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commit/galaxy-central: dan: Refactor Biostar interaction code. Add the ability to search for previously asked questions about a tool from the tool form. Allow logging out of biostar.
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/86ea88b98bb7/ Changeset: 86ea88b98bb7 User: dan Date: 2014-03-20 22:23:41 Summary: Refactor Biostar interaction code. Add the ability to search for previously asked questions about a tool from the tool form. Allow logging out of biostar. Affected #: 5 files diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/util/biostar.py --- /dev/null +++ b/lib/galaxy/util/biostar.py @@ -0,0 +1,121 @@ +""" +Support for integration with the Biostar application +""" + +import hmac +import urlparse +import re +from unicodedata import normalize +from galaxy.web.base.controller import url_for + +_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+') + +DEFAULT_GALAXY_TAG = 'galaxy' + +BIOSTAR_ACTIONS = { + None: { 'url': lambda x: '', 'uses_payload': False }, + 'new_post': { 'url': lambda x: 'p/new/post/', 'uses_payload': True }, + 'show_tags': { 'url': lambda x: 't/%s/' % ( "+".join( ( x.get( 'tag_val' ) or DEFAULT_GALAXY_TAG ).split( ',' ) ) ), 'uses_payload':False }, + 'log_out': { 'url': lambda x: 'site/logout/', 'uses_payload': False } +} + +DEFAULT_BIOSTAR_COOKIE_AGE = 1 + +def biostar_enabled( app ): + return bool( app.config.biostar_url ) + +# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/) +def slugify(text, delim=u'-'): + """Generates an slightly worse ASCII-only slug.""" + result = [] + for word in _punct_re.split(text.lower()): + word = normalize('NFKD', word).encode('ascii', 'ignore') + if word: + result.append(word) + return unicode(delim.join(result)) + +# Default values for new posts to Biostar +DEFAULT_PAYLOAD = { + 'title': '', + 'tag_val': DEFAULT_GALAXY_TAG, + 'content': '', +} + +def get_biostar_url( app, payload=None, biostar_action=None ): + # Ensure biostar integration is enabled + if not biostar_enabled( app ): + raise Exception( "Biostar integration is not enabled" ) + if biostar_action not in BIOSTAR_ACTIONS: + raise Exception( "Invalid action specified (%s)." % ( biostar_action ) ) + biostar_action = BIOSTAR_ACTIONS[ biostar_action ] + # Start building up the payload + payload = payload or {} + payload = dict( DEFAULT_PAYLOAD, **payload ) + #generate url, can parse payload info + url = str( urlparse.urljoin( app.config.biostar_url, biostar_action.get( 'url' )( payload ) ) ) + if not biostar_action.get( 'uses_payload' ): + payload = {} + url = url_for( url, **payload ) + return url + +def tag_for_tool( tool ): + """ + Generate a reasonable biostar tag for a tool. + """ + #Biostar can now handle tags with spaces, do we want to generate tags differently now? + return slugify( unicode( tool.name ), delim='-' ) + +def populate_tag_payload( payload=None, tool=None ): + if payload is None: + payload = {} + tag_val = [ DEFAULT_GALAXY_TAG ] + if tool: + tag_val.append( tag_for_tool( tool ) ) + payload[ 'tag_val' ] = ','.join( tag_val ) + return payload + +def populate_tool_payload( payload=None, tool=None ): + payload = populate_tag_payload( payload=payload, tool=tool ) + payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + return payload + +def determine_cookie_domain( galaxy_hostname, biostar_hostname ): + if galaxy_hostname == biostar_hostname: + return galaxy_hostname + + sub_biostar_hostname = biostar_hostname.split( '.', 1 )[-1] + if sub_biostar_hostname == galaxy_hostname: + return galaxy_hostname + + sub_galaxy_hostname = galaxy_hostname.split( '.', 1 )[-1] + if sub_biostar_hostname == sub_galaxy_hostname: + return sub_galaxy_hostname + + return galaxy_hostname + +def create_cookie( trans, key_name, key, email, age=DEFAULT_BIOSTAR_COOKIE_AGE ): + digest = hmac.new( key, email ).hexdigest() + value = "%s:%s" % (email, digest) + trans.set_cookie( value, name=key_name, path='/', age=age, version='1' ) + #We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work + galaxy_hostname = urlparse.urlsplit( url_for( '/', qualified=True ) ).hostname + biostar_hostname = urlparse.urlsplit( trans.app.config.biostar_url ).hostname + trans.response.cookies[ key_name ][ 'domain' ] = determine_cookie_domain( galaxy_hostname, biostar_hostname ) + +def delete_cookie( trans, key_name ): + #Set expiration of Cookie to time in past, to cause browser to delete + if key_name in trans.request.cookies: + create_cookie( trans, trans.app.config.biostar_key_name, '', '', age=-90 ) + +def biostar_logged_in( trans ): + if biostar_enabled( trans.app ): + if trans.app.config.biostar_key_name in trans.request.cookies: + return True + return False + +def biostar_logout( trans ): + if biostar_enabled( trans.app ): + delete_cookie( trans, trans.app.config.biostar_key_name ) + return get_biostar_url( trans.app, biostar_action='log_out' ) + return None diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -1,84 +1,10 @@ """ -Support for integration with the Biostar Q&A application +Controller for integration with the Biostar application """ from galaxy.web.base.controller import BaseUIController, url_for, error, web +from galaxy.util import biostar -import base64 -from galaxy.util import json -import hmac -import urlparse - -# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/) - -import re -from unicodedata import normalize - -_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+') - -BIOSTAR_ACTIONS = { - None: '', - 'new': 'p/new/post/', - 'show_tag_galaxy': 't/galaxy/' -} - - -def slugify(text, delim=u'-'): - """Generates an slightly worse ASCII-only slug.""" - result = [] - for word in _punct_re.split(text.lower()): - word = normalize('NFKD', word).encode('ascii', 'ignore') - if word: - result.append(word) - return unicode(delim.join(result)) - - -# Biostar requires all keys to be present, so we start with a template -DEFAULT_PAYLOAD = { - 'title': '', - 'tag_val': 'galaxy', - 'content': '', -} - - -def encode_data( key, data ): - """ - Encode data to send a question to Biostar - """ - text = json.to_json_string(data) - text = base64.urlsafe_b64encode(text) - digest = hmac.new(key, text).hexdigest() - return text, digest - - -def tag_for_tool( tool ): - """ - Generate a reasonable biostar tag for a tool. - """ - return slugify( unicode( tool.name ) ) - -def determine_cookie_domain( galaxy_hostname, biostar_hostname ): - if galaxy_hostname == biostar_hostname: - return galaxy_hostname - - sub_biostar_hostname = biostar_hostname.split( '.', 1 )[-1] - if sub_biostar_hostname == galaxy_hostname: - return galaxy_hostname - - sub_galaxy_hostname = galaxy_hostname.split( '.', 1 )[-1] - if sub_biostar_hostname == sub_galaxy_hostname: - return sub_galaxy_hostname - - return galaxy_hostname - -def create_cookie( trans, key_name, key, email ): - digest = hmac.new( key, email ).hexdigest() - value = "%s:%s" % (email, digest) - trans.set_cookie( value, name=key_name, path='/', age=90, version='1' ) - #We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work - galaxy_hostname = urlparse.urlsplit( url_for( '/', qualified=True ) ).hostname - biostar_hostname = urlparse.urlsplit( trans.app.config.biostar_url ).hostname - trans.response.cookies[ key_name ][ 'domain' ] = determine_cookie_domain( galaxy_hostname, biostar_hostname ) class BiostarController( BaseUIController ): """ @@ -89,24 +15,35 @@ def biostar_redirect( self, trans, payload=None, biostar_action=None ): """ Generate a redirect to a Biostar site using external authentication to - pass Galaxy user information and information about a specific tool. + pass Galaxy user information and optional information about a specific tool. """ - # Ensure biostar integration is enabled - if not trans.app.config.biostar_url: - return error( "Biostar integration is not enabled" ) - if biostar_action not in BIOSTAR_ACTIONS: - return error( "Invalid action specified (%s)." % ( biostar_action ) ) - - # Start building up the payload - payload = payload or {} - payload = dict( DEFAULT_PAYLOAD, **payload ) - # Do the best we can of providing user information for the payload + try: + url = biostar.get_biostar_url( trans.app, payload=payload, biostar_action=biostar_action ) + except Exception, e: + return error( str( e ) ) + # Only create/log in biostar user if is registered Galaxy user if trans.user: - email = trans.user.email - else: - email = "anon-%s" % ( trans.security.encode_id( trans.galaxy_session.id ) ) - create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, email ) - return trans.response.send_redirect( url_for( urlparse.urljoin( trans.app.config.biostar_url, BIOSTAR_ACTIONS[ biostar_action ] ), **payload ) ) + biostar.create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, trans.user.email ) + return trans.response.send_redirect( url ) + + @web.expose + def biostar_tool_tag_redirect( self, trans, tool_id=None ): + """ + Generate a redirect to a Biostar site using tag for tool. + """ + # tool_id is required + if tool_id is None: + return error( "No tool_id provided" ) + # Load the tool + tool_version_select_field, tools, tool = \ + self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) + # No matching tool, unlikely + if not tool: + return error( "No tool found matching '%s'" % tool_id ) + # Tool specific information for payload + payload = biostar.populate_tag_payload( tool=tool ) + # Pass on to standard redirect method + return self.biostar_redirect( trans, payload=payload, biostar_action='show_tags' ) @web.expose def biostar_question_redirect( self, trans, payload=None ): @@ -114,8 +51,8 @@ Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool. """ - payload = payload or {} - return self.biostar_redirect( trans, payload=payload, biostar_action='new' ) + # Pass on to standard redirect method + return self.biostar_redirect( trans, payload=payload, biostar_action='new_post' ) @web.expose def biostar_tool_question_redirect( self, trans, tool_id=None ): @@ -133,8 +70,19 @@ if not tool: return error( "No tool found matching '%s'" % tool_id ) # Tool specific information for payload - payload = { 'title':'Need help with "%s" tool' % ( tool.name ), - 'content': '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ), - 'tag_val': ','.join( [ 'galaxy', tag_for_tool( tool ) ] ) } + payload = biostar.populate_tool_payload( tool=tool ) # Pass on to regular question method return self.biostar_question_redirect( trans, payload ) + + @web.expose + def biostar_logout( self, trans ): + """ + Log out of biostar + """ + try: + url = biostar.biostar_log_out( trans ) + except Exception, e: + return error( str( e ) ) + if url: + return trans.response.send_redirect( url ) + return error( "Could not determine Biostar logout URL." ) diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -30,7 +30,7 @@ from galaxy.web.form_builder import build_select_field from galaxy.web.framework.helpers import time_ago, grids from datetime import datetime, timedelta -from galaxy.util import hash_util +from galaxy.util import hash_util, biostar log = logging.getLogger( __name__ ) @@ -600,6 +600,11 @@ trans.handle_user_logout( logout_all=logout_all ) message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ ( trans.request.referer, url_for( '/' ) ) + if biostar.biostar_logged_in( trans ): + biostar_url = biostar.biostar_logout( trans ) + if biostar_url: + #TODO: It would be better if we automatically logged this user out of biostar + message += '<br>To logout of Biostar, please click <a href="%s" target="_blank">here</a>.' % ( biostar_url ) return trans.fill_template( '/user/logout.mako', refresh_frames=refresh_frames, message=message, diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -40,7 +40,7 @@ 'enable_cloud_launch' : app.config.get_bool('enable_cloud_launch', False), 'lims_doc_url' : app.config.get("lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts"), 'biostar_url' : app.config.biostar_url, - 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show_tag_galaxy', qualified=True ), + 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show_tags', qualified=True ), 'support_url' : app.config.get("support_url", "http://wiki.galaxyproject.org/Support"), 'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"), 'mailing_lists' : app.config.get("mailing_lists", "http://wiki.galaxyproject.org/MailingLists"), diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -324,8 +324,13 @@ %if trans.app.config.biostar_url: ## BioStar links <span class="pull-right"> - <span class="fa fa-question-circle">&nbsp</span><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" - target="_blank">Ask a question about this tool</a>&nbsp<span class="fa fa-external-link"></span> + Help from Biostar + <div class="icon-btn-group"> + <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Search for this tool"><span class="fa fa-search"></span></a> + <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Ask a question about this tool"><span class="fa fa-question-circle"></a> + </div></span> %endif </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5996738d71ac/ Changeset: 5996738d71ac User: jmchilton Date: 2014-03-20 22:12:52 Summary: Drop unit incorrect unit tests added in 410a13e and 01933aa. Workflow run template was causing these methods to be called wrong (and has been for a LONG time), this in turn caused me to misunderstand what the spec for how other_values in tool parameters should operate when writing the tests. The real underlying bug should be fixed with 55cf8bb. Affected #: 1 file diff -r 1285d07792b31e6c1ce9d66f559afc3f49a054a8 -r 5996738d71ace34df5bee3452b8f2cdeda3e230f test/unit/tools/test_select_parameters.py --- a/test/unit/tools/test_select_parameters.py +++ b/test/unit/tools/test_select_parameters.py @@ -35,19 +35,6 @@ # Data ref currently must be same level, if not at top level. assert not self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } } ) - # Following test will fail due to bug in Galaxy. - def test_nested_context_validation_needed_in_repeat( self ): - self.type = "data_column" - self.set_ref_text = True - self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>''' - assert not self.param.need_late_validation( self.trans, { "series": [ { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } ] } ) - - def test_nested_context_validation_not_needed_in_repeat( self ): - self.type = "data_column" - self.set_ref_text = True - self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>''' - assert self.param.need_late_validation( self.trans, { "series": [ { "my_name": "42", "input_bam": basic.RuntimeValue() } ] } ) - def test_filter_param_value( self ): self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>''' assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, { "input_bam": "testname1" } ) @@ -61,11 +48,6 @@ assert ("testname2", "testpath2", False) in self.param.get_options( self.trans, { "input_bam": "testpath2" } ) assert len( self.param.get_options( self.trans, { "input_bam": "testpath3" } ) ) == 0 - def test_filter_nested( self ): - # Test filtering a parameter inside a conditional (not currently supported.) - self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>''' - assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, {"condtional1" : { "input_bam": "testpath1", "my_name": 42 } } ) - # TODO: Good deal of overlap here with DataToolParameterTestCase, # refactor. def setUp( self ): https://bitbucket.org/galaxy/galaxy-central/commits/f830918df15b/ Changeset: f830918df15b User: jmchilton Date: 2014-03-20 22:15:20 Summary: Drop functional test for jobs that fails randomly. Affected #: 1 file diff -r 5996738d71ace34df5bee3452b8f2cdeda3e230f -r f830918df15be11380a4628c9c3aad860547e092 test/functional/api/test_jobs.py --- a/test/functional/api/test_jobs.py +++ b/test/functional/api/test_jobs.py @@ -84,28 +84,6 @@ self.__assert_one_search_result( search_payload ) - def test_search_param( self ): - history_id, dataset_id = self.__history_with_ok_dataset() - - inputs = json.dumps( - dict( - input=dict( - src='hda', - id=dataset_id, - ), - num_lines=1, - ) - ) - search_payload = dict( - tool_id="random_lines1", - inputs=inputs, - state="ok", - ) - - self.__run_randomlines_tool( 1, history_id, dataset_id ) - self._wait_for_history( history_id, assert_ok=True ) - self.__assert_one_search_result( search_payload ) - def __assert_one_search_result( self, search_payload ): search_response = self._post( "jobs/search", data=search_payload ) self._assert_status_code_is( search_response, 200 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55cf8bb06007/ Changeset: 55cf8bb06007 User: jmchilton Date: 2014-03-18 17:33:05 Summary: Bring workflow parameter context inline with tool. When tool parameters are passed other_values when rendering tool forms - other_values is the context of other tools at their position in the tree, when rendering workflows other_values is the global state of the tool. The result is different handling of say parameter value filtering for tools and workflows. This changeset switches workflows/run.mako to use the same recursive calculation of context/other_values as tool_form.mako uses. Affected #: 1 file diff -r 0a9263af45ec678bea82a6d128f49cf5372d370d -r 55cf8bb0600772d4508cd725677725611e4d78d0 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -313,9 +313,10 @@ %><%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )"> - %if other_values is None: - <% other_values = values %> - %endif + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( values, other_values ) + %> %for input_index, input in enumerate( inputs.itervalues() ): %if input.type == "repeat": <div class="repeat-group"> https://bitbucket.org/galaxy/galaxy-central/commits/1285d07792b3/ Changeset: 1285d07792b3 User: jmchilton Date: 2014-03-20 22:05:49 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #349) Bring workflow parameter context calculation in line with that of tools. Affected #: 1 file diff -r 7f7b154608e3e1c54d921d1e23277379f54293d9 -r 1285d07792b31e6c1ce9d66f559afc3f49a054a8 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -313,9 +313,10 @@ %><%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )"> - %if other_values is None: - <% other_values = values %> - %endif + <% + from galaxy.util.expressions import ExpressionContext + other_values = ExpressionContext( values, other_values ) + %> %for input_index, input in enumerate( inputs.itervalues() ): %if input.type == "repeat": <div class="repeat-group"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Functional test script for installing, updating, uninstalling, and reinstalling a repository.
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/944e6ae11d5e/ Changeset: 944e6ae11d5e User: davebgx Date: 2014-03-20 21:53:25 Summary: Functional test script for installing, updating, uninstalling, and reinstalling a repository. Affected #: 2 files diff -r b95ae5f6d6f513760fa01f596ca52fbc1cff9d6e -r 944e6ae11d5e870ae17b2c928034b4b7cd3b3bb9 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -63,11 +63,13 @@ .filter( galaxy.model.tool_shed_install.ToolShedRepository.table.c.id == repository_id ) \ .first() -def get_installed_repository_by_name_owner( repository_name, owner ): - return install_session.query( galaxy.model.tool_shed_install.ToolShedRepository ) \ - .filter( and_( galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name, - galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner ) ) \ - .first() +def get_installed_repository_by_name_owner( repository_name, owner, return_multiple=False ): + query = install_session.query( galaxy.model.tool_shed_install.ToolShedRepository ) \ + .filter( and_( galaxy.model.tool_shed_install.ToolShedRepository.table.c.name == repository_name, + galaxy.model.tool_shed_install.ToolShedRepository.table.c.owner == owner ) ) + if return_multiple: + return query.all() + return query.first() def get_private_role( user ): for role in user.all_roles(): @@ -181,7 +183,7 @@ .filter( galaxy.model.User.table.c.email==email ) \ .first() -def get_repository_by_name_and_owner( name, owner_username ): +def get_repository_by_name_and_owner( name, owner_username, return_multiple=False ): owner = get_user_by_name( owner_username ) repository = sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.name == name, diff -r b95ae5f6d6f513760fa01f596ca52fbc1cff9d6e -r 944e6ae11d5e870ae17b2c928034b4b7cd3b3bb9 test/tool_shed/functional/test_1470_updating_installed_repositories.py --- /dev/null +++ b/test/tool_shed/functional/test_1470_updating_installed_repositories.py @@ -0,0 +1,138 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import logging + +log = logging.getLogger(__name__) + +repository_name = 'filtering_1470' +repository_description = "Galaxy's filtering tool" +repository_long_description = "Long description of Galaxy's filtering tool" + +category_name = 'Test 1470 - Updating Installed Repositories' +category_description = 'Functional test suite to ensure that updating installed repositories does not create white ghosts.' + +''' +1. Install a repository into Galaxy. +2. In the Tool Shed, update the repository from Step 1. +3. In Galaxy, get updates to the repository. +4. In Galaxy, uninstall the repository. +5. In Galaxy, reinstall the repository. +6. Make sure step 5 created no white ghosts. +''' + + +class TestUpdateInstalledRepository( ShedTwillTestCase ): + '''Verify that the code correctly handles updating an installed repository, then uninstalling and reinstalling.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = self.test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = self.test_db_util.get_private_role( admin_user ) + + def test_0005_create_filtering_repository( self ): + """Create and populate the filtering_0530 repository.""" + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_install_filtering_to_galaxy( self ): + '''Install the filtering_1470 repository to galaxy.''' + ''' + This is step 1 - Install a repository into Galaxy. + ''' + self.galaxy_logout() + self.galaxy_login( email=common.admin_email, username=common.admin_username ) + self.install_repository( repository_name, + common.test_user_1_name, + category_name, + install_tool_dependencies=False, + install_repository_dependencies=False, + new_tool_panel_section_label='Filtering' ) + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + strings_displayed = [ 'filtering_1470', + self.url.replace( 'http://', '' ), + installed_repository.installed_changeset_revision, + installed_repository.changeset_revision ] + self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) + self.display_installed_repository_manage_page( installed_repository, + strings_displayed=strings_displayed ) + + def test_0015_update_repository( self ): + '''Upload a readme file to the filtering_1470 repository.''' + ''' + This is step 2 - In the Tool Shed, update the repository from Step 1. + + Importantly, this update should *not* create a new installable changeset revision, because that would + eliminate the process we're testing in this script. So, we upload a readme file. + ''' + repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.upload_file( repository, + filename='filtering/readme.txt', + filepath=None, + valid_tools_only=True, + uncompress_file=False, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded readme.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_get_repository_updates( self ): + '''Get updates to the installed repository.''' + ''' + This is step 3 - In Galaxy, get updates to the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.update_installed_repository( installed_repository ) + + def test_0025_uninstall_repository( self ): + '''Uninstall the filtering_1470 repository.''' + ''' + This is step 4 - In Galaxy, uninstall the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.uninstall_repository( installed_repository ) + + def test_0030_reinstall_repository( self ): + '''Reinstall the filtering_1470 repository.''' + ''' + This is step 5 - In Galaxy, reinstall the repository. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name ) + self.reinstall_repository( installed_repository ) + + def test_0035_verify_absence_of_ghosts( self ): + '''Check the count of repositories in the database named filtering_1470 and owned by user1.''' + ''' + This is step 6 - Make sure step 5 created no white ghosts. + ''' + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, + common.test_user_1_name, + return_multiple=True ) + assert len( installed_repository ) == 1, 'Multiple filtering repositories found in the Galaxy database, possibly indicating a "white ghost" scenario.' + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: fix: dont override default initialization of bootstrap tooltip with placement 'top'
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b95ae5f6d6f5/ Changeset: b95ae5f6d6f5 User: martenson Date: 2014-03-20 21:54:43 Summary: fix: dont override default initialization of bootstrap tooltip with placement 'top' Affected #: 2 files diff -r 7155334f5ec5743188f90053a54ac851be3e2d58 -r b95ae5f6d6f513760fa01f596ca52fbc1cff9d6e static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -682,8 +682,9 @@ // Put tooltips below items in panel header so that they do not overlap masthead. $(".unified-panel-header [title]").tooltip( { placement: 'bottom' } ); - // Default tooltip location to be above item. - $("[title]").tooltip( { placement: 'top' } ); + // default tooltip initialization, it will follow the data-placement tag for tooltip location + // and fallback to 'top' if not present + $("[title]").tooltip(); } // Make popup menus. make_popup_menus(); diff -r 7155334f5ec5743188f90053a54ac851be3e2d58 -r 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commit/galaxy-central: carlfeberhard: UI: move base-mvc, annotation and tag editors, user model and quotameter to AMD; fix loading order and currUser in masthead, view, history; remove loggable mixin from scatterplot
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7155334f5ec5/ Changeset: 7155334f5ec5 User: carlfeberhard Date: 2014-03-20 21:52:06 Summary: UI: move base-mvc, annotation and tag editors, user model and quotameter to AMD; fix loading order and currUser in masthead, view, history; remove loggable mixin from scatterplot Affected #: 33 files diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js --- a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js @@ -29,7 +29,7 @@ * configuring which data will be used * configuring the plot display */ -var ScatterplotConfigEditor = Backbone.View.extend( LoggableMixin ).extend({ +var ScatterplotConfigEditor = Backbone.View.extend({ //TODO: !should be a view on a visualization model //logger : console, className : 'scatterplot-control-form', @@ -39,13 +39,13 @@ if( !this.model ){ this.model = new Visualization({ type: 'scatterplot' }); } - this.log( this + '.initialize, attributes:', attributes ); + //this.log( this + '.initialize, attributes:', attributes ); if( !attributes || !attributes.dataset ){ throw new Error( "ScatterplotConfigEditor requires a dataset" ); } this.dataset = attributes.dataset; - this.log( 'dataset:', this.dataset ); + //this.log( 'dataset:', this.dataset ); this.display = new ScatterplotDisplay({ dataset : attributes.dataset, diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 config/plugins/visualizations/scatterplot/static/scatterplot-edit.js --- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js +++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js @@ -1,1 +1,1 @@ -function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="',(f=c.xLabel)?f=f.call(b,{hash:{},data:e}):(f=b.xLabel,f=typeof f===h?f.apply(b):f),g+=i(f)+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="',(f=c.yLabel)?f=f.call(b,{hash:{},data:e}):(f=b.yLabel,f=typeof f===h?f.apply(b):f),g+=i(f)+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function";return g+='<p class="help-text">\n Use the following control to change which columns are used by the chart. Click any cell\n from the last three rows of the table to select the column for the appropriate data.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n It may be useful to select unique or categorical identifiers here (such as gene ids).\n </li>\n</ul>\n\n<div class="column-selection">\n <pre class="peek">',(f=c.peek)?f=f.call(b,{hash:{},data:e}):(f=b.peek,f=typeof f===h?f.apply(b):f),(f||0===f)&&(g+=f),g+='</pre>\n</div>\n\n<p class="help-text help-text-small">\n <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekControl({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-control.change",function(a,c){b.model.set("config",c)}).on("peek-control.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file +function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.xTicks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.yTicks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("id","x-axis-label").attr("class","axis-label").text(b.xLabel).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("id","y-axis-label").attr("class","axis-label").text(b.yLabel).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="',(f=c.xLabel)?f=f.call(b,{hash:{},data:e}):(f=b.xLabel,f=typeof f===h?f.apply(b):f),g+=i(f)+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="',(f=c.yLabel)?f=f.call(b,{hash:{},data:e}):(f=b.yLabel,f=typeof f===h?f.apply(b):f),g+=i(f)+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function";return g+='<p class="help-text">\n Use the following control to change which columns are used by the chart. Click any cell\n from the last three rows of the table to select the column for the appropriate data.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n It may be useful to select unique or categorical identifiers here (such as gene ids).\n </li>\n</ul>\n\n<div class="column-selection">\n <pre class="peek">',(f=c.peek)?f=f.call(b,{hash:{},data:e}):(f=b.peek,f=typeof f===h?f.apply(b):f),(f||0===f)&&(g+=f),g+='</pre>\n</div>\n\n<p class="help-text help-text-small">\n <b>Note</b>: If it can be determined from the dataset\'s filetype that a column is not numeric,\n that column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekControl({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-control.change",function(a,c){b.model.set("config",c)}).on("peek-control.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.xLabel,e=b.yLabel,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},xTicks:10,xLabel:"X",yTicks:10,yLabel:"Y",datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -32,7 +32,6 @@ 'libs/backbone/backbone', 'libs/d3', 'libs/handlebars.runtime', - 'mvc/base-mvc', 'mvc/ui', 'mvc/visualization/visualization-model' )} diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -1,9 +1,12 @@ define([ -], function(){ + "mvc/base-mvc" +], function( baseMVC ){ // ============================================================================= /** A view on any model that has a 'annotation' attribute */ -var AnnotationEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ +var AnnotationEditor = Backbone.View + .extend( baseMVC.LoggableMixin ) + .extend( baseMVC.HiddenUntilActivatedViewMixin ).extend({ tagName : 'div', className : 'annotation-display', diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -1,3 +1,6 @@ +define([ +], function(){ +//ASSUMES: backbone //============================================================================== /** @class Mixin to add logging capabilities to an object. * Designed to allow switching an objects log output off/on at one central @@ -188,3 +191,10 @@ return this.HUAVOptions.showFn.apply( this.HUAVOptions.$elementShown, arguments ); } }; + +//============================================================================== +return { + LoggableMixin : LoggableMixin, + SessionStorageModel : SessionStorageModel, + HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin +};}); diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -1,7 +1,8 @@ define([ - "mvc/dataset/hda-model" -], function( hdaModel ){ -/* global Backbone, LoggableMixin, HistoryDatasetAssociation, HDABaseView */ + "mvc/dataset/hda-model", + "mvc/base-mvc" +], function( hdaModel, baseMVC ){ +/* global Backbone */ //============================================================================== /** @class Read only view for HistoryDatasetAssociation. * @name HDABaseView @@ -11,7 +12,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( +var HDABaseView = Backbone.View.extend( baseMVC.LoggableMixin ).extend( /** @lends HDABaseView.prototype */{ ///** logger used to record this.log messages, commonly set to console */ diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -13,7 +13,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( +var HDAEditView = hdaBase.HDABaseView.extend( /** @lends HDAEditView.prototype */{ // ......................................................................... set up diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -1,5 +1,6 @@ define([ -], function(){ + "mvc/base-mvc" +], function( baseMVC ){ //============================================================================== /** @class (HDA) model for a Galaxy dataset * related to a history. @@ -10,7 +11,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HistoryDatasetAssociation = Backbone.Model.extend( LoggableMixin ).extend( +var HistoryDatasetAssociation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( /** @lends HistoryDatasetAssociation.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -401,7 +402,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDACollection = Backbone.Collection.extend( LoggableMixin ).extend( +var HDACollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( /** @lends HDACollection.prototype */{ model : HistoryDatasetAssociation, diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -1,11 +1,12 @@ define([ "mvc/dataset/hda-edit", - "mvc/history/history-panel" -], function( hdaEdit, hpanel ){ + "mvc/history/history-panel", + "mvc/base-mvc" +], function( hdaEdit, hpanel, baseMVC ){ // ============================================================================ /** session storage for history panel preferences (and to maintain state) */ -var HistoryPanelPrefs = SessionStorageModel.extend({ +var HistoryPanelPrefs = baseMVC.SessionStorageModel.extend({ defaults : { /** is the panel currently showing the search/filter controls? */ searching : false, diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -1,6 +1,7 @@ define([ - "mvc/dataset/hda-model" -], function( hdaModel ){ + "mvc/dataset/hda-model", + "mvc/base-mvc" +], function( hdaModel, baseMVC ){ //============================================================================== /** @class Model for a Galaxy history resource - both a record of user * tool use and a collection of the datasets those tools produced. @@ -11,7 +12,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var History = Backbone.Model.extend( LoggableMixin ).extend( +var History = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( /** @lends History.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -114,13 +115,6 @@ }, // ........................................................................ common queries - /** is this model already associated with a user? */ -//TODO: remove - hasUser : function(){ - var user = this.get( 'user' ); - return !!( user && user.id ); - }, - /** T/F is this history owned by the current user (Galaxy.currUser) * Note: that this will return false for an anon user even if the history is theirs. */ @@ -295,7 +289,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HistoryCollection = Backbone.Collection.extend( LoggableMixin ).extend( +var HistoryCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, urlRoot : galaxy_config.root + 'api/histories' diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -84,7 +84,7 @@ $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); this.$emptyMessage( $newRender ).text( this.emptyMsg ); - if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ + if( Galaxy && Galaxy.currUser && Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ this._renderTags( $newRender ); this._renderAnnotation( $newRender ); } diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -1,10 +1,11 @@ define([ "mvc/history/history-model", - "mvc/dataset/hda-base" -], function( historyModel, hdaBase ){ + "mvc/dataset/hda-base", + "mvc/base-mvc" +], function( historyModel, hdaBase, baseMVC ){ // ============================================================================ /** session storage for individual history preferences */ -var HistoryPrefs = SessionStorageModel.extend({ +var HistoryPrefs = baseMVC.SessionStorageModel.extend({ defaults : { //TODO:?? expandedHdas to array? expandedHdas : {}, @@ -71,7 +72,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var ReadOnlyHistoryPanel = Backbone.View.extend( LoggableMixin ).extend( +var ReadOnlyHistoryPanel = Backbone.View.extend( baseMVC.LoggableMixin ).extend( /** @lends ReadOnlyHistoryPanel.prototype */{ /** logger used to record this.log messages, commonly set to console */ @@ -311,11 +312,11 @@ attributes = attributes || {}; //this.log( 'JSONToModel:', newHistoryJSON, newHdaJSON.length, attributes ); - // set up the new model and render - if( Galaxy && Galaxy.currUser ){ -//TODO: global - newHistoryJSON.user = Galaxy.currUser.toJSON(); - } +// // set up the new model and render +// if( Galaxy && Galaxy.currUser ){ +////TODO: global +// newHistoryJSON.user = Galaxy.currUser.toJSON(); +// } var model = new historyModel.History( newHistoryJSON, newHdaJSON, attributes ); this.setModel( model ); return this; @@ -334,10 +335,10 @@ if( model ){ // set up the new model with user, logger, storage, events - if( Galaxy && Galaxy.currUser ){ -//TODO: global - model.user = Galaxy.currUser.toJSON(); - } +// if( Galaxy && Galaxy.currUser ){ +////TODO: global +// model.user = Galaxy.currUser.toJSON(); +// } this.model = model; if( this.logger ){ this.model.logger = this.logger; diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/tags.js --- a/static/scripts/mvc/tags.js +++ b/static/scripts/mvc/tags.js @@ -1,11 +1,12 @@ define([ -], function(){ + "mvc/base-mvc" +], function( baseMVC ){ // ============================================================================= /** A view on any model that has a 'tags' attribute (a list of tag strings) * Incorporates the select2 jQuery plugin for tags display/editing: * http://ivaynberg.github.io/select2/ */ -var TagsEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ +var TagsEditor = Backbone.View.extend( baseMVC.LoggableMixin ).extend( baseMVC.HiddenUntilActivatedViewMixin ).extend({ tagName : 'div', className : 'tags-display', diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/user/user-model.js --- a/static/scripts/mvc/user/user-model.js +++ b/static/scripts/mvc/user/user-model.js @@ -1,3 +1,7 @@ +define([ + "mvc/base-mvc" +], function( baseMVC ){ +//============================================================================== /** @class Model for a Galaxy user (including anonymous users). * @name User * @@ -6,7 +10,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var User = Backbone.Model.extend( LoggableMixin ).extend( +var User = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( /** @lends User.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -107,8 +111,14 @@ }; // (stub) collection for users (shouldn't be common unless admin UI) -var UserCollection = Backbone.Collection.extend( LoggableMixin ).extend({ +var UserCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend({ model : User, urlRoot : galaxy_config.root + 'api/users' //logger : console, }); + + +//============================================================================== +return { + User : User +};}); diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/user/user-quotameter.js --- a/static/scripts/mvc/user/user-quotameter.js +++ b/static/scripts/mvc/user/user-quotameter.js @@ -1,3 +1,7 @@ +define([ + "mvc/base-mvc" +], function( baseMVC ){ +//============================================================================== /** @class View to display a user's disk/storage usage * either as a progress bar representing the percentage of a quota used * or a simple text element displaying the human readable size used. @@ -8,7 +12,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var UserQuotaMeter = Backbone.View.extend( LoggableMixin ).extend( +var UserQuotaMeter = Backbone.View.extend( baseMVC.LoggableMixin ).extend( /** @lends UserQuotaMeter.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -149,3 +153,9 @@ return 'UserQuotaMeter(' + this.model + ')'; } }); + + +//============================================================================== +return { + UserQuotaMeter : UserQuotaMeter +};}); diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/mvc/visualization/visualization-model.js --- a/static/scripts/mvc/visualization/visualization-model.js +++ b/static/scripts/mvc/visualization/visualization-model.js @@ -5,11 +5,9 @@ /** @class Model for a saved Galaxy visualization. * * @augments Backbone.Model - * @borrows LoggableMixin#logger as #logger - * @borrows LoggableMixin#log as #log * @constructs */ -var Visualization = Backbone.Model.extend( LoggableMixin ).extend( +var Visualization = Backbone.Model.extend( /** @lends Visualization.prototype */{ ///** logger used to record this.log messages, commonly set to console */ @@ -31,7 +29,7 @@ * @see Backbone.Model#initialize */ initialize : function( data ){ - this.log( this + '.initialize', data, this.attributes ); + //this.log( this + '.initialize', data, this.attributes ); // munge config sub-object here since bbone won't handle defaults with this if( _.isObject( data.config ) && _.isObject( this.defaults.config ) ){ @@ -84,7 +82,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var VisualizationCollection = Backbone.Collection.extend( LoggableMixin ).extend( +var VisualizationCollection = Backbone.Collection.extend( /** @lends VisualizationCollection.prototype */{ model : Visualization, diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(b){b=b||{};this.tooltipConfig=b.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(b.$activator,b)},render:function(){var b=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(c){b.$annotation().text(c);b.model.save({annotation:c},{silent:true}).fail(function(){b.$annotation().text(b.model.previous("annotation"))})}});return this},_template:function(){var b=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',b,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:a}}); \ No newline at end of file +define(["mvc/base-mvc"],function(a){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(c){c=c||{};this.tooltipConfig=c.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(c.$activator,c)},render:function(){var c=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(d){c.$annotation().text(d);c.model.save({annotation:d},{silent:true}).fail(function(){c.$annotation().text(c.model.previous("annotation"))})}});return this},_template:function(){var c=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',c,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:b}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file +define([],function(){var c={logger:null,log:function(){if(this.logger){var d=this.logger.log;if(typeof this.logger.log==="object"){d=Function.prototype.bind.call(this.logger.log,this.logger)}return d.apply(this.logger,arguments)}return undefined}};var a=Backbone.Model.extend({initialize:function(e){e.id=(!_.isString(e.id))?(_.uniqueId()):(e.id);this.id=e.id;var d=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,d,e),{silent:true});this.on("change",function(){this.save()})},sync:function(g,e,d){if(!d.silent){e.trigger("request",e,{},d)}var f;switch(g){case"create":f=this._create(e);break;case"read":f=this._read(e);break;case"update":f=this._update(e);break;case"delete":f=this._delete(e);break}if(f!==undefined||f!==null){if(d.success){d.success()}}else{if(d.error){d.error()}}return f},_create:function(d){var e=d.toJSON(),f=sessionStorage.setItem(d.id,JSON.stringify(e));return(f===null)?(f):(e)},_read:function(d){return JSON.parse(sessionStorage.getItem(d.id))},_update:function(d){return d._create(d)},_delete:function(d){return sessionStorage.removeItem(d.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){a.prototype=_.omit(a.prototype,"url","urlRoot")}());var b={hiddenUntilActivated:function(d,f){f=f||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,f||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(d){var e=this;d.on("click",function(g){e.toggle(e.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};return{LoggableMixin:c,SessionStorageModel:a,HiddenUntilActivatedViewMixin:b}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display})}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend(LoggableMixin).extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$el.find(".icon-btn.dataset-delete").trigger("mouseout");h.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==f.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var h=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(h))){return null}if(_.isObject(h[0])){return this._render_visualizationsFrameworkButton(h)}if(!this.urls.visualization){return null}var j=this.model.get("dbkey"),n=this.urls.visualization,k={},o={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(j){o.dbkey=j}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function l(p){if(p==="trackster"){return c(n,o,j)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:n+"/"+p+"?"+$.param(o)})}}function m(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(h.length===1){i.attr("data-original-title",_l("Visualize in ")+_l(m(h[0])));i.click(l(h[0]))}else{_.each(h,function(p){k[_l(m(p))]=l(p)});make_popupmenu(i,k)}return i},_render_visualizationsFrameworkButton:function(h){if(!(this.model.hasData())||!(h&&!_.isEmpty(h))){return null}var j=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(h.length===1){var i=h[0];j.attr("data-original-title",_l("Visualize in ")+i.html);j.attr("href",i.href)}else{var k=[];_.each(h,function(l){l.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:l.href});return false}return true};k.push(l);return false});PopupMenu.create(j,k)}return j},_buildNewRender:function(){var h=b.HDABaseView.prototype._buildNewRender.call(this);h.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));h.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return h},_render_body_failed_metadata:function(){var i=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),h=$("<span/>").text(". "+_l("You may be able to")+" ").append(i),j=b.HDABaseView.prototype._render_body_failed_metadata.call(this);j.find(".warningmessagesmall strong").append(h);return j},_render_body_error:function(){var h=b.HDABaseView.prototype._render_body_error.call(this);h.find(".dataset-actions .left").prepend(this._render_errButton());return h},_render_body_ok:function(){var h=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return h}this.makeDbkeyEditLink(h);if(this.hasUser){h.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(h);this._renderAnnotation(h)}return h},_renderTags:function(h){var i=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:h.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true},onhide:function(){i.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(h){var i=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:h.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true},onhide:function(){i.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var h=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);i.find(".dataset-dbkey .value").replaceWith(h)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(h){this.model.undelete();return false},"click .dataset-unhide":function(h){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(h){this.model.purge();return false},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDAView("+h+")"}});function c(h,j,i){return function(){var k={};if(i){k["f-dbkey"]=i}$.ajax({url:h+"/list_tracks?"+$.param(k),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(l){var m=window.parent;m.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){m.Galaxy.modal.hide()},"View in saved visualization":function(){m.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:l,buttons:{Cancel:function(){m.Galaxy.modal.hide()},"Add to visualization":function(){$(m.document).find("input[name=id]:checked").each(function(){m.Galaxy.modal.hide();var n=$(this).val();j.id=n;m.Galaxy.frame.add({title:"Trackster",type:"url",content:h+"/trackster?"+$.param(j)})})}}})},"View in new visualization":function(){m.Galaxy.modal.hide();var n=h+"/trackster?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$el.find(".icon-btn.dataset-delete").trigger("mouseout");h.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==f.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var h=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(h))){return null}if(_.isObject(h[0])){return this._render_visualizationsFrameworkButton(h)}if(!this.urls.visualization){return null}var j=this.model.get("dbkey"),n=this.urls.visualization,k={},o={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(j){o.dbkey=j}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function l(p){if(p==="trackster"){return c(n,o,j)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:n+"/"+p+"?"+$.param(o)})}}function m(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(h.length===1){i.attr("data-original-title",_l("Visualize in ")+_l(m(h[0])));i.click(l(h[0]))}else{_.each(h,function(p){k[_l(m(p))]=l(p)});make_popupmenu(i,k)}return i},_render_visualizationsFrameworkButton:function(h){if(!(this.model.hasData())||!(h&&!_.isEmpty(h))){return null}var j=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(h.length===1){var i=h[0];j.attr("data-original-title",_l("Visualize in ")+i.html);j.attr("href",i.href)}else{var k=[];_.each(h,function(l){l.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:l.href});return false}return true};k.push(l);return false});PopupMenu.create(j,k)}return j},_buildNewRender:function(){var h=b.HDABaseView.prototype._buildNewRender.call(this);h.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));h.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return h},_render_body_failed_metadata:function(){var i=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),h=$("<span/>").text(". "+_l("You may be able to")+" ").append(i),j=b.HDABaseView.prototype._render_body_failed_metadata.call(this);j.find(".warningmessagesmall strong").append(h);return j},_render_body_error:function(){var h=b.HDABaseView.prototype._render_body_error.call(this);h.find(".dataset-actions .left").prepend(this._render_errButton());return h},_render_body_ok:function(){var h=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return h}this.makeDbkeyEditLink(h);if(this.hasUser){h.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(h);this._renderAnnotation(h)}return h},_renderTags:function(h){var i=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:h.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true},onhide:function(){i.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(h){var i=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:h.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true},onhide:function(){i.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var h=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);i.find(".dataset-dbkey .value").replaceWith(h)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(h){this.model.undelete();return false},"click .dataset-unhide":function(h){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(h){this.model.purge();return false},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDAView("+h+")"}});function c(h,j,i){return function(){var k={};if(i){k["f-dbkey"]=i}$.ajax({url:h+"/list_tracks?"+$.param(k),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(l){var m=window.parent;m.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){m.Galaxy.modal.hide()},"View in saved visualization":function(){m.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:l,buttons:{Cancel:function(){m.Galaxy.modal.hide()},"Add to visualization":function(){$(m.document).find("input[name=id]:checked").each(function(){m.Galaxy.modal.hide();var n=$(this).val();j.id=n;m.Galaxy.frame.add({title:"Trackster",type:"url",content:h+"/trackster?"+$.param(j)})})}}})},"View in new visualization":function(){m.Galaxy.modal.hide();var n=h+"/trackster?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},h)},undelete:function a(h){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},h)},hide:function b(h){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},h)},unhide:function g(h){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},h)},purge:function f(h){if(this.get("purged")){return jQuery.when()}h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set({deleted:true,purged:true})});j.fail(function(o,k,n){var l=_l("Unable to purge dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})});return j},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(j,h){var i=this.get(j);if(!h||(i===undefined||i===null)){return false}if(_.isArray(i)){return this._searchArrayAttribute(i,h)}return(i.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)},_searchArrayAttribute:function(i,h){h=h.toLowerCase();return _.any(i,function(j){return(j.toString().toLowerCase().indexOf(h.toLowerCase())!==-1)})},search:function(h){var i=this;return _.filter(this.searchAttributes,function(j){return i.searchAttribute(j,h)})},matches:function(i){var k="=",h=i.split(k);if(h.length>=2){var j=h[0];j=this.searchAliases[j]||j;return this.searchAttribute(j,h[1])}return !!this.search(i).length},matchesAll:function(i){var h=this;i=i.match(/(".*"|\w*=".*"|\S*)/g).filter(function(j){return !!j});return _.all(i,function(j){j=j.replace(/"/g,"");return h.matches(j)})},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new e(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new e(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file +define(["mvc/base-mvc"],function(b){var e=Backbone.Model.extend(b.LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var j=this.get("id");if(!j){return{}}var i={purge:galaxy_config.root+"datasets/"+j+"/purge_async",display:galaxy_config.root+"datasets/"+j+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+j+"/edit",download:galaxy_config.root+"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+j,rerun:galaxy_config.root+"tool_runner/rerun?id="+j,show_params:galaxy_config.root+"datasets/"+j+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+j,set:galaxy_config.root+"dataset/annotate_async?id="+j},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};return i},initialize:function(i){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",e.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(j,i){this.log(this+" has changed state:",j,i);if(this.inReadyState()){this.trigger("state:ready",j,i,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(j,k){var i=true;if((!j)&&(this.get("deleted")||this.get("purged"))){i=false}if((!k)&&(!this.get("visible"))){i=false}return i},hidden:function(){return !this.get("visible")},inReadyState:function(){var i=_.contains(e.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||i)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function d(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function c(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function h(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},purge:function g(i){if(this.get("purged")){return jQuery.when()}i=i||{};i.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var j=this,k=jQuery.ajax(i);k.done(function(n,l,m){j.set({deleted:true,purged:true})});k.fail(function(p,l,o){var m=_l("Unable to purge dataset");var n=("Removal of datasets by users is not allowed in this Galaxy instance");if(p.responseJSON&&p.responseJSON.error){m=p.responseJSON.error}else{if(p.responseText.indexOf(n)!==-1){m=n}}p.responseText=m;j.trigger("error",j,p,i,_l(m),{error:m})});return k},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},searchAttribute:function(k,i){var j=this.get(k);if(!i||(j===undefined||j===null)){return false}if(_.isArray(j)){return this._searchArrayAttribute(j,i)}return(j.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)},_searchArrayAttribute:function(j,i){i=i.toLowerCase();return _.any(j,function(k){return(k.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)})},search:function(i){var j=this;return _.filter(this.searchAttributes,function(k){return j.searchAttribute(k,i)})},matches:function(j){var l="=",i=j.split(l);if(i.length>=2){var k=i[0];k=this.searchAliases[k]||k;return this.searchAttribute(k,i[1])}return !!this.search(j).length},matchesAll:function(j){var i=this;j=j.match(/(".*"|\w*=".*"|\S*)/g).filter(function(k){return !!k});return _.all(j,function(k){k=k.replace(/"/g,"");return i.matches(k)})},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HDA("+i+")"}});e.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};e.READY_STATES=[e.STATES.NEW,e.STATES.OK,e.STATES.EMPTY,e.STATES.PAUSED,e.STATES.FAILED_METADATA,e.STATES.NOT_VIEWABLE,e.STATES.DISCARDED,e.STATES.ERROR];e.NOT_READY_STATES=[e.STATES.UPLOAD,e.STATES.QUEUED,e.STATES.RUNNING,e.STATES.SETTING_METADATA];var f=Backbone.Collection.extend(b.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(j,i){i=i||{};this.historyId=i.historyId},ids:function(){return this.map(function(i){return i.id})},notReady:function(){return this.filter(function(i){return !i.inReadyState()})},running:function(){var i=[];this.each(function(j){if(!j.inReadyState()){i.push(j.get("id"))}});return i},getByHid:function(i){return _.first(this.filter(function(j){return j.get("hid")===i}))},getVisible:function(i,l,k){k=k||[];var j=new f(this.filter(function(m){return m.isVisible(i,l)}));_.each(k,function(m){if(!_.isFunction(m)){return}j=new f(j.filter(m))});return j},haveDetails:function(){return this.all(function(i){return i.hasDetails()})},fetchAllDetails:function(j){j=j||{};var i={details:"all"};j.data=(j.data)?(_.extend(j.data,i)):(i);return this.fetch(j)},ajaxQueue:function(l,k){var j=jQuery.Deferred(),i=this.length,n=[];if(!i){j.resolve([]);return j}var m=this.chain().reverse().map(function(p,o){return function(){var q=l.call(p,k);q.done(function(r){j.notify({curr:o,total:i,response:r,model:p})});q.always(function(r){n.push(r);if(m.length){m.shift()()}else{j.resolve(n)}})}}).value();m.shift()();return j},matches:function(i){return this.filter(function(j){return j.matches(i)})},set:function(k,i){var j=this;k=_.map(k,function(m){var n=j.get(m.id);if(!n){return m}var l=n.toJSON();_.extend(l,m);return l});Backbone.Collection.prototype.set.call(this,k,i)},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryDatasetAssociation:e,HDACollection:f}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f)},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(g,f,h){e.HistoryPanel.prototype.setModel.call(this,g,f,h);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(h){var g=this,f=g.$emptyMessage(h),i=$(".toolMenuContainer");if((_.isEmpty(g.hdaViews)&&!g.searchFor)&&(Galaxy&&Galaxy.upload&&i.size())){f.empty();f.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));f.find(".uploader-link").click(function(j){Galaxy.upload._eventShow(j)});f.find(".get-data-link").click(function(j){i.parent().scrollTop(0);i.find('span:contains("Get Data")').click()});f.show()}else{e.HistoryPanel.prototype._renderEmptyMsg.call(this,h)}return this},toggleSearchControls:function(g,f){var h=e.HistoryPanel.prototype.toggleSearchControls.call(this,g,f);this.preferences.set("searching",h)},_renderTags:function(f){var g=this;e.HistoryPanel.prototype._renderTags.call(this,f);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("tagsEditorShown",h.hidden)})},_renderAnnotation:function(f){var g=this;e.HistoryPanel.prototype._renderAnnotation.call(this,f);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("annotationEditorShown",h.hidden)})},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel","mvc/base-mvc"],function(b,f,c){var d=c.SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});d.storageKey=function e(){return("history-panel")};var a=f.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(g){g=g||{};this.preferences=new d(_.extend({id:d.storageKey()},_.pick(g,_.keys(d.prototype.defaults))));f.HistoryPanel.prototype.initialize.call(this,g)},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},setModel:function(h,g,i){f.HistoryPanel.prototype.setModel.call(this,h,g,i);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){f.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children());g.renderBasedOnPrefs()}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(i){var h=this,g=h.$emptyMessage(i),j=$(".toolMenuContainer");if((_.isEmpty(h.hdaViews)&&!h.searchFor)&&(Galaxy&&Galaxy.upload&&j.size())){g.empty();g.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));g.find(".uploader-link").click(function(k){Galaxy.upload._eventShow(k)});g.find(".get-data-link").click(function(k){j.parent().scrollTop(0);j.find('span:contains("Get Data")').click()});g.show()}else{f.HistoryPanel.prototype._renderEmptyMsg.call(this,i)}return this},toggleSearchControls:function(h,g){var i=f.HistoryPanel.prototype.toggleSearchControls.call(this,h,g);this.preferences.set("searching",i)},_renderTags:function(g){var h=this;f.HistoryPanel.prototype._renderTags.call(this,g);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("tagsEditorShown",i.hidden)})},_renderAnnotation:function(g){var h=this;f.HistoryPanel.prototype._renderAnnotation.call(this,g);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("annotationEditorShown",i.hidden)})},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(a){var c=Backbone.Model.extend(LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var e=this.get("id");if(!e){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(f,g,e){e=e||{};this.logger=e.logger||null;this.log(this+".initialize:",f,g,e);this.hdas=new a.HDACollection(g||[],{historyId:this.get("id")});if(g&&_.isArray(g)){this.hdas.reset(g)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(f,e){if(this.hdas){this.hdas.historyId=e}},this)},errorHandler:function(f,i,e,h,g){this.clearUpdateTimeout()},hasUser:function(){var e=this.get("user");return !!(e&&e.id)},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(e,f){return e+f},0)},checkForUpdates:function(e){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(e)){e.call(this)}}return this},setUpdateTimeout:function(e){e=e||c.UPDATE_DELAY;var f=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){f.refresh()},e);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(f,e){f=f||[];e=e||{};var g=this;e.data=e.data||{};if(f.length){e.data.details=f.join(",")}var h=this.hdas.fetch(e);h.done(function(i){g.checkForUpdates(function(){this.fetch()})});return h},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});c.UPDATE_DELAY=4000;c.getHistoryData=function d(f,p){p=p||{};var j=p.hdaDetailIds||[];var l=jQuery.Deferred(),k=null;function g(q){return jQuery.ajax(galaxy_config.root+"api/histories/"+f)}function e(q){if(!q||!q.state_ids){return 0}return _.reduce(q.state_ids,function(r,t,s){return r+t.length},0)}function o(r){if(!e(r)){return[]}if(_.isFunction(j)){j=j(r)}var q=(j.length)?({details:j.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+r.id+"/contents",{data:q})}var n=p.historyFn||g,m=p.hdaFn||o;var i=n(f);i.done(function(q){k=q;l.notify({status:"history data retrieved",historyJSON:k})});i.fail(function(s,q,r){l.reject(s,"loading the history")});var h=i.then(m);h.then(function(q){l.notify({status:"dataset data retrieved",historyJSON:k,hdaJSON:q});l.resolve(k,q)});h.fail(function(s,q,r){l.reject(s,"loading the datasets",{history:k})});return l};var b=Backbone.Collection.extend(LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/histories"});return{History:c,HistoryCollection:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/base-mvc"],function(b,a){var d=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",renameUrl:function(){var f=this.get("id");if(!f){return undefined}return galaxy_config.root+"history/rename_async?id="+this.get("id")},annotateUrl:function(){var f=this.get("id");if(!f){return undefined}return galaxy_config.root+"history/annotate_async?id="+this.get("id")},tagUrl:function(){var f=this.get("id");if(!f){return undefined}return galaxy_config.root+"tag/get_tagging_elt_async?item_id="+this.get("id")+"&item_class=History"},initialize:function(g,h,f){f=f||{};this.logger=f.logger||null;this.log(this+".initialize:",g,h,f);this.hdas=new b.HDACollection(h||[],{historyId:this.get("id")});if(h&&_.isArray(h)){this.hdas.reset(h)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(g,j,f,i,h){this.errorHandler(g,j,f,i,h)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(g,f){if(this.hdas){this.hdas.historyId=f}},this)},errorHandler:function(g,j,f,i,h){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(f,g){return f+g},0)},checkForUpdates:function(f){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(f)){f.call(this)}}return this},setUpdateTimeout:function(f){f=f||d.UPDATE_DELAY;var g=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){g.refresh()},f);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(g,f){g=g||[];f=f||{};var h=this;f.data=f.data||{};if(g.length){f.data.details=g.join(",")}var i=this.hdas.fetch(f);i.done(function(j){h.checkForUpdates(function(){this.fetch()})});return i},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});d.UPDATE_DELAY=4000;d.getHistoryData=function e(g,q){q=q||{};var k=q.hdaDetailIds||[];var m=jQuery.Deferred(),l=null;function h(r){return jQuery.ajax(galaxy_config.root+"api/histories/"+g)}function f(r){if(!r||!r.state_ids){return 0}return _.reduce(r.state_ids,function(s,u,t){return s+u.length},0)}function p(s){if(!f(s)){return[]}if(_.isFunction(k)){k=k(s)}var r=(k.length)?({details:k.join(",")}):({});return jQuery.ajax(galaxy_config.root+"api/histories/"+s.id+"/contents",{data:r})}var o=q.historyFn||h,n=q.hdaFn||p;var j=o(g);j.done(function(r){l=r;m.notify({status:"history data retrieved",historyJSON:l})});j.fail(function(t,r,s){m.reject(t,"loading the history")});var i=j.then(n);i.then(function(r){m.notify({status:"dataset data retrieved",historyJSON:l,hdaJSON:r});m.resolve(l,r)});i.fail(function(t,r,s){m.reject(t,"loading the datasets",{history:l})});return m};var c=Backbone.Collection.extend(a.LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories"});return{History:d,HistoryCollection:c}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations"],function(e,b,d,a,c){var f=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(g){g=g||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=g.selecting||false;this.annotationEditorShown=g.annotationEditorShown||false;this.tagsEditorShown=g.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,g)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this)},renderModel:function(){var g=$("<div/>");g.append(f.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(g).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(g);this._renderAnnotation(g)}g.find(".history-secondary-actions").prepend(this._renderSelectButton());g.find(".history-dataset-actions").toggle(this.selecting);g.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){var h=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDATagEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDATagEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){var h=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDAAnnotationEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDAAnnotationEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_renderSelectButton:function(g){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(g){g=g||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,g);if(!this.model){return}this._setUpDatasetActionsPopup(g);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var h=this;g.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(i){var j=h.model.get("name");if(i&&i!==j){h.$el.find(".history-name").text(i);h.model.save({name:i}).fail(function(){h.$el.find(".history-name").text(h.model.previous("name"))})}else{h.$el.find(".history-name").text(j)}}})},_setUpDatasetActionsPopup:function(g){var h=this;(new PopupMenu(g.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.hide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Unhide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.unhide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Delete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype["delete"];h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Undelete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.undelete;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var i=e.HistoryDatasetAssociation.prototype.purge;h.getSelectedHdaCollection().ajaxQueue(i)}}}]))},_handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},_handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},_createHdaView:function(h){var g=h.get("id"),i=new this.HDAViewClass({model:h,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[g],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(i);return i},_setUpHdaListeners:function(h){var g=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,h);h.on("selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.union(g.selectedHdaIds,[j])});h.on("de-selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.without(g.selectedHdaIds,j)})},toggleHDATagEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.annotationEditor){i.annotationEditor.toggle.apply(i.annotationEditor,h)}})},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$emptyMessage().fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(g);_.each(this.hdaViews,function(h){h.showSelector()});this.selectedHdaIds=[]},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(g);_.each(this.hdaViews,function(h){h.hideSelector()});this.selectedHdaIds=[]},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.select(g)})},deselectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.deselect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},getSelectedHdaCollection:function(){return new e.HDACollection(_.map(this.getSelectedHdaViews(),function(g){return g.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations"],function(e,b,d,a,c){var f=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(g){g=g||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=g.selecting||false;this.annotationEditorShown=g.annotationEditorShown||false;this.tagsEditorShown=g.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,g)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this)},renderModel:function(){var g=$("<div/>");g.append(f.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(g).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(g);this._renderAnnotation(g)}g.find(".history-secondary-actions").prepend(this._renderSelectButton());g.find(".history-dataset-actions").toggle(this.selecting);g.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){var h=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDATagEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDATagEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){var h=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDAAnnotationEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDAAnnotationEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_renderSelectButton:function(g){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(g){g=g||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,g);if(!this.model){return}this._setUpDatasetActionsPopup(g);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var h=this;g.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(i){var j=h.model.get("name");if(i&&i!==j){h.$el.find(".history-name").text(i);h.model.save({name:i}).fail(function(){h.$el.find(".history-name").text(h.model.previous("name"))})}else{h.$el.find(".history-name").text(j)}}})},_setUpDatasetActionsPopup:function(g){var h=this;(new PopupMenu(g.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.hide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Unhide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.unhide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Delete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype["delete"];h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Undelete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.undelete;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var i=e.HistoryDatasetAssociation.prototype.purge;h.getSelectedHdaCollection().ajaxQueue(i)}}}]))},_handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},_handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},_createHdaView:function(h){var g=h.get("id"),i=new this.HDAViewClass({model:h,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[g],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(i);return i},_setUpHdaListeners:function(h){var g=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,h);h.on("selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.union(g.selectedHdaIds,[j])});h.on("de-selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.without(g.selectedHdaIds,j)})},toggleHDATagEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.annotationEditor){i.annotationEditor.toggle.apply(i.annotationEditor,h)}})},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$emptyMessage().fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(g);_.each(this.hdaViews,function(h){h.showSelector()});this.selectedHdaIds=[]},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(g);_.each(this.hdaViews,function(h){h.hideSelector()});this.selectedHdaIds=[]},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.select(g)})},deselectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.deselect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},getSelectedHdaCollection:function(){return new e.HDACollection(_.map(this.getSelectedHdaViews(),function(g){return g.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:f}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base"],function(h,a){var g=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){var i="expandedHdas";this.save(i,_.extend(this.get(i),_.object([j],[true])))},removeExpandedHda:function(j){var i="expandedHdas";this.save(i,_.omit(this.get(i),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});g.storageKeyPrefix="history:";g.historyStorageKey=function f(i){if(!i){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+i)}return(g.storageKeyPrefix+i)};g.get=function d(i){return new g({id:g.historyStorageKey(i)})};g.clearAll=function c(j){for(var i in sessionStorage){if(i.indexOf(g.storageKeyPrefix)===0){sessionStorage.removeItem(i)}}};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.fxSpeed=_.has(i,"fxSpeed")?(i.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=i.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var j=_.pick(i,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,j,false);if(i.onready){i.onready.call(this)}},_setUpListeners:function(){this.on("error",function(j,m,i,l,k){this.errorHandler(j,m,i,l,k)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(i){this.log(this+"",arguments)},this)}return this},errorHandler:function(k,n,j,m,l){console.error(k,n,j,m,l);if(n&&n.status===0&&n.readyState===0){}else{if(n&&n.status===502){}else{var i=this._parseErrorMessage(k,n,j,m,l);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",i.message,i.details)})}else{this.displayMessage("error",i.message,i.details)}}}},_parseErrorMessage:function(l,p,k,o,n){var j=Galaxy.currUser,i={message:this._bePolite(o),details:{user:(j instanceof User)?(j.toJSON()):(j+""),source:(l instanceof Backbone.Model)?(l.toJSON()):(l+""),xhr:p,options:(p)?(_.omit(k,"xhr")):(k)}};_.extend(i.details,n||{});if(p&&_.isFunction(p.getAllResponseHeaders)){var m=p.getAllResponseHeaders();m=_.compact(m.split("\n"));m=_.map(m,function(q){return q.split(": ")});i.details.xhr.responseHeaders=_.object(m)}return i},_bePolite:function(i){i=i||_l("An error occurred while getting updates from the server");return i+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(k,j,i,m){var l=function(n){return _.keys(g.get(n.id).get("expandedHdas"))};return this.loadHistory(k,j,i,m,l)},loadHistory:function(l,k,j,o,m){var i=this;k=k||{};i.trigger("loading-history",i);var n=h.History.getHistoryData(l,{historyFn:j,hdaFn:o,hdaDetailIds:k.initiallyExpanded||m});return i._loadHistoryFromXHR(n,k).fail(function(r,p,q){i.trigger("error",i,r,k,_l("An error was encountered while "+p),{historyId:l,history:q||{}})}).always(function(){i.trigger("loading-done",i)})},_loadHistoryFromXHR:function(k,j){var i=this;k.then(function(l,m){i.JSONToModel(l,m,j)});k.fail(function(m,l){i.render()});return k},JSONToModel:function(l,i,j){this.log("JSONToModel:",l,i,j);j=j||{};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}var k=new h.History(l,i,j);this.setModel(k);return this},setModel:function(j,i,k){i=i||{};k=(k!==undefined)?(k):(true);this.log("setModel:",j,i,k);this.freeModel();this.selectedHdaIds=[];if(j){if(Galaxy&&Galaxy.currUser){j.user=Galaxy.currUser.toJSON()}this.model=j;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(i.initiallyExpanded,i.show_deleted,i.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(k){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(j,i,k){this.storage=new g({id:g.historyStorageKey(this.model.get("id"))});if(_.isObject(j)){this.storage.set("exandedHdas",j)}if(_.isBoolean(i)){this.storage.set("show_deleted",i)}if(_.isBoolean(k)){this.storage.set("show_hidden",k)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(j,l,i,k){this.errorHandler(j,l,i,k)},this);return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(this.model){j=this.renderModel()}else{j=this.renderWithoutModel()}$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderWithoutModel:function(){var i=$("<div/>"),j=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return i.append(j)},renderModel:function(){var i=$("<div/>");i.append(b.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderEmptyMsg:function(k){var j=this,i=j.$emptyMessage(k);if(!_.isEmpty(j.hdaViews)){i.hide()}else{if(j.searchFor){i.text(j.noneFoundMsg).show()}else{i.text(j.emptyMsg).show()}}return this},_renderSearchButton:function(i){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(i.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},$messages:function(i){return(i||this.$el).find(".message-container")},$emptyMessage:function(i){return(i||this.$el).find(".empty-history-message")},renderHdas:function(j){j=j||this.$el;var i=this,l={},k=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(j).empty();if(k.length){k.each(function(n){var m=n.get("id"),o=i._createHdaView(n);l[m]=o;if(_.contains(i.selectedHdaIds,m)){o.selected=true}i.attachHdaView(o.render(),j)})}this.hdaViews=l;this._renderEmptyMsg(j);return this.hdaViews},_createHdaView:function(j){var i=j.get("id"),k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;j.on("error",function(l,n,k,m){i.errorHandler(l,n,k,m)});j.on("body-expanded",function(k){i.storage.addExpandedHda(k)});j.on("body-collapsed",function(k){i.storage.removeExpandedHda(k)});return this},attachHdaView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.prepend(k.$el);return this},addHdaView:function(l){this.log("add."+this,l);var j=this;if(!l.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return j}$({}).queue([function k(n){var m=j.$emptyMessage();if(m.is(":visible")){m.fadeOut(j.fxSpeed,n)}else{n()}},function i(m){var n=j._createHdaView(l);j.hdaViews[l.id]=n;n.render().$el.hide();j.scrollToTop();j.attachHdaView(n);n.$el.slideDown(j.fxSpeed)}]);return j},refreshHdas:function(j,i){if(this.model){return this.model.refresh(j,i)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(i){i.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(i){i=(i!==undefined)?(i):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",i);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(i){i=(i!==undefined)?(i):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",i);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(j){var k=this,l=".history-search-input";function i(m){if(k.model.hdas.haveDetails()){k.searchHdas(m);return}k.$el.find(l).searchInput("toggle-loading");k.model.hdas.fetchAllDetails({silent:true}).always(function(){k.$el.find(l).searchInput("toggle-loading")}).done(function(){k.searchHdas(m)})}j.searchInput({initialVal:k.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:i,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return j},toggleSearchControls:function(k,i){var j=this.$el.find(".history-search-controls"),l=(jQuery.type(k)==="number")?(k):(this.fxSpeed);i=(i!==undefined)?(i):(!j.is(":visible"));if(i){j.slideDown(l,function(){$(this).find("input").focus()})}else{j.slideUp(l)}return i},searchHdas:function(i){var j=this;this.searchFor=i;this.filters=[function(k){return k.matchesAll(j.searchFor)}];this.trigger("search:searching",i,this);this.renderHdas();return this},clearHdaSearch:function(i){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(j,i,k){i=(i!==undefined)?(i):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,k)}else{this.$el.fadeOut(i);this.indicator.show(j,i,k)}},_hideLoadingIndicator:function(i,j){i=(i!==undefined)?(i):(this.fxSpeed);if(this.indicator){this.indicator.hide(i,j)}},displayMessage:function(n,o,m){var k=this;this.scrollToTop();var l=this.$messages(),i=$("<div/>").addClass(n+"message").html(o);if(!_.isEmpty(m)){var j=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(k._messageToModalOptions(n,o,m));return false});i.append(" ",j)}return l.html(i)},_messageToModalOptions:function(m,o,l){var i=this,n=$("<div/>"),k={title:"Details"};function j(p){p=_.omit(p,_.functions(p));return["<table>",_.map(p,function(r,q){r=(_.isObject(r))?(j(r)):(r);return'<tr><td style="vertical-align: top; color: grey">'+q+'</td><td style="padding-left: 8px">'+r+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(l)){k.body=n.append(j(l))}else{k.body=n.html(l)}k.buttons={Ok:function(){Galaxy.modal.hide();i.clearMessages()}};return k},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(i){this.$container().scrollTop(i);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(j){if((!j)||(!this.hdaViews[j])){return this}var i=this.hdaViews[j];this.scrollTo(i.el.offsetTop);return this},scrollToHid:function(i){var j=this.model.hdas.getByHid(i);if(!j){return this}return this.scrollToId(j.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var e=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',_l("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',_l("You are over your disk quota."),_l("Tool execution is on hold until your disk usage drops below your allocated quota."),"</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',_l("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',_l("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',_l("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',_l("Your history is empty. Click 'Get Data' on the left pane to start"),"</div>"].join("");b.templates={historyPanel:function(i){return _.template(e,i,{variable:"history"})}};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/base-mvc"],function(e,a,d){var g=d.SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(k){var j="expandedHdas";this.save(j,_.extend(this.get(j),_.object([k],[true])))},removeExpandedHda:function(k){var j="expandedHdas";this.save(j,_.omit(this.get(j),k))},toString:function(){return"HistoryPrefs("+this.id+")"}});g.storageKeyPrefix="history:";g.historyStorageKey=function c(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return(g.storageKeyPrefix+j)};g.get=function b(j){return new g({id:g.historyStorageKey(j)})};g.clearAll=function f(k){for(var j in sessionStorage){if(j.indexOf(g.storageKeyPrefix)===0){sessionStorage.removeItem(j)}}};var h=Backbone.View.extend(d.LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.linkTarget=j.linkTarget||"_blank";this.fxSpeed=_.has(j,"fxSpeed")?(j.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=j.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var k=_.pick(j,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,k,false);if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}return this},errorHandler:function(l,o,k,n,m){console.error(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{var j=this._parseErrorMessage(l,o,k,n,m);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(l,k,j,n){var m=function(o){return _.keys(g.get(o.id).get("expandedHdas"))};return this.loadHistory(l,k,j,n,m)},loadHistory:function(m,l,k,p,n){var j=this;l=l||{};j.trigger("loading-history",j);var o=e.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return j._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.JSONToModel(m,n,k)});l.fail(function(n,m){j.render()});return l},JSONToModel:function(m,j,k){this.log("JSONToModel:",m,j,k);k=k||{};var l=new e.History(m,j,k);this.setModel(l);return this},setModel:function(k,j,l){j=j||{};l=(l!==undefined)?(l):(true);this.log("setModel:",k,j,l);this.freeModel();this.selectedHdaIds=[];if(k){this.model=k;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(l){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(k,j,l){this.storage=new g({id:g.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);return this},render:function(l,m){this.log("render:",l,m);l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children())}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");j.append(h.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(j).text(this.emptyMsg);j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},_renderEmptyMsg:function(l){var k=this,j=k.$emptyMessage(l);if(!_.isEmpty(k.hdaViews)){j.hide()}else{if(k.searchFor){j.text(k.noneFoundMsg).show()}else{j.text(k.emptyMsg).show()}}return this},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(j.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(j){return(j||this.$el).find(".datasets-list")},$messages:function(j){return(j||this.$el).find(".message-container")},$emptyMessage:function(j){return(j||this.$el).find(".empty-history-message")},renderHdas:function(k){k=k||this.$el;var j=this,m={},l=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(k).empty();if(l.length){l.each(function(o){var n=o.get("id"),p=j._createHdaView(o);m[n]=p;if(_.contains(j.selectedHdaIds,n)){p.selected=true}j.attachHdaView(p.render(),k)})}this.hdaViews=m;this._renderEmptyMsg(k);return this.hdaViews},_createHdaView:function(k){var j=k.get("id"),l=new this.HDAViewClass({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(l);return l},_setUpHdaListeners:function(k){var j=this;k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)});k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});return this},attachHdaView:function(l,k){k=k||this.$el;var j=this.$datasetsList(k);j.prepend(l.$el);return this},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return k}$({}).queue([function l(o){var n=k.$emptyMessage();if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(n){var o=k._createHdaView(m);k.hdaViews[m.id]=o;o.render().$el.hide();k.scrollToTop();k.attachHdaView(o);o.$el.slideDown(k.fxSpeed)}]);return k},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(j){j=(j!==undefined)?(j):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",j);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(j){j=(j!==undefined)?(j):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",j);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(k){var l=this,m=".history-search-input";function j(n){if(l.model.hdas.haveDetails()){l.searchHdas(n);return}l.$el.find(m).searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(m).searchInput("toggle-loading")}).done(function(){l.searchHdas(n)})}k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return k},toggleSearchControls:function(l,j){var k=this.$el.find(".history-search-controls"),m=(jQuery.type(l)==="number")?(l):(this.fxSpeed);j=(j!==undefined)?(j):(!k.is(":visible"));if(j){k.slideDown(m,function(){$(this).find("input").focus()})}else{k.slideUp(m)}return j},searchHdas:function(j){var k=this;this.searchFor=j;this.filters=[function(l){return l.matchesAll(k.searchFor)}];this.trigger("search:searching",j,this);this.renderHdas();return this},clearHdaSearch:function(j){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},_hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$messages(),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l._messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},_messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(j){this.$container().scrollTop(j);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k];this.scrollTo(j.el.offsetTop);return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var i=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',_l("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',_l("You are over your disk quota."),_l("Tool execution is on hold until your disk usage drops below your allocated quota."),"</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',_l("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',_l("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',_l("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',_l("Your history is empty. Click 'Get Data' on the left pane to start"),"</div>"].join("");h.templates={historyPanel:function(j){return _.template(i,j,{variable:"history"})}};return{ReadOnlyHistoryPanel:h}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/tags.js --- a/static/scripts/packed/mvc/tags.js +++ b/static/scripts/packed/mvc/tags.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(b){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(b.$activator,b)},render:function(){var b=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return b._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',_l("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var b=this.model.get("tags");if(!_.isArray(b)||_.isEmpty(b)){return""}return b.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var b=this;this.$input().on("change",function(c){b.model.save({tags:c.val},{silent:true});if(c.added){b._addNewTagToTagsUsed(c.added.text+"")}})},_addNewTagToTagsUsed:function(b){var c=Galaxy.currUser.get("tags_used");if(!_.contains(c,b)){c.push(b);c.sort();Galaxy.currUser.set("tags_used",c)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:a}}); \ No newline at end of file +define(["mvc/base-mvc"],function(a){var b=Backbone.View.extend(a.LoggableMixin).extend(a.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(c){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(c.$activator,c)},render:function(){var c=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return c._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',_l("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var c=this.model.get("tags");if(!_.isArray(c)||_.isEmpty(c)){return""}return c.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var c=this;this.$input().on("change",function(d){c.model.save({tags:d.val},{silent:true});if(d.added){c._addNewTagToTagsUsed(d.added.text+"")}})},_addNewTagToTagsUsed:function(c){var d=Galaxy.currUser.get("tags_used");if(!_.contains(d,c)){d.push(c);d.sort();Galaxy.currUser.set("tags_used",d)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:b}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/user/user-model.js --- a/static/scripts/packed/mvc/user/user-model.js +++ b/static/scripts/packed/mvc/user/user-model.js @@ -1,1 +1,1 @@ -var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return Backbone.Model.prototype.fetch.call(this,b)},clearSessionStorage:function(){for(var a in sessionStorage){if(a.indexOf("history:")===0){sessionStorage.removeItem(a)}else{if(a==="history-panel"){sessionStorage.removeItem(a)}}}},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:galaxy_config.root+"api/users"}); \ No newline at end of file +define(["mvc/base-mvc"],function(a){var c=Backbone.Model.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(d){this.log("User.initialize:",d);this.on("loaded",function(e,f){this.log(this+" has loaded:",e,f)});this.on("change",function(e,f){this.log(this+" has changed:",e,f.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(g,e){g=g||c.CURRENT_ID_STR;e=e||{};var d=this,f=e.success;e.success=function(i,h){d.trigger("loaded",i,h);if(f){f(i,h)}};if(g===c.CURRENT_ID_STR){e.url=this.urlRoot+"/"+c.CURRENT_ID_STR}return Backbone.Model.prototype.fetch.call(this,e)},clearSessionStorage:function(){for(var d in sessionStorage){if(d.indexOf("history:")===0){sessionStorage.removeItem(d)}else{if(d==="history-panel"){sessionStorage.removeItem(d)}}}},toString:function(){var d=[this.get("username")];if(this.get("id")){d.unshift(this.get("id"));d.push(this.get("email"))}return"User("+d.join(":")+")"}});c.CURRENT_ID_STR="current";c.getCurrentUserFromApi=function(e){var d=new c();d.loadFromApi(c.CURRENT_ID_STR,e);return d};var b=Backbone.Collection.extend(a.LoggableMixin).extend({model:c,urlRoot:galaxy_config.root+"api/users"});return{User:c}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/user/user-quotameter.js --- a/static/scripts/packed/mvc/user/user-quotameter.js +++ b/static/scripts/packed/mvc/user/user-quotameter.js @@ -1,1 +1,1 @@ -var UserQuotaMeter=Backbone.View.extend(LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100},initialize:function(a){this.log(this+".initialize:",a);_.extend(this.options,a);this.model.bind("change:quota_percent change:total_disk_usage",this.render,this)},update:function(a){this.log(this+" updating user data...",a);this.model.loadFromApi(this.model.get("id"),a);return this},isOverQuota:function(){return(this.model.get("quota_percent")!==null&&this.model.get("quota_percent")>=this.options.errorAtPercent)},_render_quota:function(){var a=this.model.toJSON(),c=a.quota_percent,b=$(this._templateQuotaMeter(a)),d=b.find(".progress-bar");if(this.isOverQuota()){d.attr("class","progress-bar progress-bar-danger");b.find(".quota-meter-text").css("color","white");this.trigger("quota:over",a)}else{if(c>=this.options.warnAtPercent){d.attr("class","progress-bar progress-bar-warning");this.trigger("quota:under quota:under:approaching",a)}else{d.attr("class","progress-bar progress-bar-success");this.trigger("quota:under quota:under:ok",a)}}return b},_render_usage:function(){var a=$(this._templateUsage(this.model.toJSON()));this.log(this+".rendering usage:",a);return a},render:function(){var a=null;this.log(this+".model.quota_percent:",this.model.get("quota_percent"));if((this.model.get("quota_percent")===null)||(this.model.get("quota_percent")===undefined)){a=this._render_usage()}else{a=this._render_quota()}this.$el.html(a);this.$el.find(".quota-meter-text").tooltip();return this},_templateQuotaMeter:function(a){return['<div id="quota-meter" class="quota-meter progress">','<div class="progress-bar" style="width: ',a.quota_percent,'%"></div>','<div class="quota-meter-text" style="top: 6px"',((a.nice_total_disk_usage)?(' title="Using '+a.nice_total_disk_usage+'">'):(">")),_l("Using")," ",a.quota_percent,"%","</div>","</div>"].join("")},_templateUsage:function(a){return['<div id="quota-meter" class="quota-meter" style="background-color: transparent">','<div class="quota-meter-text" style="top: 6px; color: white">',((a.nice_total_disk_usage)?(_l("Using ")+a.nice_total_disk_usage):("")),"</div>","</div>"].join("")},toString:function(){return"UserQuotaMeter("+this.model+")"}}); \ No newline at end of file +define(["mvc/base-mvc"],function(a){var b=Backbone.View.extend(a.LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100},initialize:function(c){this.log(this+".initialize:",c);_.extend(this.options,c);this.model.bind("change:quota_percent change:total_disk_usage",this.render,this)},update:function(c){this.log(this+" updating user data...",c);this.model.loadFromApi(this.model.get("id"),c);return this},isOverQuota:function(){return(this.model.get("quota_percent")!==null&&this.model.get("quota_percent")>=this.options.errorAtPercent)},_render_quota:function(){var c=this.model.toJSON(),e=c.quota_percent,d=$(this._templateQuotaMeter(c)),f=d.find(".progress-bar");if(this.isOverQuota()){f.attr("class","progress-bar progress-bar-danger");d.find(".quota-meter-text").css("color","white");this.trigger("quota:over",c)}else{if(e>=this.options.warnAtPercent){f.attr("class","progress-bar progress-bar-warning");this.trigger("quota:under quota:under:approaching",c)}else{f.attr("class","progress-bar progress-bar-success");this.trigger("quota:under quota:under:ok",c)}}return d},_render_usage:function(){var c=$(this._templateUsage(this.model.toJSON()));this.log(this+".rendering usage:",c);return c},render:function(){var c=null;this.log(this+".model.quota_percent:",this.model.get("quota_percent"));if((this.model.get("quota_percent")===null)||(this.model.get("quota_percent")===undefined)){c=this._render_usage()}else{c=this._render_quota()}this.$el.html(c);this.$el.find(".quota-meter-text").tooltip();return this},_templateQuotaMeter:function(c){return['<div id="quota-meter" class="quota-meter progress">','<div class="progress-bar" style="width: ',c.quota_percent,'%"></div>','<div class="quota-meter-text" style="top: 6px"',((c.nice_total_disk_usage)?(' title="Using '+c.nice_total_disk_usage+'">'):(">")),_l("Using")," ",c.quota_percent,"%","</div>","</div>"].join("")},_templateUsage:function(c){return['<div id="quota-meter" class="quota-meter" style="background-color: transparent">','<div class="quota-meter-text" style="top: 6px; color: white">',((c.nice_total_disk_usage)?(_l("Using ")+c.nice_total_disk_usage):("")),"</div>","</div>"].join("")},toString:function(){return"UserQuotaMeter("+this.model+")"}});return{UserQuotaMeter:b}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 static/scripts/packed/mvc/visualization/visualization-model.js --- a/static/scripts/packed/mvc/visualization/visualization-model.js +++ b/static/scripts/packed/mvc/visualization/visualization-model.js @@ -1,1 +1,1 @@ -var Visualization=Backbone.Model.extend(LoggableMixin).extend({defaults:{config:{}},urlRoot:function(){var a="/api/visualizations";return((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root+a):(a))},initialize:function(a){this.log(this+".initialize",a,this.attributes);if(_.isObject(a.config)&&_.isObject(this.defaults.config)){_.defaults(a.config,this.defaults.config)}this._setUpListeners()},_setUpListeners:function(){},set:function(b,c){if(b==="config"){var a=this.get("config");if(_.isObject(a)){c=_.extend(_.clone(a),c)}}Backbone.Model.prototype.set.call(this,b,c);return this},toString:function(){var a=this.get("id")||"";if(this.get("title")){a+=":"+this.get("title")}return"Visualization("+a+")"}});var VisualizationCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(b,a){a=a||{}},set:function(c,a){var b=this;c=_.map(c,function(e){var f=b.get(e.id);if(!f){return e}var d=f.toJSON();_.extend(d,e);return d});Backbone.Collection.prototype.set.call(this,c,a)},toString:function(){return(["VisualizationCollection(",[this.historyId,this.length].join(),")"].join(""))}}); \ No newline at end of file +var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var a="/api/visualizations";return((window.galaxy_config&&galaxy_config.root)?(galaxy_config.root+a):(a))},initialize:function(a){if(_.isObject(a.config)&&_.isObject(this.defaults.config)){_.defaults(a.config,this.defaults.config)}this._setUpListeners()},_setUpListeners:function(){},set:function(b,c){if(b==="config"){var a=this.get("config");if(_.isObject(a)){c=_.extend(_.clone(a),c)}}Backbone.Model.prototype.set.call(this,b,c);return this},toString:function(){var a=this.get("id")||"";if(this.get("title")){a+=":"+this.get("title")}return"Visualization("+a+")"}});var VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(b,a){a=a||{}},set:function(c,a){var b=this;c=_.map(c,function(e){var f=b.get(e.id);if(!f){return e}var d=f.toJSON();_.extend(d,e);return d});Backbone.Collection.prototype.set.call(this,c,a)},toString:function(){return(["VisualizationCollection(",[this.historyId,this.length].join(),")"].join(""))}}); \ No newline at end of file diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -66,25 +66,28 @@ } %> - ${h.js( "mvc/base-mvc", "utils/localization", "mvc/user/user-model", "mvc/user/user-quotameter" )} + ##${h.js( "mvc/base-mvc", "utils/localization", "mvc/user/user-model", "mvc/user/user-quotameter" )} + ${h.js( "utils/localization" )} ## load the frame manager <script type="text/javascript"> if( !window.Galaxy ){ - window.Galaxy = {}; + Galaxy = {}; } - ## fetch the current user data from trans - Galaxy.currUser = new User(${ h.to_json_string( get_user_json(), indent=2 ) }); ## load additional style sheet - if (window != window.top) - $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); + if (window != window.top){ + $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">') + .appendTo('head'); + } ## load galaxy js-modules - $(function() { - require(['galaxy.masthead', 'galaxy.menu', 'mvc/ui/ui-modal', 'galaxy.frame', 'mvc/upload/upload-view'], - function(mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload) - { + require([ + 'galaxy.masthead', 'galaxy.menu', 'mvc/ui/ui-modal', 'galaxy.frame', 'mvc/upload/upload-view', + 'mvc/user/user-model', + 'mvc/user/user-quotameter' + ], function( mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload, user, quotameter ){ + $(function() { ## check if masthead is available if (Galaxy.masthead) return; @@ -106,11 +109,14 @@ ## add upload plugin Galaxy.upload = new GalaxyUpload(masthead_config); + if( !Galaxy.currUser ){ + Galaxy.currUser = new user.User(${ h.to_json_string( get_user_json(), indent=2 ) }); + } ## set up the quota meter (And fetch the current user data from trans) ## add quota meter to masthead - Galaxy.quotaMeter = new UserQuotaMeter({ + Galaxy.quotaMeter = new quotameter.UserQuotaMeter({ model : Galaxy.currUser, - el : $(Galaxy.masthead.el).find('.quota-meter-container') + el : Galaxy.masthead.$('.quota-meter-container') }).render(); }); }); diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ b/templates/webapps/galaxy/history/history_panel.mako @@ -16,7 +16,8 @@ linkTarget : 'galaxy_main', onready : function loadAsCurrentHistoryPanel(){ var panel = this; - this.connectToQuotaMeter( Galaxy.quotaMeter ).connectToOptionsMenu( Galaxy.historyOptionsMenu ); + this.connectToQuotaMeter( Galaxy.quotaMeter ) + .connectToOptionsMenu( Galaxy.historyOptionsMenu ); this.loadCurrentHistory() .fail( function(){ panel.render(); @@ -92,7 +93,6 @@ <%def name="history_panel_javascripts()"> ${h.js( "utils/localization", - "mvc/base-mvc" )} ${localize_js_strings([ diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -73,17 +73,11 @@ ${history_panel_javascripts()} %if not use_panels: - ${h.js( 'mvc/user/user-model' )} +<script type="text/javascript"> +window.Galaxy = {}; +</script> %endif -<script type="text/javascript"> - ##TODO: remove when Galaxy is either ensured or removed from the history panel - var using_panels = ${ 'false' if not use_panels else 'true' }; - %if not use_panels: - window.Galaxy = {}; - Galaxy.currUser = new User(${h.to_json_string( get_user_json() )}); - %endif -</script></%def> ## ---------------------------------------------------------------------------- @@ -163,8 +157,12 @@ require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" - })([ panelToUse.location ], function( panelMod ){ + })([ 'mvc/user/user-model', panelToUse.location ], function( user, panelMod ){ $(function(){ + if( !Galaxy.currUser ){ + Galaxy.currUser = new user.User( ${h.to_json_string( get_user_json() )} ); + } + var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. historyModel = require( 'mvc/history/history-model' ), diff -r 08f389432f6876a5af1ad54ef2f25e4d06310999 -r 7155334f5ec5743188f90053a54ac851be3e2d58 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -22,47 +22,45 @@ <%def name="javascripts()"> ${parent.javascripts()} ${history_panel_javascripts()} -${h.js( - "mvc/user/user-model" -)} <script type="text/javascript"> - if( !window.Galaxy ){ - window.Galaxy = {}; - Galaxy.currUser = new User(${h.to_json_string( get_user_json() )}); - } +if( !window.Galaxy ){ + window.Galaxy = {}; +} +$(function(){ + $( 'body' ).addClass( 'historyPage' ).addClass( 'history-panel' ); +}); +require([ + 'mvc/user/user-model', + 'mvc/history/current-history-panel' +], function( user, historyPanel ){ $(function(){ - $( 'body' ).addClass( 'historyPage' ).addClass( 'history-panel' ); + Galaxy.currUser = new user.User( ${h.to_json_string( get_user_json() )} ); + // history module is already in the dpn chain from the panel. We can re-scope it here. + var historyModel = require( 'mvc/history/history-model' ), + debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, + historyJSON = ${h.to_json_string( history )}, + hdaJSON = ${h.to_json_string( hdas )}; + + var history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + var panel = new historyPanel.CurrentHistoryPanel({ + show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, + show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, + el : $( "body.historyPage" ), + model : history, + onready : function(){ + this.render(); + if( Galaxy ){ + Galaxy.currHistoryPanel = this; + } + } + }); }); -</script> - -<script type="text/javascript"> -onhistoryready.done( function( historyPanel ){ - - // history module is already in the dpn chain from the panel. We can re-scope it here. - var historyModel = require( 'mvc/history/history-model' ), - debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, - historyJSON = ${h.to_json_string( history )}, - hdaJSON = ${h.to_json_string( hdas )}; - - var history = new historyModel.History( historyJSON, hdaJSON, { - logger: ( debugging )?( console ):( null ) - }); - - var panel = new historyPanel.HistoryPanel({ - show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, - show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, - el : $( "body.historyPage" ), - model : history, - onready : function(){ - this.render(); - if( Galaxy ){ - Galaxy.currHistoryPanel = this; - } - } - }); -}) +}); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix: add missing js model to scatterplot
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/08f389432f68/ Changeset: 08f389432f68 User: carlfeberhard Date: 2014-03-20 21:34:54 Summary: Fix: add missing js model to scatterplot Affected #: 1 file diff -r 8fb3637b9655a55cc54e1e5fd872bf0f9b9a48c6 -r 08f389432f6876a5af1ad54ef2f25e4d06310999 config/plugins/visualizations/scatterplot/src/scatterplot-model.js --- /dev/null +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-model.js @@ -0,0 +1,39 @@ +var ScatterplotModel = Visualization.extend({ + + defaults : { + type : 'scatterplot', + + config : { + // shouldn't be needed for properly saved splots - also often incorrect + //xColumn : 0, + //yColumn : 1, + + pagination : { + currPage : 0, + perPage : 3000 + }, + + // graph style + width : 400, + height : 400, + + margin : { + top : 16, + right : 16, + bottom : 40, + left : 54 + }, + + xTicks : 10, + xLabel : 'X', + yTicks : 10, + yLabel : 'Y', + + datapointSize : 4, + animDuration : 500, + + scale : 1, + translate : [ 0, 0 ] + } + } +}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: Functional test script for granting admin privileges on a repository.
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8fb3637b9655/ Changeset: 8fb3637b9655 User: davebgx Date: 2014-03-20 20:28:26 Summary: Functional test script for granting admin privileges on a repository. Affected #: 3 files diff -r 593833a7ff5395bb585513ba6881012174909180 -r 8fb3637b9655a55cc54e1e5fd872bf0f9b9a48c6 test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -75,6 +75,19 @@ return role raise AssertionError( "Private role not found for user '%s'" % user.email ) +def get_role( user, role_name ): + for role in user.all_roles(): + if role.name == role_name: + return role + return None + +def get_repository_role_association( repository_id, role_id ): + rra = sa_session.query( model.RepositoryRoleAssociation ) \ + .filter( and_( model.RepositoryRoleAssociation.table.c.role_id == role_id, + model.RepositoryRoleAssociation.table.c.repository_id == repository_id ) ) \ + .first() + return rra + def get_repository_reviews( repository_id, reviewer_user_id=None, changeset_revision=None ): if reviewer_user_id and changeset_revision: reviews = sa_session.query( model.RepositoryReview ) \ diff -r 593833a7ff5395bb585513ba6881012174909180 -r 8fb3637b9655a55cc54e1e5fd872bf0f9b9a48c6 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -67,6 +67,14 @@ url = '/repository_review/create_component?operation=create' self.visit_url( url ) self.submit_form( 1, 'create_component_button', **kwd ) + + def assign_admin_role( self, repository, user ): + # As elsewhere, twill limits the possibility of submitting the form, this time due to not executing the javascript + # attached to the role selection form. Visit the action url directly with the necessary parameters. + url = '/repository/manage_repository_admins?id=%s&in_users=%d&manage_role_associations_button=Save' % \ + ( self.security.encode_id( repository.id ), user.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed=[ 'Role', 'has been associated' ] ) def browse_category( self, category, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/browse_valid_categories?sort=name&operation=valid_repositories_by_category&id=%s' % \ @@ -518,7 +526,7 @@ tc.submit( "manage_categories_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def edit_repository_information( self, repository, **kwd ): + def edit_repository_information( self, repository, revert=True, **kwd ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) @@ -530,12 +538,13 @@ strings_displayed.append( self.escape_html( kwd[ input_elem_name ] ) ) tc.submit( "edit_repository_button" ) self.check_for_strings( strings_displayed ) - strings_displayed = [] - for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: - tc.fv( "edit_repository", input_elem_name, original_information[ input_elem_name ] ) - strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) - tc.submit( "edit_repository_button" ) - self.check_for_strings( strings_displayed ) + if revert: + strings_displayed = [] + for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: + tc.fv( "edit_repository", input_elem_name, original_information[ input_elem_name ] ) + strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) + tc.submit( "edit_repository_button" ) + self.check_for_strings( strings_displayed ) def enable_email_alerts( self, repository, strings_displayed=[], strings_not_displayed=[] ): repository_id = self.security.encode_id( repository.id ) diff -r 593833a7ff5395bb585513ba6881012174909180 -r 8fb3637b9655a55cc54e1e5fd872bf0f9b9a48c6 test/tool_shed/functional/test_0530_repository_admin_feature.py --- /dev/null +++ b/test/tool_shed/functional/test_0530_repository_admin_feature.py @@ -0,0 +1,165 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +import logging + +log = logging.getLogger( __name__ ) + +repository_name = 'filtering_0530' +repository_description = 'Filtering repository for test 0530' +repository_long_description = 'This is the filtering repository for test 0530.' +category_name = 'Test 0530 Repository Admin Role' +category_description = 'Verify the functionality of the code that handles the repository admin role.' + +''' +1. Create new repository as user user1. + +2. Check to make sure a new role was created named <repo_name>_user1_admin. + +3. Check to make sure a new repository_role_association record was created with appropriate repository id and role id. + +4. Change the name of the repository created in step 1 - this can be done as long as the repository has not been installed or cloned. + +5. Make sure the name of the role initially inspected in Step 2 has been changed to reflect the new repository name from Step 4. + +6. Log into the Tool Shed as a user that is not the repository owner (e.g., user2) and make sure the repository name + and description cannot be changed. + +7. As user user1, add user user2 as a repository admin user. + +8. Log into the Tool Shed as user user2 and make sure the repository name and description can now be changed. +''' + + +class TestRepositoryAdminRole( ShedTwillTestCase ): + '''Verify that the code correctly handles the repository admin role.''' + + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + test_user_2 = self.test_db_util.get_user( common.test_user_2_email ) + assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % test_user_2_email + test_user_2_private_role = self.test_db_util.get_private_role( test_user_2 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = self.test_db_util.get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = self.test_db_util.get_private_role( admin_user ) + + def test_0005_create_filtering_repository( self ): + """Create and populate the filtering_0530 repository.""" + ''' + This is step 1 - Create new repository as user user1. + ''' + category = self.create_category( name=category_name, description=category_description ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + repository = self.get_or_create_repository( name=repository_name, + description=repository_description, + long_description=repository_long_description, + owner=common.test_user_1_name, + category_id=self.security.encode_id( category.id ), + strings_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0010_verify_repository_admin_role_exists( self ): + '''Verify that the role filtering_0530_user1_admin exists.''' + ''' + This is step 2 - Check to make sure a new role was created named filtering_0530_user1_admin. + ''' + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + repository_admin_role = self.test_db_util.get_role( test_user_1, 'filtering_0530_user1_admin' ) + assert repository_admin_role is not None, 'Admin role for filtering_0530 was not created.' + + def test_0015_verify_repository_role_association( self ): + '''Verify that the filtering_0530_user1_admin role is associated with the filtering_0530 repository.''' + ''' + This is step 3 - Check to make sure a new repository_role_association record was created with appropriate repository id and role id. + ''' + repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + repository_admin_role = self.test_db_util.get_role( test_user_1, 'filtering_0530_user1_admin' ) + repository_role_association = self.test_db_util.get_repository_role_association( repository.id, repository_admin_role.id ) + assert repository_role_association is not None, 'Repository filtering_0530 is not associated with the filtering_0530_user1_admin role.' + + def test_0020_rename_repository( self ): + '''Rename the repository to renamed_filtering_0530.''' + ''' + This is step 4 - Change the name of the repository created in step 1 - this can be done as long as the repository has not + been installed or cloned. + ''' + repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.edit_repository_information( repository, revert=False, repo_name='renamed_filtering_0530' ) + self.test_db_util.refresh( repository ) + assert repository.name == 'renamed_filtering_0530', 'Repository was not renamed to renamed_filtering_0530.' + + def test_0025_check_admin_role_name( self ): + return + '''Check that a role renamed_filtering_0530_user1_admin now exists, and filtering_0530_user1_admin does not.''' + ''' + This is step 5 - Make sure the name of the role initially inspected in Step 2 has been changed to reflect the + new repository name from Step 4. + ''' + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + old_repository_admin_role = self.test_db_util.get_role( test_user_1, 'filtering_0530_%s_admin' % test_user_1.username ) + assert old_repository_admin_role is None, 'Admin role filtering_0530_user1_admin incorrectly exists.' + new_repository_admin_role = self.test_db_util.get_role( test_user_1, 'renamed_filtering_0530_%s_admin' % test_user_1.username ) + assert new_repository_admin_role is not None, 'Admin role renamed_filtering_0530_user1_admin does not exist.' + + def test_0030_verify_access_denied( self ): + '''Make sure a non-admin user can't modify the repository.''' + ''' + This is step 6 - Log into the Tool Shed as a user that is not the repository owner (e.g., user2) and make sure the repository + name and description cannot be changed. + ''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = self.test_db_util.get_repository_by_name_and_owner( 'renamed_filtering_0530', common.test_user_1_name ) + strings_not_displayed = [ 'Manage repository' ] + strings_displayed = [ 'View repository' ] + self.display_manage_repository_page( repository, strings_not_displayed=strings_not_displayed ) + self.submit_form( button='edit_repository_button', description='This description has been modified.' ) + strings_displayed = [ 'You are not the owner of this repository, so you cannot administer it.' ] + strings_not_displayed = [ 'The repository information has been updated.' ] + self.check_for_strings( strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) + + def test_0035_grant_admin_role( self ): + '''Grant the repository admin role to user2.''' + ''' + This is step 7 - As user user1, add user user2 as a repository admin user. + ''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_2 = self.test_db_util.get_user( common.test_user_2_email ) + repository = self.test_db_util.get_repository_by_name_and_owner( 'renamed_filtering_0530', common.test_user_1_name ) + self.assign_admin_role( repository, test_user_2 ) + + def test_0040_rename_repository_as_repository_admin( self ): + '''Rename the repository as user2.''' + ''' + This is step 8 - Log into the Tool Shed as user user2 and make sure the repository name and description can now be changed. + ''' + self.logout() + self.login( email=common.test_user_2_email, username=common.test_user_2_name ) + repository = self.test_db_util.get_repository_by_name_and_owner( 'renamed_filtering_0530', common.test_user_1_name ) + self.edit_repository_information( repository, revert=False, repo_name='filtering_0530' ) + self.test_db_util.refresh( repository ) + assert repository.name == 'filtering_0530', 'User with admin role failed to rename repository.' + test_user_1 = self.test_db_util.get_user( common.test_user_1_email ) + old_repository_admin_role = self.test_db_util.get_role( test_user_1, 'renamed_filtering_0530_user1_admin' ) + assert old_repository_admin_role is None, 'Admin role renamed_filtering_0530_user1_admin incorrectly exists.' + new_repository_admin_role = self.test_db_util.get_role( test_user_1, 'filtering_0530_user1_admin' ) + assert new_repository_admin_role is not None, 'Admin role filtering_0530_user1_admin does not exist.' + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Small bug fix in history contents API error handling.
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/593833a7ff53/ Changeset: 593833a7ff53 User: jmchilton Date: 2014-03-20 19:56:08 Summary: Small bug fix in history contents API error handling. Affected #: 1 file diff -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af -r 593833a7ff5395bb585513ba6881012174909180 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -286,7 +286,7 @@ if contents_type == "dataset": return self.__update_dataset( trans, history_id, id, payload, **kwd ) else: - return self.__handle_unknown_contents_type( contents_type ) + return self.__handle_unknown_contents_type( trans, contents_type ) def __update_dataset( self, trans, history_id, id, payload, **kwd ): changed = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Remove handlebars common-template helpers, remove unused templates
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e8fac2f5d93f/ Changeset: e8fac2f5d93f User: carlfeberhard Date: 2014-03-20 19:16:13 Summary: Remove handlebars common-template helpers, remove unused templates Affected #: 9 files diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/packed/templates/compiled/helpers-common-templates.js --- a/static/scripts/packed/templates/compiled/helpers-common-templates.js +++ /dev/null @@ -1,1 +0,0 @@ -Handlebars.registerHelper("local",function(a){return _l(a.fn(this))});Handlebars.registerHelper("n2br",function(a){return a.fn(this).replace(/\n/g,"<br/>")}); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/packed/templates/compiled/template-iconButton.js --- a/static/scripts/packed/templates/compiled/template-iconButton.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-iconButton"]=b(function(i,j,g,e,h){this.compilerInfo=[4,">= 1.0.0"];g=this.merge(g,i.helpers);e=this.merge(e,i.partials);h=h||{};var c="",f,d=this;c+="\n";f=d.invokePartial(e.iconButton,"iconButton",j,g,e,h);if(f||f===0){c+=f}return c})})(); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/packed/templates/compiled/template-warningmessagesmall.js --- a/static/scripts/packed/templates/compiled/template-warningmessagesmall.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-warningmessagesmall"]=b(function(i,j,f,d,g){this.compilerInfo=[4,">= 1.0.0"];f=this.merge(f,i.helpers);g=g||{};var c="",e,h="function";c+=' \n <div class="warningmessagesmall"><strong>';if(e=f.warning){e=e.call(j,{hash:{},data:g})}else{e=j.warning;e=typeof e===h?e.apply(j):e}if(e||e===0){c+=e}c+="</strong></div>";return c})})(); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/templates/common-templates.html --- a/static/scripts/templates/common-templates.html +++ /dev/null @@ -1,15 +0,0 @@ -<script type="text/javascript" class="helper-common" id="helper-local"> -/** Calls _l (from base-mvc.js) to localize strings (if poosible) - * This helper is specifically for localization within templates - */ -Handlebars.registerHelper( 'local', function( options ){ - return _l( options.fn( this ) ); -}); -</script> - -<script type="text/javascript" class="helper-common" id="helper-n2br"> -/** replace newlines with breaks */ -Handlebars.registerHelper( 'n2br', function( options ){ - return options.fn( this ).replace( /\n/g, '<br/>' ); -}); -</script> diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/templates/compiled/helpers-common-templates.js --- a/static/scripts/templates/compiled/helpers-common-templates.js +++ /dev/null @@ -1,10 +0,0 @@ -/** Calls _l (from base-mvc.js) to localize strings (if poosible) - * This helper is specifically for localization within templates - */ -Handlebars.registerHelper( 'local', function( options ){ - return _l( options.fn( this ) ); -}); -/** replace newlines with breaks */ -Handlebars.registerHelper( 'n2br', function( options ){ - return options.fn( this ).replace( /\n/g, '<br/>' ); -}); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/templates/compiled/template-iconButton.js --- a/static/scripts/templates/compiled/template-iconButton.js +++ /dev/null @@ -1,14 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-iconButton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); partials = this.merge(partials, Handlebars.partials); data = data || {}; - var buffer = "", stack1, self=this; - - - buffer += "\n"; - stack1 = self.invokePartial(partials.iconButton, 'iconButton', depth0, helpers, partials, data); - if(stack1 || stack1 === 0) { buffer += stack1; } - return buffer; - }); -})(); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af static/scripts/templates/compiled/template-warningmessagesmall.js --- a/static/scripts/templates/compiled/template-warningmessagesmall.js +++ /dev/null @@ -1,16 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-warningmessagesmall'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function"; - - - buffer += " \n <div class=\"warningmessagesmall\"><strong>"; - if (stack1 = helpers.warning) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.warning; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</strong></div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af templates/webapps/galaxy/dataset/tabular_chunked.mako --- a/templates/webapps/galaxy/dataset/tabular_chunked.mako +++ b/templates/webapps/galaxy/dataset/tabular_chunked.mako @@ -6,7 +6,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "libs/require" )} - ${h.templates("helpers-common-templates")} <script type="text/javascript"> require.config({ @@ -36,4 +35,4 @@ ${parent.stylesheets()} </%def> -${ render_deleted_data_message( dataset ) } \ No newline at end of file +${ render_deleted_data_message( dataset ) } diff -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 -r e8fac2f5d93f1ab7b87041dd5b1878705e8178af templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -66,7 +66,6 @@ } %> - ${h.templates( "helpers-common-templates" )} ${h.js( "mvc/base-mvc", "utils/localization", "mvc/user/user-model", "mvc/user/user-quotameter" )} ## load the frame manager Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: reduce size of select checkboxes, decrease animation
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/261d9bab3d12/ Changeset: 261d9bab3d12 User: carlfeberhard Date: 2014-03-20 18:38:10 Summary: History panel: reduce size of select checkboxes, decrease animation Affected #: 6 files diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -495,70 +495,34 @@ /** display a (fa-icon) checkbox on the left of the hda that fires events when checked * Note: this also hides the primary actions */ - showSelector : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - + showSelector : function(){ // make sure selected state is represented properly if( this.selected ){ this.select( null, true ); } - // create a jq fx queue to do this sequentially: fadeout the buttons, embiggen the selector - var hdaView = this, - SELECTOR_WIDTH = 32; + this.selectable = true; + this.trigger( 'selectable', true, this ); - if( speed ){ - this.$el.queue( 'fx', function( next ){ - $( this ).find( '.dataset-primary-actions' ).fadeOut( speed, next ); - }); - this.$el.queue( 'fx', function( next ){ - $( this ).find( '.dataset-selector' ).show().animate({ width: SELECTOR_WIDTH }, speed, next ); - $( this ).find( '.dataset-title-bar' ).animate({ 'margin-left': SELECTOR_WIDTH }, speed, next ); - hdaView.selectable = true; - hdaView.trigger( 'selectable', true, hdaView ); - }); - // no animation - } else { - this.$el.find( '.dataset-primary-actions' ).hide(); - this.$el.find( '.dataset-selector' ).show().css({ width : SELECTOR_WIDTH }); - this.$el.find( '.dataset-title-bar' ).show().css({ 'margin-left' : SELECTOR_WIDTH }); - hdaView.selectable = true; - hdaView.trigger( 'selectable', true, hdaView ); - } + this.$( '.dataset-primary-actions' ).hide(); + this.$( '.dataset-selector' ).show(); }, /** remove the selection checkbox */ - hideSelector : function( speed ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - + hideSelector : function(){ // reverse the process from showSelect this.selectable = false; this.trigger( 'selectable', false, this ); - if( speed ){ - this.$el.queue( 'fx', function( next ){ - $( this ).find( '.dataset-title-bar' ).show().css({ 'margin-left' : '0' }); - $( this ).find( '.dataset-selector' ).animate({ width: '0px' }, speed, function(){ - $( this ).hide(); - next(); - }); - }); - this.$el.queue( 'fx', function( next ){ - $( this ).find( '.dataset-primary-actions' ).fadeIn( speed, next ); - }); - - // no animation - } else { - $( this ).find( '.dataset-selector' ).css({ width : '0px' }).hide(); - $( this ).find( '.dataset-primary-actions' ).show(); - } + this.$( '.dataset-selector' ).hide(); + this.$( '.dataset-primary-actions' ).show(); }, - toggleSelector : function( speed ){ + toggleSelector : function(){ if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){ - this.showSelector( speed ); + this.showSelector(); } else { - this.hideSelector( speed ); + this.hideSelector(); } }, @@ -694,7 +658,9 @@ '</div>', // multi-select checkbox - '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', + '<div class="dataset-selector">', + '<span class="fa fa-2x fa-square-o"></span>', + '</div>', // space for title bar buttons '<div class="dataset-primary-actions"></div>', diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -336,7 +336,7 @@ // ------------------------------------------------------------------------ panel events /** event map */ events : _.extend( _.clone( readonlyPanel.ReadOnlyHistoryPanel.prototype.events ), { - 'click .history-select-btn' : function( e ){ this.toggleSelectors( this.fxSpeed ); }, + 'click .history-select-btn' : 'toggleSelectors', 'click .history-select-all-datasets-btn' : 'selectAllDatasets', 'click .history-deselect-all-datasets-btn' : 'deselectAllDatasets' }), @@ -351,30 +351,32 @@ //TODO: to toggle showOrHide pattern /** show selectors on all visible hdas and associated controls */ showSelectors : function( speed ){ + speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); this.selecting = true; - this.$el.find( '.history-dataset-actions' ).slideDown( speed ); + this.$( '.history-dataset-actions' ).slideDown( speed ); _.each( this.hdaViews, function( view ){ - view.showSelector( speed ); + view.showSelector(); }); this.selectedHdaIds = []; }, /** hide selectors on all visible hdas and associated controls */ hideSelectors : function( speed ){ + speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); this.selecting = false; - this.$el.find( '.history-dataset-actions' ).slideUp( speed ); + this.$( '.history-dataset-actions' ).slideUp( speed ); _.each( this.hdaViews, function( view ){ - view.hideSelector( speed ); + view.hideSelector(); }); this.selectedHdaIds = []; }, /** show or hide selectors on all visible hdas and associated controls */ - toggleSelectors : function( speed ){ + toggleSelectors : function(){ if( !this.selecting ){ - this.showSelectors( speed ); + this.showSelectors(); } else { - this.hideSelectors( speed ); + this.hideSelectors(); } }, diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations"],function(e,b,d,a,c){var f=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(g){g=g||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=g.selecting||false;this.annotationEditorShown=g.annotationEditorShown||false;this.tagsEditorShown=g.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,g)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this)},renderModel:function(){var g=$("<div/>");g.append(f.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(g).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(g);this._renderAnnotation(g)}g.find(".history-secondary-actions").prepend(this._renderSelectButton());g.find(".history-dataset-actions").toggle(this.selecting);g.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){var h=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDATagEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDATagEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){var h=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDAAnnotationEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDAAnnotationEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_renderSelectButton:function(g){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(g){g=g||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,g);if(!this.model){return}this._setUpDatasetActionsPopup(g);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var h=this;g.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(i){var j=h.model.get("name");if(i&&i!==j){h.$el.find(".history-name").text(i);h.model.save({name:i}).fail(function(){h.$el.find(".history-name").text(h.model.previous("name"))})}else{h.$el.find(".history-name").text(j)}}})},_setUpDatasetActionsPopup:function(g){var h=this;(new PopupMenu(g.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.hide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Unhide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.unhide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Delete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype["delete"];h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Undelete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.undelete;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var i=e.HistoryDatasetAssociation.prototype.purge;h.getSelectedHdaCollection().ajaxQueue(i)}}}]))},_handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},_handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},_createHdaView:function(h){var g=h.get("id"),i=new this.HDAViewClass({model:h,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[g],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(i);return i},_setUpHdaListeners:function(h){var g=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,h);h.on("selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.union(g.selectedHdaIds,[j])});h.on("de-selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.without(g.selectedHdaIds,j)})},toggleHDATagEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.annotationEditor){i.annotationEditor.toggle.apply(i.annotationEditor,h)}})},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$emptyMessage().fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(g){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(g){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(g);_.each(this.hdaViews,function(h){h.showSelector(g)});this.selectedHdaIds=[]},hideSelectors:function(g){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(g);_.each(this.hdaViews,function(h){h.hideSelector(g)});this.selectedHdaIds=[]},toggleSelectors:function(g){if(!this.selecting){this.showSelectors(g)}else{this.hideSelectors(g)}},selectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.select(g)})},deselectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.deselect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},getSelectedHdaCollection:function(){return new e.HDACollection(_.map(this.getSelectedHdaViews(),function(g){return g.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations"],function(e,b,d,a,c){var f=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(g){g=g||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=g.selecting||false;this.annotationEditorShown=g.annotationEditorShown||false;this.tagsEditorShown=g.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,g)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this)},renderModel:function(){var g=$("<div/>");g.append(f.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(g).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(g);this._renderAnnotation(g)}g.find(".history-secondary-actions").prepend(this._renderSelectButton());g.find(".history-dataset-actions").toggle(this.selecting);g.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){var h=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDATagEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDATagEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){var h=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDAAnnotationEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDAAnnotationEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_renderSelectButton:function(g){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(g){g=g||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,g);if(!this.model){return}this._setUpDatasetActionsPopup(g);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var h=this;g.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(i){var j=h.model.get("name");if(i&&i!==j){h.$el.find(".history-name").text(i);h.model.save({name:i}).fail(function(){h.$el.find(".history-name").text(h.model.previous("name"))})}else{h.$el.find(".history-name").text(j)}}})},_setUpDatasetActionsPopup:function(g){var h=this;(new PopupMenu(g.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.hide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Unhide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.unhide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Delete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype["delete"];h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Undelete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.undelete;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var i=e.HistoryDatasetAssociation.prototype.purge;h.getSelectedHdaCollection().ajaxQueue(i)}}}]))},_handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},_handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},_createHdaView:function(h){var g=h.get("id"),i=new this.HDAViewClass({model:h,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[g],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(i);return i},_setUpHdaListeners:function(h){var g=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,h);h.on("selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.union(g.selectedHdaIds,[j])});h.on("de-selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.without(g.selectedHdaIds,j)})},toggleHDATagEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.annotationEditor){i.annotationEditor.toggle.apply(i.annotationEditor,h)}})},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$emptyMessage().fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(g);_.each(this.hdaViews,function(h){h.showSelector()});this.selectedHdaIds=[]},hideSelectors:function(g){g=(g!==undefined)?(g):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(g);_.each(this.hdaViews,function(h){h.hideSelector()});this.selectedHdaIds=[]},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.select(g)})},deselectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.deselect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},getSelectedHdaCollection:function(){return new e.HDACollection(_.map(this.getSelectedHdaViews(),function(g){return g.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:f}}); \ No newline at end of file diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1617,7 +1617,8 @@ .history-panel .dataset .dataset-padding{padding:6px 10px 6px 8px} .history-panel .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} .history-panel .dataset .help-text{font-weight:normal;color:#555} -.history-panel .dataset .dataset-selector{float:left;display:none;width:0px;margin:0 0 -6px 0;padding:5px 0 2px 8px;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-selector{float:left;display:none;width:32px;height:32px;margin:0 0 -6px 0;padding:8px 0 2px 7px;font-size:80%;color:#333;cursor:pointer;vertical-align:middle} +.history-panel .dataset .dataset-selector:hover{color:maroon} .history-panel .dataset .dataset-title-bar{cursor:pointer;outline:none;padding:6px 10px 6px 8px} .history-panel .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-wrap:break-word;word-break:break-all;line-height:16px} .history-panel .dataset .dataset-primary-actions{display:inline-block;float:right;margin:6px 10px 0}.history-panel .dataset .dataset-primary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} @@ -1654,7 +1655,7 @@ .history-panel .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} .history-panel .dataset .dataset-body .dataset-peek{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.history-panel .dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} .history-panel .dataset .dataset-body .dataset-peek pre.peek table,.history-panel .dataset .dataset-body .dataset-peek pre.peek th,.history-panel .dataset .dataset-body .dataset-peek pre.peek tr,.history-panel .dataset .dataset-body .dataset-peek pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} +.history-panel .dataset .state-icon{font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale;display:inline-block;margin-right:4px;vertical-align:middle;width:16px;height:16px;line-height:16px;text-align:center;font-size:16px} .state-icon-error{background-color:white;border-radius:8px}.state-icon-error:before{font-size:20px;line-height:16px;color:red;content:"\f057"} .history-panel [class$="messagesmall"]{margin:0px} .history-panel .editable-text{border:solid transparent 1px} diff -r f714a3410ec5a22fa571156c376ae2e97baafd50 -r 261d9bab3d12b2bf6fb0ab2e57a8a08e85cbc408 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -165,14 +165,19 @@ float: left; // always initially hidden and zero width display: none; - width: 0px; + width: 32px; + height: 32px; //HACK: neg. on the bottom due to padding-bottom in title-bar - very tweakish - margin: 0px 0px -@spacing-bottom 0px; - padding: ( @spacing-top - 1 ) 0px 2px @spacing-left; + margin: 0px 0px -( @spacing-bottom ) 0px; + padding: ( @spacing-top + 2 ) 0px 2px ( @spacing-left - 1 ); + font-size: 80%; + color: @btn-default-color; cursor: pointer; - //text-align: center; vertical-align: middle; } + .dataset-selector:hover { + color: maroon; + } .dataset-title-bar { cursor: pointer; @@ -360,6 +365,7 @@ .dataset .state-icon { .fa-icon; display: inline-block; + margin-right: 4px; vertical-align: middle; width: 16px; height: 16px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Fix to 3268c8606464: properly namespace display applications in template
by commits-noreply＠bitbucket.org 20 Mar '14

20 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f714a3410ec5/ Changeset: f714a3410ec5 User: carlfeberhard Date: 2014-03-20 15:13:38 Summary: Fix to 3268c8606464: properly namespace display applications in template Affected #: 2 files diff -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 -r f714a3410ec5a22fa571156c376ae2e97baafd50 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -768,12 +768,12 @@ //TODO: the following two should be compacted '<% _.each( hda.display_apps, function( app ){ %>', '<div class="display-application">', - '<span class="display-application-location"><%- app.label %></span>', + '<span class="display-application-location"><%- app.label %></span> ', '<span class="display-application-links">', '<% _.each( app.links, function( link ){ %>', - '<a target="<%= target %>" href="<%= href %>">', + '<a target="<%= link.target %>" href="<%= link.href %>">', '<% print( _l( link.text ) ); %>', - '</a>', + '</a> ', '<% }); %>', '</span>', '</div>', @@ -781,12 +781,12 @@ '<% _.each( hda.display_types, function( app ){ %>', '<div class="display-application">', - '<span class="display-application-location"><%- label %></span>', + '<span class="display-application-location"><%- app.label %></span> ', '<span class="display-application-links">', '<% _.each( app.links, function( link ){ %>', - '<a target="<%= target %>" href="<%= href %>">', + '<a target="<%= link.target %>" href="<%= link.href %>">', '<% print( _l( link.text ) ); %>', - '</a>', + '</a> ', '<% }); %>', '</span>', '</div>', diff -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 -r f714a3410ec5a22fa571156c376ae2e97baafd50 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: libraries: changed to more grid-like styling; added packed versions of recent JS updates that showed up after packing scripts
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4904f18e1cb0/ Changeset: 4904f18e1cb0 User: martenson Date: 2014-03-19 22:18:36 Summary: libraries: changed to more grid-like styling; added packed versions of recent JS updates that showed up after packing scripts Affected #: 9 files diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -121,10 +121,10 @@ // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); - tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); - tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); @@ -150,7 +150,7 @@ // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="library_table table table-condensed">'); + tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); @@ -797,7 +797,6 @@ initialize : function(){ var viewContext = this; this.collection = new Libraries(); - // this.collection.on('sort', this.render, this); this.collection.fetch({ success: function(libraries){ @@ -817,8 +816,9 @@ $("#center").css('overflow','auto'); }, - /** Renders the libraries table either from the object's own collection, or from a given array of library models, - or renders an empty list in case no data is present. */ + /** Renders the libraries table either from the object's own collection, + or from a given array of library models, + or renders an empty list in case no data is given. */ render: function (options) { var template = this.templateLibraryList(); var libraries_to_render = null; @@ -874,14 +874,18 @@ templateLibraryList: function(){ tmpl_array = []; + tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); - tmpl_array.push(''); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); + tmpl_array.push('<div id="library_toolbar">'); + tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>'); + tmpl_array.push('</div>'); + tmpl_array.push('<% if(libraries.length === 0) { %>'); tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>"); tmpl_array.push('<% } else{ %>'); - tmpl_array.push('<table class="library_table table table-condensed">'); + tmpl_array.push('<table class="grid table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th>description</th>'); @@ -898,6 +902,7 @@ tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); tmpl_array.push('<% }%>'); + tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(k,h,m){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var n=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:j});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<ol class="breadcrumb">');q.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');q.push(" <% _.each(path, function(path_item) { %>");q.push(" <% if (path_item[0] != id) { %>");q.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');q.push("<% } else { %>");q.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');q.push(" <% } %>");q.push(" <% }); %>");q.push("</ol>");q.push('<table id="folder_table" class="library_table table table-condensed">');q.push(" <thead>");q.push(' <th class="button_heading"></th>');q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date (UTC)</th>");q.push(" </thead>");q.push(" <tbody>");q.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Folder" class="fa fa-folder-o"></span>');q.push(" </td>");q.push(" <td></td>");q.push(" <td>");q.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } else { %>");q.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Dataset" class="fa fa-file-o"></span>');q.push(" </td>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } %> ");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div class="modal_table">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded (UTC)</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new e({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)},error:function(){m.error("An error occured :(")}})},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().parent().attr("id");if(typeof u==="undefined"){u=$(t.target).parent().attr("id")}if(typeof u==="undefined"){u=$(t.target).parent().parent().attr("id")}var s=new i();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)},error:function(){m.error("An error occured during fetching histories:(");q.renderModalAfterFetch(v)}})},error:function(){m.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide()}}});$(".peek").html(v.get("peek"));if(typeof history.models!==undefined){var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark");q.find("span").removeClass("fa-file-o");q.find("span").addClass("fa-file")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light");q.find("span").addClass("fa-file-o");q.find("span").removeClass("fa-file")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=Galaxy.modal;r.modal.show({closing_events:true,title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide()}}})},error:function(){m.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){q.create_new_folder_event()},Close:function(){q.modal.hide();q.modal=null}}})},create_new_folder_event:function(){var q=this.serialize_new_folder();if(this.validate_new_folder(q)){var s=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];s.url=s.urlRoot+"/"+current_folder_id;var r=this;s.save(q,{success:function(t){r.modal.hide();m.success("Folder created");r.render({id:current_folder_id})},error:function(){m.error("An error occured :(")}})}else{m.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(q){return q.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},modal:null,collection:null,initialize:function(){var q=this;this.collection=new n();this.collection.fetch({success:function(r){q.render()},error:function(s,r){if(r.statusCode().status===403){m.info("Please log in first. Redirecting to login page in 3s.");setTimeout(that.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}});$("#center").css("overflow","auto")},render:function(r){var s=this.templateLibraryList();var t=null;var q=false;var u=null;if(typeof r!=="undefined"){q=typeof r.with_deleted!=="undefined"?r.with_deleted:false;u=typeof r.models!=="undefined"?r.models:null}if(this.collection!==null&&u===null){if(q){t=this.collection.models}else{t=this.collection.where({deleted:false})}}else{if(u!==null){t=u}else{t=[]}}this.$el.html(s({libraries:t,order:this.collection.sort_order}))},sortLibraries:function(r,q){if(r==="name"){if(q==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return 1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}return 0}}else{if(q==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return -1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="library_table table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}})},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new f();var q=this;r.save(s,{success:function(t){q.collection.add(t);q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""}});var p=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){galaxyLibraryview=new a();library_router=new p();folderContentView=new l();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:sort_libraries",function(r,q){galaxyLibraryview.sortLibraries(r,q);galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(k,h,m){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var n=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:j});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<ol class="breadcrumb">');q.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');q.push(" <% _.each(path, function(path_item) { %>");q.push(" <% if (path_item[0] != id) { %>");q.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');q.push("<% } else { %>");q.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');q.push(" <% } %>");q.push(" <% }); %>");q.push("</ol>");q.push('<table id="folder_table" class="grid table table-condensed">');q.push(" <thead>");q.push(' <th class="button_heading"></th>');q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date (UTC)</th>");q.push(" </thead>");q.push(" <tbody>");q.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Folder" class="fa fa-folder-o"></span>');q.push(" </td>");q.push(" <td></td>");q.push(" <td>");q.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } else { %>");q.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Dataset" class="fa fa-file-o"></span>');q.push(" </td>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } %> ");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div class="modal_table">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded (UTC)</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new e({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)},error:function(){m.error("An error occured :(")}})},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().parent().attr("id");if(typeof u==="undefined"){u=$(t.target).parent().attr("id")}if(typeof u==="undefined"){u=$(t.target).parent().parent().attr("id")}var s=new i();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)},error:function(){m.error("An error occured during fetching histories:(");q.renderModalAfterFetch(v)}})},error:function(){m.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide()}}});$(".peek").html(v.get("peek"));if(typeof history.models!==undefined){var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark");q.find("span").removeClass("fa-file-o");q.find("span").addClass("fa-file")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light");q.find("span").addClass("fa-file-o");q.find("span").removeClass("fa-file")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=Galaxy.modal;r.modal.show({closing_events:true,title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide()}}})},error:function(){m.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){q.create_new_folder_event()},Close:function(){q.modal.hide();q.modal=null}}})},create_new_folder_event:function(){var q=this.serialize_new_folder();if(this.validate_new_folder(q)){var s=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];s.url=s.urlRoot+"/"+current_folder_id;var r=this;s.save(q,{success:function(t){r.modal.hide();m.success("Folder created");r.render({id:current_folder_id})},error:function(){m.error("An error occured :(")}})}else{m.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(q){return q.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},modal:null,collection:null,initialize:function(){var q=this;this.collection=new n();this.collection.fetch({success:function(r){q.render()},error:function(s,r){if(r.statusCode().status===403){m.info("Please log in first. Redirecting to login page in 3s.");setTimeout(that.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}});$("#center").css("overflow","auto")},render:function(r){var s=this.templateLibraryList();var t=null;var q=false;var u=null;if(typeof r!=="undefined"){q=typeof r.with_deleted!=="undefined"?r.with_deleted:false;u=typeof r.models!=="undefined"?r.models:null}if(this.collection!==null&&u===null){if(q){t=this.collection.models}else{t=this.collection.where({deleted:false})}}else{if(u!==null){t=u}else{t=[]}}this.$el.html(s({libraries:t,order:this.collection.sort_order}))},sortLibraries:function(r,q){if(r==="name"){if(q==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return 1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}return 0}}else{if(q==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return -1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push("</div>");tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}})},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new f();var q=this;r.save(s,{success:function(t){q.collection.add(t);q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""}});var p=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){galaxyLibraryview=new a();library_router=new p();folderContentView=new l();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:sort_libraries",function(r,q){galaxyLibraryview.sortLibraries(r,q);galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -var AnnotationEditor=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',a,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(b){b=b||{};this.tooltipConfig=b.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(b.$activator,b)},render:function(){var b=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(c){b.$annotation().text(c);b.model.save({annotation:c},{silent:true}).fail(function(){b.$annotation().text(b.model.previous("annotation"))})}});return this},_template:function(){var b=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',b,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:a}}); \ No newline at end of file diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var e=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(f){a.HDABaseView.prototype.initialize.call(this,f);this.hasUser=f.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=f.tagsEditorShown||false;this.annotationEditorShown=f.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this.model.get("purged"),f=this.model.get("deleted"),g={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(f||h){g.disabled=true;if(h){g.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(f){g.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be edited")}}g.faIcon="fa-pencil";return faIconButton(g)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var f=this,g={title:_l("Delete"),classes:"dataset-delete",onclick:function(){f.$el.find(".icon-btn.dataset-delete").trigger("mouseout");f.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){g={title:_l("Dataset is already deleted"),disabled:true}}g.faIcon="fa-times";return faIconButton(g)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var f=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(f))){return null}if(_.isObject(f[0])){return this._render_visualizationsFrameworkButton(f)}if(!this.urls.visualization){return null}var h=this.model.get("dbkey"),l=this.urls.visualization,i={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(h){m.dbkey=h}var g=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function j(n){if(n==="trackster"){return b(l,m,h)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}function k(n){return n.charAt(0).toUpperCase()+n.slice(1)}if(f.length===1){g.attr("data-original-title",_l("Visualize in ")+_l(k(f[0])));g.click(j(f[0]))}else{_.each(f,function(n){i[_l(k(n))]=j(n)});make_popupmenu(g,i)}return g},_render_visualizationsFrameworkButton:function(f){if(!(this.model.hasData())||!(f&&!_.isEmpty(f))){return null}var h=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(f.length===1){var g=f[0];h.attr("data-original-title",_l("Visualize in ")+g.html);h.attr("href",g.href)}else{var i=[];_.each(f,function(j){j.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:j.href});return false}return true};i.push(j);return false});PopupMenu.create(h,i)}return h},_buildNewRender:function(){var f=a.HDABaseView.prototype._buildNewRender.call(this);f.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));f.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return f},_render_body_failed_metadata:function(){var g=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),f=$("<span/>").text(". "+_l("You may be able to")+" ").append(g),h=a.HDABaseView.prototype._render_body_failed_metadata.call(this);h.find(".warningmessagesmall strong").append(f);return h},_render_body_error:function(){var f=a.HDABaseView.prototype._render_body_error.call(this);f.find(".dataset-actions .left").prepend(this._render_errButton());return f},_render_body_ok:function(){var f=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return f}this.makeDbkeyEditLink(f);if(this.hasUser){f.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(f);this._renderAnnotation(f)}return f},_renderTags:function(f){var g=this;this.tagsEditor=new TagsEditor({model:this.model,el:f.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){g.tagsEditorShown=true},onhide:function(){g.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(f.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(f){var g=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:f.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){g.annotationEditorShown=true},onhide:function(){g.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(f.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var f=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);g.find(".dataset-dbkey .value").replaceWith(f)}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(f){this.model.undelete();return false},"click .dataset-unhide":function(f){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(f){this.model.purge();return false},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDAView("+f+")"}});function b(f,h,g){return function(){var i={};if(g){i["f-dbkey"]=g}$.ajax({url:f+"/list_tracks?"+$.param(i),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(j){var k=window.parent;k.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){k.Galaxy.modal.hide()},"View in saved visualization":function(){k.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:j,buttons:{Cancel:function(){k.Galaxy.modal.hide()},"Add to visualization":function(){$(k.document).find("input[name=id]:checked").each(function(){k.Galaxy.modal.hide();var l=$(this).val();h.id=l;k.Galaxy.frame.add({title:"Trackster",type:"url",content:f+"/trackster?"+$.param(h)})})}}})},"View in new visualization":function(){k.Galaxy.modal.hide();var l=f+"/trackster?"+$.param(h);k.Galaxy.frame.add({title:"Trackster",type:"url",content:l})}}})}});return false}}return{HDAEditView:e}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations"],function(f,b,a,e){var g=b.HDABaseView.extend(LoggableMixin).extend({initialize:function(h){b.HDABaseView.prototype.initialize.call(this,h);this.hasUser=h.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=h.tagsEditorShown||false;this.annotationEditorShown=h.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var j=this.model.get("purged"),h=this.model.get("deleted"),i={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(h||j){i.disabled=true;if(j){i.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(h){i.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===f.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=_l("This dataset must finish uploading before it can be edited")}}i.faIcon="fa-pencil";return faIconButton(i)},_render_deleteButton:function(){if((this.model.get("state")===f.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===f.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var h=this,i={title:_l("Delete"),classes:"dataset-delete",onclick:function(){h.$el.find(".icon-btn.dataset-delete").trigger("mouseout");h.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),disabled:true}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==f.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var h=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(h))){return null}if(_.isObject(h[0])){return this._render_visualizationsFrameworkButton(h)}if(!this.urls.visualization){return null}var j=this.model.get("dbkey"),n=this.urls.visualization,k={},o={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(j){o.dbkey=j}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function l(p){if(p==="trackster"){return c(n,o,j)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:n+"/"+p+"?"+$.param(o)})}}function m(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(h.length===1){i.attr("data-original-title",_l("Visualize in ")+_l(m(h[0])));i.click(l(h[0]))}else{_.each(h,function(p){k[_l(m(p))]=l(p)});make_popupmenu(i,k)}return i},_render_visualizationsFrameworkButton:function(h){if(!(this.model.hasData())||!(h&&!_.isEmpty(h))){return null}var j=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(h.length===1){var i=h[0];j.attr("data-original-title",_l("Visualize in ")+i.html);j.attr("href",i.href)}else{var k=[];_.each(h,function(l){l.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:l.href});return false}return true};k.push(l);return false});PopupMenu.create(j,k)}return j},_buildNewRender:function(){var h=b.HDABaseView.prototype._buildNewRender.call(this);h.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));h.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return h},_render_body_failed_metadata:function(){var i=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),h=$("<span/>").text(". "+_l("You may be able to")+" ").append(i),j=b.HDABaseView.prototype._render_body_failed_metadata.call(this);j.find(".warningmessagesmall strong").append(h);return j},_render_body_error:function(){var h=b.HDABaseView.prototype._render_body_error.call(this);h.find(".dataset-actions .left").prepend(this._render_errButton());return h},_render_body_ok:function(){var h=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return h}this.makeDbkeyEditLink(h);if(this.hasUser){h.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(h);this._renderAnnotation(h)}return h},_renderTags:function(h){var i=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:h.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.tagsEditorShown=true},onhide:function(){i.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(h.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(h){var i=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:h.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){i.annotationEditorShown=true},onhide:function(){i.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(h.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(i){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var h=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);i.find(".dataset-dbkey .value").replaceWith(h)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(h){this.model.undelete();return false},"click .dataset-unhide":function(h){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(h){this.model.purge();return false},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDAView("+h+")"}});function c(h,j,i){return function(){var k={};if(i){k["f-dbkey"]=i}$.ajax({url:h+"/list_tracks?"+$.param(k),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(l){var m=window.parent;m.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){m.Galaxy.modal.hide()},"View in saved visualization":function(){m.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:l,buttons:{Cancel:function(){m.Galaxy.modal.hide()},"Add to visualization":function(){$(m.document).find("input[name=id]:checked").each(function(){m.Galaxy.modal.hide();var n=$(this).val();j.id=n;m.Galaxy.frame.add({title:"Trackster",type:"url",content:h+"/trackster?"+$.param(j)})})}}})},"View in new visualization":function(){m.Galaxy.modal.hide();var n=h+"/trackster?"+$.param(j);m.Galaxy.frame.add({title:"Trackster",type:"url",content:n})}}})}});return false}}return{HDAEditView:g}}); \ No newline at end of file diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(e).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;b.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,e);if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},_handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},_handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},_createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$emptyMessage().fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations"],function(e,b,d,a,c){var f=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(g){g=g||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=g.selecting||false;this.annotationEditorShown=g.annotationEditorShown||false;this.tagsEditorShown=g.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,g)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(g){this.model.fetch()},this)},renderModel:function(){var g=$("<div/>");g.append(f.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(g).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(g);this._renderAnnotation(g)}g.find(".history-secondary-actions").prepend(this._renderSelectButton());g.find(".history-dataset-actions").toggle(this.selecting);g.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(g);this.renderHdas(g);return g},_renderTags:function(g){var h=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:g.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDATagEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDATagEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".history-secondary-actions"))})},_renderAnnotation:function(g){var h=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:g.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.toggleHDAAnnotationEditors(true,h.fxSpeed)},onhide:function(){h.toggleHDAAnnotationEditors(false,h.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".history-secondary-actions"))})},_renderSelectButton:function(g){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(g){g=g||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,g);if(!this.model){return}this._setUpDatasetActionsPopup(g);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var h=this;g.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(i){var j=h.model.get("name");if(i&&i!==j){h.$el.find(".history-name").text(i);h.model.save({name:i}).fail(function(){h.$el.find(".history-name").text(h.model.previous("name"))})}else{h.$el.find(".history-name").text(j)}}})},_setUpDatasetActionsPopup:function(g){var h=this;(new PopupMenu(g.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.hide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Unhide datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.unhide;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Delete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype["delete"];h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Undelete datasets"),func:function(){var i=e.HistoryDatasetAssociation.prototype.undelete;h.getSelectedHdaCollection().ajaxQueue(i)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var i=e.HistoryDatasetAssociation.prototype.purge;h.getSelectedHdaCollection().ajaxQueue(i)}}}]))},_handleHdaDeletionChange:function(g){if(g.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[g.id])}},_handleHdaVisibleChange:function(g){if(g.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[g.id])}},_createHdaView:function(h){var g=h.get("id"),i=new this.HDAViewClass({model:h,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[g],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(i);return i},_setUpHdaListeners:function(h){var g=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,h);h.on("selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.union(g.selectedHdaIds,[j])});h.on("de-selected",function(i){var j=i.model.get("id");g.selectedHdaIds=_.without(g.selectedHdaIds,j)})},toggleHDATagEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.tagsEditor){i.tagsEditor.toggle.apply(i.tagsEditor,h)}})},toggleHDAAnnotationEditors:function(g){var h=arguments;_.each(this.hdaViews,function(i){if(i.annotationEditor){i.annotationEditor.toggle.apply(i.annotationEditor,h)}})},removeHdaView:function(h){if(!h){return}var g=this;h.$el.fadeOut(g.fxSpeed,function(){h.off();h.remove();delete g.hdaViews[h.model.id];if(_.isEmpty(g.hdaViews)){g.$emptyMessage().fadeIn(g.fxSpeed,function(){g.trigger("empty-history",g)})}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(g){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(g){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(g);_.each(this.hdaViews,function(h){h.showSelector(g)});this.selectedHdaIds=[]},hideSelectors:function(g){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(g);_.each(this.hdaViews,function(h){h.hideSelector(g)});this.selectedHdaIds=[]},toggleSelectors:function(g){if(!this.selecting){this.showSelectors(g)}else{this.hideSelectors(g)}},selectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.select(g)})},deselectAllDatasets:function(g){_.each(this.hdaViews,function(h){h.deselect(g)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(g){return g.selected})},getSelectedHdaCollection:function(){return new e.HDACollection(_.map(this.getSelectedHdaViews(),function(g){return g.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:f}}); \ No newline at end of file diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/scripts/packed/mvc/tags.js --- a/static/scripts/packed/mvc/tags.js +++ b/static/scripts/packed/mvc/tags.js @@ -1,1 +1,1 @@ -var TagsEditor=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(a){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return a._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',_l("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var a=this.model.get("tags");if(!_.isArray(a)||_.isEmpty(a)){return""}return a.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var a=this;this.$input().on("change",function(b){a.model.save({tags:b.val},{silent:true});if(b.added){a._addNewTagToTagsUsed(b.added.text+"")}})},_addNewTagToTagsUsed:function(a){var b=Galaxy.currUser.get("tags_used");if(!_.contains(b,a)){b.push(a);b.sort();Galaxy.currUser.set("tags_used",b)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(b){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(b.$activator,b)},render:function(){var b=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return b._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['<label class="prompt">',_l("Tags"),"</label>",'<input class="tags-input" value="',this.tagsToCSV(),'" />'].join("")},tagsToCSV:function(){var b=this.model.get("tags");if(!_.isArray(b)||_.isEmpty(b)){return""}return b.sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var b=this;this.$input().on("change",function(c){b.model.save({tags:c.val},{silent:true});if(c.added){b._addNewTagToTagsUsed(c.added.text+"")}})},_addNewTagToTagsUsed:function(b){var c=Galaxy.currUser.get("tags_used");if(!_.contains(c,b)){c.push(b);c.sort();Galaxy.currUser.set("tags_used",c)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:a}}); \ No newline at end of file diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1292,15 +1292,16 @@ .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} tr.light td{background-color:white;color:black} -tr.light:hover td{background-color:#A2A9C8} -tr.dark td{background-color:#8389a1;color:white} -tr.dark:hover td{background-color:#bbbfd0;color:white} +tr.light:hover td{background-color:#f5e8cc} +tr.dark td{background-color:#d6b161;color:white} +tr.dark:hover td{background-color:#ebd4a4;color:white} a.dark{color:white} .modal_table tr{border-bottom:1px solid #5f6990 !important} .modal_table th{border:none !important} .modal_table td{border:none !important} th.button_heading{width:2em} #library_folder_toolbar{margin-bottom:1em} +#library_toolbar{margin-bottom:1em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -10,15 +10,16 @@ .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} tr.light td{background-color:white;color:black} -tr.light:hover td{background-color:#A2A9C8} -tr.dark td{background-color:#8389a1;color:white} -tr.dark:hover td{background-color:#bbbfd0;color:white} +tr.light:hover td{background-color:#f5e8cc} +tr.dark td{background-color:#d6b161;color:white} +tr.dark:hover td{background-color:#ebd4a4;color:white} a.dark{color:white} .modal_table tr{border-bottom:1px solid #5f6990 !important} .modal_table th{border:none !important} .modal_table td{border:none !important} th.button_heading{width:2em} #library_folder_toolbar{margin-bottom:1em} +#library_toolbar{margin-bottom:1em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} diff -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 -r 4904f18e1cb0aaeb4ed2fb838eea3a40a682e231 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -52,17 +52,16 @@ } tr.light:hover td { - background-color: #A2A9C8; - // color: #8389a1; + background-color: #f5e8cc; } tr.dark td { - background-color: #8389a1; + background-color: #d6b161; color: white; } tr.dark:hover td { - background-color: #bbbfd0; + background-color: #ebd4a4; color: white; } a.dark @@ -70,8 +69,6 @@ color: white; } - - .modal_table{ tr { border-bottom: 1px solid #5f6990 !important; @@ -84,15 +81,6 @@ } } - - - - - - - - - th.button_heading { width: 2em; @@ -101,6 +89,9 @@ #library_folder_toolbar { margin-bottom: 1em; } +#library_toolbar { + margin-bottom: 1em; +} img.expanderIcon { padding-right: 4px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: use require definitions for tag and annotation editor views
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd27b9e4cda8/ Changeset: fd27b9e4cda8 User: carlfeberhard Date: 2014-03-19 21:26:31 Summary: History panel: use require definitions for tag and annotation editor views Affected #: 5 files diff -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -1,3 +1,6 @@ +define([ +], function(){ +// ============================================================================= /** A view on any model that has a 'annotation' attribute */ var AnnotationEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ @@ -69,3 +72,8 @@ /** string rep */ toString : function(){ return [ 'AnnotationEditor(', this.model + '', ')' ].join(''); } }); +// ============================================================================= +return { + AnnotationEditor : AnnotationEditor +}; +}); diff -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -1,7 +1,9 @@ define([ "mvc/dataset/hda-model", - "mvc/dataset/hda-base" -], function( hdaModel, hdaBase ){ + "mvc/dataset/hda-base", + "mvc/tags", + "mvc/annotations" +], function( hdaModel, hdaBase, tagsMod, annotationsMod ){ //============================================================================== /** @class Editing view for HistoryDatasetAssociation. * @name HDAEditView @@ -338,7 +340,7 @@ _renderTags : function( $where ){ var view = this; - this.tagsEditor = new TagsEditor({ + this.tagsEditor = new tagsMod.TagsEditor({ model : this.model, el : $where.find( '.tags-display' ), onshowFirstTime : function(){ this.render(); }, @@ -355,7 +357,7 @@ }, _renderAnnotation : function( $where ){ var view = this; - this.annotationEditor = new AnnotationEditor({ + this.annotationEditor = new annotationsMod.AnnotationEditor({ model : this.model, el : $where.find( '.annotation-display' ), onshowFirstTime : function(){ this.render(); }, diff -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -1,8 +1,10 @@ define([ "mvc/dataset/hda-model", "mvc/dataset/hda-edit", - "mvc/history/readonly-history-panel" -], function( hdaModel, hdaEdit, readonlyPanel ){ + "mvc/history/readonly-history-panel", + "mvc/tags", + "mvc/annotations" +], function( hdaModel, hdaEdit, readonlyPanel, tagsMod, annotationsMod ){ /* ============================================================================= TODO: @@ -101,7 +103,7 @@ /** render the tags sub-view controller */ _renderTags : function( $where ){ var panel = this; - this.tagsEditor = new TagsEditor({ + this.tagsEditor = new tagsMod.TagsEditor({ model : this.model, el : $where.find( '.history-controls .tags-display' ), onshowFirstTime : function(){ this.render(); }, @@ -122,7 +124,7 @@ /** render the annotation sub-view controller */ _renderAnnotation : function( $where ){ var panel = this; - this.annotationEditor = new AnnotationEditor({ + this.annotationEditor = new annotationsMod.AnnotationEditor({ model : this.model, el : $where.find( '.history-controls .annotation-display' ), onshowFirstTime : function(){ this.render(); }, diff -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 static/scripts/mvc/tags.js --- a/static/scripts/mvc/tags.js +++ b/static/scripts/mvc/tags.js @@ -1,3 +1,6 @@ +define([ +], function(){ +// ============================================================================= /** A view on any model that has a 'tags' attribute (a list of tag strings) * Incorporates the select2 jQuery plugin for tags display/editing: * http://ivaynberg.github.io/select2/ @@ -103,3 +106,9 @@ /** string rep */ toString : function(){ return [ 'TagsEditor(', this.model + '', ')' ].join(''); } }); + +// ============================================================================= +return { + TagsEditor : TagsEditor +}; +}); diff -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee -r fd27b9e4cda804e3bfbb9d94f076539ec1465ce5 templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ b/templates/webapps/galaxy/history/history_panel.mako @@ -92,9 +92,7 @@ <%def name="history_panel_javascripts()"> ${h.js( "utils/localization", - "mvc/base-mvc", - "mvc/tags", - "mvc/annotations" + "mvc/base-mvc" )} ${localize_js_strings([ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Remove older history and hda templates
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ce48f2a34dd/ Changeset: 7ce48f2a34dd User: carlfeberhard Date: 2014-03-19 20:47:39 Summary: Remove older history and hda templates Affected #: 21 files diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -660,11 +660,6 @@ }); //------------------------------------------------------------------------------ TEMPLATES -//HDABaseView.templates = { -// skeleton : Handlebars.templates[ 'template-hda-skeleton' ], -// body : Handlebars.templates[ 'template-hda-body' ] -//}; - var skeletonTemplate = [ '<div class="dataset hda">', '<div class="dataset-warnings">', diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -966,9 +966,6 @@ } }); //------------------------------------------------------------------------------ TEMPLATES -//ReadOnlyHistoryPanel.templates = { -// historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] -//}; var _panelTemplate = [ '<div class="history-controls">', '<div class="history-search-controls">', @@ -1027,6 +1024,7 @@ _l( 'Your history is empty. Click \'Get Data\' on the left pane to start' ), '</div>' ].join( '' ); + ReadOnlyHistoryPanel.templates = { historyPanel : function( historyJSON ){ return _.template( _panelTemplate, historyJSON, { variable: 'history' }); diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div 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y(B,A){return"database"}function x(D,C){var A="",B;A+='\n <div class="dataset-info">\n <span class="value">';if(B=p.misc_info){B=B.call(D,{hash:{},data:C})}else{B=D.misc_info;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function w(D,C){var A="",B;A+='\n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="dataset-display-applications">\n ';B=p.each.call(D,D.display_apps,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p.each.call(D,D.display_types,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-peek">\n ';B=p["if"].call(D,D.peek,{hash:{},inverse:o.noop,fn:o.program(19,s,C),data:C});if(B||B===0){A+=B}A+="\n </div>\n\n ";return A}function v(D,C){var A="",B;A+='\n <div class="display-application">\n <span class="display-application-location">';if(B=p.label){B=B.call(D,{hash:{},data:C})}else{B=D.label;B=typeof 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\ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/packed/templates/compiled/template-hda-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-hda-warning-messages.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-warning-messages"]=b(function(h,u,s,n,C){this.compilerInfo=[4,">= 1.0.0"];s=this.merge(s,h.helpers);C=C||{};var t="",j,e="function",d=this.escapeExpression,r=this,c=s.blockHelperMissing;function q(H,G){var D="",F,E;D+='\n<div class="errormessagesmall">\n ';E={hash:{},inverse:r.noop,fn:r.program(2,p,G),data:G};if(F=s.local){F=F.call(H,E)}else{F=H.local;F=typeof F===e?F.apply(H):F}if(!s.local){F=c.call(H,F,E)}if(F||F===0){D+=F}D+=":\n ";E={hash:{},inverse:r.noop,fn:r.program(4,o,G),data:G};if(F=s.local){F=F.call(H,E)}else{F=H.local;F=typeof F===e?F.apply(H):F}if(!s.local){F=c.call(H,F,E)}if(F||F===0){D+=F}D+="\n</div>\n";return D}function p(E,D){return"There was an error getting the data for this dataset"}function o(F,E){var D;if(D=s.error){D=D.call(F,{hash:{},data:E})}else{D=F.error;D=typeof D===e?D.apply(F):D}return d(D)}function m(F,E){var D;D=s.unless.call(F,F.purged,{hash:{},inverse:r.noop,fn:r.program(7,l,E),data:E});if(D||D===0){return D}else{return""}}function l(H,G){var D="",F,E;D+="\n";E={hash:{},inverse:r.noop,fn:r.program(8,i,G),data:G};if(F=s.warningmessagesmall){F=F.call(H,E)}else{F=H.warningmessagesmall;F=typeof F===e?F.apply(H):F}if(!s.warningmessagesmall){F=c.call(H,F,E)}if(F||F===0){D+=F}D+="\n";return D}function i(I,H){var D="",G,F,E;D+="\n ";E={hash:{},inverse:r.noop,fn:r.program(9,g,H),data:H};if(G=s.local){G=G.call(I,E)}else{G=I.local;G=typeof G===e?G.apply(I):G}if(!s.local){G=c.call(I,G,E)}if(G||G===0){D+=G}D+="\n ";F=s["if"].call(I,((G=I.urls),G==null||G===false?G:G.undelete),{hash:{},inverse:r.noop,fn:r.program(11,B,H),data:H});if(F||F===0){D+=F}D+="\n";return D}function g(E,D){return"This dataset has been deleted."}function B(H,G){var D="",F,E;D+='\n \n Click <a href="'+d(((F=((F=H.urls),F==null||F===false?F:F.undelete)),typeof F===e?F.apply(H):F))+'" class="historyItemUndelete" id="historyItemUndeleter-';if(E=s.id){E=E.call(H,{hash:{},data:G})}else{E=H.id;E=typeof E===e?E.apply(H):E}D+=d(E)+'"\n target="galaxy_history">here</a> to undelete it\n ';E=s["if"].call(H,((F=H.urls),F==null||F===false?F:F.purge),{hash:{},inverse:r.noop,fn:r.program(12,A,G),data:G});if(E||E===0){D+=E}D+="\n ";return D}function A(H,G){var D="",F,E;D+='\n or <a href="'+d(((F=((F=H.urls),F==null||F===false?F:F.purge)),typeof F===e?F.apply(H):F))+'" class="historyItemPurge" id="historyItemPurger-';if(E=s.id){E=E.call(H,{hash:{},data:G})}else{E=H.id;E=typeof E===e?E.apply(H):E}D+=d(E)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return D}function z(G,F){var E,D;D={hash:{},inverse:r.noop,fn:r.program(15,y,F),data:F};if(E=s.warningmessagesmall){E=E.call(G,D)}else{E=G.warningmessagesmall;E=typeof E===e?E.apply(G):E}if(!s.warningmessagesmall){E=c.call(G,E,D)}if(E||E===0){return E}else{return""}}function y(H,G){var D="",F,E;D+="\n ";E={hash:{},inverse:r.noop,fn:r.program(16,x,G),data:G};if(F=s.local){F=F.call(H,E)}else{F=H.local;F=typeof F===e?F.apply(H):F}if(!s.local){F=c.call(H,F,E)}if(F||F===0){D+=F}D+="\n";return D}function x(E,D){return"This dataset has been deleted and removed from disk."}function w(G,F){var E,D;D={hash:{},inverse:r.noop,fn:r.program(19,v,F),data:F};if(E=s.warningmessagesmall){E=E.call(G,D)}else{E=G.warningmessagesmall;E=typeof E===e?E.apply(G):E}if(!s.warningmessagesmall){E=c.call(G,E,D)}if(E||E===0){return E}else{return""}}function v(I,H){var D="",G,F,E;D+="\n ";E={hash:{},inverse:r.noop,fn:r.program(20,k,H),data:H};if(G=s.local){G=G.call(I,E)}else{G=I.local;G=typeof G===e?G.apply(I):G}if(!s.local){G=c.call(I,G,E)}if(G||G===0){D+=G}D+="\n ";F=s["if"].call(I,((G=I.urls),G==null||G===false?G:G.unhide),{hash:{},inverse:r.noop,fn:r.program(22,f,H),data:H});if(F||F===0){D+=F}D+="\n";return D}function k(E,D){return"This dataset has been hidden."}function f(H,G){var D="",F,E;D+='\n Click <a href="'+d(((F=((F=H.urls),F==null||F===false?F:F.unhide)),typeof F===e?F.apply(H):F))+'" class="historyItemUnhide" id="historyItemUnhider-';if(E=s.id){E=E.call(H,{hash:{},data:G})}else{E=H.id;E=typeof E===e?E.apply(H):E}D+=d(E)+'"\n target="galaxy_history">here</a> to unhide it\n ';return D}j=s["if"].call(u,u.error,{hash:{},inverse:r.noop,fn:r.program(1,q,C),data:C});if(j||j===0){t+=j}t+="\n\n";j=s["if"].call(u,u.deleted,{hash:{},inverse:r.noop,fn:r.program(6,m,C),data:C});if(j||j===0){t+=j}t+="\n\n";j=s["if"].call(u,u.purged,{hash:{},inverse:r.noop,fn:r.program(14,z,C),data:C});if(j||j===0){t+=j}t+="\n\n";j=s.unless.call(u,u.visible,{hash:{},inverse:r.noop,fn:r.program(18,w,C),data:C});if(j||j===0){t+=j}return t})})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,s,q,m,y){this.compilerInfo=[4,">= 1.0.0"];q=this.merge(q,g.helpers);y=y||{};var r="",i,f,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(C,B){var z="",A;z+='\n <div class="history-name">\n ';if(A=q.name){A=A.call(C,{hash:{},data:B})}else{A=C.name;A=typeof A===e?A.apply(C):A}z+=d(A)+"\n </div>\n ";return z}function n(C,B){var z="",A;z+='\n <div class="history-size">';if(A=q.nice_size){A=A.call(C,{hash:{},data:B})}else{A=C.nice_size;A=typeof A===e?A.apply(C):A}z+=d(A)+"</div>\n ";return z}function l(D,C){var z="",B,A;z+='\n <div class="warningmessagesmall"><strong>\n ';A={hash:{},inverse:p.noop,fn:p.program(6,k,C),data:C};if(B=q.local){B=B.call(D,A)}else{B=D.local;B=typeof B===e?B.apply(D):B}if(!q.local){B=c.call(D,B,A)}if(B||B===0){z+=B}z+="\n </strong></div>\n ";return z}function k(A,z){return"You are currently viewing a deleted history!"}function h(C,B){var z="",A;z+='\n \n <div class="';if(A=q.status){A=A.call(C,{hash:{},data:B})}else{A=C.status;A=typeof A===e?A.apply(C):A}z+=d(A)+'message">';if(A=q.message){A=A.call(C,{hash:{},data:B})}else{A=C.message;A=typeof A===e?A.apply(C):A}z+=d(A)+"</div>\n ";return z}function x(A,z){return"You are over your disk quota"}function w(A,z){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function v(A,z){return"All"}function u(A,z){return"None"}function t(A,z){return"For all selected"}function j(A,z){return"Your history is empty. Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(3,n,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(5,l,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(8,h,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(10,x,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(12,w,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <div class="btn-group">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(14,v,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n <button class="history-deselect-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(16,u,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n </div>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:p.noop,fn:p.program(18,t,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(20,j,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ /dev/null @@ -1,455 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-body'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-summary\">\n "; - if (stack1 = helpers.body) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.body; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"dataset-actions clear\">\n <div class=\"left\"></div>\n <div class=\"right\"></div>\n </div>\n\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-summary\">\n "; - stack1 = helpers['if'].call(depth0, depth0.misc_blurb, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.data_type, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.metadata_dbkey, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>" - + "\n\n <div class=\"dataset-actions clear\">\n <div class=\"left\"></div>\n <div class=\"right\"></div>\n </div>\n\n "; - stack1 = helpers.unless.call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - return buffer; - } -function program4(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-blurb\">\n <span class=\"value\">"; - if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } - -function program6(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-datatype\">\n <label class=\"prompt\">"; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</label>\n <span class=\"value\">"; - if (stack1 = helpers.data_type) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } -function program7(depth0,data) { - - - return "format"; - } - -function program9(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-dbkey\">\n <label class=\"prompt\">"; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</label>\n <span class=\"value\">\n "; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </span>\n </div>\n "; - return buffer; - } -function program10(depth0,data) { - - - return "database"; - } - -function program12(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-info\">\n <span class=\"value\">"; - if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } - -function program14(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"dataset-display-applications\">\n "; - stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-peek\">\n "; - stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n "; - return buffer; - } -function program15(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"display-application\">\n <span class=\"display-application-location\">"; - if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"display-application-links\">\n "; - stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </span>\n </div>\n "; - return buffer; - } -function program16(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <a target=\""; - if (stack1 = helpers.target) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\" href=\""; - if (stack1 = helpers.href) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - return buffer; - } -function program17(depth0,data) { - - var stack1; - if (stack1 = helpers.text) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program19(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <pre class=\"peek\">"; - if (stack1 = helpers.peek) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.peek; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</pre>\n "; - return buffer; - } - - buffer += "<div class=\"dataset-body\">\n "; - stack1 = helpers['if'].call(depth0, depth0.body, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"errormessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":\n "; - options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "There was an error getting the data for this dataset"; - } - -function program4(depth0,data) { - - var stack1; - if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program6(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n\n "; - return buffer; - } -function program8(depth0,data) { - - - return "This dataset has been deleted and removed from disk."; - } - -function program10(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program11(depth0,data) { - - - return "This dataset has been deleted."; - } - -function program13(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program14(depth0,data) { - - - return "This dataset has been hidden."; - } - - buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; - stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n " - + "\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; - if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"dataset-name\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program6(depth0,data) { - - - return "You are currently viewing a deleted history!"; - } - -function program8(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program10(depth0,data) { - - - return "You are over your disk quota"; - } - -function program12(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program14(depth0,data) { - - - return "All"; - } - -function program16(depth0,data) { - - - return "None"; - } - -function program18(depth0,data) { - - - return "For all selected"; - } - -function program20(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/compiled/template-hda-body.js --- a/static/scripts/templates/compiled/template-hda-body.js +++ /dev/null @@ -1,180 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-body'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-summary\">\n "; - if (stack1 = helpers.body) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.body; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n <div class=\"dataset-actions clear\">\n <div class=\"left\"></div>\n <div class=\"right\"></div>\n </div>\n\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-summary\">\n "; - stack1 = helpers['if'].call(depth0, depth0.misc_blurb, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.data_type, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.metadata_dbkey, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>" - + "\n\n <div class=\"dataset-actions clear\">\n <div class=\"left\"></div>\n <div class=\"right\"></div>\n </div>\n\n "; - stack1 = helpers.unless.call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - return buffer; - } -function program4(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-blurb\">\n <span class=\"value\">"; - if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } - -function program6(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-datatype\">\n <label class=\"prompt\">"; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</label>\n <span class=\"value\">"; - if (stack1 = helpers.data_type) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } -function program7(depth0,data) { - - - return "format"; - } - -function program9(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-dbkey\">\n <label class=\"prompt\">"; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</label>\n <span class=\"value\">\n "; - if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </span>\n </div>\n "; - return buffer; - } -function program10(depth0,data) { - - - return "database"; - } - -function program12(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"dataset-info\">\n <span class=\"value\">"; - if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n "; - return buffer; - } - -function program14(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"dataset-display-applications\">\n "; - stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-peek\">\n "; - stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n "; - return buffer; - } -function program15(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"display-application\">\n <span class=\"display-application-location\">"; - if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"display-application-links\">\n "; - stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </span>\n </div>\n "; - return buffer; - } -function program16(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <a target=\""; - if (stack1 = helpers.target) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\" href=\""; - if (stack1 = helpers.href) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\">"; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - return buffer; - } -function program17(depth0,data) { - - var stack1; - if (stack1 = helpers.text) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program19(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <pre class=\"peek\">"; - if (stack1 = helpers.peek) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.peek; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</pre>\n "; - return buffer; - } - - buffer += "<div class=\"dataset-body\">\n "; - stack1 = helpers['if'].call(depth0, depth0.body, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/compiled/template-hda-skeleton.js --- a/static/scripts/templates/compiled/template-hda-skeleton.js +++ /dev/null @@ -1,124 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"errormessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":\n "; - options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "There was an error getting the data for this dataset"; - } - -function program4(depth0,data) { - - var stack1; - if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program6(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n\n "; - return buffer; - } -function program8(depth0,data) { - - - return "This dataset has been deleted and removed from disk."; - } - -function program10(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program11(depth0,data) { - - - return "This dataset has been deleted."; - } - -function program13(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program14(depth0,data) { - - - return "This dataset has been hidden."; - } - - buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; - stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n " - + "\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; - if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"dataset-name\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ /dev/null @@ -1,153 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program6(depth0,data) { - - - return "You are currently viewing a deleted history!"; - } - -function program8(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program10(depth0,data) { - - - return "You are over your disk quota"; - } - -function program12(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program14(depth0,data) { - - - return "All"; - } - -function program16(depth0,data) { - - - return "None"; - } - -function program18(depth0,data) { - - - return "For all selected"; - } - -function program20(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n \n <div class=\"tags-display\"></div>\n <div class=\"annotation-display\"></div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(18, program18, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/hda-templates.html --- a/static/scripts/templates/hda-templates.html +++ /dev/null @@ -1,133 +0,0 @@ - -<script type="text/template" class="template-hda" id="template-hda-skeleton"> -<div class="dataset hda"> - <div class="dataset-warnings"> - {{#if error}} - <div class="errormessagesmall"> - {{#local}}There was an error getting the data for this dataset{{/local}}: - {{#local}}{{error}}{{/local}} - </div> - {{/if}} - - {{#if deleted}} - {{#if purged}} - <div class="dataset-purged-msg warningmessagesmall"><strong> - {{#local}}This dataset has been deleted and removed from disk.{{/local}} - </strong></div> - - {{else}}{{! deleted, not purged }} - <div class="dataset-deleted-msg warningmessagesmall"><strong> - {{#local}}This dataset has been deleted.{{/local}} - </strong></div> - {{/if}} - {{/if}} - - {{#unless visible}} - <div class="dataset-hidden-msg warningmessagesmall"><strong> - {{#local}}This dataset has been hidden.{{/local}} - </strong></div> - {{/unless}} - </div> - - <div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div> - <div class="dataset-primary-actions"></div> - {{! adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display }} - <div class="dataset-title-bar clear" tabindex="0"> - <span class="dataset-state-icon state-icon"></span> - <div class="dataset-title"> - <span class="hda-hid">{{ hid }}</span> - <span class="dataset-name">{{ name }}</span> - </div> - </div> - - <div class="dataset-body"></div> -</div> -</script> - - -<script type="text/template" class="template-hda" id="template-hda-body"> -<div class="dataset-body"> - {{#if body}} - <div class="dataset-summary"> - {{{ body }}} - </div> - <div class="dataset-actions clear"> - <div class="left"></div> - <div class="right"></div> - </div> - - {{else}} - <div class="dataset-summary"> - {{#if misc_blurb }} - <div class="dataset-blurb"> - <span class="value">{{ misc_blurb }}</span> - </div> - {{/if}} - - {{#if data_type }} - <div class="dataset-datatype"> - <label class="prompt">{{#local}}format{{/local}}</label> - <span class="value">{{ data_type }}</span> - </div> - {{/if}} - - {{#if metadata_dbkey }} - <div class="dataset-dbkey"> - <label class="prompt">{{#local}}database{{/local}}</label> - <span class="value"> - {{ metadata_dbkey }} - </span> - </div> - {{/if}} - - {{#if misc_info}} - <div class="dataset-info"> - <span class="value">{{ misc_info }}</span> - </div> - {{/if}} - </div>{{! end dataset-summary }} - - <div class="dataset-actions clear"> - <div class="left"></div> - <div class="right"></div> - </div> - - {{#unless deleted }} - <div class="tags-display"></div> - <div class="annotation-display"></div> - - <div class="dataset-display-applications"> - {{#each display_apps}} - <div class="display-application"> - <span class="display-application-location">{{label}}</span> - <span class="display-application-links"> - {{#each links}} - <a target="{{target}}" href="{{href}}">{{#local}}{{text}}{{/local}}</a> - {{/each}} - </span> - </div> - {{/each}} - - {{#each display_types}} - <div class="display-application"> - <span class="display-application-location">{{label}}</span> - <span class="display-application-links"> - {{#each links}} - <a target="{{target}}" href="{{href}}">{{#local}}{{text}}{{/local}}</a> - {{/each}} - </span> - </div> - {{/each}} - </div> - - <div class="dataset-peek"> - {{#if peek }} - <pre class="peek">{{{ peek }}}</pre> - {{/if}} - </div> - - {{/unless}}{{! unless deleted }} - - {{/if}}{{! end if body }} -</div> -</script> diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ /dev/null @@ -1,65 +0,0 @@ - -<script type="text/template" class="template-history" id="template-history-historyPanel"> - - <div class="history-controls"> - <div class="history-search-controls"> - <div class="history-search-input"></div> - </div> - - <div class="history-title"> - {{#if name }} - <div class="history-name"> - {{name}} - </div> - {{/if}} - </div> - - <div class="history-subtitle clear"> - {{#if nice_size }} - <div class="history-size">{{nice_size}}</div> - {{/if}} - - <div class="history-secondary-actions"></div> - </div> - - {{#if deleted}} - <div class="warningmessagesmall"><strong> - {{#local}}You are currently viewing a deleted history!{{/local}} - </strong></div> - {{/if}} - - <div class="message-container"> - {{#if message}} - {{! should already be localized }} - <div class="{{status}}message">{{message}}</div> - {{/if}} - </div> - - <div class="quota-message errormessage"> - {{#local}}You are over your disk quota{{/local}}. - {{#local}}Tool execution is on hold until your disk usage drops below your allocated quota{{/local}}. - </div> - - <div class="tags-display"></div> - <div class="annotation-display"></div> - - <div class="history-dataset-actions"> - <div class="btn-group"> - <button class="history-select-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}All{{/local}}</button> - <button class="history-deselect-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}None{{/local}}</button> - </div> - <button class="history-dataset-action-popup-btn btn btn-default" - >{{#local}}For all selected{{/local}}...</button> - </div> - - </div>{{! end history-controls }} - - {{! where the datasets/hdas are added }} - <div class="datasets-list"></div> - - <div class="empty-history-message infomessagesmall"> - {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} - </div> -</script> diff -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 -r 7ce48f2a34dd5d4cbac5d85bf94119380b15eeee templates/webapps/galaxy/history/history_panel.mako --- a/templates/webapps/galaxy/history/history_panel.mako +++ b/templates/webapps/galaxy/history/history_panel.mako @@ -97,12 +97,6 @@ "mvc/annotations" )} -##TODO: concat these -${h.templates( - "history-templates", - "helpers-common-templates" -)} - ${localize_js_strings([ # not needed?: "Galaxy History", 'refresh', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: libraries: imrpoved to_dict handling; corrected unencoded ID treatment; eceptions refactoring for API; docs
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7ebd14c2f9b/ Changeset: f7ebd14c2f9b User: martenson Date: 2014-03-19 20:38:14 Summary: libraries: imrpoved to_dict handling; corrected unencoded ID treatment; eceptions refactoring for API; docs Affected #: 3 files diff -r 40213f2f80646d21013c1ec7fe461aef3542c6e0 -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1951,6 +1951,14 @@ self.description = description self.synopsis = synopsis self.root_folder = root_folder + def to_dict( self, view='collection', value_mapper=None ): + """ + We prepend an F to folders. + """ + rval = super( Library, self ).to_dict( view=view, value_mapper=value_mapper ) + if 'root_folder_id' in rval: + rval[ 'root_folder_id' ] = 'F' + rval[ 'root_folder_id' ] + return rval def get_active_folders( self, folder, folders=None ): # TODO: should we make sure the library is not deleted? def sort_by_attr( seq, attr ): diff -r 40213f2f80646d21013c1ec7fe461aef3542c6e0 -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -54,8 +54,7 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) libraries = [] for library in query: - item = self.prepend_folder_prefix( library.to_dict( view='element', - value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) ) + item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) libraries.append( item ) return libraries @@ -93,8 +92,7 @@ library = None if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ): raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) - return self.prepend_folder_prefix( library.to_dict( view='element', - value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) ) + return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) @expose_api def create( self, trans, payload, **kwd ): @@ -131,8 +129,7 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - return self.prepend_folder_prefix( library.to_dict( view='element', - value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) ) + return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) @expose_api def update( self, trans, id, **kwd ): @@ -183,8 +180,7 @@ raise exceptions.RequestParameterMissingException( "You did not specify any payload." ) trans.sa_session.add( library ) trans.sa_session.flush() - return self.prepend_folder_prefix( library.to_dict( view='element', - value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) ) + return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) @expose_api def delete( self, trans, id, **kwd ): @@ -229,33 +225,5 @@ trans.sa_session.add( library ) trans.sa_session.flush() - return self.prepend_folder_prefix( library.to_dict( view='element', - value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) ) + return library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) - def prepend_folder_prefix (self, dictionary, type='library' ): - """ - prepend_folder_prefix (self, dictionary, type='library' ) - In Galaxy folders have an 'F' as a prefix to the encoded id to distinguish between folders and libraries - - :param dictionary: a supported object after to_dict containing _encoded_ ids - :type dictionary: dictionary - - :param type: string representing the type of dictionary that is passed in, defaults to 'library' - :type type: string - - :raises: TypeError, ValueError - """ - if not ( type in [ 'library', 'folder' ] ): - raise TypeError( 'Prepending is not implemented for given type of dictionary.' ) - return_dict = dictionary - if type == 'library': - if return_dict[ 'root_folder_id' ]: - return_dict[ 'root_folder_id' ] = 'F' + return_dict[ 'root_folder_id' ] - else: - raise ValueError( 'Given library does not contain root_folder_id to prepend to.' ) - elif type == 'folder': - if return_dict[ 'id' ]: - return_dict[ 'id' ] = 'F' + return_dict[ 'id' ] - else: - raise ValueError( 'Given folder does not contain an id to prepend to.' ) - return return_dict diff -r 40213f2f80646d21013c1ec7fe461aef3542c6e0 -r f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -1,39 +1,47 @@ """ -API operations on the contents of a library. +API operations on the contents of a data library. """ -import logging -from galaxy import web, exceptions -from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex +from galaxy import util +from galaxy import web +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import HTTPBadRequest, url_for -from galaxy import util +from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound +import logging log = logging.getLogger( __name__ ) class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): - @web.expose_api - # TODO: Add parameter to only get top level of datasets/subfolders. + @expose_api def index( self, trans, library_id, **kwd ): """ index( self, trans, library_id, **kwd ) * GET /api/libraries/{library_id}/contents: - return a list of library files and folders + Returns a list of library files and folders. - :type library_id: str - :param library_id: encoded id string of the library that contains this item + .. note:: May be slow! Returns all content traversing recursively through all folders. + .. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a non-recursive solution - :rtype: list + :param library_id: encoded id string of the library + :type library_id: string + :returns: list of dictionaries of the form: - * id: the encoded id of the library item * name: the 'libary path' or relationship of the library item to the root * type: 'file' or 'folder' * url: the url to get detailed information on the library item + :rtype: list + + :raises: MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError """ rval = [] current_user_roles = trans.get_current_user_roles() @@ -56,33 +64,32 @@ ld.library_dataset_dataset_association.dataset ) if (admin or can_access) and not ld.deleted: - #log.debug( "type(folder): %s" % type( folder ) ) - #log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) ) - #log.debug( "attributes of folder: %s" % str(dir(folder)) ) ld.api_path = folder.api_path + '/' + ld.name ld.api_type = 'file' rval.append( ld ) return rval try: decoded_library_id = trans.security.decode_id( library_id ) - except TypeError: - trans.response.status = 400 - return "Malformed library id ( %s ) specified, unable to decode." % str( library_id ) + except Exception: + raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % library_id ) try: - library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) - except: - library = None - if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): - trans.response.status = 400 - return "Invalid library id ( %s ) specified." % str( library_id ) - #log.debug( "Root folder type: %s" % type( library.root_folder ) ) + library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.id == decoded_library_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple libraries found with the same id.' ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): + raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) + # appending root folder rval.append( dict( id=encoded_id, type='folder', name='/', url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) - #log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) ) library.root_folder.api_path = '' + # appending all other items in the library recursively for content in traverse( library.root_folder ): encoded_id = trans.security.encode_id( content.id ) if content.api_type == 'folder': @@ -93,20 +100,22 @@ url=url_for( 'library_content', library_id=library_id, id=encoded_id, ) ) ) return rval - @web.expose_api + @expose_api def show( self, trans, id, library_id, **kwd ): """ show( self, trans, id, library_id, **kwd ) * GET /api/libraries/{library_id}/contents/{id} - return information about library file or folder + Returns information about library file or folder. + :param id: the encoded id of the library item to return :type id: str - :param id: the encoded id of the library item to return + + :param library_id: encoded id string of the library that contains this item :type library_id: str - :param library_id: encoded id string of the library that contains this item + :returns: detailed library item information :rtype: dict - :returns: detailed library item information + .. seealso:: :func:`galaxy.model.LibraryDataset.to_dict` and :attr:`galaxy.model.LibraryFolder.dict_element_visible_keys` @@ -116,7 +125,9 @@ content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) else: content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) - return self.encode_all_ids( trans, content.to_dict( view='element' ) ) + + return content.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } ) + # return self.encode_all_ids( trans, content.to_dict( view='element' ) ) @web.expose_api def create( self, trans, library_id, payload, **kwd ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 3268c8606464: correct localization call
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40213f2f8064/ Changeset: 40213f2f8064 User: carlfeberhard Date: 2014-03-19 20:03:12 Summary: Fix to 3268c8606464: correct localization call Affected #: 2 files diff -r 3268c8606464debc5270530ae80435c2671bb6ba -r 40213f2f80646d21013c1ec7fe461aef3542c6e0 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -685,7 +685,7 @@ // deleted not purged '<% } else { %>', '<div class="dataset-deleted-msg warningmessagesmall"><strong>', - _( 'This dataset has been deleted.' ), + _l( 'This dataset has been deleted.' ), '</strong></div>', '<% } %>', '<% } %>', diff -r 3268c8606464debc5270530ae80435c2671bb6ba -r 40213f2f80646d21013c1ec7fe461aef3542c6e0 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History panel: switch to underscore-based templating for all views
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3268c8606464/ Changeset: 3268c8606464 User: carlfeberhard Date: 2014-03-19 19:55:22 Summary: History panel: switch to underscore-based templating for all views Affected #: 6 files diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -660,9 +660,165 @@ }); //------------------------------------------------------------------------------ TEMPLATES +//HDABaseView.templates = { +// skeleton : Handlebars.templates[ 'template-hda-skeleton' ], +// body : Handlebars.templates[ 'template-hda-body' ] +//}; + +var skeletonTemplate = [ +'<div class="dataset hda">', + '<div class="dataset-warnings">', + // error during index fetch - show error on dataset + '<% if( hda.error ){ %>', + '<div class="errormessagesmall">', + _l( 'There was an error getting the data for this dataset' ), ':<%- hda.error %>', + '</div>', + '<% } %>', + + '<% if( hda.deleted ){ %>', + // purged and deleted + '<% if( hda.purged ){ %>', + '<div class="dataset-purged-msg warningmessagesmall"><strong>', + _l( 'This dataset has been deleted and removed from disk.' ), + '</strong></div>', + + // deleted not purged + '<% } else { %>', + '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + _( 'This dataset has been deleted.' ), + '</strong></div>', + '<% } %>', + '<% } %>', + + // hidden + '<% if( !hda.visible ){ %>', + '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + _l( 'This dataset has been hidden.' ), + '</strong></div>', + '<% } %>', + '</div>', + + // multi-select checkbox + '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', + // space for title bar buttons + '<div class="dataset-primary-actions"></div>', + + // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display + '<div class="dataset-title-bar clear" tabindex="0">', + '<span class="dataset-state-icon state-icon"></span>', + '<div class="dataset-title">', + //TODO: remove whitespace and use margin-right + '<span class="hda-hid"><%- hda.hid %></span> ', + '<span class="dataset-name"><%- hda.name %></span>', + '</div>', + '</div>', + + '<div class="dataset-body"></div>', +'</div>' +].join( '' ); + +var bodyTemplate = [ +'<div class="dataset-body">', + '<% if( hda.body ){ %>', + '<div class="dataset-summary">', + '<%= hda.body %>', + '</div>', + '<div class="dataset-actions clear">', + '<div class="left"></div>', + '<div class="right"></div>', + '</div>', + + '<% } else { %>', + '<div class="dataset-summary">', + '<% if( hda.misc_blurb ){ %>', + '<div class="dataset-blurb">', + '<span class="value"><%- hda.misc_blurb %></span>', + '</div>', + '<% } %>', + + '<% if( hda.data_type ){ %>', + '<div class="dataset-datatype">', + '<label class="prompt">', _l( 'format' ), '</label>', + '<span class="value"><%- hda.data_type %></span>', + '</div>', + '<% } %>', + + '<% if( hda.metadata_dbkey ){ %>', + '<div class="dataset-dbkey">', + '<label class="prompt">', _l( 'database' ), '</label>', + '<span class="value">', + '<%- hda.metadata_dbkey %>', + '</span>', + '</div>', + '<% } %>', + + '<% if( hda.misc_info ){ %>', + '<div class="dataset-info">', + '<span class="value"><%- hda.misc_info %></span>', + '</div>', + '<% } %>', + '</div>', + // end dataset-summary + + '<div class="dataset-actions clear">', + '<div class="left"></div>', + '<div class="right"></div>', + '</div>', + + '<% if( !hda.deleted ){ %>', + '<div class="tags-display"></div>', + '<div class="annotation-display"></div>', + + '<div class="dataset-display-applications">', + //TODO: the following two should be compacted + '<% _.each( hda.display_apps, function( app ){ %>', + '<div class="display-application">', + '<span class="display-application-location"><%- app.label %></span>', + '<span class="display-application-links">', + '<% _.each( app.links, function( link ){ %>', + '<a target="<%= target %>" href="<%= href %>">', + '<% print( _l( link.text ) ); %>', + '</a>', + '<% }); %>', + '</span>', + '</div>', + '<% }); %>', + + '<% _.each( hda.display_types, function( app ){ %>', + '<div class="display-application">', + '<span class="display-application-location"><%- label %></span>', + '<span class="display-application-links">', + '<% _.each( app.links, function( link ){ %>', + '<a target="<%= target %>" href="<%= href %>">', + '<% print( _l( link.text ) ); %>', + '</a>', + '<% }); %>', + '</span>', + '</div>', + '<% }); %>', + '</div>', + + '<div class="dataset-peek">', + '<% if( hda.peek ){ %>', + '<pre class="peek"><%= hda.peek %></pre>', + '<% } %>', + '</div>', + + '<% } %>', + // end if !deleted + + '<% } %>', + // end if body +'</div>' +].join( '' ); + HDABaseView.templates = { - skeleton : Handlebars.templates[ 'template-hda-skeleton' ], - body : Handlebars.templates[ 'template-hda-body' ] + skeleton : function( hdaJSON ){ + return _.template( skeletonTemplate, hdaJSON, { variable: 'hda' }); + }, + body : function( hdaJSON ){ + return _.template( bodyTemplate, hdaJSON, { variable: 'hda' }); + } }; //============================================================================== diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -966,8 +966,71 @@ } }); //------------------------------------------------------------------------------ TEMPLATES +//ReadOnlyHistoryPanel.templates = { +// historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] +//}; +var _panelTemplate = [ + '<div class="history-controls">', + '<div class="history-search-controls">', + '<div class="history-search-input"></div>', + '</div>', + + '<div class="history-title">', + '<% if( history.name ){ %>', + '<div class="history-name"><%= history.name %></div>', + '<% } %>', + '</div>', + + '<div class="history-subtitle clear">', + '<% if( history.nice_size ){ %>', + '<div class="history-size"><%= history.nice_size %></div>', + '<% } %>', + '<div class="history-secondary-actions"></div>', + '</div>', + + '<% if( history.deleted ){ %>', + '<div class="warningmessagesmall"><strong>', + _l( 'You are currently viewing a deleted history!' ), + '</strong></div>', + '<% } %>', + + '<div class="message-container">', + '<% if( history.message ){ %>', + // should already be localized + '<div class="<%= history.status %>message"><%= history.message %></div>', + '<% } %>', + '</div>', + + '<div class="quota-message errormessage">', + _l( 'You are over your disk quota.' ), + _l( 'Tool execution is on hold until your disk usage drops below your allocated quota.' ), + '</div>', + + '<div class="tags-display"></div>', + '<div class="annotation-display"></div>', + '<div class="history-dataset-actions">', + '<div class="btn-group">', + '<button class="history-select-all-datasets-btn btn btn-default"', + 'data-mode="select">', _l( 'All' ), '</button>', + '<button class="history-deselect-all-datasets-btn btn btn-default"', + 'data-mode="select">', _l( 'None' ), '</button>', + '</div>', + '<button class="history-dataset-action-popup-btn btn btn-default">', + _l( 'For all selected' ), '...</button>', + '</div>', + '</div>', + // end history controls + + // where the datasets/hdas are added + '<div class="datasets-list"></div>', + '<div class="empty-history-message infomessagesmall">', + _l( 'Your history is empty. Click \'Get Data\' on the left pane to start' ), + '</div>' +].join( '' ); ReadOnlyHistoryPanel.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ] + historyPanel : function( historyJSON ){ + return _.template( _panelTemplate, historyJSON, { variable: 'history' }); + } }; diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=this._buildNewRender();if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_buildNewRender:function(){var c=$(a.templates.skeleton(this.model.toJSON()));c.find(".dataset-primary-actions").append(this._render_titleButtons());c.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(c);return c},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){c.urls=c.model.urls();d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(c){var b=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(e){if(e.logger){this.logger=this.model.logger=e.logger}this.log(this+".initialize:",e);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=e.linkTarget||"_blank";this.selectable=e.selectable||false;this.selected=e.selected||false;this.expanded=e.expanded||false;this.draggable=e.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(f,e){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(g){g=(g===undefined)?(true):(g);var e=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var f=this._buildNewRender();if(g){$(e).queue(function(h){this.$el.fadeOut(e.fxSpeed,h)})}$(e).queue(function(h){this.$el.empty().attr("class",e.className).addClass("state-"+e.model.get("state")).append(f.children());if(this.selectable){this.showSelector(0)}h()});if(g){$(e).queue(function(h){this.$el.fadeIn(e.fxSpeed,h)})}$(e).queue(function(h){this.trigger("rendered",e);if(this.model.inReadyState()){this.trigger("rendered:ready",e)}if(this.draggable){this.draggableOn()}h()});return this},_buildNewRender:function(){var e=$(b.templates.skeleton(this.model.toJSON()));e.find(".dataset-primary-actions").append(this._render_titleButtons());e.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(e);return e},_setUpBehaviors:function(e){e=e||this.$el;make_popup_menus(e);e.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var f={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){f.disabled=true;f.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===c.HistoryDatasetAssociation.STATES.UPLOAD){f.disabled=true;f.title=_l("This dataset must finish uploading before it can be viewed")}else{f.title=_l("View data");f.href=this.urls.display;var e=this;f.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+e.model.get("name"),type:"url",content:e.urls.display})}}}}f.faIcon="fa-eye";return faIconButton(f)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var f=this.urls,g=this.model.get("meta_files");if(_.isEmpty(g)){return $(['<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var h="dataset-"+this.model.get("id")+"-popup",e=['<div popupmenu="'+h+'">','<a href="'+f.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(g,function(i){return['<a class="action-button" href="',f.meta_download+i.file_type,'">',_l("Download")," ",i.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+f.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+h+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(e)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var f=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),e=this["_render_body_"+this.model.get("state")];if(_.isFunction(e)){f=e.call(this)}this._setUpBehaviors(f);if(this.expanded){f.show()}return f},_render_stateBodyHelper:function(e,h){h=h||[];var f=this,g=$(b.templates.body(_.extend(this.model.toJSON(),{body:e})));g.find(".dataset-actions .left").append(_.map(h,function(i){return i.call(f)}));return g},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var e=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){e="<div>"+this.model.get("misc_blurb")+"</div>"+e}return this._render_stateBodyHelper(e,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var e=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),f=this._render_body_ok();f.prepend(e);return f},_render_body_ok:function(){var e=this,g=$(b.templates.body(this.model.toJSON())),f=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);g.find(".dataset-actions .left").append(_.map(f,function(h){return h.call(e)}));if(this.model.isDeletedOrPurged()){return g}return g},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(h,f){var e=32,g=13;if(h&&(h.type==="keydown")&&!(h.keyCode===e||h.keyCode===g)){return true}var i=this.$el.find(".dataset-body");f=(f===undefined)?(!i.is(":visible")):(f);if(f){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var e=this;function f(){e.$el.children(".dataset-body").replaceWith(e._render_body());e.$el.children(".dataset-body").slideDown(e.fxSpeed,function(){e.expanded=true;e.trigger("body-expanded",e.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(g){e.urls=e.model.urls();f()})}else{f()}},collapseBody:function(){var e=this;this.$el.children(".dataset-body").slideUp(e.fxSpeed,function(){e.expanded=false;e.trigger("body-collapsed",e.model.get("id"))})},showSelector:function(g){g=(g!==undefined)?(g):(this.fxSpeed);if(this.selected){this.select(null,true)}var f=this,e=32;if(g){this.$el.queue("fx",function(h){$(this).find(".dataset-primary-actions").fadeOut(g,h)});this.$el.queue("fx",function(h){$(this).find(".dataset-selector").show().animate({width:e},g,h);$(this).find(".dataset-title-bar").animate({"margin-left":e},g,h);f.selectable=true;f.trigger("selectable",true,f)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:e});this.$el.find(".dataset-title-bar").show().css({"margin-left":e});f.selectable=true;f.trigger("selectable",true,f)}},hideSelector:function(e){e=(e!==undefined)?(e):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},e,function(){$(this).hide();f()})});this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeIn(e,f)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(e){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(e)}else{this.hideSelector(e)}},select:function(e){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(e){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(e){if(this.selected){this.deselect(e)}else{this.select(e)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var e=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);e.addEventListener("dragstart",this.dragStartHandler,false);e.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var e=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);e.removeEventListener("dragstart",this.dragStartHandler,false);e.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(e){this.trigger("dragstart",this);e.dataTransfer.effectAllowed="move";e.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(e){this.trigger("dragend",this);return false},remove:function(f){var e=this;this.$el.fadeOut(e.fxSpeed,function(){e.$el.remove();e.off();if(f){f()}})},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+e+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var d=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- label %></span>','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= target %>" href="<%= href %>">',"<% print( _l( link.text ) ); %>","</a>","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");b.templates={skeleton:function(e){return _.template(a,e,{variable:"hda"})},body:function(e){return _.template(d,e,{variable:"hda"})}};return{HDABaseView:b}}); \ No newline at end of file diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base"],function(g,a){var f=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(i){var h="expandedHdas";this.save(h,_.extend(this.get(h),_.object([i],[true])))},removeExpandedHda:function(i){var h="expandedHdas";this.save(h,_.omit(this.get(h),i))},toString:function(){return"HistoryPrefs("+this.id+")"}});f.storageKeyPrefix="history:";f.historyStorageKey=function e(h){if(!h){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+h)}return(f.storageKeyPrefix+h)};f.get=function d(h){return new f({id:f.historyStorageKey(h)})};f.clearAll=function c(i){for(var h in sessionStorage){if(h.indexOf(f.storageKeyPrefix)===0){sessionStorage.removeItem(h)}}};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.linkTarget=h.linkTarget||"_blank";this.fxSpeed=_.has(h,"fxSpeed")?(h.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=h.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var i=_.pick(h,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,i,false);if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}return this},errorHandler:function(j,m,i,l,k){console.error(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{var h=this._parseErrorMessage(j,m,i,l,k);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(j,i,h,l){var k=function(m){return _.keys(f.get(m.id).get("expandedHdas"))};return this.loadHistory(j,i,h,l,k)},loadHistory:function(k,j,i,n,l){var h=this;j=j||{};h.trigger("loading-history",h);var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return h._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.JSONToModel(k,l,i)});j.fail(function(l,k){h.render()});return j},JSONToModel:function(k,h,i){this.log("JSONToModel:",k,h,i);i=i||{};if(Galaxy&&Galaxy.currUser){k.user=Galaxy.currUser.toJSON()}var j=new g.History(k,h,i);this.setModel(j);return this},setModel:function(i,h,j){h=h||{};j=(j!==undefined)?(j):(true);this.log("setModel:",i,h,j);this.freeModel();this.selectedHdaIds=[];if(i){if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=i;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(j){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(i,h,j){this.storage=new f({id:f.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);return this},render:function(j,k){this.log("render:",j,k);j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");h.append(b.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(h).text(this.emptyMsg);h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderEmptyMsg:function(j){var i=this,h=i.$emptyMessage(j);if(!_.isEmpty(i.hdaViews)){h.hide()}else{if(i.searchFor){h.text(i.noneFoundMsg).show()}else{h.text(i.emptyMsg).show()}}return this},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(h.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(h){return(h||this.$el).find(".datasets-list")},$messages:function(h){return(h||this.$el).find(".message-container")},$emptyMessage:function(h){return(h||this.$el).find(".empty-history-message")},renderHdas:function(i){i=i||this.$el;var h=this,k={},j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(i).empty();if(j.length){j.each(function(m){var l=m.get("id"),n=h._createHdaView(m);k[l]=n;if(_.contains(h.selectedHdaIds,l)){n.selected=true}h.attachHdaView(n.render(),i)})}this.hdaViews=k;this._renderEmptyMsg(i);return this.hdaViews},_createHdaView:function(i){var h=i.get("id"),j=new this.HDAViewClass({model:i,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[h],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(j);return j},_setUpHdaListeners:function(i){var h=this;i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)});i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});return this},attachHdaView:function(j,i){i=i||this.$el;var h=this.$datasetsList(i);h.prepend(j.$el);return this},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return i}$({}).queue([function j(m){var l=i.$emptyMessage();if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(l){var m=i._createHdaView(k);i.hdaViews[k.id]=m;m.render().$el.hide();i.scrollToTop();i.attachHdaView(m);m.$el.slideDown(i.fxSpeed)}]);return i},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",h);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",h);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(i){var j=this,k=".history-search-input";function h(l){if(j.model.hdas.haveDetails()){j.searchHdas(l);return}j.$el.find(k).searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(k).searchInput("toggle-loading")}).done(function(){j.searchHdas(l)})}i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return i},toggleSearchControls:function(j,h){var i=this.$el.find(".history-search-controls"),k=(jQuery.type(j)==="number")?(j):(this.fxSpeed);h=(h!==undefined)?(h):(!i.is(":visible"));if(h){i.slideDown(k,function(){$(this).find("input").focus()})}else{i.slideUp(k)}return h},searchHdas:function(h){var i=this;this.searchFor=h;this.filters=[function(j){return j.matchesAll(i.searchFor)}];this.trigger("search:searching",h,this);this.renderHdas();return this},clearHdaSearch:function(h){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},_hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$messages(),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j._messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},_messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(h){this.$container().scrollTop(h);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i];this.scrollTo(h.el.offsetTop);return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base"],function(h,a){var g=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){var i="expandedHdas";this.save(i,_.extend(this.get(i),_.object([j],[true])))},removeExpandedHda:function(j){var i="expandedHdas";this.save(i,_.omit(this.get(i),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});g.storageKeyPrefix="history:";g.historyStorageKey=function f(i){if(!i){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+i)}return(g.storageKeyPrefix+i)};g.get=function d(i){return new g({id:g.historyStorageKey(i)})};g.clearAll=function c(j){for(var i in sessionStorage){if(i.indexOf(g.storageKeyPrefix)===0){sessionStorage.removeItem(i)}}};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.fxSpeed=_.has(i,"fxSpeed")?(i.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=i.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var j=_.pick(i,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,j,false);if(i.onready){i.onready.call(this)}},_setUpListeners:function(){this.on("error",function(j,m,i,l,k){this.errorHandler(j,m,i,l,k)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(i){this.log(this+"",arguments)},this)}return this},errorHandler:function(k,n,j,m,l){console.error(k,n,j,m,l);if(n&&n.status===0&&n.readyState===0){}else{if(n&&n.status===502){}else{var i=this._parseErrorMessage(k,n,j,m,l);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",i.message,i.details)})}else{this.displayMessage("error",i.message,i.details)}}}},_parseErrorMessage:function(l,p,k,o,n){var j=Galaxy.currUser,i={message:this._bePolite(o),details:{user:(j instanceof User)?(j.toJSON()):(j+""),source:(l instanceof Backbone.Model)?(l.toJSON()):(l+""),xhr:p,options:(p)?(_.omit(k,"xhr")):(k)}};_.extend(i.details,n||{});if(p&&_.isFunction(p.getAllResponseHeaders)){var m=p.getAllResponseHeaders();m=_.compact(m.split("\n"));m=_.map(m,function(q){return q.split(": ")});i.details.xhr.responseHeaders=_.object(m)}return i},_bePolite:function(i){i=i||_l("An error occurred while getting updates from the server");return i+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(k,j,i,m){var l=function(n){return _.keys(g.get(n.id).get("expandedHdas"))};return this.loadHistory(k,j,i,m,l)},loadHistory:function(l,k,j,o,m){var i=this;k=k||{};i.trigger("loading-history",i);var n=h.History.getHistoryData(l,{historyFn:j,hdaFn:o,hdaDetailIds:k.initiallyExpanded||m});return i._loadHistoryFromXHR(n,k).fail(function(r,p,q){i.trigger("error",i,r,k,_l("An error was encountered while "+p),{historyId:l,history:q||{}})}).always(function(){i.trigger("loading-done",i)})},_loadHistoryFromXHR:function(k,j){var i=this;k.then(function(l,m){i.JSONToModel(l,m,j)});k.fail(function(m,l){i.render()});return k},JSONToModel:function(l,i,j){this.log("JSONToModel:",l,i,j);j=j||{};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}var k=new h.History(l,i,j);this.setModel(k);return this},setModel:function(j,i,k){i=i||{};k=(k!==undefined)?(k):(true);this.log("setModel:",j,i,k);this.freeModel();this.selectedHdaIds=[];if(j){if(Galaxy&&Galaxy.currUser){j.user=Galaxy.currUser.toJSON()}this.model=j;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(i.initiallyExpanded,i.show_deleted,i.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(k){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(j,i,k){this.storage=new g({id:g.historyStorageKey(this.model.get("id"))});if(_.isObject(j)){this.storage.set("exandedHdas",j)}if(_.isBoolean(i)){this.storage.set("show_deleted",i)}if(_.isBoolean(k)){this.storage.set("show_hidden",k)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(j,l,i,k){this.errorHandler(j,l,i,k)},this);return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(this.model){j=this.renderModel()}else{j=this.renderWithoutModel()}$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderWithoutModel:function(){var i=$("<div/>"),j=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return i.append(j)},renderModel:function(){var i=$("<div/>");i.append(b.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderEmptyMsg:function(k){var j=this,i=j.$emptyMessage(k);if(!_.isEmpty(j.hdaViews)){i.hide()}else{if(j.searchFor){i.text(j.noneFoundMsg).show()}else{i.text(j.emptyMsg).show()}}return this},_renderSearchButton:function(i){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(i.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},$messages:function(i){return(i||this.$el).find(".message-container")},$emptyMessage:function(i){return(i||this.$el).find(".empty-history-message")},renderHdas:function(j){j=j||this.$el;var i=this,l={},k=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(j).empty();if(k.length){k.each(function(n){var m=n.get("id"),o=i._createHdaView(n);l[m]=o;if(_.contains(i.selectedHdaIds,m)){o.selected=true}i.attachHdaView(o.render(),j)})}this.hdaViews=l;this._renderEmptyMsg(j);return this.hdaViews},_createHdaView:function(j){var i=j.get("id"),k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;j.on("error",function(l,n,k,m){i.errorHandler(l,n,k,m)});j.on("body-expanded",function(k){i.storage.addExpandedHda(k)});j.on("body-collapsed",function(k){i.storage.removeExpandedHda(k)});return this},attachHdaView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.prepend(k.$el);return this},addHdaView:function(l){this.log("add."+this,l);var j=this;if(!l.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return j}$({}).queue([function k(n){var m=j.$emptyMessage();if(m.is(":visible")){m.fadeOut(j.fxSpeed,n)}else{n()}},function i(m){var n=j._createHdaView(l);j.hdaViews[l.id]=n;n.render().$el.hide();j.scrollToTop();j.attachHdaView(n);n.$el.slideDown(j.fxSpeed)}]);return j},refreshHdas:function(j,i){if(this.model){return this.model.refresh(j,i)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(i){i.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(i){i=(i!==undefined)?(i):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",i);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(i){i=(i!==undefined)?(i):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",i);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(j){var k=this,l=".history-search-input";function i(m){if(k.model.hdas.haveDetails()){k.searchHdas(m);return}k.$el.find(l).searchInput("toggle-loading");k.model.hdas.fetchAllDetails({silent:true}).always(function(){k.$el.find(l).searchInput("toggle-loading")}).done(function(){k.searchHdas(m)})}j.searchInput({initialVal:k.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:i,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return j},toggleSearchControls:function(k,i){var j=this.$el.find(".history-search-controls"),l=(jQuery.type(k)==="number")?(k):(this.fxSpeed);i=(i!==undefined)?(i):(!j.is(":visible"));if(i){j.slideDown(l,function(){$(this).find("input").focus()})}else{j.slideUp(l)}return i},searchHdas:function(i){var j=this;this.searchFor=i;this.filters=[function(k){return k.matchesAll(j.searchFor)}];this.trigger("search:searching",i,this);this.renderHdas();return this},clearHdaSearch:function(i){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(j,i,k){i=(i!==undefined)?(i):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,k)}else{this.$el.fadeOut(i);this.indicator.show(j,i,k)}},_hideLoadingIndicator:function(i,j){i=(i!==undefined)?(i):(this.fxSpeed);if(this.indicator){this.indicator.hide(i,j)}},displayMessage:function(n,o,m){var k=this;this.scrollToTop();var l=this.$messages(),i=$("<div/>").addClass(n+"message").html(o);if(!_.isEmpty(m)){var j=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(k._messageToModalOptions(n,o,m));return false});i.append(" ",j)}return l.html(i)},_messageToModalOptions:function(m,o,l){var i=this,n=$("<div/>"),k={title:"Details"};function j(p){p=_.omit(p,_.functions(p));return["<table>",_.map(p,function(r,q){r=(_.isObject(r))?(j(r)):(r);return'<tr><td style="vertical-align: top; color: grey">'+q+'</td><td style="padding-left: 8px">'+r+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(l)){k.body=n.append(j(l))}else{k.body=n.html(l)}k.buttons={Ok:function(){Galaxy.modal.hide();i.clearMessages()}};return k},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(i){this.$container().scrollTop(i);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(j){if((!j)||(!this.hdaViews[j])){return this}var i=this.hdaViews[j];this.scrollTo(i.el.offsetTop);return this},scrollToHid:function(i){var j=this.model.hdas.getByHid(i);if(!j){return this}return this.scrollToId(j.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var e=['<div class="history-controls">','<div class="history-search-controls">','<div class="history-search-input"></div>',"</div>",'<div class="history-title">',"<% if( history.name ){ %>",'<div class="history-name"><%= history.name %></div>',"<% } %>","</div>",'<div class="history-subtitle clear">',"<% if( history.nice_size ){ %>",'<div class="history-size"><%= history.nice_size %></div>',"<% } %>",'<div class="history-secondary-actions"></div>',"</div>","<% if( history.deleted ){ %>",'<div class="warningmessagesmall"><strong>',_l("You are currently viewing a deleted history!"),"</strong></div>","<% } %>",'<div class="message-container">',"<% if( history.message ){ %>",'<div class="<%= history.status %>message"><%= history.message %></div>',"<% } %>","</div>",'<div class="quota-message errormessage">',_l("You are over your disk quota."),_l("Tool execution is on hold until your disk usage drops below your allocated quota."),"</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="history-dataset-actions">','<div class="btn-group">','<button class="history-select-all-datasets-btn btn btn-default"','data-mode="select">',_l("All"),"</button>",'<button class="history-deselect-all-datasets-btn btn btn-default"','data-mode="select">',_l("None"),"</button>","</div>",'<button class="history-dataset-action-popup-btn btn btn-default">',_l("For all selected"),"...</button>","</div>","</div>",'<div class="datasets-list"></div>','<div class="empty-history-message infomessagesmall">',_l("Your history is empty. Click 'Get Data' on the left pane to start"),"</div>"].join("");b.templates={historyPanel:function(i){return _.template(e,i,{variable:"history"})}};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1627,10 +1627,10 @@ .history-panel .dataset .dataset-body{display:none;padding:0 10px 6px 8px}.history-panel .dataset .dataset-body [class$=messagesmall]{margin:0px 0px 8px 0px} .history-panel .dataset .dataset-body label{margin:0px;padding:0px;font-weight:normal} .history-panel .dataset .dataset-body .prompt{font-weight:normal;color:#555} -.history-panel .dataset .dataset-body .prompt:after{content:':'} +.history-panel .dataset .dataset-body .prompt:after{content:':';margin-right:4px} .history-panel .dataset .dataset-body .dataset-summary{margin-bottom:8px}.history-panel .dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} .history-panel .dataset .dataset-body .dataset-summary .dataset-datatype,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value,.history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555} +.history-panel .dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;color:#555;margin-right:4px} .history-panel .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} .history-panel .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto}.history-panel .dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} .history-panel .dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} diff -r 9adf899807e7e618c11734e62cdede517048aa8b -r 3268c8606464debc5270530ae80435c2671bb6ba static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -220,6 +220,7 @@ } .prompt:after { content: ':'; + margin-right: 4px; } .dataset-summary { @@ -235,6 +236,7 @@ .dataset-datatype .value:after { content: ','; .help-text; + margin-right: 4px; } .dataset-dbkey:after { content: ' '; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Testing: update browser tests to use new empty history message
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9adf899807e7/ Changeset: 9adf899807e7 User: carlfeberhard Date: 2014-03-19 19:19:23 Summary: Testing: update browser tests to use new empty history message Affected #: 1 file diff -r fe392bff79db569562d771beaecf9f3cbb215fdf -r 9adf899807e7e618c11734e62cdede517048aa8b test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -388,7 +388,7 @@ }, newName : 'Unnamed history', newSize : '0 bytes', - emptyMsg : "This history is empty. Click 'Get Data' on the left pane to start" + emptyMsg : "This history is empty. You can load your own data or get data from an external source" }, hda : { datasetFetchErrorMsg : 'There was an error getting the data for this dataset' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Add settings parser, apply fixes, remove history identifier
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fe392bff79db/ Changeset: fe392bff79db User: guerler Date: 2014-03-19 17:53:59 Summary: Charts: Add settings parser, apply fixes, remove history identifier Affected #: 13 files diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof 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Please make sure that 'R-kit' is installed.")})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in 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t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data 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n=self.app.charts.get(e);this.portlet.title(n.get("title")),this.portlet.setOperation("edit",function(){self.app.chart.copy(n),self.app.charts_view.hide(),self.app.chart_view.$el.show()}),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s}),i=u.mode;i=="execute"?t.app.jobs.submit(e,t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t({content:"Add charts to this table.",ondblclick:function(e){var t=u.app.charts.get(e);u.app.chart.copy(t),u.hide(),u.app.chart_view.$el.show()},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.hide(),u.app.chart.reset(),u.app.chart_view.$el.show()}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.table.size()==0?(this.hide(),this.app.chart.reset(),this.app.chart_view.$el.show()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom"}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=n.$title.find("#delete");r.tooltip({title:"Delete this tab",placement:"bottom"}),r.on("click",function(){return r.tooltip("destroy"),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be reseted.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.chart.groups.length==0&&o._addGroupModel(),o._saveChart(),o.hide(),o.app.charts_view.$el.show()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.hide(),o.app.charts_view.$el.show()}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.dataset.id),this.chart.set("dataset_hid",this.app.options.dataset.hid),this.chart.set("history_id",this.app.options.dataset.history_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()});var 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d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){return Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden",operations:{edit:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize"})}}),this.setElement(this.portlet.$el);var s=this;this.app.charts.on("remove",function(e){s._removeChart(e.id)}),this.app.charts.on("redraw",function(e){e.ready()?s._refreshChart(e):e.on("change:state",function(){e.ready()&&s._refreshChart(e)})})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=self.app.charts.get(e);this.portlet.title(n.get("title")),this.portlet.setOperation("edit",function(){self.app.chart.copy(n),self.app.charts_view.hide(),self.app.chart_view.$el.show()}),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t({content:"Add charts to this table.",ondblclick:function(e){var t=u.app.charts.get(e);u.app.chart.copy(t),u.hide(),u.app.chart_view.$el.show()},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.hide(),u.app.chart.reset(),u.app.chart_view.$el.show()}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.table.size()==0?(this.hide(),this.app.chart.reset(),this.app.chart_view.$el.show()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend(LoggableMixin).extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){this.log(this+".initialize",e,this.attributes),_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"},save:function(){}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be reseted.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.chart.groups.length==0&&o._addGroupModel(),o._saveChart(),o.hide(),o.app.charts_view.$el.show()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.hide(),o.app.charts_view.$el.show()}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()});var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.save(),e.trigger("redraw",e)}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500,title:"Create a new chart"}})}),define("plugin/models/charts",["plugin/models/chart"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"},separator_custom:{title:"Advanced",type:"separator"},bin_size:{title:"Bin size",info:"Provide the bin size for the histogram.",type:"select",init:1,data:[{label:"0.001",value:"0.001"},{label:"0.01",value:"0.01"},{label:"0.1",value:"0.1"},{label:"1",value:"1"},{label:"10",value:"10"},{label:"100",value:"100"},{label:"1000",value:"1000"}]}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/views/charts","plugin/views/chart","plugin/models/config","plugin/models/chart","plugin/models/charts","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(n){this.options=n,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new a,this.jobs=new i(this),this.types=new c,this.chart=new f,this.charts=new l,this.datasets=new s(this),this.charts_view=new o(this),this.chart_view=new u(this),this.options.config.widget?this.portlet=$("<div></div>"):this.portlet=new t.View({icon:"fa-bar-chart-o"}),this.portlet.append(this.charts_view.$el),this.portlet.append(this.chart_view.$el),this.options.config.widget?this.setElement(this.portlet):this.setElement(this.portlet.$el),this.charts_view.$el.hide();var r=this;this.config.on("change:title",function(){r._refreshTitle()}),this.render()},render:function(){this._refreshTitle()},_refreshTitle:function(){var e=this.config.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/charts/histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/histogram/config.js +++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js @@ -2,7 +2,7 @@ return $.extend(true, {}, nvd3_config, { title : 'Histogram', - mode : 'execute', + execute : true, columns : { y : { title : 'Observations' @@ -23,12 +23,40 @@ type : 'separator' }, bin_size : { - title : 'Number of bins', - info : 'Provide the number of histogram bins. The parsed data will be evenly distributed into bins according to the minimum and maximum values of the dataset.', - type : 'slider', - init : 10, - min : 10, - max : 1000, + title : 'Bin size', + info : 'Provide the bin size for the histogram.', + type : 'select', + init : 1, + data : [ + { + label : '0.001', + value : '0.001' + }, + { + label : '0.01', + value : '0.01' + }, + { + label : '0.1', + value : '0.1' + }, + { + label : '1', + value : '1' + }, + { + label : '10', + value : '10' + }, + { + label : '100', + value : '100' + }, + { + label : '1000', + value : '1000' + } + ] } } }); diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -14,7 +14,7 @@ }, // create job - submit: function(chart, request_string, callback) { + submit: function(chart, settings_string, columns_string, callback) { // link this var self = this; @@ -28,11 +28,14 @@ // configure tool data = { 'tool_id' : 'rkit', - 'history_id' : chart.get('history_id'), 'inputs' : { - 'input' : chart.get('dataset_hid'), + 'input' : { + 'id' : chart.get('dataset_id'), + 'src' : 'hda' + }, 'module' : chart_type, - 'options' : request_string + 'columns' : columns_string, + 'settings' : settings_string } } @@ -85,7 +88,11 @@ }, // error handler function(response) { - chart.state('failed', 'Job submission failed. Please make sure that \'R-kit\' is installed.'); + var message = ''; + if (response && response.message && response.message.data && response.message.data.input) { + message = response.message.data.input + '.'; + } + chart.state('failed', 'This visualization requires processing by the R-kit. Please make sure that it is installed. ' + message); } ); }, diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -81,7 +81,8 @@ float : 'right', icon : '', tooltip : '', - placement : 'bottom' + placement : 'bottom', + title : '' }, // initialize @@ -98,7 +99,10 @@ // element _template: function(options) { - return '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/>'; + return '<div>' + + '<span class="fa ' + options.icon + '" style="font-size: 1.2em;"/> ' + + options.title + + '</div>'; } }); diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/models/chart.js --- a/config/plugins/visualizations/charts/static/models/chart.js +++ b/config/plugins/visualizations/charts/static/models/chart.js @@ -1,5 +1,5 @@ // dependencies -define(['plugin/models/groups'], function(Groups) { +define(['plugin/models/groups', 'mvc/visualization/visualization-model'], function(Groups) { // model @@ -58,6 +58,25 @@ ready: function() { return (this.get('state') == 'ok') || (this.get('state') == 'failed'); + }, + + // save charts + save: function() { + /*/ create visualization + var vis = new Visualization({ + type : 'charts', + config : this.attributes + }); + + // copy attributes + //vis.set(this.attributes); + + // save visualization + vis.save() + .fail( function( xhr, status, message ){ + console.error( xhr, status, message ); + alert( 'Error loading data:\n' + xhr.responseText ); + });*/ } }); diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -76,7 +76,11 @@ for (var id in types){ var chart_type = types[id]; this.table.add (++types_n + '.'); - this.table.add (chart_type.title); + if (chart_type.execute) { + this.table.add(chart_type.title + ' (requires processing)'); + } else { + this.table.add (chart_type.title); + } this.table.append(id); } @@ -280,9 +284,7 @@ // reset chart details this.chart.set('id', Utils.uuid()); this.chart.set('type', 'bardiagram'); - this.chart.set('dataset_id', this.app.options.dataset.id); - this.chart.set('dataset_hid', this.app.options.dataset.hid); - this.chart.set('history_id', this.app.options.dataset.history_id); + this.chart.set('dataset_id', this.app.options.config.dataset_id); this.chart.set('title', 'New Chart'); }, @@ -305,6 +307,9 @@ current.copy(this.chart); } + // save + current.save(); + // trigger redraw current.trigger('redraw', current); } diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -199,9 +199,8 @@ var view = new ChartView(self.app, {svg : svg}); // request data - var mode = chart_settings.mode; - if (mode == 'execute') { - self.app.jobs.submit(chart, self._defaultRequestString(chart), function() { + if (chart_settings.execute) { + self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { view.draw(chart, self._defaultRequestDictionary(chart)); }); } else { @@ -255,6 +254,21 @@ }, // create default chart request + _defaultSettingsString : function(chart) { + + // configure settings + var settings_string = ''; + + // add settings to settings string + for (key in chart.settings.attributes) { + settings_string += key + ':' + chart.settings.get(key) + ', '; + }; + + // return + return settings_string.substring(0, settings_string.length - 2); + }, + + // create default chart request _defaultRequestDictionary : function(chart) { // get chart settings diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -15,7 +15,8 @@ 'libs/require', 'libs/underscore', 'libs/backbone/backbone', - 'libs/d3' )} + 'libs/d3', + 'mvc/base-mvc')} ## css ${h.css( 'base' )} @@ -71,10 +72,9 @@ require(['plugin/app'], function(App) { // load options var options = { - config : ${h.to_json_string( config )}, - dataset : ${h.to_json_string( trans.security.encode_dict_ids( hda.to_dict() ) )} + config : ${h.to_json_string( config )} } - + console.log(options); // create application app = new App(options); diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js --- a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js @@ -16,7 +16,7 @@ Embedding Small multiples Drag & Drop other splots onto current (redraw with new axis and differentiate the datasets) - Remove 'chart' names + Remove 'chart' namessave Somehow link out from info box? Subclass on specific datatypes? (vcf, cuffdiff, etc.) diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf static/scripts/mvc/ui/ui-tabs.js --- a/static/scripts/mvc/ui/ui-tabs.js +++ b/static/scripts/mvc/ui/ui-tabs.js @@ -47,7 +47,7 @@ if (this.options.operations) { $.each(this.options.operations, function(name, item) { item.$el.prop('id', name); - self.$nav.append(item.$el); + self.$nav.find('.operations').append(item.$el); }); } @@ -60,7 +60,7 @@ this.$nav.append($tab_new); // add tooltip - $tab_new.tooltip({title: 'Add a new tab', placement: 'bottom'}); + $tab_new.tooltip({title: 'Add a new tab', placement: 'bottom', container: self.$el}); // link click event $tab_new.on('click', function(e) { @@ -105,10 +105,12 @@ // add click event to remove tab if (options.ondel) { + var self = this; var $del_icon = tab.$title.find('#delete'); - $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom'}); + $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom', container: self.$el}); $del_icon.on('click', function() { $del_icon.tooltip('destroy'); + self.$el.find('.tooltip').remove(); options.ondel(); return false; }); @@ -199,7 +201,9 @@ // fill template _template: function(options) { return '<div class="tabbable tabs-left">' + - '<ul class="tab-navigation nav nav-tabs"/>' + + '<ul class="tab-navigation nav nav-tabs">' + + '<div class="operations" style="float: right; margin-bottom: 4px;"></div>' + + '</ul>'+ '<div class="tab-content"/>' + '</div>'; }, diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf static/scripts/packed/mvc/ui/ui-tabs.js --- a/static/scripts/packed/mvc/ui/ui-tabs.js +++ b/static/scripts/packed/mvc/ui/ui-tabs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom"});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(d){var f=d.id;var e={$title:$(this._template_tab(d)),$content:$(this._template_tab_content(d)),removable:d.ondel?true:false};this.list[f]=e;if(this.options.onnew){this.$nav.find("#new-tab").before(e.$title)}else{this.$nav.append(e.$title)}e.$content.append(d.$el);this.$content.append(e.$content);if(_.size(this.list)==1){e.$title.addClass("active");e.$content.addClass("active");this.first_tab=f}if(d.ondel){var c=e.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom"});c.on("click",function(){c.tooltip("destroy");d.ondel();return false})}if(d.onclick){e.$title.on("click",function(){d.onclick()})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"/><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(e){this.options=a.merge(e,this.optionsDefault);var c=$(this._template(this.options));this.$nav=c.find(".tab-navigation");this.$content=c.find(".tab-content");this.setElement(c);this.list={};var d=this;if(this.options.operations){$.each(this.options.operations,function(g,h){h.$el.prop("id",g);d.$nav.find(".operations").append(h.$el)})}if(this.options.onnew){var f=$(this._template_tab_new(this.options));this.$nav.append(f);f.tooltip({title:"Add a new tab",placement:"bottom",container:d.$el});f.on("click",function(g){f.tooltip("hide");d.options.onnew()})}},add:function(e){var g=e.id;var f={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?true:false};this.list[g]=f;if(this.options.onnew){this.$nav.find("#new-tab").before(f.$title)}else{this.$nav.append(f.$title)}f.$content.append(e.$el);this.$content.append(f.$content);if(_.size(this.list)==1){f.$title.addClass("active");f.$content.addClass("active");this.first_tab=g}if(e.ondel){var d=this;var c=f.$title.find("#delete");c.tooltip({title:"Delete this tab",placement:"bottom",container:d.$el});c.on("click",function(){c.tooltip("destroy");d.$el.find(".tooltip").remove();e.ondel();return false})}if(e.onclick){f.$title.on("click",function(){e.onclick()})}},del:function(d){var c=this.list[d];c.$title.remove();c.$content.remove();delete c;if(this.first_tab==d){this.first_tab=null}if(this.first_tab!=null){this.show(this.first_tab)}},delRemovable:function(){for(var d in this.list){var c=this.list[d];if(c.removable){this.del(d)}}},show:function(c){this.$el.fadeIn("fast");this.visible=true;if(c){this.list[c].$title.find("a").tab("show")}},hide:function(){this.$el.fadeOut("fast");this.visible=false},hideOperation:function(c){this.$nav.find("#"+c).hide()},showOperation:function(c){this.$nav.find("#"+c).show()},setOperation:function(e,d){var c=this.$nav.find("#"+e);c.off("click");c.on("click",d)},title:function(e,d){var c=this.list[e].$title.find("#text");if(d){c.html(d)}return c.html()},_template:function(c){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(c){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+c.title_new+"</a></li>"},_template_tab:function(d){var c='<li id="title-'+d.id+'"><a title="" href="#tab-'+d.id+'" data-toggle="tab" data-original-title=""><span id="text">'+d.title+"</span>";if(d.ondel){c+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'}c+="</a></li>";return c},_template_tab_content:function(c){return'<div id="tab-'+c.id+'" class="tab-pane"/>'}});return{View:b}}); \ No newline at end of file diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;if(q==200){try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}o&&o(response)}else{k&&k(q)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return(new Date().getTime()).toString(36)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file +define(["libs/underscore"],function(j){function d(l,m,k){g("GET",l,{},m,k)}function g(p,l,m,o,k){if(p=="GET"||p=="DELETE"){if(l.indexOf("?")==-1){l+="?"}else{l+="&"}l+=$.param(m)}var n=new XMLHttpRequest();n.open(p,l,true);n.setRequestHeader("Accept","application/json");n.setRequestHeader("Cache-Control","no-cache");n.setRequestHeader("X-Requested-With","XMLHttpRequest");n.setRequestHeader("Content-Type","application/json");n.onloadend=function(){var q=n.status;try{response=jQuery.parseJSON(n.responseText)}catch(r){response=n.responseText}if(q==200){o&&o(response)}else{k&&k(response)}};if(p=="GET"||p=="DELETE"){n.send()}else{n.send(JSON.stringify(m))}}function h(n,k){var l=$('<div class="'+n+'"></div>');l.appendTo(":eq(0)");var m=l.css(k);l.remove();return m}function f(k){if(!$('link[href^="'+k+'"]').length){$('<link href="'+galaxy_config.root+k+'" rel="stylesheet">').appendTo("head")}}function i(k,l){if(k){return j.defaults(k,l)}else{return l}}function b(l,n){var m="";if(l>=100000000000){l=l/100000000000;m="TB"}else{if(l>=100000000){l=l/100000000;m="GB"}else{if(l>=100000){l=l/100000;m="MB"}else{if(l>=100){l=l/100;m="KB"}else{if(l>0){l=l*10;m="b"}else{return"<strong>-</strong>"}}}}}var k=(Math.round(l)/10);if(n){return k+" "+m}else{return"<strong>"+k+"</strong> "+m}}function a(){return(new Date().getTime()).toString(36)}function c(k){var l=$("<p></p>");l.append(k);return l}function e(){var m=new Date();var k=(m.getHours()<10?"0":"")+m.getHours();var l=(m.getMinutes()<10?"0":"")+m.getMinutes();var n=m.getDate()+"/"+(m.getMonth()+1)+"/"+m.getFullYear()+", "+k+":"+l;return n}return{cssLoadFile:f,cssGetAttribute:h,get:d,merge:i,bytesToString:b,uuid:a,time:e,wrap:c,request:g}}); \ No newline at end of file diff -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e -r fe392bff79db569562d771beaecf9f3cbb215fdf static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -32,16 +32,21 @@ xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); xhr.setRequestHeader('Content-Type', 'application/json'); xhr.onloadend = function() { + // get status var status = xhr.status; + + // read response + try { + response = jQuery.parseJSON(xhr.responseText); + } catch (e) { + response = xhr.responseText; + } + + // parse response if (status == 200) { - try { - response = jQuery.parseJSON(xhr.responseText); - } catch (e) { - response = xhr.responseText; - } success && success(response); } else { - error && error(status); + error && error(response); } }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: add assistive UI links to empty history message
by commits-noreply＠bitbucket.org 19 Mar '14

19 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cb2d13e55a5c/ Changeset: cb2d13e55a5c User: carlfeberhard Date: 2014-03-19 16:08:15 Summary: History panel: add assistive UI links to empty history message Affected #: 6 files diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -47,7 +47,7 @@ /** class to use for constructing the HDA views */ HDAViewClass : hdaEdit.HDAEditView, - emptyMsg : _l( "This history is empty. Click 'Get Data' on the left pane to start" ), + emptyMsg : _l( "This history is empty. Click 'Get Data' on the left tool menu to start" ), noneFoundMsg : _l( "No matching datasets found" ), // ......................................................................... SET UP @@ -204,6 +204,47 @@ } }, + /** In this override, add links to open data uploader or get data in the tools section */ + _renderEmptyMsg : function( $whereTo ){ + var panel = this, + $emptyMsg = panel.$emptyMessage( $whereTo ), + $toolMenu = $( '.toolMenuContainer' ); + + if( ( _.isEmpty( panel.hdaViews ) && !panel.searchFor ) + && ( Galaxy && Galaxy.upload && $toolMenu.size() ) ){ + $emptyMsg.empty(); + + $emptyMsg.html([ + _l( 'This history is empty. ' ), _l( 'You can ' ), + '<a class="uploader-link" href="javascript:void(0)">', + _l( 'load your own data' ), + '</a>', + _l( ' or ' ), '<a class="get-data-link" href="javascript:void(0)">', + _l( 'get data from an external source' ), + '</a>' + ].join('') ); + $emptyMsg.find( '.uploader-link' ).click( function( ev ){ + Galaxy.upload._eventShow( ev ); + }); + $emptyMsg.find( '.get-data-link' ).click( function( ev ){ + $toolMenu.parent().scrollTop( 0 ); + $toolMenu.find( 'span:contains("Get Data")' ) + .click(); + //.fadeTo( 200, 0.1, function(){ + // console.debug( this ) + // $( this ).fadeTo( 200, 1.0 ); + //}); + }); + + $emptyMsg.show(); + + + } else { + hpanel.HistoryPanel.prototype._renderEmptyMsg.call( this, $whereTo ); + } + return this; + }, + /** In this override, save the search control visibility state to preferences */ toggleSearchControls : function( eventOrSpeed, show ){ var visible = hpanel.HistoryPanel.prototype.toggleSearchControls.call( this, eventOrSpeed, show ); diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -81,6 +81,7 @@ var $newRender = $( '<div/>' ); $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); + this.$emptyMessage( $newRender ).text( this.emptyMsg ); if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ this._renderTags( $newRender ); this._renderAnnotation( $newRender ); diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -497,6 +497,7 @@ // render based on anonymity, set up behaviors $newRender.append( ReadOnlyHistoryPanel.templates.historyPanel( this.model.toJSON() ) ); + this.$emptyMessage( $newRender ).text( this.emptyMsg ); // search and select available to both anon/logged-in users $newRender.find( '.history-secondary-actions' ).prepend( this._renderSearchButton() ); @@ -507,6 +508,23 @@ return $newRender; }, + /** render the empty/none-found message */ + _renderEmptyMsg : function( $whereTo ){ + var panel = this, + $emptyMsg = panel.$emptyMessage( $whereTo ); + + if( !_.isEmpty( panel.hdaViews ) ){ + $emptyMsg.hide(); + + } else if( panel.searchFor ){ + $emptyMsg.text( panel.noneFoundMsg ).show(); + + } else { + $emptyMsg.text( panel.emptyMsg ).show(); + } + return this; + }, + /** button for opening search */ _renderSearchButton : function( $where ){ return faIconButton({ @@ -555,7 +573,7 @@ newHdaViews = {}, // only render the shown hdas //TODO: switch to more general filtered pattern - visibleHdas = this.model.hdas.getVisible( + visibleHdas = this.model.hdas.getVisible( this.storage.get( 'show_deleted' ), this.storage.get( 'show_hidden' ), this.filters @@ -571,20 +589,15 @@ var hdaId = hda.get( 'id' ), hdaView = panel._createHdaView( hda ); newHdaViews[ hdaId ] = hdaView; + // persist selection if( _.contains( panel.selectedHdaIds, hdaId ) ){ hdaView.selected = true; } panel.attachHdaView( hdaView.render(), $whereTo ); }); - panel.$emptyMessage( $whereTo ).hide(); - - } else { - //this.log( 'emptyMsg:', panel.$emptyMessage( $whereTo ) ) - panel.$emptyMessage( $whereTo ) - .text( ( this.model.hdas.length && this.searchFor )?( this.noneFoundMsg ):( this.emptyMsg ) ) - .show(); } this.hdaViews = newHdaViews; + this._renderEmptyMsg( $whereTo ); return this.hdaViews; }, diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left pane to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f)},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(g,f,h){e.HistoryPanel.prototype.setModel.call(this,g,f,h);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},toggleSearchControls:function(g,f){var h=e.HistoryPanel.prototype.toggleSearchControls.call(this,g,f);this.preferences.set("searching",h)},_renderTags:function(f){var g=this;e.HistoryPanel.prototype._renderTags.call(this,f);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("tagsEditorShown",h.hidden)})},_renderAnnotation:function(f){var g=this;e.HistoryPanel.prototype._renderAnnotation.call(this,f);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("annotationEditorShown",h.hidden)})},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f)},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(g,f,h){e.HistoryPanel.prototype.setModel.call(this,g,f,h);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(h){var g=this,f=g.$emptyMessage(h),i=$(".toolMenuContainer");if((_.isEmpty(g.hdaViews)&&!g.searchFor)&&(Galaxy&&Galaxy.upload&&i.size())){f.empty();f.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));f.find(".uploader-link").click(function(j){Galaxy.upload._eventShow(j)});f.find(".get-data-link").click(function(j){i.parent().scrollTop(0);i.find('span:contains("Get Data")').click()});f.show()}else{e.HistoryPanel.prototype._renderEmptyMsg.call(this,h)}return this},toggleSearchControls:function(g,f){var h=e.HistoryPanel.prototype.toggleSearchControls.call(this,g,f);this.preferences.set("searching",h)},_renderTags:function(f){var g=this;e.HistoryPanel.prototype._renderTags.call(this,f);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("tagsEditorShown",h.hidden)})},_renderAnnotation:function(f){var g=this;e.HistoryPanel.prototype._renderAnnotation.call(this,f);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(h){g.preferences.set("annotationEditorShown",h.hidden)})},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;b.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,e);if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},_handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},_handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},_createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$emptyMessage().fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(e).text(this.emptyMsg);if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;b.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,e);if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},_handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},_handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},_createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$emptyMessage().fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:d}}); \ No newline at end of file diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r cb2d13e55a5ca1e51f50d11e79e70c69a399cd1e static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base"],function(g,a){var f=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(i){var h="expandedHdas";this.save(h,_.extend(this.get(h),_.object([i],[true])))},removeExpandedHda:function(i){var h="expandedHdas";this.save(h,_.omit(this.get(h),i))},toString:function(){return"HistoryPrefs("+this.id+")"}});f.storageKeyPrefix="history:";f.historyStorageKey=function e(h){if(!h){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+h)}return(f.storageKeyPrefix+h)};f.get=function d(h){return new f({id:f.historyStorageKey(h)})};f.clearAll=function c(i){for(var h in sessionStorage){if(h.indexOf(f.storageKeyPrefix)===0){sessionStorage.removeItem(h)}}};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.linkTarget=h.linkTarget||"_blank";this.fxSpeed=_.has(h,"fxSpeed")?(h.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=h.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var i=_.pick(h,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,i,false);if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}return this},errorHandler:function(j,m,i,l,k){console.error(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{var h=this._parseErrorMessage(j,m,i,l,k);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(j,i,h,l){var k=function(m){return _.keys(f.get(m.id).get("expandedHdas"))};return this.loadHistory(j,i,h,l,k)},loadHistory:function(k,j,i,n,l){var h=this;j=j||{};h.trigger("loading-history",h);var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return h._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.JSONToModel(k,l,i)});j.fail(function(l,k){h.render()});return j},JSONToModel:function(k,h,i){this.log("JSONToModel:",k,h,i);i=i||{};if(Galaxy&&Galaxy.currUser){k.user=Galaxy.currUser.toJSON()}var j=new g.History(k,h,i);this.setModel(j);return this},setModel:function(i,h,j){h=h||{};j=(j!==undefined)?(j):(true);this.log("setModel:",i,h,j);this.freeModel();this.selectedHdaIds=[];if(i){if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=i;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(j){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(i,h,j){this.storage=new f({id:f.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);return this},render:function(j,k){this.log("render:",j,k);j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");h.append(b.templates.historyPanel(this.model.toJSON()));h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(h.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(h){return(h||this.$el).find(".datasets-list")},$messages:function(h){return(h||this.$el).find(".message-container")},$emptyMessage:function(h){return(h||this.$el).find(".empty-history-message")},renderHdas:function(i){i=i||this.$el;var h=this,k={},j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(i).empty();if(j.length){j.each(function(m){var l=m.get("id"),n=h._createHdaView(m);k[l]=n;if(_.contains(h.selectedHdaIds,l)){n.selected=true}h.attachHdaView(n.render(),i)});h.$emptyMessage(i).hide()}else{h.$emptyMessage(i).text((this.model.hdas.length&&this.searchFor)?(this.noneFoundMsg):(this.emptyMsg)).show()}this.hdaViews=k;return this.hdaViews},_createHdaView:function(i){var h=i.get("id"),j=new this.HDAViewClass({model:i,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[h],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(j);return j},_setUpHdaListeners:function(i){var h=this;i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)});i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});return this},attachHdaView:function(j,i){i=i||this.$el;var h=this.$datasetsList(i);h.prepend(j.$el);return this},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return i}$({}).queue([function j(m){var l=i.$emptyMessage();if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(l){var m=i._createHdaView(k);i.hdaViews[k.id]=m;m.render().$el.hide();i.scrollToTop();i.attachHdaView(m);m.$el.slideDown(i.fxSpeed)}]);return i},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",h);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",h);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(i){var j=this,k=".history-search-input";function h(l){if(j.model.hdas.haveDetails()){j.searchHdas(l);return}j.$el.find(k).searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(k).searchInput("toggle-loading")}).done(function(){j.searchHdas(l)})}i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return i},toggleSearchControls:function(j,h){var i=this.$el.find(".history-search-controls"),k=(jQuery.type(j)==="number")?(j):(this.fxSpeed);h=(h!==undefined)?(h):(!i.is(":visible"));if(h){i.slideDown(k,function(){$(this).find("input").focus()})}else{i.slideUp(k)}return h},searchHdas:function(h){var i=this;this.searchFor=h;this.filters=[function(j){return j.matchesAll(i.searchFor)}];this.trigger("search:searching",h,this);this.renderHdas();return this},clearHdaSearch:function(h){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},_hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$messages(),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j._messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},_messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(h){this.$container().scrollTop(h);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i];this.scrollTo(h.el.offsetTop);return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base"],function(g,a){var f=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(i){var h="expandedHdas";this.save(h,_.extend(this.get(h),_.object([i],[true])))},removeExpandedHda:function(i){var h="expandedHdas";this.save(h,_.omit(this.get(h),i))},toString:function(){return"HistoryPrefs("+this.id+")"}});f.storageKeyPrefix="history:";f.historyStorageKey=function e(h){if(!h){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+h)}return(f.storageKeyPrefix+h)};f.get=function d(h){return new f({id:f.historyStorageKey(h)})};f.clearAll=function c(i){for(var h in sessionStorage){if(h.indexOf(f.storageKeyPrefix)===0){sessionStorage.removeItem(h)}}};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(h){h=h||{};if(h.logger){this.logger=h.logger}this.log(this+".initialize:",h);this.linkTarget=h.linkTarget||"_blank";this.fxSpeed=_.has(h,"fxSpeed")?(h.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor="";this.findContainerFn=h.findContainerFn;this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this._setUpListeners();var i=_.pick(h,"initiallyExpanded","show_deleted","show_hidden");this.setModel(this.model,i,false);if(h.onready){h.onready.call(this)}},_setUpListeners:function(){this.on("error",function(i,l,h,k,j){this.errorHandler(i,l,h,k,j)});this.on("loading-history",function(){this._showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this._hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(h){this.log(this+"",arguments)},this)}return this},errorHandler:function(j,m,i,l,k){console.error(j,m,i,l,k);if(m&&m.status===0&&m.readyState===0){}else{if(m&&m.status===502){}else{var h=this._parseErrorMessage(j,m,i,l,k);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",h.message,h.details)})}else{this.displayMessage("error",h.message,h.details)}}}},_parseErrorMessage:function(k,o,j,n,m){var i=Galaxy.currUser,h={message:this._bePolite(n),details:{user:(i instanceof User)?(i.toJSON()):(i+""),source:(k instanceof Backbone.Model)?(k.toJSON()):(k+""),xhr:o,options:(o)?(_.omit(j,"xhr")):(j)}};_.extend(h.details,m||{});if(o&&_.isFunction(o.getAllResponseHeaders)){var l=o.getAllResponseHeaders();l=_.compact(l.split("\n"));l=_.map(l,function(p){return p.split(": ")});h.details.xhr.responseHeaders=_.object(l)}return h},_bePolite:function(h){h=h||_l("An error occurred while getting updates from the server");return h+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(j,i,h,l){var k=function(m){return _.keys(f.get(m.id).get("expandedHdas"))};return this.loadHistory(j,i,h,l,k)},loadHistory:function(k,j,i,n,l){var h=this;j=j||{};h.trigger("loading-history",h);var m=g.History.getHistoryData(k,{historyFn:i,hdaFn:n,hdaDetailIds:j.initiallyExpanded||l});return h._loadHistoryFromXHR(m,j).fail(function(q,o,p){h.trigger("error",h,q,j,_l("An error was encountered while "+o),{historyId:k,history:p||{}})}).always(function(){h.trigger("loading-done",h)})},_loadHistoryFromXHR:function(j,i){var h=this;j.then(function(k,l){h.JSONToModel(k,l,i)});j.fail(function(l,k){h.render()});return j},JSONToModel:function(k,h,i){this.log("JSONToModel:",k,h,i);i=i||{};if(Galaxy&&Galaxy.currUser){k.user=Galaxy.currUser.toJSON()}var j=new g.History(k,h,i);this.setModel(j);return this},setModel:function(i,h,j){h=h||{};j=(j!==undefined)?(j):(true);this.log("setModel:",i,h,j);this.freeModel();this.selectedHdaIds=[];if(i){if(Galaxy&&Galaxy.currUser){i.user=Galaxy.currUser.toJSON()}this.model=i;if(this.logger){this.model.logger=this.logger}this._setUpWebStorage(h.initiallyExpanded,h.show_deleted,h.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this)}if(j){this.render()}return this},freeModel:function(){if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.freeHdaViews();return this},freeHdaViews:function(){this.hdaViews={};return this},_setUpWebStorage:function(i,h,j){this.storage=new f({id:f.historyStorageKey(this.model.get("id"))});if(_.isObject(i)){this.storage.set("exandedHdas",i)}if(_.isBoolean(h)){this.storage.set("show_deleted",h)}if(_.isBoolean(j)){this.storage.set("show_hidden",j)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(i,k,h,j){this.errorHandler(i,k,h,j)},this);return this},render:function(j,k){this.log("render:",j,k);j=(j===undefined)?(this.fxSpeed):(j);var h=this,i;if(this.model){i=this.renderModel()}else{i=this.renderWithoutModel()}$(h).queue("fx",[function(l){if(j&&h.$el.is(":visible")){h.$el.fadeOut(j,l)}else{l()}},function(l){h.$el.empty();if(i){h.$el.append(i.children())}l()},function(l){if(j&&!h.$el.is(":visible")){h.$el.fadeIn(j,l)}else{l()}},function(l){if(k){k.call(this)}h.trigger("rendered",this);l()}]);return this},renderWithoutModel:function(){var h=$("<div/>"),i=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return h.append(i)},renderModel:function(){var h=$("<div/>");h.append(b.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(h).text(this.emptyMsg);h.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(h);this.renderHdas(h);return h},_renderEmptyMsg:function(j){var i=this,h=i.$emptyMessage(j);if(!_.isEmpty(i.hdaViews)){h.hide()}else{if(i.searchFor){h.text(i.noneFoundMsg).show()}else{h.text(i.emptyMsg).show()}}return this},_renderSearchButton:function(h){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(h){h=h||this.$el;h.find("[title]").tooltip({placement:"bottom"});this._setUpSearchInput(h.find(".history-search-controls .history-search-input"));return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(h){return(h||this.$el).find(".datasets-list")},$messages:function(h){return(h||this.$el).find(".message-container")},$emptyMessage:function(h){return(h||this.$el).find(".empty-history-message")},renderHdas:function(i){i=i||this.$el;var h=this,k={},j=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);this.$datasetsList(i).empty();if(j.length){j.each(function(m){var l=m.get("id"),n=h._createHdaView(m);k[l]=n;if(_.contains(h.selectedHdaIds,l)){n.selected=true}h.attachHdaView(n.render(),i)})}this.hdaViews=k;this._renderEmptyMsg(i);return this.hdaViews},_createHdaView:function(i){var h=i.get("id"),j=new this.HDAViewClass({model:i,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[h],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(j);return j},_setUpHdaListeners:function(i){var h=this;i.on("error",function(k,m,j,l){h.errorHandler(k,m,j,l)});i.on("body-expanded",function(j){h.storage.addExpandedHda(j)});i.on("body-collapsed",function(j){h.storage.removeExpandedHda(j)});return this},attachHdaView:function(j,i){i=i||this.$el;var h=this.$datasetsList(i);h.prepend(j.$el);return this},addHdaView:function(k){this.log("add."+this,k);var i=this;if(!k.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return i}$({}).queue([function j(m){var l=i.$emptyMessage();if(l.is(":visible")){l.fadeOut(i.fxSpeed,m)}else{m()}},function h(l){var m=i._createHdaView(k);i.hdaViews[k.id]=m;m.render().$el.hide();i.scrollToTop();i.attachHdaView(m);m.$el.slideDown(i.fxSpeed)}]);return i},refreshHdas:function(i,h){if(this.model){return this.model.refresh(i,h)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(h){h.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{});return this},toggleShowDeleted:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",h);this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(h){h=(h!==undefined)?(h):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",h);this.renderHdas();return this.storage.get("show_hidden")},_setUpSearchInput:function(i){var j=this,k=".history-search-input";function h(l){if(j.model.hdas.haveDetails()){j.searchHdas(l);return}j.$el.find(k).searchInput("toggle-loading");j.model.hdas.fetchAllDetails({silent:true}).always(function(){j.$el.find(k).searchInput("toggle-loading")}).done(function(){j.searchHdas(l)})}i.searchInput({initialVal:j.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:h,onsearch:_.bind(this.searchHdas,this),onclear:_.bind(this.clearHdaSearch,this)});return i},toggleSearchControls:function(j,h){var i=this.$el.find(".history-search-controls"),k=(jQuery.type(j)==="number")?(j):(this.fxSpeed);h=(h!==undefined)?(h):(!i.is(":visible"));if(h){i.slideDown(k,function(){$(this).find("input").focus()})}else{i.slideUp(k)}return h},searchHdas:function(h){var i=this;this.searchFor=h;this.filters=[function(j){return j.matchesAll(i.searchFor)}];this.trigger("search:searching",h,this);this.renderHdas();return this},clearHdaSearch:function(h){this.searchFor="";this.filters=[];this.trigger("search:clear",this);this.renderHdas();return this},_showLoadingIndicator:function(i,h,j){h=(h!==undefined)?(h):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,j)}else{this.$el.fadeOut(h);this.indicator.show(i,h,j)}},_hideLoadingIndicator:function(h,i){h=(h!==undefined)?(h):(this.fxSpeed);if(this.indicator){this.indicator.hide(h,i)}},displayMessage:function(m,n,l){var j=this;this.scrollToTop();var k=this.$messages(),h=$("<div/>").addClass(m+"message").html(n);if(!_.isEmpty(l)){var i=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(j._messageToModalOptions(m,n,l));return false});h.append(" ",i)}return k.html(h)},_messageToModalOptions:function(l,n,k){var h=this,m=$("<div/>"),j={title:"Details"};function i(o){o=_.omit(o,_.functions(o));return["<table>",_.map(o,function(q,p){q=(_.isObject(q))?(i(q)):(q);return'<tr><td style="vertical-align: top; color: grey">'+p+'</td><td style="padding-left: 8px">'+q+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(k)){j.body=m.append(i(k))}else{j.body=m.html(k)}j.buttons={Ok:function(){Galaxy.modal.hide();h.clearMessages()}};return j},clearMessages:function(){this.$messages().empty();return this},scrollPosition:function(){return this.$container().scrollTop()},scrollTo:function(h){this.$container().scrollTop(h);return this},scrollToTop:function(){this.$container().scrollTop(0);return this},scrollToId:function(i){if((!i)||(!this.hdaViews[i])){return this}var h=this.hdaViews[i];this.scrollTo(h.el.offsetTop);return this},scrollToHid:function(h){var i=this.model.hdas.getByHid(h);if(!i){return this}return this.scrollToId(i.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- 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commit/galaxy-central: carlfeberhard: Page-embedded histories: allow embedding the same history more than once by removing the reliance on DOM ids and selecting/traversing based on sibling relation of the history's script
by commits-noreply＠bitbucket.org 18 Mar '14

18 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/215f23b27be9/ Changeset: 215f23b27be9 User: carlfeberhard Date: 2014-03-18 21:14:52 Summary: Page-embedded histories: allow embedding the same history more than once by removing the reliance on DOM ids and selecting/traversing based on sibling relation of the history's script Affected #: 1 file diff -r c2ee53fa3589fa2852c056ac65c4656e1d88632a -r 215f23b27be962047909c7676fb8a42fa44ea053 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -38,36 +38,44 @@ </div><script type="text/javascript"> +// Embedding the same history more than once will confuse DOM ids. +// In order to handle this, find this script and cache the previous node (the div above). +// (Since we need thisScript to be locally scoped or it will get overwritten, enclose in self-calling function) +(function(){ + var scripts = document.getElementsByTagName( 'script' ), + // this is executed immediately, so the last script will be this script + thisScript = scripts[ scripts.length - 1 ], + $embeddedHistory = $( thisScript ).prev(); -require.config({ - baseUrl : "${h.url_for( '/static/scripts' )}" -}); -require([ 'mvc/history/annotated-history-panel' ], function( panelMod ){ + require.config({ + baseUrl : "${h.url_for( '/static/scripts' )}" + }); + require([ 'mvc/history/annotated-history-panel' ], function( panelMod ){ - function toggleExpanded( ev ){ - var $embeddedHistory = $( "#history-${encoded_history_id}" ); - $embeddedHistory.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' ); - $embeddedHistory.find( ".summary-content" ).slideToggle( "fast" ); - $embeddedHistory.find( ".annotation" ).slideToggle( "fast" ); - $embeddedHistory.find( ".expanded-content" ).slideToggle( "fast" ); - ev.preventDefault(); - } + function toggleExpanded( ev ){ + var $embeddedHistory = $( thisScript ).prev(); + $embeddedHistory.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' ); + $embeddedHistory.find( ".summary-content" ).slideToggle( "fast" ); + $embeddedHistory.find( ".annotation" ).slideToggle( "fast" ); + $embeddedHistory.find( ".expanded-content" ).slideToggle( "fast" ); + ev.preventDefault(); + } - $(function(){ - var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, - historyModel = require( 'mvc/history/history-model' ), - $embeddedHistory = $( "#history-${encoded_history_id}" ), - panel = new panelMod.AnnotatedHistoryPanel({ - el : $embeddedHistory.find( ".history-panel" ), - model : new historyModel.History( - ${h.to_json_string( history_dict )}, - ${h.to_json_string( hda_dicts )}, - { logger: ( debugging )?( console ):( null ) } - ) - }).render(); + $(function(){ + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, + historyModel = require( 'mvc/history/history-model' ), + panel = new panelMod.AnnotatedHistoryPanel({ + el : $embeddedHistory.find( ".history-panel" ), + model : new historyModel.History( + ${h.to_json_string( history_dict )}, + ${h.to_json_string( hda_dicts )}, + { logger: ( debugging )?( console ):( null ) } + ) + }).render(); - $embeddedHistory.find( '.expand-content-btn' ).click( toggleExpanded ); - $embeddedHistory.find( '.toggle-embed' ).click( toggleExpanded ); + $embeddedHistory.find( '.expand-content-btn' ).click( toggleExpanded ); + $embeddedHistory.find( '.toggle-embed' ).click( toggleExpanded ); + }); }); -}); +})(); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Mar '14

18 Mar '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fa9860db38e2/ Changeset: fa9860db38e2 User: dannon Date: 2014-03-18 19:55:11 Summary: Pep8, cruft cleanup -- s3_multipart_upload Affected #: 1 file diff -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a -r fa9860db38e2209d91648f09e5fbf9937a2ff7f9 lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -5,13 +5,13 @@ Code mostly taken form CloudBioLinux. """ -import os -import glob -import subprocess import contextlib import functools +import glob +import multiprocessing +import os +import subprocess -import multiprocessing from multiprocessing.pool import IMapIterator try: @@ -32,6 +32,7 @@ return apply(f, *args, **kwargs) return wrapper + def mp_from_ids(mp_id, mp_keyname, mp_bucketname): """Get the multipart upload from the bucket and multipart IDs. @@ -45,21 +46,22 @@ mp.id = mp_id return mp + @map_wrap def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part): """Transfer a part of a multipart upload. Designed to be run in parallel. """ mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname) - #print " Transferring", i, part with open(part) as t_handle: - mp.upload_part_from_file(t_handle, i+1) + mp.upload_part_from_file(t_handle, i + 1) os.remove(part) + def multipart_upload(bucket, s3_key_name, tarball, mb_size, use_rr=True): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() - #print "Initiating multipart upload using %s cores" % cores + def split_file(in_file, mb_size, split_num=5): prefix = os.path.join(os.path.dirname(in_file), "%sS3PART" % (os.path.basename(s3_key_name))) @@ -78,6 +80,7 @@ pass mp.complete_upload() + @contextlib.contextmanager def multimap(cores=None): """Provide multiprocessing imap like function. @@ -87,6 +90,7 @@ """ if cores is None: cores = max(multiprocessing.cpu_count() - 1, 1) + def wrapper(func): def wrap(self, timeout=None): return func(self, timeout=timeout if timeout is not None else 1e100) https://bitbucket.org/galaxy/galaxy-central/commits/c115742f0c63/ Changeset: c115742f0c63 User: dannon Date: 2014-03-18 20:41:06 Summary: Force multipart upload to, instead of using environment variables via connect_s3, use keys provided in the objectstore. Affected #: 1 file diff -r fa9860db38e2209d91648f09e5fbf9937a2ff7f9 -r c115742f0c6319b823c277c80cfece08150bea45 lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -22,6 +22,7 @@ try: import boto + from boto.s3.connection import S3Connection except ImportError: boto = None @@ -33,13 +34,13 @@ return wrapper -def mp_from_ids(mp_id, mp_keyname, mp_bucketname): +def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key): """Get the multipart upload from the bucket and multipart IDs. This allows us to reconstitute a connection to the upload from within multiprocessing functions. """ - conn = boto.connect_s3() + conn = S3Connection(aws_access_key_id, aws_secret_access_key) bucket = conn.lookup(mp_bucketname) mp = boto.s3.multipart.MultiPartUpload(bucket) mp.key_name = mp_keyname @@ -48,16 +49,16 @@ @map_wrap -def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part): +def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, aws_access_key_id, aws_secret_access_key): """Transfer a part of a multipart upload. Designed to be run in parallel. """ - mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname) + mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key) with open(part) as t_handle: mp.upload_part_from_file(t_handle, i + 1) os.remove(part) -def multipart_upload(bucket, s3_key_name, tarball, mb_size, use_rr=True): +def multipart_upload(bucket, s3_key_name, tarball, mb_size, aws_access_key_id, aws_secret_access_key, use_rr=True): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() @@ -74,7 +75,7 @@ mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr) with multimap(cores) as pmap: - for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part) + for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part, aws_access_key_id, aws_secret_access_key) for (i, part) in enumerate(split_file(tarball, mb_size, cores)))): pass https://bitbucket.org/galaxy/galaxy-central/commits/c2ee53fa3589/ Changeset: c2ee53fa3589 User: dannon Date: 2014-03-18 20:42:08 Summary: S3ObjectStore import cleanup, fix (forgotten) new multipart upload params. Affected #: 1 file diff -r c115742f0c6319b823c277c80cfece08150bea45 -r c2ee53fa3589fa2852c056ac65c4656e1d88632a lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -2,22 +2,23 @@ Object Store plugin for the Amazon Simple Storage Service (S3) """ +import logging +import multiprocessing import os +import shutil +import subprocess +import threading import time -import shutil -import logging -import threading -import subprocess + from datetime import datetime +from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms +from galaxy.util.directory_hash import directory_hash_id from galaxy.util.sleeper import Sleeper -from galaxy.util.directory_hash import directory_hash_id +from .s3_multipart_upload import multipart_upload from ..objectstore import ObjectStore, convert_bytes -from galaxy.exceptions import ObjectNotFound -import multiprocessing -from .s3_multipart_upload import multipart_upload try: import boto from boto.s3.key import Key @@ -326,7 +327,7 @@ cb=self._transfer_cb, num_cb=10) else: - multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr) + multipart_upload(self.bucket, key.name, source_file, mb_size, self.access_key, self.secret_key, use_rr=self.use_rr) end_time = datetime.now() log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Mar '14

18 Mar '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/152fe1084f16/ Changeset: 152fe1084f16 User: dannon Date: 2014-03-18 18:34:59 Summary: Correctly initialize bucket for S3ObjectStore Affected #: 1 file diff -r 0a9263af45ec678bea82a6d128f49cf5372d370d -r 152fe1084f160bf18d44ca3c7f12ea98c14cfd98 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -47,6 +47,7 @@ self.transfer_progress = 0 self._parse_config_xml(config_xml) self._configure_connection() + self.bucket = self._get_bucket(self.bucket) # Clean cache only if value is set in universe_wsgi.ini if self.cache_size != -1: # Convert GBs to bytes for comparison https://bitbucket.org/galaxy/galaxy-central/commits/77a655d1ae4b/ Changeset: 77a655d1ae4b User: dannon Date: 2014-03-18 19:36:52 Summary: Tweak debugging output for s3 upload. Cruft cleanup. Pep8 fixes. Affected #: 1 file diff -r 152fe1084f160bf18d44ca3c7f12ea98c14cfd98 -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -110,8 +110,8 @@ # Initiate cleaning once within 10% of the defined cache size? cache_limit = self.cache_size * 0.9 if total_size > cache_limit: - log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s" \ - % (convert_bytes(total_size), convert_bytes(cache_limit))) + log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s" + % (convert_bytes(total_size), convert_bytes(cache_limit))) # How much to delete? If simply deleting up to the cache-10% limit, # is likely to be deleting frequently and may run the risk of hitting # the limit - maybe delete additional #%? @@ -226,7 +226,6 @@ except S3ResponseError, ex: log.error("Trouble checking existence of S3 key '%s': %s" % (rel_path, ex)) return False - #print "Checking if '%s' exists in S3: %s" % (rel_path, exists) if rel_path[0] == '/': raise return exists @@ -279,8 +278,8 @@ key = self.bucket.get_key(rel_path) # Test if cache is large enough to hold the new file if self.cache_size > 0 and key.size > self.cache_size: - log.critical("File %s is larger (%s) than the cache size (%s). Cannot download." \ - % (rel_path, key.size, self.cache_size)) + log.critical("File %s is larger (%s) than the cache size (%s). Cannot download." + % (rel_path, key.size, self.cache_size)) return False if self.use_axel: log.debug("Parallel pulled key '%s' into cache to %s" % (rel_path, self._get_cache_path(rel_path))) @@ -318,23 +317,22 @@ log.debug("Pushed data from string '%s' to key '%s'" % (from_string, rel_path)) else: start_time = datetime.now() - # print "Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path) - # print "+ Push started at '%s'" % start_time + log.debug("Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)) mb_size = os.path.getsize(source_file) / 1e6 - #DBTODO Hack, refactor this logic. - if mb_size < 60 or type(self) == SwiftObjectStore: + if mb_size < 10 or type(self) == SwiftObjectStore: self.transfer_progress = 0 # Reset transfer progress counter - key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, - cb=self._transfer_cb, num_cb=10) + key.set_contents_from_filename(source_file, + reduced_redundancy=self.use_rr, + cb=self._transfer_cb, + num_cb=10) else: multipart_upload(self.bucket, key.name, source_file, mb_size, use_rr=self.use_rr) end_time = datetime.now() - # print "+ Push ended at '%s'; %s bytes transfered in %ssec" % (end_time, os.path.getsize(source_file), end_time-start_time) log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True else: log.error("Tried updating key '%s' from source file '%s', but source file does not exist." - % (rel_path, source_file)) + % (rel_path, source_file)) except S3ResponseError, ex: log.error("Trouble pushing S3 key '%s' from file '%s': %s" % (rel_path, source_file, ex)) return False @@ -350,7 +348,7 @@ if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path): return True log.debug("Waiting for dataset {0} to transfer from OS: {1}/{2}".format(rel_path, - os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))) + os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))) return False def exists(self, obj, **kwargs): @@ -380,13 +378,11 @@ def create(self, obj, **kwargs): if not self.exists(obj, **kwargs): - #print "S3 OS creating a dataset with ID %s" % kwargs # Pull out locally used fields extra_dir = kwargs.get('extra_dir', None) extra_dir_at_root = kwargs.get('extra_dir_at_root', False) dir_only = kwargs.get('dir_only', False) alt_name = kwargs.get('alt_name', None) - # print "---- Processing: %s; %s" % (alt_name, locals()) # Construct hashed path rel_path = os.path.join(*directory_hash_id(obj.id)) @@ -416,7 +412,7 @@ return bool(self.size(obj, **kwargs) > 0) else: raise ObjectNotFound( 'objectstore.empty, object does not exist: %s, kwargs: %s' - % ( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def size(self, obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) @@ -465,8 +461,6 @@ # Check cache first and get file if not there if not self._in_cache(rel_path): self._pull_into_cache(rel_path) - #else: - # print "(cccc) Getting '%s' from cache" % self._get_cache_path(rel_path) # Read the file content from cache data_file = open(self._get_cache_path(rel_path), 'r') data_file.seek(start) @@ -475,7 +469,6 @@ return content def get_filename(self, obj, **kwargs): - #print "S3 get_filename for dataset: %s" % dataset_id dir_only = kwargs.get('dir_only', False) rel_path = self._construct_path(obj, **kwargs) cache_path = self._get_cache_path(rel_path) @@ -502,7 +495,7 @@ # if dir_only: # return cache_path raise ObjectNotFound( 'objectstore.get_filename, no cache_path: %s, kwargs: %s' - % ( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path def update_from_file(self, obj, file_name=None, create=False, **kwargs): @@ -528,7 +521,7 @@ self._push_to_os(rel_path, source_file) else: raise ObjectNotFound( 'objectstore.update_from_file, object does not exist: %s, kwargs: %s' - % ( str( obj ), str( kwargs ) ) ) + % ( str( obj ), str( kwargs ) ) ) def get_object_url(self, obj, **kwargs): if self.exists(obj, **kwargs): @@ -554,9 +547,9 @@ def _configure_connection(self): log.debug("Configuring Swift Connection") self.conn = boto.connect_s3(aws_access_key_id=self.access_key, - aws_secret_access_key=self.secret_key, - is_secure=self.is_secure, - host=self.host, - port=self.port, - calling_format=boto.s3.connection.OrdinaryCallingFormat(), - path=self.conn_path) + aws_secret_access_key=self.secret_key, + is_secure=self.is_secure, + host=self.host, + port=self.port, + calling_format=boto.s3.connection.OrdinaryCallingFormat(), + path=self.conn_path) https://bitbucket.org/galaxy/galaxy-central/commits/2043fb8cec50/ Changeset: 2043fb8cec50 User: dannon Date: 2014-03-18 19:37:52 Summary: Merge. Affected #: 6 files diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -451,18 +451,21 @@ // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form // item_class='History'). var item_elt_id = item_info.iclass + "-" + item_id; - var item_embed_html = - "<div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + - " placeholder'> \ - <p class='title'>Embedded Galaxy " + item_info.singular + " '" + item_name + "'</p> \ - <p class='content'> \ - [Do not edit this block; Galaxy will fill it in with the annotated " + - item_info.singular.toLowerCase() + " when it is displayed.] \ - </p> \ - </div>"; + var item_embed_html = [ + "<div id='", item_elt_id, "' class='embedded-item ", + item_info.singular.toLowerCase(), " placeholder'>", + "<p class='title'>", + "Embedded Galaxy ", item_info.singular, " '", item_name, "'", + "</p>", + "<p class='content'>", + "[Do not edit this block; Galaxy will fill it in with the annotated ", + item_info.singular.toLowerCase(), " when it is displayed.]", + "</p>", + "</div>" ].join( '' ); + console.debug( item_embed_html ); // Insert embedded item into document. - wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. + //wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. wym.insert(item_embed_html); // TODO: can we fix this? diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var 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Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case 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Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){c.each(h,function(i){if(g[i.key]){i.value=g[i.key]}})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);this.config.each(function(af){console.log(af.id,af.get("value"))});if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],ab.prefs)},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){console.log(this.config.to_key_value_dict());return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=(ac.reference_track?J.RefBasedReadPainter:J.ReadPainter);this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=(ac.reference_track?J.RefBasedReadPainter:J.ReadPainter);this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -45,13 +45,20 @@ fetcher = self.__dataset_fetcher( history_id ) ## TODO: Twill version verifys dataset is 'ok' in here. self.twill_test_case.verify_hid( outfile, hda_id=hid, attributes=attributes, dataset_fetcher=fetcher, shed_tool_id=shed_tool_id ) - metadata = attributes.get( 'metadata', {} ) + metadata = attributes.get( 'metadata', {} ).copy() + for key, value in metadata.copy().iteritems(): + new_key = "metadata_%s" % key + metadata[ new_key ] = metadata[ key ] + del metadata[ key ] + expected_file_type = attributes.get( 'ftype', None ) + if expected_file_type: + metadata[ "file_ext" ] = expected_file_type + if metadata: dataset = self._get( "histories/%s/contents/%s" % ( history_id, hid ) ).json() for key, value in metadata.iteritems(): - dataset_key = "metadata_%s" % key try: - dataset_value = dataset.get( dataset_key, None ) + dataset_value = dataset.get( key, None ) if dataset_value != value: msg = "Dataset metadata verification for [%s] failed, expected [%s] but found [%s]." msg_params = ( key, value, dataset_value ) diff -r 77a655d1ae4b2049d4a86bbdfd8850468788f214 -r 2043fb8cec50582ba5620b399bb55ad7dffbd72a test/functional/tools/metadata.xml --- a/test/functional/tools/metadata.xml +++ b/test/functional/tools/metadata.xml @@ -16,7 +16,7 @@ <metadata name="base_name" value="Example Metadata" /></param> - <output name="output_of_input_metadata"> + <output name="output_of_input_metadata" ftype="txt"><assert_contents><has_line line="Example Metadata" /></assert_contents> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Pages: fix insertion of embedded in webkit browsers; pack scripts
by commits-noreply＠bitbucket.org 18 Mar '14

18 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/acdc987f817a/ Changeset: acdc987f817a User: carlfeberhard Date: 2014-03-18 19:32:33 Summary: Pages: fix insertion of embedded in webkit browsers; pack scripts Affected #: 4 files diff -r 327583f6b0581c2bdf22b933b2659298af2ed699 -r acdc987f817a339b0524e5f700be83009bbe67a3 static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -451,18 +451,21 @@ // all non-standard attributes when it returns its content (e.g. it will not return an element attribute of the form // item_class='History'). var item_elt_id = item_info.iclass + "-" + item_id; - var item_embed_html = - "<div id='" + item_elt_id + "' class='embedded-item " + item_info.singular.toLowerCase() + - " placeholder'> \ - <p class='title'>Embedded Galaxy " + item_info.singular + " '" + item_name + "'</p> \ - <p class='content'> \ - [Do not edit this block; Galaxy will fill it in with the annotated " + - item_info.singular.toLowerCase() + " when it is displayed.] \ - </p> \ - </div>"; + var item_embed_html = [ + "<div id='", item_elt_id, "' class='embedded-item ", + item_info.singular.toLowerCase(), " placeholder'>", + "<p class='title'>", + "Embedded Galaxy ", item_info.singular, " '", item_name, "'", + "</p>", + "<p class='content'>", + "[Do not edit this block; Galaxy will fill it in with the annotated ", + item_info.singular.toLowerCase(), " when it is displayed.]", + "</p>", + "</div>" ].join( '' ); + console.debug( item_embed_html ); // Insert embedded item into document. - wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. + //wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers. wym.insert(item_embed_html); // TODO: can we fix this? diff -r 327583f6b0581c2bdf22b933b2659298af2ed699 -r acdc987f817a339b0524e5f700be83009bbe67a3 static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" '"+p.name+"'</a>")}else{$("a[href="+b+"]",a._doc.body).attr(WYMeditor.HREF,p.link).attr(WYMeditor.TITLE,j.singular+n)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_DATASET||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_PAGE||i==Galaxy.DIALOG_EMBED_VISUALIZATION){var j;switch(i){case (Galaxy.DIALOG_EMBED_HISTORY):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_EMBED_DATASET):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_EMBED_WORKFLOW):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_EMBED_PAGE):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_EMBED_VISUALIZATION):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_VISUALIZATION){k=k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>"}show_modal("Embed "+j.plural,k,{Embed:function(){var l=false;if($("#make-importable:checked").val()!=null){l=true}$("input[name=id]:checked").each(function(){var m=$(this).val();var p=$("label[for='"+m+"']:first").text();if(l){make_item_importable(j.controller,m,j.singular)}var n=j.iclass+"-"+m;var o="<div id='"+n+"' class='embedded-item "+j.singular.toLowerCase()+" placeholder'><p class='title'>Embedded Galaxy "+j.singular+" '"+p+"'</p><p class='content'> [Do not edit this block; Galaxy will fill it in with the annotated "+j.singular.toLowerCase()+" when it is displayed.] </p></div>";a.insert(" ");a.insert(o)});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_ANNOTATE_HISTORY){$.ajax({url:list_histories_for_selection_url,data:{},error:function(){alert("Grid refresh failed")},success:function(k){show_modal("Insert Link to History",k,{Annotate:function(){var l=new Array();$("input[name=id]:checked").each(function(){var m=$(this).val();$.ajax({url:get_history_annotation_table_url,data:{id:m},error:function(){alert("Grid refresh failed")},success:function(n){a.insert(n);init_galaxy_elts(a)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}};$(function(){$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});$("[name=page_content]").wymeditor({skin:"galaxy",basePath:editor_base_path,iframeBasePath:iframe_base_path,boxHtml:"<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>"+WYMeditor.IFRAME+WYMeditor.STATUS+"</div></div></td></tr></table>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},]});var d=$.wymeditors(0);var f=function(g){show_modal("Saving page","progress");$.ajax({url:save_url,type:"POST",data:{id:page_id,content:d.xhtml(),annotations:JSON.stringify(new Object()),_:"true"},success:function(){g()}})};$("#save-button").click(function(){f(function(){hide_modal()})});$("#close-button").click(function(){var h=false;if(h){var g=function(){window.onbeforeunload=undefined;window.document.location=page_list_url};show_modal("Close editor","There are unsaved changes to your page which will be lost.",{Cancel:hide_modal,"Save Changes":function(){f(g)}},{"Don't Save":g})}else{window.document.location=page_list_url}});var a=$("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>");$(".wym_area_top").append(a);var b={};$.each(d._options.containersItems,function(h,g){var i=g.name;b[g.title.replace("_"," ")]=function(){d.container(i)}});make_popupmenu(a,b);var c=$("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file +var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" '"+p.name+"'</a>")}else{$("a[href="+b+"]",a._doc.body).attr(WYMeditor.HREF,p.link).attr(WYMeditor.TITLE,j.singular+n)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_DATASET||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_PAGE||i==Galaxy.DIALOG_EMBED_VISUALIZATION){var j;switch(i){case (Galaxy.DIALOG_EMBED_HISTORY):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_EMBED_DATASET):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_EMBED_WORKFLOW):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_EMBED_PAGE):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_EMBED_VISUALIZATION):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_VISUALIZATION){k=k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>"}show_modal("Embed "+j.plural,k,{Embed:function(){var l=false;if($("#make-importable:checked").val()!=null){l=true}$("input[name=id]:checked").each(function(){var m=$(this).val();var p=$("label[for='"+m+"']:first").text();if(l){make_item_importable(j.controller,m,j.singular)}var n=j.iclass+"-"+m;var o=["<div id='",n,"' class='embedded-item ",j.singular.toLowerCase()," placeholder'>","<p class='title'>","Embedded Galaxy ",j.singular," '",p,"'","</p>","<p class='content'>","[Do not edit this block; Galaxy will fill it in with the annotated ",j.singular.toLowerCase()," when it is 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Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})}); \ No newline at end of file diff -r 327583f6b0581c2bdf22b933b2659298af2ed699 -r acdc987f817a339b0524e5f700be83009bbe67a3 static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){c.each(h,function(i){if(g[i.key]){i.value=g[i.key]}})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r 327583f6b0581c2bdf22b933b2659298af2ed699 -r acdc987f817a339b0524e5f700be83009bbe67a3 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);this.config.each(function(af){console.log(af.id,af.get("value"))});if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],ab.prefs)},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){console.log(this.config.to_key_value_dict());return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=(ac.reference_track?J.RefBasedReadPainter:J.ReadPainter);this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=(ac.reference_track?J.RefBasedReadPainter:J.ReadPainter);this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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