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commit/galaxy-central: greg: Fix for viewing invalid tools in the tool shed.
by Bitbucket 12 Nov '12

12 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/74a7bc65f1ed/ changeset: 74a7bc65f1ed user: greg date: 2012-11-12 22:05:55 summary: Fix for viewing invalid tools in the tool shed. affected #: 1 file diff -r 8cc09edeafb2b01b034c8c4abff1b0bc95a66d47 -r 74a7bc65f1ed8bde40425d1823ad8761b6cdcea8 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1577,7 +1577,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) 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: greg: Correct method name in the repository controller.
by Bitbucket 12 Nov '12

12 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8cc09edeafb2/ changeset: 8cc09edeafb2 user: greg date: 2012-11-12 22:00:31 summary: Correct method name in the repository controller. affected #: 1 file diff -r d60deede2b6a1d360bfd7479a68ab72eb162e84b -r 8cc09edeafb2b01b034c8c4abff1b0bc95a66d47 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1577,7 +1577,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - repository_clone_url = generate_clone_url( trans, repository_id ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) 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: greg: Make the directory containing the tool shed's hgweb.config file a setting in the tool shed config.
by Bitbucket 12 Nov '12

12 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d60deede2b6a/ changeset: d60deede2b6a user: greg date: 2012-11-12 21:55:24 summary: Make the directory containing the tool shed's hgweb.config file a setting in the tool shed config. affected #: 31 files diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b community_wsgi.ini.sample --- a/community_wsgi.ini.sample +++ b/community_wsgi.ini.sample @@ -26,6 +26,9 @@ # You may use a SQLAlchemy connection string to specify an external database instead #database_connection = postgres:///community_test?host=/var/run/postgresql +# Where the hgweb.config file is stored. The default is the Galaxy installation directory. +#hgweb_config_dir = None + # Where dataset files are saved file_path = database/community_files # Temporary storage for additional datasets, this should be shared through the cluster diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -42,10 +42,11 @@ class ShedCounter( object ): def __init__( self, model ): + # TODO: Enhance the ShedCounter to retrieve information from the db instead of displaying what's currently in memory. self.model = model self.generation_time = strftime( "%b %d, %Y", gmtime() ) self.repositories = 0 - self.new_repositories = 0 + #self.new_repositories = 0 self.deleted_repositories = 0 self.invalid_tools = 0 self.valid_tools = 0 @@ -59,7 +60,7 @@ return self.model.context def generate_statistics( self ): self.repositories = 0 - self.new_repositories = 0 + #self.new_repositories = 0 self.deleted_repositories = 0 self.invalid_tools = 0 self.valid_tools = 0 @@ -70,14 +71,15 @@ self.repositories += 1 self.total_clones += repository.times_downloaded is_deleted = repository.deleted - is_new = repository.is_new - if is_deleted and is_new: + #is_new = repository.is_new + #if is_deleted and is_new: + if is_deleted: self.deleted_repositories += 1 - self.new_repositories += 1 - elif is_deleted: - self.deleted_repositories += 1 - elif is_new: - self.new_repositories += 1 + # self.new_repositories += 1 + #elif is_deleted: + # self.deleted_repositories += 1 + #elif is_new: + # self.new_repositories += 1 else: processed_guids = [] processed_invalid_tool_configs = [] @@ -763,8 +765,8 @@ """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's - disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be an absolute path to a temporary directory - containing a clone). If it is an absolute path, the value of relative_install_dir must contain repository.repo_path. + disk files, so the value of repository_files_dir will not always be repository.repo_path( app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of relative_install_dir must contain repository.repo_path( app ). The value of persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by app.config.shed_tool_data_table_config. @@ -784,7 +786,7 @@ original_tool_data_table_config_path = app.config.tool_data_table_config_path if resetting_all_metadata_on_repository: if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + raise Exception( "The value of repository.repo_path( app ) must be sent when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can strip the path when setting metadata. The value of # repository_files_dir is the full path to the temporary directory to which the repository was cloned. work_dir = repository_files_dir @@ -907,7 +909,7 @@ app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups -def generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ): +def generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ): if as_html: new_line = '<br/>' bold_start = '<b>' @@ -919,10 +921,10 @@ message = '' if not displaying_invalid_tool: if metadata_dict: - message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) + message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup @@ -1351,6 +1353,11 @@ ctx = get_changectx_for_changeset( repo, changeset_revision ) named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir ) return named_tmp_file +def get_hgweb_config( app ): + hgweb_config = os.path.join( app.config.hgweb_config_dir, 'hgweb.config' ) + if not os.path.exists( hgweb_config ): + raise Exception( "Required file %s does not exist - check config setting for hgweb_config_dir." % hgweb_config ) + return hgweb_config def get_installed_tool_shed_repository( trans, id ): """Get a repository on the Galaxy side from the database via id""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) @@ -2229,7 +2236,7 @@ trans.sa_session.flush() repository = get_repository_in_tool_shed( trans, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop @@ -2329,7 +2336,7 @@ repository = get_installed_tool_shed_repository( trans, repository_id ) invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) if invalid_file_tups: - message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False ) + message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -92,6 +92,8 @@ self.job_handlers = [] self.tool_handlers = [] self.tool_runners = [] + # Where the tool shed hgweb.config file is stored - the default is the Galaxy installation directory. + self.hgweb_config_dir = resolve_path( kwargs.get( 'hgweb_config_dir', '' ), self.root ) # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) @@ -112,7 +114,7 @@ return default def check( self ): # Check that required directories exist. - paths_to_check = [ self.root, self.file_path, self.tool_data_path, self.template_path ] + paths_to_check = [ self.root, self.file_path, self.hgweb_config_dir, self.tool_data_path, self.template_path ] for path in paths_to_check: if path not in [ None, False ] and not os.path.isdir( path ): try: diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -344,7 +344,7 @@ class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): @@ -516,7 +516,7 @@ if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) repository = get_repository_in_tool_shed( trans, repository_id ) - if repository.tip != v: + if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', operation='view_or_manage_repository', diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -139,7 +139,7 @@ if not file_path or not os.path.exists( file_path ): # The file no longer exists on disk, so it must have been deleted at some previous point in the change log. return False - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): return True file_name = strip_path( file_path ) latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision ) @@ -327,7 +327,7 @@ previous_changeset_revision = current_changeset_revision def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] previous_reviews_dict = odict() for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): @@ -340,10 +340,10 @@ previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews ) return previous_reviews_dict -def get_rev_label_changeset_revision_from_repository_metadata( repository_metadata, repository=None ): +def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ): if repository is None: repository = repository_metadata.repository - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) changeset_revision = repository_metadata.changeset_revision ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: @@ -424,7 +424,7 @@ Return a string consisting of the human read-able changeset rev and the changeset revision string. """ - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) @@ -454,7 +454,7 @@ # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the # user is not an admin user, the email will not include any information about both HTML and image content # that was included in the change set. - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server if smtp_server and ( new_repo_alert or repository.email_alerts ): @@ -522,7 +522,7 @@ log.exception( "An error occurred sending a tool shed repository update alert by email." ) def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) @@ -537,7 +537,7 @@ """ original_tool_data_path = trans.app.config.tool_data_path repository = get_repository_in_tool_shed( trans, repository_id ) - repo_files_dir = repository.repo_path + repo_files_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_files_dir ) message = '' tool = None @@ -555,7 +555,8 @@ tool, sample_files ) if invalid_files_and_errors_tups: - message2 = generate_message_for_invalid_tools( invalid_files_and_errors_tups, + message2 = generate_message_for_invalid_tools( trans, + invalid_files_and_errors_tups, repository, metadata_dict=None, as_html=True, @@ -631,7 +632,7 @@ status = 'done' encoded_id = trans.security.encode_id( repository.id ) repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, @@ -649,7 +650,7 @@ repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, - repository.tip, + repository.tip( trans.app ), metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. if len( repository.downloadable_revisions ) == 1: @@ -659,7 +660,7 @@ if repository_metadata: downloadable = is_downloadable( metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip + repository_metadata.changeset_revision = repository.tip( trans.app ) repository_metadata.metadata = metadata_dict repository_metadata.downloadable = downloadable trans.sa_session.add( repository_metadata ) @@ -669,7 +670,7 @@ repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, - repository.tip, + repository.tip( trans.app ), metadata_dict ) if 'tools' in metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. @@ -680,11 +681,11 @@ changeset_revisions.append( changeset_revision ) add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions ) elif len( repo ) == 1 and not invalid_file_tups: - message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) + message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip( trans.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" if invalid_file_tups: - message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) + message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) @@ -704,7 +705,7 @@ # is not supported by the mercurial API. # Make a copy of a repository's files for browsing, remove from disk all files that are not tracked, and commit all # added, modified or removed files that have not yet been committed. - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -1,7 +1,7 @@ import os, logging from galaxy.web.base.controller import * from galaxy.webapps.community.controllers.common import * -from galaxy.util.shed_util import update_repository +from galaxy.util.shed_util import get_hgweb_config from galaxy import eggs eggs.require('mercurial') @@ -14,10 +14,16 @@ class HgController( BaseUIController ): @web.expose def handle_request( self, trans, **kwd ): - # The os command that results in this method being called will look something like + # The os command that results in this method being called will look something like: # hg clone http://test@127.0.0.1:9009/repos/test/convert_characters1 hg_version = mercurial.__version__.version cmd = kwd.get( 'cmd', None ) + hgweb_config = get_hgweb_config( trans.app ) + if not os.path.exists( hgweb_config ): + raise Exception( "Required file %s does not exist." % str( hgweb_config ) ) + def make_web_app(): + hgwebapp = hgwebdir( hgweb_config ) + return hgwebapp wsgi_app = wsgiapplication( make_web_app ) if hg_version >= '2.2.3' and cmd == 'pushkey': # When doing an "hg push" from the command line, the following commands, in order, will be retrieved from environ, depending @@ -33,15 +39,8 @@ if hg_version >= '2.2.3': # Set metadata using the repository files on disk. error_message, status = set_repository_metadata( trans, repository ) - if status not in [ 'ok' ] and error_message: - log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) - elif status in [ 'ok' ] and error_message: - log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( str( repository.name ), str( error_message ) ) ) + if status == 'ok' and error_message: + log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( repository.name, error_message ) ) + elif status != 'ok' and error_message: + log.debug( "Error resetting metadata on repository %s: %s" % ( repository.name, error_message ) ) return wsgi_app - -def make_web_app(): - hgweb_config = "%s/hgweb.config" % os.getcwd() - if not os.path.exists( hgweb_config ): - raise Exception( "Required file hgweb.config does not exist in directory %s" % os.getcwd() ) - hgwebapp = hgwebdir( hgweb_config ) - return hgwebapp diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -11,12 +11,12 @@ from galaxy.model.orm import * # TODO: re-factor shed_util to eliminate the following restricted imports from galaxy.util.shed_util import create_repo_info_dict, generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision, get_repository_file_contents -from galaxy.util.shed_util import get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision, handle_sample_files_and_load_tool_from_disk -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, remove_dir, reset_all_metadata_on_repository_in_tool_shed -from galaxy.util.shed_util import reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path, to_html_escaped -from galaxy.util.shed_util import update_repository, url_join +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_file_from_changeset_revision, get_hgweb_config +from galaxy.util.shed_util import get_repository_file_contents, get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config +from galaxy.util.shed_util import INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS, open_repository_files_folder, remove_dir +from galaxy.util.shed_util import reset_all_metadata_on_repository_in_tool_shed, reversed_lower_upper_bounded_changelog +from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, update_repository, url_join from galaxy.tool_shed.encoding_util import * from common import * @@ -129,7 +129,7 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display the repository tip revision label.""" - return escape_html( repository.revision ) + return escape_html( repository.revision( trans.app ) ) class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return escape_html( repository.description ) @@ -361,7 +361,7 @@ for repository in trans.sa_session.query( model.Repository ) \ .filter( and_( model.Repository.table.c.deprecated == False, model.Repository.table.c.deleted == False ) ): - allow_push = repository.allow_push + allow_push = repository.allow_push( trans.app ) if allow_push: allow_push_usernames = allow_push.split( ',' ) if username in allow_push_usernames: @@ -533,7 +533,7 @@ def __add_hgweb_config_entry( self, trans, repository, repository_path ): # Add an entry in the hgweb.config file for a new repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. - hgweb_config = "%s/hgweb.config" % trans.app.config.root + hgweb_config = get_hgweb_config( trans.app ) if repository_path.startswith( './' ): repository_path = repository_path.replace( './', '', 1 ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path ) @@ -700,7 +700,7 @@ if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) repository = get_repository_in_tool_shed( trans, repository_id ) - if repository.tip != v: + if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', operation='view_or_manage_repository', @@ -714,11 +714,11 @@ status = params.get( 'status', 'done' ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository_in_tool_shed( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) # Update repository files for browsing. update_repository( repo ) - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - metadata = self.get_metadata( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repository=repository, metadata=metadata, @@ -799,7 +799,7 @@ if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) repository = get_repository_in_tool_shed( trans, repository_id ) - if repository.tip != v: + if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), @@ -828,10 +828,10 @@ # Change an entry in the hgweb.config file for a repository. This only happens when # the owner changes the name of the repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. - hgweb_config = "%s/hgweb.config" % trans.app.config.root + hgweb_config = get_hgweb_config( trans.app ) # Make a backup of the hgweb.config file since we're going to be changing it. self.__make_hgweb_config_copy( trans, hgweb_config ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) tmp_fd, tmp_fname = tempfile.mkstemp() @@ -855,7 +855,7 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) # Default to the current changeset revision. update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) @@ -869,7 +869,7 @@ url = url_join( galaxy_url, 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: return no_update @@ -894,7 +894,7 @@ changeset_hash = str( repo.changectx( changeset ) ) ctx = get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: - if changeset_hash == repository.tip: + if changeset_hash == repository.tip( trans.app ): update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash break @@ -926,7 +926,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, id ) - metadata = self.get_metadata( trans, id, repository.tip ) + metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: return trans.fill_template( "/webapps/community/repository/contact_owner.mako", repository=repository, @@ -936,12 +936,12 @@ else: # Do all we can to eliminate spam. return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) - def __create_hgrc_file( self, repository ): - # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path. - # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. - # The hg purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll - # remove unknown files and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( get_configured_ui(), path=repository.repo_path ) + def __create_hgrc_file( self, trans, repository ): + # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path( trans.app ). + # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. The hg + # purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll remove unknown files + # and empty directories. This is not currently used because it is not supported in the mercurial API. + repo = hg.repository( get_configured_ui(), path=repository.repo_path( trans.app ) ) fp = repo.opener( 'hgrc', 'wb' ) fp.write( '[paths]\n' ) fp.write( 'default = .\n' ) @@ -1001,11 +1001,10 @@ os.makedirs( repository_path ) # Create the local repository repo = hg.repository( get_configured_ui(), repository_path, create=True ) - # Add an entry in the hgweb.config file for the local repository - # This enables calls to repository.repo_path + # Add an entry in the hgweb.config file for the local repository, enabling calls to repository.repo_path( trans.app ) self.__add_hgweb_config_entry( trans, repository, repository_path ) # Create a .hg/hgrc file for the local repository - self.__create_hgrc_file( repository ) + self.__create_hgrc_file( trans, repository ) flush_needed = False if category_ids: # Create category associations @@ -1057,7 +1056,7 @@ status = params.get( 'status', 'done' ) repository, tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) - is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: return trans.fill_template( "/webapps/community/repository/tool_form.mako", @@ -1284,7 +1283,7 @@ repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: @@ -1320,7 +1319,7 @@ includes_tools = True if not includes_tool_dependencies and 'tool_dependencies' in metadata: includes_tool_dependencies = True - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = create_repo_info_dict( repository, repository.user.username, repository_clone_url, changeset_revision, str( ctx.rev() ), metadata ) @@ -1378,7 +1377,7 @@ owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) tool_version_dicts = [] for changeset in repo.changelog: @@ -1402,14 +1401,14 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. return tool_shed_encode( update_dict ) else: @@ -1429,7 +1428,7 @@ if update_to_changeset_hash: if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): # We found a RepositoryMetadata record. - if changeset_hash == repository.tip: + if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash @@ -1446,7 +1445,7 @@ def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" encoded_id = trans.security.encode_id( repository.id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) # Initialize the tool lineage tool_guid_lineage = [ guid ] @@ -1462,7 +1461,7 @@ current_child_guid = parent_guid # Get all descendant guids of the received guid. current_parent_guid = guid - for changeset in reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, repository.tip ): + for changeset in reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, repository.tip( trans.app ) ): ctx = repo.changectx( changeset ) rm = get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) ) if rm: @@ -1581,16 +1580,16 @@ repository_clone_url = generate_clone_url( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) - is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) invalid_file_tups = [] if tool: invalid_file_tups = check_tool_input_params( trans.app, - repository.repo_path, + repository.repo_path( trans.app ), tool_config, tool, [] ) if invalid_file_tups: - message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) + message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) elif error_message: message = error_message try: @@ -1622,7 +1621,8 @@ # Make a backup of the hgweb.config file today = date.today() backup_date = today.strftime( "%Y_%m_%d" ) - hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) + hgweb_config_backup_filename = 'hgweb.config_%s_backup' % backup_date + hgweb_config_copy = os.path.join( trans.app.config.hgweb_config_dir, hgweb_config_backup_filename ) shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __make_same_length( self, list1, list2 ): # If either list is 1 item, we'll append to it until its length is the same as the other. @@ -1672,10 +1672,10 @@ status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) repository = get_repository_in_tool_shed( trans, id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) repo_name = util.restore_text( params.get( 'repo_name', repository.name ) ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) description = util.restore_text( params.get( 'description', repository.description ) ) long_description = util.restore_text( params.get( 'long_description', repository.long_description ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) @@ -1746,7 +1746,7 @@ user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) usernames.append( user.username ) usernames = ','.join( usernames ) - repository.set_allow_push( usernames, remove_auth=remove_auth ) + repository.set_allow_push( trans.app, usernames, remove_auth=remove_auth ) message = "The repository information has been updated." elif params.get( 'receive_email_alerts_button', False ): flush_needed = False @@ -1766,8 +1766,9 @@ message = "The repository information has been updated." if error: status = 'error' - if repository.allow_push: - current_allow_push_list = repository.allow_push.split( ',' ) + current_allow_push = repository.allow_push( trans.app ) + if current_allow_push: + current_allow_push_list = current_allow_push.split( ',' ) else: current_allow_push_list = [] allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) @@ -1778,7 +1779,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - revision_label = get_revision_label( trans, repository, repository.tip ) + revision_label = get_revision_label( trans, repository, repository.tip( trans.app ) ) repository_metadata_id = None metadata = None is_malicious = False @@ -1800,7 +1801,7 @@ metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if is_malicious: - if trans.app.security_agent.can_push( trans.user, repository ): + if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push else: message += malicious_error @@ -1896,7 +1897,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, repository_id ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ), @@ -1935,7 +1936,7 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) # Get the lower bound changeset revision lower_bound_changeset_revision = get_previous_downloadable_changset_revision( repository, repo, changeset_revision ) @@ -1961,7 +1962,7 @@ message='Select a repository to rate', status='error' ) ) repository = get_repository_in_tool_shed( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', @@ -1974,8 +1975,8 @@ avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - metadata = self.get_metadata( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/rate_repository.mako', repository=repository, metadata=metadata, @@ -1993,7 +1994,7 @@ invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: repository = get_repository_in_tool_shed( trans, id ) - message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) + message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict ) status = 'error' else: message = "All repository metadata has been reset." @@ -2099,14 +2100,14 @@ status = params.get( 'status', 'done' ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository_in_tool_shed( trans, id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) if params.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: selected_files_to_delete = selected_files_to_delete.split( ',' ) # Get the current repository tip. - tip = repository.tip + tip = repository.tip( trans.app ) for selected_file in selected_files_to_delete: try: commands.remove( repo.ui, repo, selected_file, force=True ) @@ -2139,7 +2140,7 @@ update_repository( repo ) # Get the new repository tip. repo = hg.repository( get_configured_ui(), repo_dir ) - if tip == repository.tip: + if tip == repository.tip( trans.app ): message += 'No changes to repository. ' kwd[ 'message' ] = message @@ -2150,7 +2151,7 @@ else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" - is_malicious = changeset_is_malicious( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', repo=repo, repository=repository, @@ -2283,7 +2284,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -2305,8 +2306,8 @@ 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - metadata = self.get_metadata( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) + metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) return trans.fill_template( '/webapps/community/repository/view_changelog.mako', repository=repository, metadata=metadata, @@ -2320,7 +2321,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) @@ -2336,7 +2337,7 @@ diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): diffs.append( to_html_escaped( diff ) ) - is_malicious = changeset_is_malicious( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, ctx_str ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, @@ -2379,7 +2380,7 @@ metadata = None if metadata and 'readme' in metadata: readme_file = str( metadata[ 'readme' ] ) - repo_files_dir = repository.repo_path + repo_files_dir = repository.repo_path( trans.app ) try: f = open( readme_file, 'r' ) raw_text = f.read() @@ -2423,9 +2424,9 @@ status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) repository = get_repository_in_tool_shed( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) @@ -2464,9 +2465,9 @@ else: repository_metadata_id = None metadata = None - is_malicious = changeset_is_malicious( trans, id, repository.tip ) + is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) ) if is_malicious: - if trans.app.security_agent.can_push( trans.user, repository ): + if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push else: message += malicious_error @@ -2505,7 +2506,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, repository_id ) - repo_files_dir = repository.repo_path + repo_files_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_files_dir ) tool_metadata_dict = {} tool_lineage = [] @@ -2547,7 +2548,7 @@ tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) else: metadata = None - is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, @@ -2611,7 +2612,7 @@ # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( repository_metadata, repository=repository ) + rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -56,7 +56,7 @@ # Restrict to revisions that have been reviewed. if repository.reviews: rval = '' - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) for review in repository.reviews: changeset_revision = review.changeset_revision rev, label = get_rev_label_from_changeset_revision( repo, changeset_revision ) @@ -71,7 +71,9 @@ if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( repository_metadata, repository=repository ) + rev, label, changeset_revision = get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) rval += '<a href="manage_repository_reviews_of_revision' rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval @@ -309,7 +311,7 @@ status = params.get( 'status', 'done' ) review = get_review( trans, kwd[ 'id' ] ) repository = review.repository - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/browse_review.mako', repository=repository, @@ -468,7 +470,7 @@ for component in get_components( trans ): components_dict[ component.name ] = dict( component=component, component_review=None ) repository = review.repository - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) for component_review in review.component_reviews: if component_review and component_review.component: component_name = component_review.component.name @@ -652,7 +654,7 @@ repository_id = kwd.get( 'id', None ) if repository_id: repository = get_repository_in_tool_shed( trans, repository_id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] @@ -699,7 +701,7 @@ repository_id = kwd.get( 'id', None ) changeset_revision = kwd.get( 'changeset_revision', None ) repository = get_repository_in_tool_shed( trans, repository_id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, changeset_revision ) @@ -765,7 +767,7 @@ status = params.get( 'status', 'done' ) repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] ) changeset_revision = kwd.get( 'changeset_revision', None ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = get_previous_repository_reviews( trans, repository, changeset_revision ) rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, changeset_revision ) return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako', diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -31,19 +31,19 @@ categories = get_categories( trans ) repository_id = params.get( 'repository_id', '' ) repository = get_repository_in_tool_shed( trans, repository_id ) - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) ) remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = self.__get_upload_point( repository, **kwd ) - tip = repository.tip + tip = repository.tip( trans.app ) file_data = params.get( 'file_data', '' ) url = params.get( 'url', '' ) # Part of the upload process is sending email notification to those that have registered to # receive them. One scenario occurs when the first change set is produced for the repository. # See the handle_email_alerts() method for the definition of the scenarios. - new_repo_alert = repository.is_new + new_repo_alert = repository.is_new( trans.app ) uploaded_directory = None if params.get( 'upload_button', False ): if file_data == '' and url == '': @@ -158,7 +158,7 @@ # Update the repository files for browsing. update_repository( repo ) # Get the new repository tip. - if tip == repository.tip: + if tip == repository.tip( trans.app ): message = 'No changes to repository. ' status = 'warning' else: @@ -215,7 +215,7 @@ message=message, status=status ) def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 @@ -251,7 +251,7 @@ return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) undesirable_dirs_removed = 0 undesirable_files_removed = 0 @@ -284,12 +284,12 @@ uploaded_file.close() return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed) def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ): - repo_dir = repository.repo_path + repo_dir = repository.repo_path( trans.app ) repo = hg.repository( get_configured_ui(), repo_dir ) content_alert_str = '' files_to_remove = [] filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ] - if remove_repo_files_not_in_tar and not repository.is_new: + if remove_repo_files_not_in_tar and not repository.is_new( trans.app ): # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. for root, dirs, files in os.walk( full_path ): diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/framework/middleware/remoteuser.py --- a/lib/galaxy/webapps/community/framework/middleware/remoteuser.py +++ b/lib/galaxy/webapps/community/framework/middleware/remoteuser.py @@ -53,8 +53,7 @@ if host in self.display_servers: environ[ 'HTTP_REMOTE_USER' ] = 'remote_display_server@%s' % ( self.maildomain or 'example.org' ) return self.app( environ, start_response ) - # Apache sets REMOTE_USER to the string '(null)' when using the - # Rewrite* method for passing REMOTE_USER and a user is + # Apache sets REMOTE_USER to the string '(null)' when using the Rewrite* method for passing REMOTE_USER and a user is # un-authenticated. Any other possible values need to go here as well. path_info = environ.get('PATH_INFO', '') if environ.has_key( 'HTTP_REMOTE_USER' ) and environ[ 'HTTP_REMOTE_USER' ] != '(null)': @@ -62,16 +61,14 @@ if self.maildomain is not None: environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain else: - title = "Access to Galaxy is denied" + title = "Access to this Galaxy tool shed is denied" message = """ - Galaxy is configured to authenticate users via an external - method (such as HTTP authentication in Apache), but only a - username (not an email address) was provided by the - upstream (proxy) server. Since Galaxy usernames are email - addresses, a default mail domain must be set.</p> - <p>Please contact your local Galaxy administrator. The - variable <code>remote_user_maildomain</code> must be set - before you may access Galaxy. + This Galaxy tool shed is configured to authenticate users via an external + method (such as HTTP authentication in Apache), but only a username (not + an email address) was provided by the upstream (proxy) server. Since tool + shed usernames are email addresses, a default mail domain must be set.</[> + <p>The variable <code>remote_user_maildomain</code> must be set before you + can access this tool shed. Contact your local tool shed administrator. """ return self.error( start_response, title, message ) return self.app( environ, start_response ) @@ -79,15 +76,15 @@ # The API handles its own authentication via keys return self.app( environ, start_response ) else: - title = "Access to Galaxy is denied" + title = "Access to this Galaxy tool shed is denied" message = """ - Galaxy is configured to authenticate users via an external - method (such as HTTP authentication in Apache), but a username - was not provided by the upstream (proxy) server. This is - generally due to a misconfiguration in the upstream server.</p> - <p>Please contact your local Galaxy administrator. + This Galaxy tool shed is configured to authenticate users via an external + method (such as HTTP authentication in Apache), but a username was not + provided by the upstream (proxy) server. This is generally due to a + misconfiguration in the upstream server.</p> + <p>Contact your local Galaxy tool shed administrator. """ return self.error( start_response, title, message ) - def error( self, start_response, title="Access denied", message="Please contact your local Galaxy administrator." ): + def error( self, start_response, title="Access denied", message="Contact your local Galaxy tool shed administrator." ): start_response( '403 Forbidden', [('Content-type', 'text/html')] ) return [errorpage % (title, message)] diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -6,6 +6,7 @@ """ import os.path, os, errno, sys, codecs, operator, logging, tarfile, mimetypes, ConfigParser from galaxy import util +from galaxy.util.shed_util import get_hgweb_config from galaxy.util.bunch import Bunch from galaxy.util.hash_util import * from galaxy.web.form_builder import * @@ -15,7 +16,7 @@ from mercurial import hg, ui log = logging.getLogger( __name__ ) - + class User( object ): def __init__( self, email=None, password=None ): self.email = email @@ -109,6 +110,10 @@ MARKED_FOR_REMOVAL = 'r', MARKED_FOR_ADDITION = 'a', NOT_TRACKED = '?' ) + # Handle to the hgweb.config file on disk. + hgweb_config_file = None + # This repository's entry in the hgweb.config file on disk. + hgweb_path = None def __init__( self, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, times_downloaded=0, deprecated=False ): self.name = name or "Unnamed repository" @@ -119,42 +124,43 @@ self.email_alerts = email_alerts self.times_downloaded = times_downloaded self.deprecated = deprecated - @property - def repo_path( self ): - # Repository locations on disk are defined in the hgweb.config file - # in the Galaxy install directory. An entry looks something like: - # repos/test/mira_assembler = database/community_files/000/repo_123 - # TODO: handle this using the mercurial api. - lhs = "repos/%s/%s" % ( self.user.username, self.name ) - hgweb_config = "%s/hgweb.config" % os.getcwd() - if not os.path.exists( hgweb_config ): - raise Exception( "Required file hgweb.config does not exist in directory %s" % os.getcwd() ) - config = ConfigParser.ConfigParser() - config.read( hgweb_config ) - for option in config.options( "paths" ): - if option == lhs: - return config.get( "paths", option ) - raise Exception( "Entry for repository %s missing in %s/hgweb.config file." % ( lhs, os.getcwd() ) ) - @property - def revision( self ): - repo = hg.repository( ui.ui(), self.repo_path ) + def get_hgweb_config_file( self, app ): + if self.hgweb_config_file is None: + self.hgweb_config_file = get_hgweb_config( app ) + return self.hgweb_config_file + def get_hgweb_path( self, app ): + # TODO: If possible, handle this using the mercurial api. + if self.hgweb_path is None: + lhs = os.path.join( "repos", self.user.username, self.name ) + config = ConfigParser.ConfigParser() + config.read( self.get_hgweb_config_file( app ) ) + for option in config.options( "paths" ): + if option == lhs: + self.hgweb_path = config.get( "paths", option ) + break + if self.hgweb_path is None: + raise Exception( "Entry for repository %s missing in file %s." % ( lhs, hgweb_config ) ) + return self.hgweb_path + def repo_path( self, app ): + # Repository locations on disk are stored in the hgweb.config file located in the directory defined by the config setting hgweb_config_dir. + # An entry looks something like: repos/test/mira_assembler = database/community_files/000/repo_123 + return self.get_hgweb_path( app ) + def revision( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) tip_ctx = repo.changectx( repo.changelog.tip() ) return "%s:%s" % ( str( tip_ctx.rev() ), str( repo.changectx( repo.changelog.tip() ) ) ) - @property - def tip( self ): - repo = hg.repository( ui.ui(), self.repo_path ) + def tip( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) return str( repo.changectx( repo.changelog.tip() ) ) - @property - def is_new( self ): - repo = hg.repository( ui.ui(), self.repo_path ) + def is_new( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) tip_ctx = repo.changectx( repo.changelog.tip() ) return tip_ctx.rev() < 0 - @property - def allow_push( self ): - repo = hg.repository( ui.ui(), self.repo_path ) + def allow_push( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) return repo.ui.config( 'web', 'allow_push' ) - def set_allow_push( self, usernames, remove_auth='' ): - allow_push = util.listify( self.allow_push ) + def set_allow_push( self, app, usernames, remove_auth='' ): + allow_push = util.listify( self.allow_push( app ) ) if remove_auth: allow_push.remove( remove_auth ) else: diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -315,7 +315,7 @@ result.engine = engine result.session = Session result.create_tables = create_tables - #load local galaxy security policy + # Load local tool shed security policy result.security_agent = CommunityRBACAgent( result ) result.shed_counter = ShedCounter( result ) return result diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py +++ b/lib/galaxy/webapps/community/security/__init__.py @@ -159,9 +159,9 @@ self.associate_components( user=user, role=role ) for group in groups: self.associate_components( user=user, group=group ) - def can_push( self, user, repository ): + def can_push( self, app, user, repository ): if user: - return user.username in listify( repository.allow_push ) + return user.username in listify( repository.allow_push( app ) ) return False def user_can_review_repositories( self, user ): if user: diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ b/templates/webapps/community/admin/statistics.mako @@ -18,10 +18,10 @@ <td>Total repositories</td><td>${trans.app.shed_counter.repositories | h}</td></tr> - <tr> - <td>Empty repositories</td> - <td>${trans.app.shed_counter.new_repositories | h}</td> - </tr> + ##<tr> + ## <td>Empty repositories</td> + ## <td>${trans.app.shed_counter.new_repositories | h}</td> + ##</tr><tr><td>Deleted repositories</td><td>${trans.app.shed_counter.deleted_repositories | h}</td> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/common/view_readme.mako --- a/templates/webapps/community/common/view_readme.mako +++ b/templates/webapps/community/common/view_readme.mako @@ -5,9 +5,9 @@ <% if trans.webapp.name == 'community': is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) @@ -26,9 +26,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -6,9 +6,9 @@ <% from galaxy.web.framework.helpers import time_ago is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new @@ -70,15 +70,15 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -87,9 +87,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -101,7 +101,7 @@ %if can_browse_contents: <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name | h} revision ${repository.tip | h} (repository tip)</div> + <div class="toolFormTitle">Browse ${repository.name | h} revision ${repository.tip( trans.app ) | h} (repository tip)</div> %if can_download: <div class="form-row"><label>Clone this repository:</label> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -22,7 +22,7 @@ // initAjax is hard to fake, so we pass the children as object array: initAjax: {url: "${h.url_for( controller='repository', action='open_folder' )}", dataType: "json", - data: { folder_path: "${repository.repo_path}" }, + data: { folder_path: "${repository.repo_path( trans.app )}" }, }, onLazyRead: function(dtnode){ dtnode.appendAjax({ @@ -51,7 +51,7 @@ var cell = $("#file_contents"); var selected_value; if (dtnode.data.key == 'root') { - selected_value = "${repository.repo_path}/"; + selected_value = "${repository.repo_path( trans.app )}/"; } else { selected_value = dtnode.data.key; }; diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -3,9 +3,9 @@ <% is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new @@ -44,7 +44,7 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -53,9 +53,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label | h}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> %endif </div> %endif diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -6,10 +6,10 @@ <% from galaxy.web.framework.helpers import time_ago is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) is_deprecated = repository.deprecated can_contact_owner = trans.user and trans.user != repository.user - can_push = not is_deprecated and trans.app.security_agent.can_push( trans.user, repository ) + can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new @@ -20,14 +20,14 @@ browse_label = 'Browse or delete repository tip files' else: browse_label = 'Browse repository tip files' - can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip + can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip( trans.app ) can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0 has_readme = metadata and 'readme' in metadata can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) reviewing_repository = cntrller and cntrller == 'repository_review' - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): tip_str = 'repository tip' else: tip_str = '' @@ -191,7 +191,7 @@ %if is_admin: <div class="form-row"><label>Location:</label> - ${repository.repo_path | h} + ${repository.repo_path( trans.app ) | h} </div><div class="form-row"><label>Deleted:</label> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -4,9 +4,9 @@ <%namespace file="/webapps/community/repository/common.mako" import="*" /><% - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) @@ -59,7 +59,7 @@ <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): tip_str = 'repository tip' else: tip_str = '' diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -6,9 +6,9 @@ from galaxy.web.framework.helpers import time_ago from urllib import quote_plus is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new @@ -77,15 +77,15 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -97,9 +97,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -122,7 +122,7 @@ </div><div class="form-row"><label>Version:</label> - ${repository.revision | h} + ${repository.revision( trans.app ) | h} <div style="clear: both"></div></div><div class="form-row"> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -8,9 +8,9 @@ from galaxy.web.form_builder import SelectField is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = not is_new diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -3,7 +3,7 @@ <% is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_browse_contents = not is_new can_browse_contents = not is_new can_rate = repository.user != trans.user @@ -48,9 +48,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -154,7 +154,7 @@ </div><div style="clear: both"></div></div> - %if not repository.is_new: + %if not repository.is_new( trans.app ): <div class="form-row" ><label>Contents:</label><div id="tree" > diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -6,11 +6,11 @@ <% from galaxy.web.framework.helpers import time_ago is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user can_browse_contents = not is_new can_manage = is_admin or trans.user == repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) @@ -48,12 +48,12 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.security.encode_id( repository.id ) )}">Rate repository</a> @@ -65,9 +65,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> %endif </div></ul> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -6,12 +6,12 @@ <% from galaxy.web.framework.helpers import time_ago is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user can_browse_contents = not is_new can_rate = trans.user and repository.user != trans.user can_manage = is_admin or trans.user == repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_view_change_log = not is_new can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) @@ -49,12 +49,12 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View README</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -69,9 +69,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> %endif </div></ul> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -5,10 +5,10 @@ <% from galaxy.web.framework.helpers import time_ago - is_new = repository.is_new + is_new = repository.is_new( trans.app ) is_deprecated = repository.deprecated can_contact_owner = trans.user and trans.user != repository.user - can_push = not is_deprecated and trans.app.security_agent.can_push( trans.user, repository ) + can_push = not is_deprecated and trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_deprecated and not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_deprecated and not is_new and ( not is_malicious or can_push ) @@ -114,7 +114,7 @@ <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% - if changeset_revision == repository.tip: + if changeset_revision == repository.tip( trans.app ): tip_str = 'repository tip' else: tip_str = '' @@ -172,7 +172,7 @@ %if trans.user_is_admin(): <div class="form-row"><label>Location:</label> - ${repository.repo_path | h} + ${repository.repo_path( trans.app ) | h} </div><div class="form-row"><label>Deleted:</label> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -7,9 +7,9 @@ from galaxy.web.framework.helpers import time_ago from urllib import quote_plus is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) can_browse_contents = trans.webapp.name == 'community' and not is_new diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -9,10 +9,10 @@ in_tool_shed = trans.webapp.name == 'community' is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_manage = is_admin or trans.user == repository.user can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user - can_push = in_tool_shed and trans.app.security_agent.can_push( trans.user, repository ) + can_push = in_tool_shed and trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push can_download = in_tool_shed and not is_new and ( not is_malicious or can_push ) can_browse_contents = in_tool_shed and not is_new @@ -51,9 +51,9 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if has_readme: <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository_review/reviews_of_changeset_revision.mako --- a/templates/webapps/community/repository_review/reviews_of_changeset_revision.mako +++ b/templates/webapps/community/repository_review/reviews_of_changeset_revision.mako @@ -7,11 +7,11 @@ from galaxy.webapps.community.controllers.repository_review import build_approved_select_field from galaxy.webapps.community.controllers.common import STRSEP is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_browse_contents = not is_new can_contact_owner = trans.user and trans.user != repository.user can_manage = is_admin or repository.user == trans.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository_review/reviews_of_repository.mako --- a/templates/webapps/community/repository_review/reviews_of_repository.mako +++ b/templates/webapps/community/repository_review/reviews_of_repository.mako @@ -5,11 +5,11 @@ <% is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_browse_contents = not is_new can_contact_owner = trans.user and trans.user != repository.user can_manage = is_admin or repository.user == trans.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: @@ -44,9 +44,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.security.encode_id( repository.id ) )}">View change log</a> diff -r 15543df2c2428ffadbce946433ae43edff8cb197 -r d60deede2b6a1d360bfd7479a68ab72eb162e84b templates/webapps/community/repository_review/select_previous_review.mako --- a/templates/webapps/community/repository_review/select_previous_review.mako +++ b/templates/webapps/community/repository_review/select_previous_review.mako @@ -5,11 +5,11 @@ <% is_admin = trans.user_is_admin() - is_new = repository.is_new + is_new = repository.is_new( trans.app ) can_browse_contents = not is_new can_contact_owner = trans.user and trans.user != repository.user can_manage = is_admin or repository.user == trans.user - can_push = trans.app.security_agent.can_push( trans.user, repository ) + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: @@ -43,9 +43,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.security.encode_id( repository.id ) )}">View change log</a> 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 Bitbucket 12 Nov '12

12 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4dee72426a65/ changeset: 4dee72426a65 user: jmchilton date: 2012-09-22 05:04:15 summary: Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged. Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app. Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh Added usage documentation to run_reports.sh. Added extension points to tweak pid and log location for reports application via environment variables. affected #: 3 files diff -r 3574c1fa4cb3494f82fd1915c63da6154b230756 -r 4dee72426a656988fdf6c70c2c3ff4ba9774fb5c run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -1,4 +1,29 @@ #!/bin/sh + +# Usage: ./run_reports.sh [--sync-config] <start|stop> +# +# +# Description: This script can be used to start or stop the galaxy +# reports web application. Passing in --sync-config as the first +# argument to this will cause Galaxy's database and path parameters +# from universe_wsgi.ini to be copied over into reports_wsgi.ini. + cd `dirname $0` -python ./scripts/paster.py serve reports_wsgi.ini --pid-file=reports_webapp.pid --log-file=reports_webapp.log $@ + +GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} +GALAXY_REPORTS_PID=${GALAXY_REPORTS_PID:-reports_webapp.pid} +GALAXY_REPORTS_LOG=${GALAXY_REPORTS_LOG:-reports_webapp.log} + +if [ -n "$GALAXY_REPORTS_CONFIG_DIR" ]; then + python ./scripts/build_universe_config.py "$GALAXY_REPORTS_CONFIG_DIR" "$GALAXY_REPORTS_CONFIG" +fi + + +if [ "$1" = "--sync-config" ]; +then + python ./scripts/sync_reports_config.py + shift +fi + +python ./scripts/paster.py serve "$GALAXY_REPORTS_CONFIG" --pid-file="$GALAXY_REPORTS_PID" --log-file="$GALAXY_REPORTS_LOG" $@ diff -r 3574c1fa4cb3494f82fd1915c63da6154b230756 -r 4dee72426a656988fdf6c70c2c3ff4ba9774fb5c scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -20,7 +20,11 @@ ## TODO: Expand enviroment variables here, that would ## also make Galaxy much easier to configure. - parser.write(open("universe_wsgi.ini", 'w')) + destination= "universe_wsgi.ini" + if len(argv) > 2: + destination = argv[2] + + parser.write(open(destination, 'w')) if __name__ == '__main__': merge() diff -r 3574c1fa4cb3494f82fd1915c63da6154b230756 -r 4dee72426a656988fdf6c70c2c3ff4ba9774fb5c scripts/sync_reports_config.py --- /dev/null +++ b/scripts/sync_reports_config.py @@ -0,0 +1,58 @@ +from ConfigParser import ConfigParser +from sys import argv + +REPLACE_PROPERTIES = ["file_path", "database_connection", "new_file_path"] +MAIN_SECTION = "app:main" + +def sync(): + # Add or replace the relevant properites from universe_wsgi.ini + # into reports_wsgi.ini + reports_config_file = "reports_wsgi.ini" + if len(argv) > 1: + reports_config_file = argv[1] + + universe_config_file = "universe_wsgi.ini" + if len(argv) > 2: + universe_config_file = argv[2] + + parser = ConfigParser() + parser.read(universe_config_file) + + with open(reports_config_file, "r") as f: + reports_config_lines = f.readlines() + + replaced_properties = set([]) + with open(reports_config_file, "w") as f: + # Write all properties from reports config replacing as + # needed. + for reports_config_line in reports_config_lines: + (line, replaced_property) = get_synced_line(reports_config_line, parser) + if replaced_property: + replaced_properties.add(replaced_property) + f.write(line) + + # If any properties appear in universe config and not in + # reports write these as well. + for replacement_property in REPLACE_PROPERTIES: + if parser.has_option(MAIN_SECTION, replacement_property) and \ + not (replacement_property in replaced_properties): + f.write(get_universe_line(replacement_property, parser)) + +def get_synced_line(reports_line, universe_config): + # Cycle through properties to replace and perform replacement on + # this line if needed. + synced_line = reports_line + replaced_property = None + for replacement_property in REPLACE_PROPERTIES: + if reports_line.startswith(replacement_property) and \ + universe_config.has_option(MAIN_SECTION, replacement_property): + synced_line = get_universe_line(replacement_property, universe_config) + replaced_property = replacement_property + break + return (synced_line, replaced_property) + +def get_universe_line(property_name, universe_config): + return "%s=%s\n" % (property_name, universe_config.get(MAIN_SECTION, property_name)) + +if __name__ == '__main__': + sync() https://bitbucket.org/galaxy/galaxy-central/changeset/15543df2c242/ changeset: 15543df2c242 user: dannon date: 2012-11-12 18:00:18 summary: Merged in jmchilton/galaxy-central-reports-config-enhancements (pull request #71) affected #: 3 files diff -r 38ce114e06f965dfd7eca383849a91b07d1473c6 -r 15543df2c2428ffadbce946433ae43edff8cb197 run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -1,4 +1,29 @@ #!/bin/sh + +# Usage: ./run_reports.sh [--sync-config] <start|stop> +# +# +# Description: This script can be used to start or stop the galaxy +# reports web application. Passing in --sync-config as the first +# argument to this will cause Galaxy's database and path parameters +# from universe_wsgi.ini to be copied over into reports_wsgi.ini. + cd `dirname $0` -python ./scripts/paster.py serve reports_wsgi.ini --pid-file=reports_webapp.pid --log-file=reports_webapp.log $@ + +GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} +GALAXY_REPORTS_PID=${GALAXY_REPORTS_PID:-reports_webapp.pid} +GALAXY_REPORTS_LOG=${GALAXY_REPORTS_LOG:-reports_webapp.log} + +if [ -n "$GALAXY_REPORTS_CONFIG_DIR" ]; then + python ./scripts/build_universe_config.py "$GALAXY_REPORTS_CONFIG_DIR" "$GALAXY_REPORTS_CONFIG" +fi + + +if [ "$1" = "--sync-config" ]; +then + python ./scripts/sync_reports_config.py + shift +fi + +python ./scripts/paster.py serve "$GALAXY_REPORTS_CONFIG" --pid-file="$GALAXY_REPORTS_PID" --log-file="$GALAXY_REPORTS_LOG" $@ diff -r 38ce114e06f965dfd7eca383849a91b07d1473c6 -r 15543df2c2428ffadbce946433ae43edff8cb197 scripts/build_universe_config.py --- a/scripts/build_universe_config.py +++ b/scripts/build_universe_config.py @@ -20,7 +20,11 @@ ## TODO: Expand enviroment variables here, that would ## also make Galaxy much easier to configure. - parser.write(open("universe_wsgi.ini", 'w')) + destination= "universe_wsgi.ini" + if len(argv) > 2: + destination = argv[2] + + parser.write(open(destination, 'w')) if __name__ == '__main__': merge() diff -r 38ce114e06f965dfd7eca383849a91b07d1473c6 -r 15543df2c2428ffadbce946433ae43edff8cb197 scripts/sync_reports_config.py --- /dev/null +++ b/scripts/sync_reports_config.py @@ -0,0 +1,58 @@ +from ConfigParser import ConfigParser +from sys import argv + +REPLACE_PROPERTIES = ["file_path", "database_connection", "new_file_path"] +MAIN_SECTION = "app:main" + +def sync(): + # Add or replace the relevant properites from universe_wsgi.ini + # into reports_wsgi.ini + reports_config_file = "reports_wsgi.ini" + if len(argv) > 1: + reports_config_file = argv[1] + + universe_config_file = "universe_wsgi.ini" + if len(argv) > 2: + universe_config_file = argv[2] + + parser = ConfigParser() + parser.read(universe_config_file) + + with open(reports_config_file, "r") as f: + reports_config_lines = f.readlines() + + replaced_properties = set([]) + with open(reports_config_file, "w") as f: + # Write all properties from reports config replacing as + # needed. + for reports_config_line in reports_config_lines: + (line, replaced_property) = get_synced_line(reports_config_line, parser) + if replaced_property: + replaced_properties.add(replaced_property) + f.write(line) + + # If any properties appear in universe config and not in + # reports write these as well. + for replacement_property in REPLACE_PROPERTIES: + if parser.has_option(MAIN_SECTION, replacement_property) and \ + not (replacement_property in replaced_properties): + f.write(get_universe_line(replacement_property, parser)) + +def get_synced_line(reports_line, universe_config): + # Cycle through properties to replace and perform replacement on + # this line if needed. + synced_line = reports_line + replaced_property = None + for replacement_property in REPLACE_PROPERTIES: + if reports_line.startswith(replacement_property) and \ + universe_config.has_option(MAIN_SECTION, replacement_property): + synced_line = get_universe_line(replacement_property, universe_config) + replaced_property = replacement_property + break + return (synced_line, replaced_property) + +def get_universe_line(property_name, universe_config): + return "%s=%s\n" % (property_name, universe_config.get(MAIN_SECTION, property_name)) + +if __name__ == '__main__': + sync() 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 Bitbucket 12 Nov '12

12 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c691188b11ad/ changeset: c691188b11ad user: kellrott date: 2012-10-28 08:28:42 summary: Adding the initial componenents of an extended metadata system for datasets. The idea behind an 'extended metadata' for datasets is to provide a mechanism to encode and index user generated metadata and keep it attached to files. Users can provide a JSON style data structure which will then be indexed and stored. Later this index can be used to search and discover datasets via a pseudo-formal schema. This patch introduces the tables, and makes it possible to inject user metadata into a file load using the 'extended_metadata' field in the query. affected #: 5 files diff -r ecd131b136d00d5753992061d12b12156be8b277 -r c691188b11ad81ae21d1135501a5ede81135bffa lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -977,7 +977,7 @@ permitted_actions = Dataset.permitted_actions def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ): + parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None ): self.name = name or "Unnamed dataset" self.id = id self.info = info @@ -987,6 +987,7 @@ self.extension = extension self.designation = designation self.metadata = metadata or dict() + self.extended_metadata = extended_metadata if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' self.dbkey = dbkey self.deleted = deleted @@ -1891,6 +1892,18 @@ ldda_name = unicode( ldda_name, 'utf-8' ) return ldda_name +class ExtendedMetadata( object ): + def __init__(self, data): + self.data = data + + +class ExtendedMetadataIndex( object ): + def __init__( self, extended_metadata, path, value): + self.extended_metadata = extended_metadata + self.path = path + self.value = value + + class LibraryInfoAssociation( object ): def __init__( self, library, form_definition, info, inheritable=False ): self.library = library diff -r ecd131b136d00d5753992061d12b12156be8b277 -r c691188b11ad81ae21d1135501a5ede81135bffa lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -323,7 +323,24 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "visible", Boolean ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "message", TrimmedString( 255 ) ) ) + Column( "message", TrimmedString( 255 ) ), + Column( "extended_metadata_id", Integer, + ForeignKey( "extended_metadata.id" ), index=True ) + ) + + +ExtendedMetadata.table = Table("extended_metadata", metadata, + Column( "id", Integer, primary_key=True ), + Column( "data", JSONType ) ) + +ExtendedMetadataIndex.table = Table("extended_metadata_index", metadata, + Column( "id", Integer, primary_key=True ), + Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id", + onupdate="CASCADE", + ondelete="CASCADE" ), + index=True ), + Column( "path", String( 255 )), + Column( "value", TEXT)) Library.table = Table( "library", metadata, Column( "id", Integer, primary_key=True ), @@ -1436,6 +1453,28 @@ ) ) +assign_mapper(context, ExtendedMetadata, ExtendedMetadata.table, + properties=dict( + children=relation( + ExtendedMetadataIndex, + primaryjoin=( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ), + backref=backref("parent", + primaryjoin=( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) + ) + ) + ) +) + +assign_mapper(context, ExtendedMetadataIndex, ExtendedMetadataIndex.table, + properties=dict( + extended_metadata=relation( + ExtendedMetadata, + primaryjoin=( ( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) ) + ) + ) +) + + assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, properties=dict( library=relation( Library, primaryjoin=( ( LibraryInfoAssociation.table.c.library_id == Library.table.c.id ) & ( not_( LibraryInfoAssociation.table.c.deleted ) ) ), backref="info_association" ), @@ -1515,8 +1554,12 @@ backref=backref( "parent", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), visible_children=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) - ) ) + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ), + extended_metadata=relation( + ExtendedMetadata, + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) ) + ) + )) assign_mapper( context, LibraryDatasetDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation.table, properties=dict( library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, diff -r ecd131b136d00d5753992061d12b12156be8b277 -r c691188b11ad81ae21d1135501a5ede81135bffa lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -0,0 +1,75 @@ +""" +Add the ExtendedMetadata and ExtendedMetadataIndex tables +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import JSONType + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +#db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + + +ExtendedMetadata_table = Table("extended_metadata", metadata, + Column( "id", Integer, primary_key=True ), + Column( "data", JSONType ) ) + +ExtendedMetadataIndex_table = Table("extended_metadata_index", metadata, + Column( "id", Integer, primary_key=True ), + Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id", + onupdate="CASCADE", + ondelete="CASCADE" ), + index=True ), + Column( "path", String( 255 )), + Column( "value", TEXT)) + +extended_metadata_ldda_col = Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), nullable=True ) + + +def display_migration_details(): + print "" + print "This migration script adds a 'handler' column to the Job table." + +def upgrade(): + print __doc__ + metadata.reflect() + try: + ExtendedMetadata_table.create() + except: + log.debug("Could not create ExtendedMetadata Table.") + try: + ExtendedMetadataIndex_table.create() + except: + log.debug("Could not create ExtendedMetadataIndex Table.") + + + # Add the extended_metadata_id to the ldda table + try: + ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_ldda_col.create( ldda_table ) + assert extended_metadata_ldda_col is ldda_table.c.extended_metadata_id + except Exception, e: + print str(e) + log.error( "Adding column 'extended_metadata_id' to library_dataset_dataset_association table failed: %s" % str( e ) ) + return + + +def downgrade(): + metadata.reflect() + ExtendedMetadata_table.drop() + ExtendedMetadataIndex_table.drop() + + # Drop the Job table's exit_code column. + try: + job_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_id = job_table.c.extended_metadata_id + extended_metadata_id.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_id' column from library_dataset_dataset_association table failed: %s" % ( str( e ) ) ) + + diff -r ecd131b136d00d5753992061d12b12156be8b277 -r c691188b11ad81ae21d1135501a5ede81135bffa 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 @@ -7,6 +7,7 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex log = logging.getLogger( __name__ ) @@ -114,6 +115,13 @@ return str( e ) # The rest of the security happens in the library_common controller. real_folder_id = trans.security.encode_id( parent.id ) + + #check for extended metadata, store it and pop it out of the param + #otherwise sanitize_param will have a fit + ex_meta_payload = None + if 'extended_metadata' in payload: + ex_meta_payload = payload.pop('extended_metadata') + # Now create the desired content object, either file or folder. if create_type == 'file': status, output = trans.webapp.controllers['library_common'].upload_library_dataset( trans, 'api', library_id, real_folder_id, **payload ) @@ -125,6 +133,19 @@ else: rval = [] for k, v in output.items(): + if ex_meta_payload is not None: + """ + If there is extended metadata, store it, attach it to the dataset, and index it + """ + ex_meta = ExtendedMetadata(ex_meta_payload) + trans.sa_session.add( ex_meta ) + v.extended_metadata = ex_meta + trans.sa_session.add(v) + trans.sa_session.flush() + for path, value in self._scan_json_block(ex_meta_payload): + meta_i = ExtendedMetadataIndex(ex_meta, path, value) + trans.sa_session.add(meta_i) + trans.sa_session.flush() if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( v.id ) @@ -135,6 +156,33 @@ url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) return rval + def _scan_json_block(self, meta, prefix=""): + """ + Scan a json style data structure, and emit all fields and their values. + Example paths + + Data + { "data" : [ 1, 2, 3 ] } + + Path: + /data == [1,2,3] + + /data/[0] == 1 + + """ + if isinstance(meta, dict): + for a in meta: + for path, value in self._scan_json_block(meta[a], prefix + "/" + a): + yield path, value + elif isinstance(meta, list): + for i, a in enumerate(meta): + for path, value in self._scan_json_block(a, prefix + "[%d]" % (i)): + yield path, value + else: + #BUG: Everything is cast to string, which can lead to false positives + #for cross type comparisions, ie "True" == True + yield prefix, str(meta) + @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ diff -r ecd131b136d00d5753992061d12b12156be8b277 -r c691188b11ad81ae21d1135501a5ede81135bffa scripts/api/load_data_with_metadata.py --- /dev/null +++ b/scripts/api/load_data_with_metadata.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python +""" + +This script scans a directory for files with companion '.json' files, then loads +the data from the file, and attaches the .json contents using the 'extended_metadata' +system in the library + +Sample call: +python load_data_with_metadata.py <api_key><api_url> /tmp/g_inbox/ /tmp/g_inbox/done/ "API Imports" + +NOTE: The upload method used requires the data library filesystem upload allow_library_path_paste +""" +import os +import shutil +import sys +import json +import time +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit, display + +def main(api_key, api_url, in_folder, out_folder, data_library): + # Find/Create data library with the above name. Assume we're putting datasets in the root folder '/' + libs = display(api_key, api_url + 'libraries', return_formatted=False) + library_id = None + for library in libs: + if library['name'] == data_library: + library_id = library['id'] + if not library_id: + lib_create_data = {'name':data_library} + library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False) + library_id = library[0]['id'] + folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted = False) + for f in folders: + if f['name'] == "/": + library_folder_id = f['id'] + if not library_id or not library_folder_id: + print "Failure to configure library destination." + sys.exit(1) + # Watch in_folder, upload anything that shows up there to data library and get ldda, + # invoke workflow, move file to out_folder. + for fname in os.listdir(in_folder): + fullpath = os.path.join(in_folder, fname) + if os.path.isfile(fullpath) and os.path.exists(fullpath + ".json"): + data = {} + data['folder_id'] = library_folder_id + data['file_type'] = 'auto' + data['dbkey'] = '' + data['upload_option'] = 'upload_paths' + data['filesystem_paths'] = fullpath + data['create_type'] = 'file' + + handle = open( fullpath + ".json" ) + smeta = handle.read() + handle.close() + data['extended_metadata'] = json.loads(smeta) + libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted = True) + print libset + +if __name__ == '__main__': + try: + api_key = sys.argv[1] + api_url = sys.argv[2] + in_folder = sys.argv[3] + out_folder = sys.argv[4] + data_library = sys.argv[5] + except IndexError: + print 'usage: %s key url in_folder out_folder data_library' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) + main(api_key, api_url, in_folder, out_folder, data_library ) + https://bitbucket.org/galaxy/galaxy-central/changeset/38ce114e06f9/ changeset: 38ce114e06f9 user: dannon date: 2012-11-12 17:54:45 summary: Merged in kellrott/galaxy-central (pull request #81) affected #: 5 files diff -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 -r 38ce114e06f965dfd7eca383849a91b07d1473c6 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -993,7 +993,7 @@ permitted_actions = Dataset.permitted_actions def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None ): + parent_id=None, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None ): self.name = name or "Unnamed dataset" self.id = id self.info = info @@ -1003,6 +1003,7 @@ self.extension = extension self.designation = designation self.metadata = metadata or dict() + self.extended_metadata = extended_metadata if dbkey: #dbkey is stored in metadata, only set if non-zero, or else we could clobber one supplied by input 'metadata' self.dbkey = dbkey self.deleted = deleted @@ -1908,6 +1909,18 @@ ldda_name = unicode( ldda_name, 'utf-8' ) return ldda_name +class ExtendedMetadata( object ): + def __init__(self, data): + self.data = data + + +class ExtendedMetadataIndex( object ): + def __init__( self, extended_metadata, path, value): + self.extended_metadata = extended_metadata + self.path = path + self.value = value + + class LibraryInfoAssociation( object ): def __init__( self, library, form_definition, info, inheritable=False ): self.library = library diff -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 -r 38ce114e06f965dfd7eca383849a91b07d1473c6 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -323,7 +323,24 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "visible", Boolean ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), - Column( "message", TrimmedString( 255 ) ) ) + Column( "message", TrimmedString( 255 ) ), + Column( "extended_metadata_id", Integer, + ForeignKey( "extended_metadata.id" ), index=True ) + ) + + +ExtendedMetadata.table = Table("extended_metadata", metadata, + Column( "id", Integer, primary_key=True ), + Column( "data", JSONType ) ) + +ExtendedMetadataIndex.table = Table("extended_metadata_index", metadata, + Column( "id", Integer, primary_key=True ), + Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id", + onupdate="CASCADE", + ondelete="CASCADE" ), + index=True ), + Column( "path", String( 255 )), + Column( "value", TEXT)) Library.table = Table( "library", metadata, Column( "id", Integer, primary_key=True ), @@ -1436,6 +1453,28 @@ ) ) +assign_mapper(context, ExtendedMetadata, ExtendedMetadata.table, + properties=dict( + children=relation( + ExtendedMetadataIndex, + primaryjoin=( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ), + backref=backref("parent", + primaryjoin=( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) + ) + ) + ) +) + +assign_mapper(context, ExtendedMetadataIndex, ExtendedMetadataIndex.table, + properties=dict( + extended_metadata=relation( + ExtendedMetadata, + primaryjoin=( ( ExtendedMetadataIndex.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) ) + ) + ) +) + + assign_mapper( context, LibraryInfoAssociation, LibraryInfoAssociation.table, properties=dict( library=relation( Library, primaryjoin=( ( LibraryInfoAssociation.table.c.library_id == Library.table.c.id ) & ( not_( LibraryInfoAssociation.table.c.deleted ) ) ), backref="info_association" ), @@ -1515,8 +1554,12 @@ backref=backref( "parent", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), visible_children=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ) - ) ) + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.parent_id == LibraryDatasetDatasetAssociation.table.c.id ) & ( LibraryDatasetDatasetAssociation.table.c.visible == True ) ) ), + extended_metadata=relation( + ExtendedMetadata, + primaryjoin=( ( LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == ExtendedMetadata.table.c.id ) ) + ) + )) assign_mapper( context, LibraryDatasetDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation.table, properties=dict( library_dataset_dataset_association=relation( LibraryDatasetDatasetAssociation, diff -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 -r 38ce114e06f965dfd7eca383849a91b07d1473c6 lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py @@ -0,0 +1,75 @@ +""" +Add the ExtendedMetadata and ExtendedMetadataIndex tables +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import JSONType + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +#db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + + +ExtendedMetadata_table = Table("extended_metadata", metadata, + Column( "id", Integer, primary_key=True ), + Column( "data", JSONType ) ) + +ExtendedMetadataIndex_table = Table("extended_metadata_index", metadata, + Column( "id", Integer, primary_key=True ), + Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id", + onupdate="CASCADE", + ondelete="CASCADE" ), + index=True ), + Column( "path", String( 255 )), + Column( "value", TEXT)) + +extended_metadata_ldda_col = Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), nullable=True ) + + +def display_migration_details(): + print "" + print "This migration script adds a 'handler' column to the Job table." + +def upgrade(): + print __doc__ + metadata.reflect() + try: + ExtendedMetadata_table.create() + except: + log.debug("Could not create ExtendedMetadata Table.") + try: + ExtendedMetadataIndex_table.create() + except: + log.debug("Could not create ExtendedMetadataIndex Table.") + + + # Add the extended_metadata_id to the ldda table + try: + ldda_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_ldda_col.create( ldda_table ) + assert extended_metadata_ldda_col is ldda_table.c.extended_metadata_id + except Exception, e: + print str(e) + log.error( "Adding column 'extended_metadata_id' to library_dataset_dataset_association table failed: %s" % str( e ) ) + return + + +def downgrade(): + metadata.reflect() + ExtendedMetadata_table.drop() + ExtendedMetadataIndex_table.drop() + + # Drop the Job table's exit_code column. + try: + job_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) + extended_metadata_id = job_table.c.extended_metadata_id + extended_metadata_id.drop() + except Exception, e: + log.debug( "Dropping 'extended_metadata_id' column from library_dataset_dataset_association table failed: %s" % ( str( e ) ) ) + + diff -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 -r 38ce114e06f965dfd7eca383849a91b07d1473c6 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 @@ -7,6 +7,7 @@ from galaxy.web.base.controller import * from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * +from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex log = logging.getLogger( __name__ ) @@ -114,6 +115,13 @@ return str( e ) # The rest of the security happens in the library_common controller. real_folder_id = trans.security.encode_id( parent.id ) + + #check for extended metadata, store it and pop it out of the param + #otherwise sanitize_param will have a fit + ex_meta_payload = None + if 'extended_metadata' in payload: + ex_meta_payload = payload.pop('extended_metadata') + # Now create the desired content object, either file or folder. if create_type == 'file': status, output = trans.webapp.controllers['library_common'].upload_library_dataset( trans, 'api', library_id, real_folder_id, **payload ) @@ -125,6 +133,19 @@ else: rval = [] for k, v in output.items(): + if ex_meta_payload is not None: + """ + If there is extended metadata, store it, attach it to the dataset, and index it + """ + ex_meta = ExtendedMetadata(ex_meta_payload) + trans.sa_session.add( ex_meta ) + v.extended_metadata = ex_meta + trans.sa_session.add(v) + trans.sa_session.flush() + for path, value in self._scan_json_block(ex_meta_payload): + meta_i = ExtendedMetadataIndex(ex_meta, path, value) + trans.sa_session.add(meta_i) + trans.sa_session.flush() if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id( v.id ) @@ -135,6 +156,33 @@ url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) return rval + def _scan_json_block(self, meta, prefix=""): + """ + Scan a json style data structure, and emit all fields and their values. + Example paths + + Data + { "data" : [ 1, 2, 3 ] } + + Path: + /data == [1,2,3] + + /data/[0] == 1 + + """ + if isinstance(meta, dict): + for a in meta: + for path, value in self._scan_json_block(meta[a], prefix + "/" + a): + yield path, value + elif isinstance(meta, list): + for i, a in enumerate(meta): + for path, value in self._scan_json_block(a, prefix + "[%d]" % (i)): + yield path, value + else: + #BUG: Everything is cast to string, which can lead to false positives + #for cross type comparisions, ie "True" == True + yield prefix, str(meta) + @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ diff -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 -r 38ce114e06f965dfd7eca383849a91b07d1473c6 scripts/api/load_data_with_metadata.py --- /dev/null +++ b/scripts/api/load_data_with_metadata.py @@ -0,0 +1,70 @@ +#!/usr/bin/env python +""" + +This script scans a directory for files with companion '.json' files, then loads +the data from the file, and attaches the .json contents using the 'extended_metadata' +system in the library + +Sample call: +python load_data_with_metadata.py <api_key><api_url> /tmp/g_inbox/ /tmp/g_inbox/done/ "API Imports" + +NOTE: The upload method used requires the data library filesystem upload allow_library_path_paste +""" +import os +import shutil +import sys +import json +import time +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import submit, display + +def main(api_key, api_url, in_folder, out_folder, data_library): + # Find/Create data library with the above name. Assume we're putting datasets in the root folder '/' + libs = display(api_key, api_url + 'libraries', return_formatted=False) + library_id = None + for library in libs: + if library['name'] == data_library: + library_id = library['id'] + if not library_id: + lib_create_data = {'name':data_library} + library = submit(api_key, api_url + 'libraries', lib_create_data, return_formatted=False) + library_id = library[0]['id'] + folders = display(api_key, api_url + "libraries/%s/contents" % library_id, return_formatted = False) + for f in folders: + if f['name'] == "/": + library_folder_id = f['id'] + if not library_id or not library_folder_id: + print "Failure to configure library destination." + sys.exit(1) + # Watch in_folder, upload anything that shows up there to data library and get ldda, + # invoke workflow, move file to out_folder. + for fname in os.listdir(in_folder): + fullpath = os.path.join(in_folder, fname) + if os.path.isfile(fullpath) and os.path.exists(fullpath + ".json"): + data = {} + data['folder_id'] = library_folder_id + data['file_type'] = 'auto' + data['dbkey'] = '' + data['upload_option'] = 'upload_paths' + data['filesystem_paths'] = fullpath + data['create_type'] = 'file' + + handle = open( fullpath + ".json" ) + smeta = handle.read() + handle.close() + data['extended_metadata'] = json.loads(smeta) + libset = submit(api_key, api_url + "libraries/%s/contents" % library_id, data, return_formatted = True) + print libset + +if __name__ == '__main__': + try: + api_key = sys.argv[1] + api_url = sys.argv[2] + in_folder = sys.argv[3] + out_folder = sys.argv[4] + data_library = sys.argv[5] + except IndexError: + print 'usage: %s key url in_folder out_folder data_library' % os.path.basename( sys.argv[0] ) + sys.exit( 1 ) + main(api_key, api_url, in_folder, out_folder, data_library ) + 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 Bitbucket 11 Nov '12

11 Nov '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6a10ee8260f5/ changeset: 6a10ee8260f5 user: jgoecks date: 2012-11-11 02:31:03 summary: Use a single generic method for asynchronously setting an item's slug. affected #: 5 files diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r 6a10ee8260f5682bca6637ba855263426bee57de lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1487,16 +1487,19 @@ user.username = username trans.sa_session.flush return self.sharing( trans, id, **kwargs ) + + @web.expose + @web.require_login( "modify Galaxy items" ) + def set_slug_async( self, trans, id, new_slug ): + item = self.get_item( trans, id ) + if item: + item.slug = new_slug + trans.sa_session.flush() + return item.slug # -- Abstract methods. -- @web.expose - @web.require_login( "modify Galaxy items" ) - def set_slug_async( self, trans, id, new_slug ): - """ Set item slug asynchronously. """ - raise "Unimplemented Method" - - @web.expose @web.require_login( "share Galaxy items" ) def sharing( self, trans, id, **kwargs ): """ Handle item sharing. """ diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r 6a10ee8260f5682bca6637ba855263426bee57de lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -725,15 +725,6 @@ return @web.expose - @web.require_login( "modify Galaxy items" ) - def set_slug_async( self, trans, id, new_slug ): - history = self.get_history( trans, id ) - if history: - history.slug = new_slug - trans.sa_session.flush() - return history.slug - - @web.expose def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r 6a10ee8260f5682bca6637ba855263426bee57de lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -621,15 +621,6 @@ return @web.expose - @web.require_login( "modify Galaxy items" ) - def set_slug_async( self, trans, id, new_slug ): - page = self.get_page( trans, id ) - if page: - page.slug = new_slug - trans.sa_session.flush() - return page.slug - - @web.expose @web.require_login( "rate items" ) @web.json def rate_async( self, trans, id, rating ): diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r 6a10ee8260f5682bca6637ba855263426bee57de lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -366,17 +366,7 @@ # Display the management page trans.set_message( 'Copy created with name "%s"' % cloned_visualization.title ) return self.list( trans ) - - @web.expose - @web.require_login( "modify Galaxy visualizations" ) - def set_slug_async( self, trans, id, new_slug ): - """ Set item slug asynchronously. """ - visualization = self.get_visualization( trans, id ) - if visualization: - visualization.slug = new_slug - trans.sa_session.flush() - return visualization.slug - + @web.expose @web.require_login( "use Galaxy visualizations" ) def set_accessible_async( self, trans, id=None, accessible=False ): diff -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b -r 6a10ee8260f5682bca6637ba855263426bee57de lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -468,15 +468,6 @@ return @web.expose - @web.require_login( "modify Galaxy items" ) - def set_slug_async( self, trans, id, new_slug ): - stored = self.get_stored_workflow( trans, id ) - if stored: - stored.slug = new_slug - trans.sa_session.flush() - return stored.slug - - @web.expose def get_embed_html_async( self, trans, id ): """ Returns HTML for embedding a workflow in a page. """ https://bitbucket.org/galaxy/galaxy-central/changeset/5c1420204d84/ changeset: 5c1420204d84 user: jgoecks date: 2012-11-11 04:50:33 summary: Ignore shed_tool_data_table_conf.xml in repository. affected #: 1 file diff -r 6a10ee8260f5682bca6637ba855263426bee57de -r 5c1420204d84e980ee5c2f3828d188cb0037505a .hgignore --- a/.hgignore +++ b/.hgignore @@ -28,6 +28,7 @@ reports_wsgi.ini community_wsgi.ini +# Config files. datatypes_conf.xml tool_conf.xml external_service_types_conf.xml @@ -37,6 +38,7 @@ tool_sheds_conf.xml integrated_tool_panel.xml openid_conf.xml +shed_tool_data_table_conf.xml static/welcome.html.* static/welcome.html https://bitbucket.org/galaxy/galaxy-central/changeset/dd63b34f8139/ changeset: dd63b34f8139 user: jgoecks date: 2012-11-11 04:53:35 summary: Ensure that slugs cannot be duplicated for active, importable items. affected #: 1 file diff -r 5c1420204d84e980ee5c2f3828d188cb0037505a -r dd63b34f813972b00f7bf492aec1e74ef9bd5f59 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1493,9 +1493,57 @@ def set_slug_async( self, trans, id, new_slug ): item = self.get_item( trans, id ) if item: - item.slug = new_slug - trans.sa_session.flush() - return item.slug + # Only update slug if slug is not already in use. + if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0: + item.slug = new_slug + trans.sa_session.flush() + + return item.slug + + def _make_item_accessible( self, sa_session, item ): + """ Makes item accessible--viewable and importable--and sets item's slug. + Does not flush/commit changes, however. Item must have name, user, + importable, and slug attributes. """ + item.importable = True + self.create_item_slug( sa_session, item ) + + def create_item_slug( self, sa_session, item ): + """ Create/set item slug. Slug is unique among user's importable items + for item's class. Returns true if item's slug was set/changed; false + otherwise. + """ + cur_slug = item.slug + + # Setup slug base. + if cur_slug is None or cur_slug == "": + # Item can have either a name or a title. + if hasattr( item, 'name' ): + item_name = item.name + elif hasattr( item, 'title' ): + item_name = item.title + # Replace whitespace with '-' + slug_base = re.sub( "\s+", "-", item_name.lower() ) + # Remove all non-alphanumeric characters. + slug_base = re.sub( "[^a-zA-Z0-9\-]", "", slug_base ) + # Remove trailing '-'. + if slug_base.endswith('-'): + slug_base = slug_base[:-1] + else: + slug_base = cur_slug + + # Using slug base, find a slug that is not taken. If slug is taken, + # add integer to end. + new_slug = slug_base + count = 1 + while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() != 0: + # Slug taken; choose a new slug based on count. This approach can + # handle numerous items with the same name gracefully. + new_slug = '%s-%i' % ( slug_base, count ) + count += 1 + + # Set slug and return. + item.slug = new_slug + return item.slug == cur_slug # -- Abstract methods. -- @@ -1527,39 +1575,6 @@ def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ raise "Unimplemented Method" - - # -- Helper methods. -- - - def _make_item_accessible( self, sa_session, item ): - """ Makes item accessible--viewable and importable--and sets item's slug. Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ - item.importable = True - self.create_item_slug( sa_session, item ) - - def create_item_slug( self, sa_session, item ): - """ Create item slug. Slug is unique among user's importable items for item's class. Returns true if item's slug was set; false otherwise. """ - if item.slug is None or item.slug == "": - # Item can have either a name or a title. - if hasattr( item, 'name' ): - item_name = item.name - elif hasattr( item, 'title' ): - item_name = item.title - # Replace whitespace with '-' - slug_base = re.sub( "\s+", "-", item_name.lower() ) - # Remove all non-alphanumeric characters. - slug_base = re.sub( "[^a-zA-Z0-9\-]", "", slug_base ) - # Remove trailing '-'. - if slug_base.endswith('-'): - slug_base = slug_base[:-1] - # Make sure that slug is not taken; if it is, add a number to it. - slug = slug_base - count = 1 - while sa_session.query( item.__class__ ).filter_by( user=item.user, slug=slug, importable=True ).count() != 0: - # Slug taken; choose a new slug based on count. This approach can handle numerous items with the same name gracefully. - slug = '%s-%i' % ( slug_base, count ) - count += 1 - item.slug = slug - return True - return False def get_item( self, trans, id ): """ Return item based on id. """ 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: clements: Pared Sphinx's mock module list down to those that actually get rid of errors at ReadTheDocs.
by Bitbucket 10 Nov '12

10 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5fdb5348d968/ changeset: 5fdb5348d968 user: clements date: 2012-11-03 18:25:21 summary: Pared Sphinx's mock module list down to those that actually get rid of errors at ReadTheDocs. affected #: 1 file diff -r f980df29adff1964f5978e56ce7414ee23eb3a25 -r 5fdb5348d968f5bb38aedba23e26bdb9032a0c0b doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -273,7 +273,7 @@ else: return Mock() -# adding pbs_python, DRMAA_python. markupsafe, and drmaa here had no effect. +# adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect. MOCK_MODULES = ['tables', 'decorator'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() 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 Bitbucket 10 Nov '12

10 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b1d704208702/ changeset: b1d704208702 user: clements date: 2012-11-03 18:00:12 summary: More changes to get Sphinx to run with fewer erros on ReadTheDocs.org. affected #: 1 file diff -r 029237b5d5a2a511c7a787b7d7abbc6de94c01f3 -r b1d704208702feac085d9cf04d56bd08ebdbb3b0 doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -273,6 +273,7 @@ else: return Mock() -MOCK_MODULES = ['tables', 'pbs_python', 'DRMAA_python', 'decorator'] +# adding pbs_python and DRMAA_python here had no effect. +MOCK_MODULES = ['tables', 'markupsafe', 'drmaa', 'decorator'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() https://bitbucket.org/galaxy/galaxy-central/changeset/f980df29adff/ changeset: f980df29adff user: clements date: 2012-11-03 18:10:15 summary: Took out mock modules that weren't helping from Sphinx config file. affected #: 1 file diff -r b1d704208702feac085d9cf04d56bd08ebdbb3b0 -r f980df29adff1964f5978e56ce7414ee23eb3a25 doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -273,7 +273,7 @@ else: return Mock() -# adding pbs_python and DRMAA_python here had no effect. -MOCK_MODULES = ['tables', 'markupsafe', 'drmaa', 'decorator'] +# adding pbs_python, DRMAA_python. markupsafe, and drmaa here had no effect. +MOCK_MODULES = ['tables', 'decorator'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() 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: clements: Added ReadTheDocs section to Sphinx's conf.py. This lists modules that need to be mocked up, Ithink.
by Bitbucket 10 Nov '12

10 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/029237b5d5a2/ changeset: 029237b5d5a2 user: clements date: 2012-11-03 17:34:06 summary: Added ReadTheDocs section to Sphinx's conf.py. This lists modules that need to be mocked up, Ithink. affected #: 1 file diff -r f8c03b26fd59f8546959789af33b2ae0370b8551 -r 029237b5d5a2a511c7a787b7d7abbc6de94c01f3 doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -252,3 +252,27 @@ # How to display URL addresses: 'footnote', 'no', or 'inline'. #texinfo_show_urls = 'footnote' + +# -- ReadTheDocs.org Settings ------------------------------------------------ + +class Mock(object): + def __init__(self, *args, **kwargs): + pass + + def __call__(self, *args, **kwargs): + return Mock() + + @classmethod + def __getattr__(cls, name): + if name in ('__file__', '__path__'): + return '/dev/null' + elif name[0] == name[0].upper(): + mockType = type(name, (), {}) + mockType.__module__ = __name__ + return mockType + else: + return Mock() + +MOCK_MODULES = ['tables', 'pbs_python', 'DRMAA_python', 'decorator'] +for mod_name in MOCK_MODULES: + sys.modules[mod_name] = Mock() 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: clements: All Sphinx related changes:
by Bitbucket 09 Nov '12

09 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f8c03b26fd59/ changeset: f8c03b26fd59 user: clements date: 2012-11-03 16:51:09 summary: All Sphinx related changes: - Changed from Galaxy Documentation to Galaxy Code Documentation to be clearer - Dropped galaxy.jobs.rules, as it is now empty. affected #: 3 files diff -r d30d2888780f44d815d4463e337bf0f62996e2df -r f8c03b26fd59f8546959789af33b2ae0370b8551 doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -52,7 +52,7 @@ master_doc = 'index' # General information about the project. -project = u'Galaxy' +project = u'Galaxy Code' copyright = u'2012, Galaxy Team' # The version info for the project you're documenting, acts as replacement for @@ -195,7 +195,7 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'Galaxy.tex', u'Galaxy Documentation', + ('index', 'Galaxy.tex', u'Galaxy Code Documentation', u'Galaxy Team', 'manual'), ] @@ -225,7 +225,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('index', 'galaxy', u'Galaxy Documentation', + ('index', 'galaxy', u'Galaxy Code Documentation', [u'Galaxy Team'], 1) ] @@ -239,7 +239,7 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'Galaxy', u'Galaxy Documentation', + ('index', 'Galaxy', u'Galaxy Code Documentation', u'Galaxy Team', 'Galaxy', 'Data intensive biology for everyone.', 'Miscellaneous'), ] diff -r d30d2888780f44d815d4463e337bf0f62996e2df -r f8c03b26fd59f8546959789af33b2ae0370b8551 doc/source/index.rst --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -1,5 +1,5 @@ -Galaxy Documentation -******************** +Galaxy Code Documentation +************************* Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. diff -r d30d2888780f44d815d4463e337bf0f62996e2df -r f8c03b26fd59f8546959789af33b2ae0370b8551 doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -48,7 +48,6 @@ galaxy.jobs.actions galaxy.jobs.deferred - galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters 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: (alt)history: subclass on for_editing flag: now hda-edit.js, hda-base.js; split hda and history templates; compile_templates.py: don't stop removal loop for error on single file; pack_scripts;
by Bitbucket 09 Nov '12

09 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d30d2888780f/ changeset: d30d2888780f user: carlfeberhard date: 2012-11-09 21:38:51 summary: (alt)history: subclass on for_editing flag: now hda-edit.js, hda-base.js; split hda and history templates; compile_templates.py: don't stop removal loop for error on single file; pack_scripts; affected #: 44 files diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/mvc/dataset/hda-base.js --- /dev/null +++ b/static/scripts/mvc/dataset/hda-base.js @@ -0,0 +1,447 @@ +//define([ +// "../mvc/base-mvc" +//], function(){ +//============================================================================== +/** read only view for HistoryDatasetAssociations + * + */ +var HDABaseView = BaseView.extend( LoggableMixin ).extend({ + //??TODO: add alias in initialize this.hda = this.model? + // view for HistoryDatasetAssociation model above + + // uncomment this out see log messages + //logger : console, + + tagName : "div", + className : "historyItemContainer", + + // ................................................................................ SET UP + initialize : function( attributes ){ + this.log( this + '.initialize:', attributes ); + + // which buttons go in most states (ok/failed meta are more complicated) + this.defaultPrimaryActionButtonRenderers = [ + this._render_showParamsButton + ]; + + // render urlTemplates (gen. provided by GalaxyPaths) to urls + if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } + this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); + + // whether the body of this hda is expanded (shown) + this.expanded = attributes.expanded || false; + + // re-render the entire view on any model change + this.model.bind( 'change', this.render, this ); + //this.bind( 'all', function( event ){ + // this.log( event ); + //}, this ); + }, + + // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) + // use the templates to create the apropo urls for each action this ds could use + renderUrls : function( urlTemplates, modelJson ){ + var hdaView = this, + urls = {}; + _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ + // object == nested templates: recurse + if( _.isObject( urlTemplateOrObj ) ){ + urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); + + // string == template: + } else { + // meta_down load is a special case (see renderMetaDownloadUrls) + //TODO: should be a better (gen.) way to handle this case + if( urlKey === 'meta_download' ){ + urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); + } else { + urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); + } + } + }); + return urls; + }, + + // there can be more than one meta_file to download, so return a list of url and file_type for each + renderMetaDownloadUrls : function( urlTemplate, modelJson ){ + return _.map( modelJson.meta_files, function( meta_file ){ + return { + url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), + file_type : meta_file.file_type + }; + }); + }, + + // ................................................................................ RENDER MAIN + // events: rendered, rendered:ready, rendered:initial, rendered:ready:initial + render : function(){ + var view = this, + id = this.model.get( 'id' ), + state = this.model.get( 'state' ), + itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), + initialRender = ( this.$el.children().size() === 0 ); + + //console.debug( this + '.render, initial?:', initialRender ); + this.$el.attr( 'id', 'historyItemContainer-' + id ); + + itemWrapper + .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) + .addClass( 'historyItem-' + state ); + + itemWrapper.append( this._render_warnings() ); + itemWrapper.append( this._render_titleBar() ); + this.body = $( this._render_body() ); + itemWrapper.append( this.body ); + + //TODO: move to own function: setUpBehaviours + // we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( itemWrapper ); + + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + + // transition... + this.$el.fadeOut( 'fast', function(){ + view.$el.children().remove(); + view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.log( view + ' rendered:', view.$el ); + + var renderedEventName = 'rendered'; + if( initialRender ){ + renderedEventName += ':initial'; + } else if( view.model.inReadyState() ){ + renderedEventName += ':ready'; + } + view.trigger( renderedEventName ); + }); + }); + return this; + }, + + // ................................................................................ RENDER WARNINGS + // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) + _render_warnings : function(){ + // jQ errs on building dom with whitespace - if there are no messages, trim -> '' + return $( jQuery.trim( HDABaseView.templates.messages( this.model.toJSON() ))); + }, + + // ................................................................................ RENDER TITLEBAR + // the part of an hda always shown (whether the body is expanded or not): title link, title buttons + _render_titleBar : function(){ + var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); + titleBar.append( this._render_titleButtons() ); + titleBar.append( '<span class="state-icon"></span>' ); + titleBar.append( this._render_titleLink() ); + return titleBar; + }, + + // ................................................................................ display, edit attr, delete + // icon-button group for the common, most easily accessed actions + //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) + _render_titleButtons : function(){ + // render the display, edit attr and delete icon-buttons + var buttonDiv = $( '<div class="historyItemButtons"></div>' ); + buttonDiv.append( this._render_displayButton() ); + return buttonDiv; + }, + + // icon-button to display this hda in the galaxy main iframe + _render_displayButton : function(){ + // don't show display if not in ready state, error'd, or not accessible + if( ( !this.model.inReadyState() ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + || ( !this.model.get( 'accessible' ) ) ){ + this.displayButton = null; + return null; + } + + var displayBtnData = { + icon_class : 'display', + target : 'galaxy_main' + }; + + // show a disabled display if the data's been purged + if( this.model.get( 'purged' ) ){ + displayBtnData.enabled = false; + displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); + + } else { + displayBtnData.title = _l( 'Display data in browser' ); + displayBtnData.href = this.urls.display; + } + + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); + return this.displayButton.render().$el; + }, + + // ................................................................................ titleLink + // render the hid and hda.name as a link (that will expand the body) + _render_titleLink : function(){ + return $( jQuery.trim( HDABaseView.templates.titleLink( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ))); + }, + + // ................................................................................ RENDER BODY + // render the data/metadata summary (format, size, misc info, etc.) + _render_hdaSummary : function(){ + var modelData = _.extend( this.model.toJSON(), { urls: this.urls } ); + return HDABaseView.templates.hdaSummary( modelData ); + }, + + // ................................................................................ primary actions + // render the icon-buttons gen. placed underneath the hda summary + _render_primaryActionButtons : function( buttonRenderingFuncs ){ + var view = this, + primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ); + _.each( buttonRenderingFuncs, function( fn ){ + primaryActionButtons.append( fn.call( view ) ); + }); + return primaryActionButtons; + }, + + // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda + _render_downloadButton : function(){ + // don't show anything if the data's been purged + if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; } + + // return either: a single download icon-button (if there are no meta files) + // or a popupmenu with links to download assoc. meta files (if there are meta files) + var downloadLinkHTML = HDABaseView.templates.downloadLinks( + _.extend( this.model.toJSON(), { urls: this.urls } ) + ); + //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); + return $( downloadLinkHTML ); + }, + + // icon-button to show the input and output (stdout/err) for the job that created this hda + _render_showParamsButton : function(){ + // gen. safe to show in all cases + this.showParamsButton = new IconButtonView({ model : new IconButton({ + title : _l( 'View details' ), + href : this.urls.show_params, + target : 'galaxy_main', + icon_class : 'information' + }) }); + return this.showParamsButton.render().$el; + }, + + // ................................................................................ other elements + // render links to external genome display applications (igb, gbrowse, etc.) + //TODO: not a fan of the style on these + _render_displayApps : function(){ + if( !this.model.hasData() ){ return null; } + + var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); + if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ + //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); + //TODO:?? does this ever get used? + displayAppsDiv.append( + HDABaseView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) + ); + } + if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ + //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); + displayAppsDiv.append( + HDABaseView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) + ); + } + return displayAppsDiv; + }, + + // render the data peek + //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible + _render_peek : function(){ + if( !this.model.get( 'peek' ) ){ return null; } + return $( '<div/>' ).append( + $( '<pre/>' ) + .attr( 'id', 'peek' + this.model.get( 'id' ) ) + .addClass( 'peek' ) + .append( this.model.get( 'peek' ) ) + ); + }, + + // ................................................................................ state body renderers + // _render_body fns for the various states + //TODO: only render these on expansion (or already expanded) + _render_body_not_viewable : function( parent ){ + //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right + parent.append( $( '<div>' + _l( 'You do not have permission to view dataset' ) + '.</div>' ) ); + }, + + _render_body_uploading : function( parent ){ + parent.append( $( '<div>' + _l( 'Dataset is uploading' ) + '</div>' ) ); + }, + + _render_body_queued : function( parent ){ + parent.append( $( '<div>' + _l( 'Job is waiting to run' ) + '.</div>' ) ); + parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); + }, + + _render_body_running : function( parent ){ + parent.append( '<div>' + _l( 'Job is currently running' ) + '.</div>' ); + parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); + }, + + _render_body_error : function( parent ){ + if( !this.model.get( 'purged' ) ){ + parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); + } + parent.append( ( _l( 'An error occurred running this job' ) + ': ' + + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); + parent.append( this._render_primaryActionButtons( + this.defaultPrimaryActionButtonRenderers.concat([ this._render_downloadButton ]) + )); + }, + + _render_body_discarded : function( parent ){ + parent.append( '<div>' + _l( 'The job creating this dataset was cancelled before completion' ) + '.</div>' ); + parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); + }, + + _render_body_setting_metadata : function( parent ){ + parent.append( $( '<div>' + _l( 'Metadata is being auto-detected' ) + '.</div>' ) ); + }, + + _render_body_empty : function( parent ){ + //TODO: replace i with dataset-misc-info class + //?? why are we showing the file size when we know it's zero?? + parent.append( $( '<div>' + _l( 'No data' ) + ': <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); + parent.append( this._render_primaryActionButtons( this.defaultPrimaryActionButtonRenderers )); + }, + + _render_body_failed_metadata : function( parent ){ + //TODO: the css for this box is broken (unlike the others) + // add a message box about the failure at the top of the body... + parent.append( $( HDABaseView.templates.failedMetadata( this.model.toJSON() ) ) ); + //...then render the remaining body as STATES.OK (only diff between these states is the box above) + this._render_body_ok( parent ); + }, + + _render_body_ok : function( parent ){ + // most common state renderer and the most complicated + parent.append( this._render_hdaSummary() ); + + // return shortened form if del'd + //TODO: is this correct? maybe only on purged + if( this.model.isDeletedOrPurged() ){ + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_showParamsButton + ])); + return; + } + + //NOTE: change the order here + parent.append( this._render_primaryActionButtons([ + this._render_downloadButton, + this._render_showParamsButton + ])); + parent.append( '<div class="clear"/>' ); + + parent.append( this._render_displayApps() ); + parent.append( this._render_peek() ); + }, + + _render_body : function(){ + //this.log( this + '_render_body' ); + + var body = $( '<div/>' ) + .attr( 'id', 'info-' + this.model.get( 'id' ) ) + .addClass( 'historyItemBody' ) + .attr( 'style', 'display: block' ); + + //TODO: not a fan of this dispatch + switch( this.model.get( 'state' ) ){ + case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : + this._render_body_not_viewable( body ); + break; + case HistoryDatasetAssociation.STATES.UPLOAD : + this._render_body_uploading( body ); + break; + case HistoryDatasetAssociation.STATES.QUEUED : + this._render_body_queued( body ); + break; + case HistoryDatasetAssociation.STATES.RUNNING : + this._render_body_running( body ); + break; + case HistoryDatasetAssociation.STATES.ERROR : + this._render_body_error( body ); + break; + case HistoryDatasetAssociation.STATES.DISCARDED : + this._render_body_discarded( body ); + break; + case HistoryDatasetAssociation.STATES.SETTING_METADATA : + this._render_body_setting_metadata( body ); + break; + case HistoryDatasetAssociation.STATES.EMPTY : + this._render_body_empty( body ); + break; + case HistoryDatasetAssociation.STATES.FAILED_METADATA : + this._render_body_failed_metadata( body ); + break; + case HistoryDatasetAssociation.STATES.OK : + this._render_body_ok( body ); + break; + default: + //??: no body? + body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); + } + body.append( '<div style="clear: both"></div>' ); + + if( this.expanded ){ + body.show(); + } else { + body.hide(); + } + return body; + }, + + // ................................................................................ EVENTS + events : { + 'click .historyItemTitle' : 'toggleBodyVisibility' + }, + + // expand/collapse body + // event: body-visible, body-hidden + toggleBodyVisibility : function( event, expanded ){ + var hdaView = this, + $body = this.$el.find( '.historyItemBody' ); + expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); + //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); + + if( expanded ){ + $body.slideDown( 'fast', function(){ + hdaView.trigger( 'body-visible', hdaView.model.get( 'id' ) ); + }); + } else { + $body.slideUp( 'fast', function(){ + hdaView.trigger( 'body-hidden', hdaView.model.get( 'id' ) ); + }); + } + }, + + // ................................................................................ UTILTIY + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDABaseView(' + modelString + ')'; + } +}); + +//------------------------------------------------------------------------------ +HDABaseView.templates = { + warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], + + messages : Handlebars.templates[ 'template-hda-warning-messages' ], + titleLink : Handlebars.templates[ 'template-hda-titleLink' ], + hdaSummary : Handlebars.templates[ 'template-hda-hdaSummary' ], + downloadLinks : Handlebars.templates[ 'template-hda-downloadLinks' ], + failedMetadata : Handlebars.templates[ 'template-hda-failedMetaData' ], + displayApps : Handlebars.templates[ 'template-hda-displayApps' ] +}; + +//============================================================================== +//return { +// HDABaseView : HDABaseView, +//};}); diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -2,155 +2,32 @@ // "../mvc/base-mvc" //], function(){ //============================================================================== -/** View for editing (working with - as opposed to viewing/read-only) an hda +/** editing view for HistoryDatasetAssociations * */ -var HDAView = BaseView.extend( LoggableMixin ).extend({ - //??TODO: add alias in initialize this.hda = this.model? - // view for HistoryDatasetAssociation model above +var HDAEditView = HDABaseView.extend({ - // uncomment this out see log messages - //logger : console, - - tagName : "div", - className : "historyItemContainer", - // ................................................................................ SET UP initialize : function( attributes ){ - this.log( this + '.initialize:', attributes ); + HDABaseView.prototype.initialize.call( this, attributes ); - // render urlTemplates (gen. provided by GalaxyPaths) to urls - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - this.urls = this.renderUrls( attributes.urlTemplates, this.model.toJSON() ); - - // whether the body of this hda is expanded (shown) - this.expanded = attributes.expanded || false; - - // re-render the entire view on any model change - this.model.bind( 'change', this.render, this ); - //this.bind( 'all', function( event ){ - // this.log( event ); - //}, this ); - }, - - // urlTemplates is a map (or nested map) of underscore templates (currently, anyhoo) - // use the templates to create the apropo urls for each action this ds could use - renderUrls : function( urlTemplates, modelJson ){ - var hdaView = this, - urls = {}; - _.each( urlTemplates, function( urlTemplateOrObj, urlKey ){ - // object == nested templates: recurse - if( _.isObject( urlTemplateOrObj ) ){ - urls[ urlKey ] = hdaView.renderUrls( urlTemplateOrObj, modelJson ); - - // string == template: - } else { - // meta_down load is a special case (see renderMetaDownloadUrls) - //TODO: should be a better (gen.) way to handle this case - if( urlKey === 'meta_download' ){ - urls[ urlKey ] = hdaView.renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); - } else { - urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); - } - } - }); - return urls; + // which buttons go in most states (ok/failed meta are more complicated) + // HDAEdit gets the rerun button on almost all states + this.defaultPrimaryActionButtonRenderers = [ + this._render_showParamsButton, + this._render_rerunButton + ]; }, - // there can be more than one meta_file to download, so return a list of url and file_type for each - renderMetaDownloadUrls : function( urlTemplate, modelJson ){ - return _.map( modelJson.meta_files, function( meta_file ){ - return { - url : _.template( urlTemplate, { id: modelJson.id, file_type: meta_file.file_type }), - file_type : meta_file.file_type - }; - }); - }, - - // ................................................................................ RENDER MAIN - // events: rendered, rendered:ready, rendered:initial, rendered:ready:initial - render : function(){ - var view = this, - id = this.model.get( 'id' ), - state = this.model.get( 'state' ), - itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), - initialRender = ( this.$el.children().size() === 0 ); - - //console.debug( this + '.render, initial?:', initialRender ); - - this._clearReferences(); - this.$el.attr( 'id', 'historyItemContainer-' + id ); - - itemWrapper - .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) - .addClass( 'historyItem-' + state ); - - itemWrapper.append( this._render_warnings() ); - itemWrapper.append( this._render_titleBar() ); - this.body = $( this._render_body() ); - itemWrapper.append( this.body ); - - //TODO: move to own function: setUpBehaviours - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - - // transition... - this.$el.fadeOut( 'fast', function(){ - view.$el.children().remove(); - view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ - view.log( view + ' rendered:', view.$el ); - - var renderedEventName = 'rendered'; - if( initialRender ){ - renderedEventName += ':initial'; - } else if( view.model.inReadyState() ){ - renderedEventName += ':ready'; - } - view.trigger( renderedEventName ); - }); - }); - return this; - }, - - //NOTE: button renderers have the side effect of caching their IconButtonViews to this view - // clear out cached sub-views, dom refs, etc. from prev. render - _clearReferences : function(){ - //??TODO: we should reset these in the button logic checks (i.e. if not needed this.button = null; return null) - //?? do we really need these - not so far - //TODO: at least move these to a map - this.displayButton = null; - this.editButton = null; - this.deleteButton = null; - this.errButton = null; - this.showParamsButton = null; - this.rerunButton = null; - this.visualizationsButton = null; - this.tagButton = null; - this.annotateButton = null; - }, - // ................................................................................ RENDER WARNINGS // hda warnings including: is deleted, is purged, is hidden (including links to further actions (undelete, etc.)) _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' - return $( jQuery.trim( HDAView.templates.messages( + return $( jQuery.trim( HDABaseView.templates.messages( _.extend( this.model.toJSON(), { urls: this.urls } ) ))); }, - // ................................................................................ RENDER TITLEBAR - // the part of an hda always shown (whether the body is expanded or not): title link, title buttons - _render_titleBar : function(){ - var titleBar = $( '<div class="historyItemTitleBar" style="overflow: hidden"></div>' ); - titleBar.append( this._render_titleButtons() ); - titleBar.append( '<span class="state-icon"></span>' ); - titleBar.append( this._render_titleLink() ); - return titleBar; - }, - // ................................................................................ display, edit attr, delete // icon-button group for the common, most easily accessed actions //NOTE: these are generally displayed for almost every hda state (tho poss. disabled) @@ -163,46 +40,16 @@ return buttonDiv; }, - // icon-button to display this hda in the galaxy main iframe - _render_displayButton : function(){ - // don't show display if not in ready state, error'd, or not accessible - if( ( !this.model.inReadyState() ) + // icon-button to edit the attributes (format, permissions, etc.) this hda + _render_editButton : function(){ + // don't show edit while uploading + //TODO??: error? + //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ - return null; - } - - var displayBtnData = { - icon_class : 'display' - }; - - // show a disabled display if the data's been purged - if( this.model.get( 'purged' ) ){ - displayBtnData.enabled = false; - displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); - - } else { - displayBtnData.title = _l( 'Display data in browser' ); - displayBtnData.href = this.urls.display; - } - - if( this.model.get( 'for_editing' ) ){ - displayBtnData.target = 'galaxy_main'; - } - - this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); - return this.displayButton.render().$el; - }, - - // icon-button to edit the attributes (format, permissions, etc.) this hda - _render_editButton : function(){ - // don't show edit while uploading, or if editable - if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( !this.model.get( 'accessible' ) ) - || ( !this.model.get( 'for_editing' ) ) ){ + this.editButton = null; return null; } @@ -216,7 +63,6 @@ }; // disable if purged or deleted and explain why in the tooltip - //TODO: if for_editing if( deleted || purged ){ editBtnData.enabled = false; if( purged ){ @@ -233,9 +79,10 @@ // icon-button to delete this hda _render_deleteButton : function(){ // don't show delete if... - if( ( !this.model.get( 'for_editing' ) ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) + //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) + if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ + this.deleteButton = null; return null; } @@ -255,14 +102,6 @@ this.deleteButton = new IconButtonView({ model : new IconButton( deleteBtnData ) }); return this.deleteButton.render().$el; }, - - // ................................................................................ titleLink - // render the hid and hda.name as a link (that will expand the body) - _render_titleLink : function(){ - return $( jQuery.trim( HDAView.templates.titleLink( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ))); - }, // ................................................................................ RENDER BODY // render the data/metadata summary (format, size, misc info, etc.) @@ -271,40 +110,19 @@ // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' if( this.model.get( 'metadata_dbkey' ) === '?' && !this.model.isDeletedOrPurged() ){ + //TODO: use HDABaseView and select/replace base on this switch _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return HDAView.templates.hdaSummary( modelData ); + return HDABaseView.templates.hdaSummary( modelData ); }, // ................................................................................ primary actions - // render the icon-buttons gen. placed underneath the hda summary - _render_primaryActionButtons : function( buttonRenderingFuncs ){ - var primaryActionButtons = $( '<div/>' ).attr( 'id', 'primary-actions-' + this.model.get( 'id' ) ), - view = this; - _.each( buttonRenderingFuncs, function( fn ){ - primaryActionButtons.append( fn.call( view ) ); - }); - return primaryActionButtons; - }, - - // icon-button/popupmenu to down the data (and/or the associated meta files (bai, etc.)) for this hda - _render_downloadButton : function(){ - // don't show anything if the data's been purged - if( this.model.get( 'purged' ) ){ return null; } - - // return either: a single download icon-button (if there are no meta files) - // or a popupmenu with links to download assoc. meta files (if there are meta files) - var downloadLinkHTML = HDAView.templates.downloadLinks( - _.extend( this.model.toJSON(), { urls: this.urls } ) - ); - //this.log( this + '_render_downloadButton, downloadLinkHTML:', downloadLinkHTML ); - return $( downloadLinkHTML ); - }, - // icon-button to show the input and output (stdout/err) for the job that created this hda - _render_errButton : function(){ - if( ( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ) - || ( !this.model.get( 'for_editing' ) ) ){ return null; } + _render_errButton : function(){ + if( this.model.get( 'state' ) !== HistoryDatasetAssociation.STATES.ERROR ){ + this.errButton = null; + return null; + } this.errButton = new IconButtonView({ model : new IconButton({ title : _l( 'View or report this error' ), @@ -315,21 +133,8 @@ return this.errButton.render().$el; }, - // icon-button to show the input and output (stdout/err) for the job that created this hda - _render_showParamsButton : function(){ - // gen. safe to show in all cases - this.showParamsButton = new IconButtonView({ model : new IconButton({ - title : _l( 'View details' ), - href : this.urls.show_params, - target : 'galaxy_main', - icon_class : 'information' - }) }); - return this.showParamsButton.render().$el; - }, - // icon-button to re run the job that created this hda _render_rerunButton : function(){ - if( !this.model.get( 'for_editing' ) ){ return null; } this.rerunButton = new IconButtonView({ model : new IconButton({ title : _l( 'Run this job again' ), href : this.urls.rerun, @@ -352,10 +157,10 @@ }; if( !( this.model.hasData() ) - || !( this.model.get( 'for_editing' ) ) || !( visualizations && visualizations.length ) || !( visualization_url ) ){ //console.warn( 'NOT rendering visualization icon' ) + this.visualizationsButton = null; return null; } @@ -422,9 +227,12 @@ // icon-button to load and display tagging html //TODO: these should be a sub-MV _render_tagButton : function(){ + //TODO: check for User if( !( this.model.hasData() ) - || !( this.model.get( 'for_editing' ) ) - || ( !this.urls.tags.get ) ){ return null; } + || ( !this.urls.tags.get ) ){ + this.tagButton = null; + return null; + } this.tagButton = new IconButtonView({ model : new IconButton({ title : _l( 'Edit dataset tags' ), @@ -438,9 +246,12 @@ // icon-button to load and display annotation html //TODO: these should be a sub-MV _render_annotateButton : function(){ + //TODO: check for User if( !( this.model.hasData() ) - || !( this.model.get( 'for_editing' ) ) - || ( !this.urls.annotation.get ) ){ return null; } + || ( !this.urls.annotation.get ) ){ + this.annotateButton = null; + return null; + } this.annotateButton = new IconButtonView({ model : new IconButton({ title : _l( 'Edit dataset annotation' ), @@ -451,130 +262,34 @@ }, // ................................................................................ other elements - // render links to external genome display applications (igb, gbrowse, etc.) - //TODO: not a fan of the style on these - _render_displayApps : function(){ - if( !this.model.hasData() ){ return null; } - - var displayAppsDiv = $( '<div/>' ).addClass( 'display-apps' ); - if( !_.isEmpty( this.model.get( 'display_types' ) ) ){ - //this.log( this + 'display_types:', this.model.get( 'urls' ).display_types ); - //TODO:?? does this ever get used? - displayAppsDiv.append( - HDAView.templates.displayApps({ displayApps : this.model.get( 'display_types' ) }) - ); - } - if( !_.isEmpty( this.model.get( 'display_apps' ) ) ){ - //this.log( this + 'display_apps:', this.model.get( 'urls' ).display_apps ); - displayAppsDiv.append( - HDAView.templates.displayApps({ displayApps : this.model.get( 'display_apps' ) }) - ); - } - return displayAppsDiv; - }, - //TODO: into sub-MV + //TODO: check for User // render the area used to load tag display _render_tagArea : function(){ if( !this.urls.tags.set ){ return null; } //TODO: move to mvc/tags.js - return $( HDAView.templates.tagArea( + return $( HDAEditView.templates.tagArea( _.extend( this.model.toJSON(), { urls: this.urls } ) )); }, //TODO: into sub-MV + //TODO: check for User // render the area used to load annotation display _render_annotationArea : function(){ if( !this.urls.annotation.get ){ return null; } //TODO: move to mvc/annotations.js - return $( HDAView.templates.annotationArea( + return $( HDAEditView.templates.annotationArea( _.extend( this.model.toJSON(), { urls: this.urls } ) )); }, - - // render the data peek - //TODO: curr. pre-formatted into table on the server side - may not be ideal/flexible - _render_peek : function(){ - if( !this.model.get( 'peek' ) ){ return null; } - return $( '<div/>' ).append( - $( '<pre/>' ) - .attr( 'id', 'peek' + this.model.get( 'id' ) ) - .addClass( 'peek' ) - .append( this.model.get( 'peek' ) ) - ); - }, // ................................................................................ state body renderers - // _render_body fns for the various states - //TODO: only render these on expansion (or already expanded) - _render_body_not_viewable : function( parent ){ - //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right - parent.append( $( '<div>' + _l( 'You do not have permission to view dataset' ) + '.</div>' ) ); - }, - - _render_body_uploading : function( parent ){ - parent.append( $( '<div>' + _l( 'Dataset is uploading' ) + '</div>' ) ); - }, - - _render_body_queued : function( parent ){ - parent.append( $( '<div>' + _l( 'Job is waiting to run' ) + '.</div>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_running : function( parent ){ - parent.append( '<div>' + _l( 'Job is currently running' ) + '.</div>' ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - _render_body_error : function( parent ){ - if( !this.model.get( 'purged' ) ){ - parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); - } - parent.append( ( _l( 'An error occurred running this job' ) + ': ' - + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_downloadButton, - this._render_errButton, - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_discarded : function( parent ){ - parent.append( '<div>' + _l( 'The job creating this dataset was cancelled before completion' ) + '.</div>' ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_setting_metadata : function( parent ){ - parent.append( $( '<div>' + _l( 'Metadata is being auto-detected' ) + '.</div>' ) ); - }, - - _render_body_empty : function( parent ){ - //TODO: replace i with dataset-misc-info class - //?? why are we showing the file size when we know it's zero?? - parent.append( $( '<div>' + _l( 'No data' ) + ': <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); - parent.append( this._render_primaryActionButtons([ - this._render_showParamsButton, - this._render_rerunButton - ])); - }, - - _render_body_failed_metadata : function( parent ){ - //TODO: the css for this box is broken (unlike the others) - // add a message box about the failure at the top of the body... - parent.append( $( HDAView.templates.failedMetadata( this.model.toJSON() ) ) ); - //...then render the remaining body as STATES.OK (only diff between these states is the box above) - this._render_body_ok( parent ); + // overridden to prepend error report button to primary actions strip + HDABaseView.prototype._render_body_error.call( this, parent ); + var primaryActions = parent.find( '#primary-actions-' + this.model.get( 'id' ) ); + primaryActions.prepend( this._render_errButton() ); }, _render_body_ok : function( parent ){ @@ -595,7 +310,6 @@ //NOTE: change the order here parent.append( this._render_primaryActionButtons([ this._render_downloadButton, - this._render_errButton, this._render_showParamsButton, this._render_rerunButton, this._render_visualizationsButton @@ -611,70 +325,6 @@ parent.append( this._render_displayApps() ); parent.append( this._render_peek() ); - - //TODO??: still needed? - //// If Mozilla, hide scrollbars in hidden items since they cause animation bugs - //if ( $.browser.mozilla ) { - // $( "div.historyItemBody" ).each( function() { - // if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } - // }); - //} - }, - - _render_body : function(){ - //this.log( this + '_render_body' ); - //this.log( 'state:', state, 'for_editing', for_editing ); - - //TODO: incorrect id (encoded - use hid?) - var body = $( '<div/>' ) - .attr( 'id', 'info-' + this.model.get( 'id' ) ) - .addClass( 'historyItemBody' ) - .attr( 'style', 'display: block' ); - - //TODO: not a fan of this dispatch - switch( this.model.get( 'state' ) ){ - case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : - this._render_body_not_viewable( body ); - break; - case HistoryDatasetAssociation.STATES.UPLOAD : - this._render_body_uploading( body ); - break; - case HistoryDatasetAssociation.STATES.QUEUED : - this._render_body_queued( body ); - break; - case HistoryDatasetAssociation.STATES.RUNNING : - this._render_body_running( body ); - break; - case HistoryDatasetAssociation.STATES.ERROR : - this._render_body_error( body ); - break; - case HistoryDatasetAssociation.STATES.DISCARDED : - this._render_body_discarded( body ); - break; - case HistoryDatasetAssociation.STATES.SETTING_METADATA : - this._render_body_setting_metadata( body ); - break; - case HistoryDatasetAssociation.STATES.EMPTY : - this._render_body_empty( body ); - break; - case HistoryDatasetAssociation.STATES.FAILED_METADATA : - this._render_body_failed_metadata( body ); - break; - case HistoryDatasetAssociation.STATES.OK : - this._render_body_ok( body ); - break; - default: - //??: no body? - body.append( $( '<div>Error: unknown dataset state "' + state + '".</div>' ) ); - } - body.append( '<div style="clear: both"></div>' ); - - if( this.expanded ){ - body.show(); - } else { - body.hide(); - } - return body; }, // ................................................................................ EVENTS @@ -761,25 +411,6 @@ return false; }, - // expand/collapse body - // event: body-visible, body-hidden - toggleBodyVisibility : function( event, expanded ){ - var hdaView = this, - $body = this.$el.find( '.historyItemBody' ); - expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); - //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); - - if( expanded ){ - $body.slideDown( 'fast', function(){ - hdaView.trigger( 'body-visible', hdaView.model.get( 'id' ) ); - }); - } else { - $body.slideUp( 'fast', function(){ - hdaView.trigger( 'body-hidden', hdaView.model.get( 'id' ) ); - }); - } - }, - // ................................................................................ UTILTIY toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); @@ -788,17 +419,9 @@ }); //------------------------------------------------------------------------------ -HDAView.templates = { - warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], - - messages : Handlebars.templates[ 'template-history-warning-messages' ], - titleLink : Handlebars.templates[ 'template-history-titleLink' ], - hdaSummary : Handlebars.templates[ 'template-history-hdaSummary' ], - downloadLinks : Handlebars.templates[ 'template-history-downloadLinks' ], - failedMetadata : Handlebars.templates[ 'template-history-failedMetaData' ], - tagArea : Handlebars.templates[ 'template-history-tagArea' ], - annotationArea : Handlebars.templates[ 'template-history-annotationArea' ], - displayApps : Handlebars.templates[ 'template-history-displayApps' ] +HDAEditView.templates = { + tagArea : Handlebars.templates[ 'template-hda-tagArea' ], + annotationArea : Handlebars.templates[ 'template-hda-annotationArea' ] }; //============================================================================== diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -43,10 +43,7 @@ // aka. !hidden visible : false, // based on trans.user (is_admin or security_agent.can_access_dataset( <user_roles>, hda.dataset )) - accessible : false, - - //TODO: this needs to be removed (it is a function of the view type (e.g. HDAForEditingView)) - for_editing : true + accessible : false }, // fetch location of this history in the api diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -5,26 +5,26 @@ Backbone.js implementation of history panel TODO: + refactoring on for_editing: + uhoh: purge link in warning message in history_common.mako conditional on trans.app.config.allow_user_dataset_purge + bug: rerun still doesn't take encoded ids + anon user, mako template init: - bug: rename url seems to be wrong url BUG: shouldn't have tag/anno buttons (on hdas) Check for user in hdaView somehow logged in, mako template: - BUG: quotaMsg not showing when 100% (on load) bug: rename not being changed locally - render() shows old name, refresh: new name + TODO: editable text to MV, might also just use REST.update on history BUG: meter is not updating RELIABLY on change:nice_size BUG: am able to start upload even if over quota - 'runs' forever bug: quotaMeter bar rendering square in chrome - BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history - (entire history is inaccessible) - ??: still happening? from loadFromApi: + + fixed: BUG: not loading deleted datasets FIXED: history_contents, show: state_ids returns all ids now (incl. deleted) - - fixed: BUG: upload, history size, doesn't change FIXED: using change:nice_size to trigger re-render of history size BUG: delete uploading hda - now in state 'discarded'! ...new state to handle @@ -112,6 +112,8 @@ // direct attachment to existing element el : 'body.historyPage', + //HDAView : HDABaseView, + HDAView : HDAEditView, // init with the model, urlTemplates, set up storage, bind HDACollection events //NOTE: this will create or load PersistantStorage keyed under 'HistoryView.<id>' @@ -122,9 +124,9 @@ // set up url templates //TODO: prob. better to put this in class scope (as the handlebars templates), but... // they're added to GalaxyPaths on page load (after this file is loaded) - if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - if( !attributes.urlTemplates.history ){ throw( 'HDAView needs urlTemplates.history on initialize' ); } - if( !attributes.urlTemplates.hda ){ throw( 'HDAView needs urlTemplates.hda on initialize' ); } + if( !attributes.urlTemplates ){ throw( this + ' needs urlTemplates on initialize' ); } + if( !attributes.urlTemplates.history ){ throw( this + ' needs urlTemplates.history on initialize' ); } + if( !attributes.urlTemplates.hda ){ throw( this + ' needs urlTemplates.hda on initialize' ); } this.urlTemplates = attributes.urlTemplates.history; this.hdaUrlTemplates = attributes.urlTemplates.hda; @@ -283,7 +285,7 @@ var hdaId = hda.get( 'id' ), expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); - historyView.hdaViews[ hdaId ] = new HDAView({ + historyView.hdaViews[ hdaId ] = new historyView.HDAView({ model : hda, expanded : expanded, urlTemplates : historyView.hdaUrlTemplates @@ -301,12 +303,11 @@ setUpHdaListeners : function( hdaView ){ var historyView = this; // use storage to maintain a list of hdas whose bodies are expanded - hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ - if( visible ){ - historyView.storage.get( 'expandedHdas' ).set( id, true ); - } else { - historyView.storage.get( 'expandedHdas' ).deleteKey( id ); - } + hdaView.bind( 'body-visible', function( id ){ + historyView.storage.get( 'expandedHdas' ).set( id, true ); + }); + hdaView.bind( 'body-hidden', function( id ){ + historyView.storage.get( 'expandedHdas' ).deleteKey( id ); }); }, diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/mvc/dataset/hda-base.js --- /dev/null +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -0,0 +1,1 @@ +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-visible",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-hidden",b.model.get("id"))})}},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetaData"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this._clearReferences();this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-visible",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-hidden",b.model.get("id"))})}},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df 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 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false,for_editing:true},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",OK:"ok",EMPTY:"empty",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",OK:"ok",EMPTY:"empty",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}}); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("body-visible",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-hidden",function(c){a.storage.get("expandedHdas").deleteKey(c)})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-annotationArea.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-annotationArea.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-annotationArea"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this,o=f.blockHelperMissing;function e(r,q){return"Annotation"}function c(r,q){return"Edit dataset annotation"}j+='\n<div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}if(d||d===0){j+=d}j+=':</strong>\n <div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-anotation-elt" class="annotation-elt tooltip editable-text"\n style="margin: 1px 0px 1px 0px" title="';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}if(d||d===0){j+=d}j+='">\n </div>\n</div>';return j})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-displayApps.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-displayApps.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-displayApps"]=b(function(h,m,g,l,k){g=g||h.helpers;var d,i="function",j=this.escapeExpression,o=this,n=g.blockHelperMissing;function f(t,s){var q="",r,p;q+="\n ";p=g.label;if(p){r=p.call(t,{hash:{}})}else{r=t.label;r=typeof r===i?r():r}q+=j(r)+"\n ";r=t.links;r=g.each.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,e,s)});if(r||r===0){q+=r}q+="\n <br />\n";return q}function e(t,s){var q="",r,p;q+='\n <a target="';p=g.target;if(p){r=p.call(t,{hash:{}})}else{r=t.target;r=typeof r===i?r():r}q+=j(r)+'" href="';p=g.href;if(p){r=p.call(t,{hash:{}})}else{r=t.href;r=typeof r===i?r():r}q+=j(r)+'">';p=g.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}else{r=t.local;r=typeof r===i?r():r}if(!g.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}if(r||r===0){q+=r}q+="</a>\n ";return q}function c(s,r){var q,p;p=g.text;if(p){q=p.call(s,{hash:{}})}else{q=s.text;q=typeof q===i?q():q}return j(q)}d=m.displayApps;d=g.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(1,f,k)});if(d||d===0){return d}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-downloadLinks.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-downloadLinks.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-downloadLinks"]=b(function(g,q,p,k,t){p=p||g.helpers;var h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(y,x){var v="",w,u;v+="\n";v+='\n<div popupmenu="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a class="action-button" href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}if(w||w===0){v+=w}v+="</a>\n <a>";u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}if(w||w===0){v+=w}v+="</a>\n ";w=y.urls;w=w==null||w===false?w:w.meta_download;w=p.each.call(y,w,{hash:{},inverse:o.noop,fn:o.program(6,j,x)});if(w||w===0){v+=w}v+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n</div>\n';return v}function m(v,u){return"Download Dataset"}function l(v,u){return"Additional Files"}function j(y,x){var v="",w,u;v+='\n <a class="action-button" href="';u=p.url;if(u){w=u.call(y,{hash:{}})}else{w=y.url;w=typeof w===e?w():w}v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}if(w||w===0){v+=w}v+=" ";u=p.file_type;if(u){w=u.call(y,{hash:{}})}else{w=y.file_type;w=typeof w===e?w():w}v+=d(w)+"</a>\n ";return v}function i(v,u){return"Download"}function f(v,u){return"Download"}function s(y,x){var v="",w,u;v+="\n";v+='\n<a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n';return v}function r(v,u){return"Download"}h=q.urls;h=h==null||h===false?h:h.meta_download;h=p["if"].call(q,h,{hash:{},inverse:o.program(11,s,t),fn:o.program(1,n,t)});if(h||h===0){return h}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-failedMetaData.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-failedMetaData.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-failedMetaData"]=b(function(g,m,f,l,k){f=f||g.helpers;var c,i,o=this,h="function",n=f.blockHelperMissing,j=this.escapeExpression;function e(t,s){var q="",r,p;q+="\n";p=f.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}else{r=t.local;r=typeof r===h?r():r}if(!f.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}if(r||r===0){q+=r}q+='\nYou may be able to <a href="';r=t.urls;r=r==null||r===false?r:r.edit;r=typeof r===h?r():r;q+=j(r)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return q}function d(q,p){return"An error occurred setting the metadata for this dataset."}i=f.warningmessagesmall;if(i){c=i.call(m,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}else{c=m.warningmessagesmall;c=typeof c===h?c():c}if(!f.warningmessagesmall){c=n.call(m,c,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-hdaSummary.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-hdaSummary.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a class="metadata-dbkey" href="';s=u.urls;s=s==null||s===false?s:s.edit;s=typeof s===h?s():s;r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="metadata-dbkey ';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info"> ';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+" </div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n ";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:p.program(3,c,l),fn:p.program(1,e,l)});if(d||d===0){j+=d}j+="\n</div>\n";d=n.misc_info;d=f["if"].call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-tagArea.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-tagArea.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-tagArea"]=b(function(f,l,e,k,j){e=e||f.helpers;var i="",c,h,n=this,g="function",m=e.blockHelperMissing;function d(p,o){return"Tags"}i+='\n<div class="tag-area" style="display: none;">\n <strong>';h=e.local;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.local;c=typeof c===g?c():c}if(!e.local){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){i+=c}i+=':</strong>\n <div class="tag-elt">\n </div>\n</div>';return i})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-titleLink.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-titleLink.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-titleLink"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<span class="historyItemTitle">';g=d.hid;if(g){c=g.call(l,{hash:{}})}else{c=l.hid;c=typeof c===f?c():c}h+=i(c)+": ";g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+"</span>";return h})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-hda-warning-messages.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-hda-warning-messages.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-warning-messages"]=b(function(g,s,q,k,z){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(C,B){var A;A=C.purged;A=q.unless.call(C,A,{hash:{},inverse:p.noop,fn:p.program(2,n,B)});if(A||A===0){return A}else{return""}}function n(E,D){var B="",C,A;B+="\n";A=q.warningmessagesmall;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}else{C=E.warningmessagesmall;C=typeof C===e?C():C}if(!q.warningmessagesmall){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}if(C||C===0){B+=C}B+="\n";return B}function m(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.undelete;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(6,j,D)});if(C||C===0){B+=C}B+="\n";return B}function l(B,A){return"This dataset has been deleted."}function j(E,D){var B="",C,A;B+="\n ";B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.undelete;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUndelete" id="historyItemUndeleter-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to undelete it\n ';C=E.urls;C=C==null||C===false?C:C.purge;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(7,i,D)});if(C||C===0){B+=C}B+="\n ";return B}function i(E,D){var B="",C,A;B+='\n or <a href="';C=E.urls;C=C==null||C===false?C:C.purge;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemPurge" id="historyItemPurger-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return B}function f(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}if(B||B===0){return B}else{return""}}function y(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}if(C||C===0){B+=C}B+="\n";return B}function x(B,A){return"This dataset has been deleted and removed from disk."}function w(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}if(B||B===0){return B}else{return""}}function v(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.unhide;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(17,t,D)});if(C||C===0){B+=C}B+="\n";return B}function u(B,A){return"This dataset has been hidden."}function t(E,D){var B="",C,A;B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.unhide;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUnhide" id="historyItemUnhider-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to unhide it\n ';return B}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,z)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,z)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(13,w,z)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-annotationArea.js --- a/static/scripts/packed/templates/compiled/template-history-annotationArea.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-annotationArea"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this,o=f.blockHelperMissing;function e(r,q){return"Annotation"}function c(r,q){return"Edit dataset annotation"}j+='\n<div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}if(d||d===0){j+=d}j+=':</strong>\n <div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-anotation-elt" class="annotation-elt tooltip editable-text"\n style="margin: 1px 0px 1px 0px" title="';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}if(d||d===0){j+=d}j+='">\n </div>\n</div>';return j})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-displayApps.js --- a/static/scripts/packed/templates/compiled/template-history-displayApps.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-displayApps"]=b(function(h,m,g,l,k){g=g||h.helpers;var d,i="function",j=this.escapeExpression,o=this,n=g.blockHelperMissing;function f(t,s){var q="",r,p;q+="\n ";p=g.label;if(p){r=p.call(t,{hash:{}})}else{r=t.label;r=typeof r===i?r():r}q+=j(r)+"\n ";r=t.links;r=g.each.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,e,s)});if(r||r===0){q+=r}q+="\n <br />\n";return q}function e(t,s){var q="",r,p;q+='\n <a target="';p=g.target;if(p){r=p.call(t,{hash:{}})}else{r=t.target;r=typeof r===i?r():r}q+=j(r)+'" href="';p=g.href;if(p){r=p.call(t,{hash:{}})}else{r=t.href;r=typeof r===i?r():r}q+=j(r)+'">';p=g.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}else{r=t.local;r=typeof r===i?r():r}if(!g.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}if(r||r===0){q+=r}q+="</a>\n ";return q}function c(s,r){var q,p;p=g.text;if(p){q=p.call(s,{hash:{}})}else{q=s.text;q=typeof q===i?q():q}return j(q)}d=m.displayApps;d=g.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(1,f,k)});if(d||d===0){return d}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,q,p,k,t){p=p||g.helpers;var h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(y,x){var v="",w,u;v+="\n";v+='\n<div popupmenu="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a class="action-button" href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}if(w||w===0){v+=w}v+="</a>\n <a>";u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}if(w||w===0){v+=w}v+="</a>\n ";w=y.urls;w=w==null||w===false?w:w.meta_download;w=p.each.call(y,w,{hash:{},inverse:o.noop,fn:o.program(6,j,x)});if(w||w===0){v+=w}v+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n</div>\n';return v}function m(v,u){return"Download Dataset"}function l(v,u){return"Additional Files"}function j(y,x){var v="",w,u;v+='\n <a class="action-button" href="';u=p.url;if(u){w=u.call(y,{hash:{}})}else{w=y.url;w=typeof w===e?w():w}v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}if(w||w===0){v+=w}v+=" ";u=p.file_type;if(u){w=u.call(y,{hash:{}})}else{w=y.file_type;w=typeof w===e?w():w}v+=d(w)+"</a>\n ";return v}function i(v,u){return"Download"}function f(v,u){return"Download"}function s(y,x){var v="",w,u;v+="\n";v+='\n<a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n';return v}function r(v,u){return"Download"}h=q.urls;h=h==null||h===false?h:h.meta_download;h=p["if"].call(q,h,{hash:{},inverse:o.program(11,s,t),fn:o.program(1,n,t)});if(h||h===0){return h}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/packed/templates/compiled/template-history-failedMetaData.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(g,m,f,l,k){f=f||g.helpers;var c,i,o=this,h="function",n=f.blockHelperMissing,j=this.escapeExpression;function e(t,s){var q="",r,p;q+="\n";p=f.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}else{r=t.local;r=typeof r===h?r():r}if(!f.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}if(r||r===0){q+=r}q+='\nYou may be able to <a href="';r=t.urls;r=r==null||r===false?r:r.edit;r=typeof r===h?r():r;q+=j(r)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return q}function d(q,p){return"An error occurred setting the metadata for this dataset."}i=f.warningmessagesmall;if(i){c=i.call(m,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}else{c=m.warningmessagesmall;c=typeof c===h?c():c}if(!f.warningmessagesmall){c=n.call(m,c,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/packed/templates/compiled/template-history-hdaSummary.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <a href="';s=u.urls;s=s==null||s===false?s:s.edit;s=typeof s===h?s():s;r+=k(s)+'" target="galaxy_main">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</a>\n ";return r}function c(u,t){var r="",s,q;r+='\n <span class="';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+'">';q=f.metadata_dbkey;if(q){s=q.call(u,{hash:{}})}else{s=u.metadata_dbkey;s=typeof s===h?s():s}r+=k(s)+"</span>\n ";return r}function o(u,t){var r="",s,q;r+='\n<div class="hda-info">';q=f.misc_info;if(q){s=q.call(u,{hash:{}})}else{s=u.misc_info;s=typeof s===h?s():s}r+=k(s)+"</div>\n";return r}j+='<div class="hda-summary">\n ';i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\n format: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\n database:\n 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c===g?c():c}if(!e.local){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){i+=c}i+=':</strong>\n <div class="tag-elt">\n </div>\n</div>';return i})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-titleLink.js --- a/static/scripts/packed/templates/compiled/template-history-titleLink.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-titleLink"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<a href="javascript:void(0);"><span class="historyItemTitle">';g=d.hid;if(g){c=g.call(l,{hash:{}})}else{c=l.hid;c=typeof c===f?c():c}h+=i(c)+": ";g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+"</span></a>";return h})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/packed/templates/compiled/template-history-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-history-warning-messages.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,z){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(C,B){var A;A=C.purged;A=q.unless.call(C,A,{hash:{},inverse:p.noop,fn:p.program(2,n,B)});if(A||A===0){return A}else{return""}}function n(E,D){var B="",C,A;B+="\n";A=q.warningmessagesmall;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}else{C=E.warningmessagesmall;C=typeof C===e?C():C}if(!q.warningmessagesmall){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}if(C||C===0){B+=C}B+="\n";return B}function m(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.undelete;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(6,j,D)});if(C||C===0){B+=C}B+="\n";return B}function l(B,A){return"This dataset has been deleted."}function j(E,D){var B="",C,A;B+="\n ";B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.undelete;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUndelete" id="historyItemUndeleter-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to undelete it\n ';C=E.urls;C=C==null||C===false?C:C.purge;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(7,i,D)});if(C||C===0){B+=C}B+="\n ";return B}function i(E,D){var B="",C,A;B+='\n or <a href="';C=E.urls;C=C==null||C===false?C:C.purge;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemPurge" id="historyItemPurger-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return B}function f(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}if(B||B===0){return B}else{return""}}function y(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}if(C||C===0){B+=C}B+="\n";return B}function x(B,A){return"This dataset has been deleted and removed from disk."}function w(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}if(B||B===0){return B}else{return""}}function v(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.unhide;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(17,t,D)});if(C||C===0){B+=C}B+="\n";return B}function u(B,A){return"This dataset has been hidden."}function t(E,D){var B="",C,A;B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.unhide;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUnhide" id="historyItemUnhider-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to unhide it\n ';return B}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,z)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,z)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(13,w,z)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compile_templates.py --- a/static/scripts/templates/compile_templates.py +++ b/static/scripts/templates/compile_templates.py @@ -210,9 +210,11 @@ # delete multi template intermediate files print "\nCleaning up intermediate multi-template template files:" for filename in multi_template_template_filenames: - print 'removing', filename - os.remove( filename ) - + try: + print 'removing', filename + os.remove( filename ) + except Exception, exc: + print exc # ------------------------------------------------------------------------------ if __name__ == '__main__': diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-annotationArea.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-annotationArea.js @@ -0,0 +1,39 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-annotationArea'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + + return "Annotation";} + +function program3(depth0,data) { + + + return "Edit dataset annotation";} + + buffer += "\n<div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-annotation-area\" class=\"annotation-area\" style=\"display: none;\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-anotation-elt\" class=\"annotation-elt tooltip editable-text\"\n style=\"margin: 1px 0px 1px 0px\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">\n </div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-displayApps.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-displayApps.js @@ -0,0 +1,51 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-displayApps'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.label; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n "; + stack1 = depth0.links; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n <br />\n"; + return buffer;} +function program2(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <a target=\""; + foundHelper = helpers.target; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" href=\""; + foundHelper = helpers.href; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n "; + return buffer;} +function program3(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.text; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + return escapeExpression(stack1);} + + stack1 = depth0.displayApps; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-downloadLinks.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-downloadLinks.js @@ -0,0 +1,117 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-downloadLinks'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + buffer += "\n<div popupmenu=\"dataset-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-popup\">\n <a class=\"action-button\" href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n <a>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n<div style=\"float:left;\" class=\"menubutton split popup\" id=\"dataset-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-popup\">\n <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; + return buffer;} +function program2(depth0,data) { + + + return "Download Dataset";} + +function program4(depth0,data) { + + + return "Additional Files";} + +function program6(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <a class=\"action-button\" href=\""; + foundHelper = helpers.url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " "; + foundHelper = helpers.file_type; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</a>\n "; + return buffer;} +function program7(depth0,data) { + + + return "Download";} + +function program9(depth0,data) { + + + return "Download";} + +function program11(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + buffer += "\n<a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button disk tooltip\"></a>\n"; + return buffer;} +function program12(depth0,data) { + + + return "Download";} + + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(11, program11, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-failedMetaData.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-failedMetaData.js @@ -0,0 +1,33 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-failedMetaData'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\nYou may be able to <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">set it manually or retry auto-detection</a>.\n"; + return buffer;} +function program2(depth0,data) { + + + return "An error occurred setting the metadata for this dataset.";} + + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-hdaSummary.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-hdaSummary.js @@ -0,0 +1,66 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <a class=\"metadata-dbkey\" href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">"; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</a>\n "; + return buffer;} + +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <span class=\"metadata-dbkey "; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>\n "; + return buffer;} + +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n<div class=\"hda-info\"> "; + foundHelper = helpers.misc_info; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + " </div>\n"; + return buffer;} + + buffer += "<div class=\"hda-summary\">\n "; + foundHelper = helpers.misc_blurb; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "<br />\n format: <span class=\""; + foundHelper = helpers.data_type; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.data_type; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>,\n database:\n "; + stack1 = depth0.dbkey_unknown_and_editable; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</div>\n"; + stack1 = depth0.misc_info; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-tagArea.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-tagArea.js @@ -0,0 +1,20 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-tagArea'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + + return "Tags";} + + buffer += "\n<div class=\"tag-area\" style=\"display: none;\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div class=\"tag-elt\">\n </div>\n</div>"; + return buffer;}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-titleLink.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-titleLink.js @@ -0,0 +1,18 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-titleLink'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + buffer += "<span class=\"historyItemTitle\">"; + foundHelper = helpers.hid; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + ": "; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>"; + return buffer;}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-hda-warning-messages.js --- /dev/null +++ b/static/scripts/templates/compiled/template-hda-warning-messages.js @@ -0,0 +1,160 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-hda-warning-messages'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + +function program1(depth0,data) { + + var stack1; + stack1 = depth0.purged; + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program2(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program4(depth0,data) { + + + return "This dataset has been deleted.";} + +function program6(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + buffer += "\n Click <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer;} +function program7(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n or <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; + return buffer;} + +function program9(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program10(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program11(depth0,data) { + + + return "This dataset has been deleted and removed from disk.";} + +function program13(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program14(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program15(depth0,data) { + + + return "This dataset has been hidden.";} + +function program17(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n Click <a href=\""; + stack1 = depth0.urls; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; + stack1 = typeof stack1 === functionType ? stack1() : stack1; + buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to unhide it\n "; + return buffer;} + + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.purged; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n\n"; + stack1 = depth0.visible; + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-annotationArea.js --- a/static/scripts/templates/compiled/template-history-annotationArea.js +++ /dev/null @@ -1,39 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-annotationArea'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - - return "Annotation";} - -function program3(depth0,data) { - - - return "Edit dataset annotation";} - - buffer += "\n<div id=\""; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-annotation-area\" class=\"annotation-area\" style=\"display: none;\">\n <strong>"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div id=\""; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-anotation-elt\" class=\"annotation-elt tooltip editable-text\"\n style=\"margin: 1px 0px 1px 0px\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\">\n </div>\n</div>"; - return buffer;}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-displayApps.js --- a/static/scripts/templates/compiled/template-history-displayApps.js +++ /dev/null @@ -1,51 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-displayApps'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.label; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\n "; - stack1 = depth0.links; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n <br />\n"; - return buffer;} -function program2(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <a target=\""; - foundHelper = helpers.target; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" href=\""; - foundHelper = helpers.href; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - return buffer;} -function program3(depth0,data) { - - var stack1, foundHelper; - foundHelper = helpers.text; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - return escapeExpression(stack1);} - - stack1 = depth0.displayApps; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ /dev/null @@ -1,117 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-downloadLinks'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n"; - buffer += "\n<div popupmenu=\"dataset-"; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-popup\">\n <a class=\"action-button\" href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n <a>"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n<div style=\"float:left;\" class=\"menubutton split popup\" id=\"dataset-"; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-popup\">\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; - return buffer;} -function program2(depth0,data) { - - - return "Download Dataset";} - -function program4(depth0,data) { - - - return "Additional Files";} - -function program6(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <a class=\"action-button\" href=\""; - foundHelper = helpers.url; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += " "; - foundHelper = helpers.file_type; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</a>\n "; - return buffer;} -function program7(depth0,data) { - - - return "Download";} - -function program9(depth0,data) { - - - return "Download";} - -function program11(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n"; - buffer += "\n<a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button disk tooltip\"></a>\n"; - return buffer;} -function program12(depth0,data) { - - - return "Download";} - - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(11, program11, data),fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/templates/compiled/template-history-failedMetaData.js +++ /dev/null @@ -1,33 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-failedMetaData'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; - -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\nYou may be able to <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">set it manually or retry auto-detection</a>.\n"; - return buffer;} -function program2(depth0,data) { - - - return "An error occurred setting the metadata for this dataset.";} - - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/templates/compiled/template-history-hdaSummary.js +++ /dev/null @@ -1,66 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; - -function program1(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">"; - foundHelper = helpers.metadata_dbkey; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</a>\n "; - return buffer;} - -function program3(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <span class=\""; - foundHelper = helpers.metadata_dbkey; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.metadata_dbkey; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</span>\n "; - return buffer;} - -function program5(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div class=\"hda-info\">"; - foundHelper = helpers.misc_info; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n"; - return buffer;} - - buffer += "<div class=\"hda-summary\">\n "; - foundHelper = helpers.misc_blurb; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "<br />\n format: <span class=\""; - foundHelper = helpers.data_type; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.data_type; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</span>,\n database:\n "; - stack1 = depth0.dbkey_unknown_and_editable; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n"; - stack1 = depth0.misc_info; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - return buffer;}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-tagArea.js --- a/static/scripts/templates/compiled/template-history-tagArea.js +++ /dev/null @@ -1,20 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-tagArea'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - - return "Tags";} - - buffer += "\n<div class=\"tag-area\" style=\"display: none;\">\n <strong>"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div class=\"tag-elt\">\n </div>\n</div>"; - return buffer;}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-titleLink.js --- a/static/scripts/templates/compiled/template-history-titleLink.js +++ /dev/null @@ -1,18 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-titleLink'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; - - - buffer += "<a href=\"javascript:void(0);\"><span class=\"historyItemTitle\">"; - foundHelper = helpers.hid; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + ": "; - foundHelper = helpers.name; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</span></a>"; - return buffer;}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/compiled/template-history-warning-messages.js --- a/static/scripts/templates/compiled/template-history-warning-messages.js +++ /dev/null @@ -1,160 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-warning-messages'] = template(function (Handlebars,depth0,helpers,partials,data) { - helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var stack1; - stack1 = depth0.purged; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program2(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n"; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program3(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program4(depth0,data) { - - - return "This dataset has been deleted.";} - -function program6(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - buffer += "\n Click <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer;} -function program7(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n or <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; - return buffer;} - -function program9(depth0,data) { - - var stack1, foundHelper; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program10(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program11(depth0,data) { - - - return "This dataset has been deleted and removed from disk.";} - -function program13(depth0,data) { - - var stack1, foundHelper; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program14(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program15(depth0,data) { - - - return "This dataset has been hidden.";} - -function program17(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n Click <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; - foundHelper = helpers.id; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to unhide it\n "; - return buffer;} - - stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - stack1 = depth0.purged; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - stack1 = depth0.visible; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - return buffer;}); -})(); \ No newline at end of file diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/hda-templates.html --- /dev/null +++ b/static/scripts/templates/hda-templates.html @@ -0,0 +1,118 @@ + +<script type="text/template" class="template-hda" id="template-hda-warning-messages"> +{{#if deleted}}{{#unless purged}} +{{#warningmessagesmall}} + {{#local}}This dataset has been deleted.{{/local}} + {{#if urls.undelete}} + {{! how in the hell would you localize this? }} + Click <a href="{{ urls.undelete }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + target="galaxy_history">here</a> to undelete it + {{#if urls.purge}} + or <a href="{{ urls.purge }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + target="galaxy_history">here</a> to immediately remove it from disk + {{/if}} + {{/if}} +{{/warningmessagesmall}} +{{/unless}}{{/if}} + +{{#if purged}}{{#warningmessagesmall}} + {{#local}}This dataset has been deleted and removed from disk.{{/local}} +{{/warningmessagesmall}}{{/if}} + +{{#unless visible}}{{#warningmessagesmall}} + {{#local}}This dataset has been hidden.{{/local}} + {{#if urls.unhide}} + Click <a href="{{ urls.unhide }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + target="galaxy_history">here</a> to unhide it + {{/if}} +{{/warningmessagesmall}}{{/unless}} +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-titleLink"> +<span class="historyItemTitle">{{ hid }}: {{ name }}</span> +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-hdaSummary"> +<div class="hda-summary"> + {{ misc_blurb }}<br /> + format: <span class="{{ data_type }}">{{ data_type }}</span>, + database: + {{#if dbkey_unknown_and_editable }} + <a class="metadata-dbkey" href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> + {{else}} + <span class="metadata-dbkey {{ metadata_dbkey }}">{{ metadata_dbkey }}</span> + {{/if}} +</div> +{{#if misc_info}} +<div class="hda-info"> {{ misc_info }} </div> +{{/if}} +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-failedMetaData"> +{{#warningmessagesmall}} +{{#local}}An error occurred setting the metadata for this dataset.{{/local}} +You may be able to <a href="{{ urls.edit }}" target="galaxy_main">set it manually or retry auto-detection</a>. +{{/warningmessagesmall}} +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-downloadLinks"> +{{#if urls.meta_download}} +{{! this will be built using a popupmenu }} +<div popupmenu="dataset-{{ id }}-popup"> + <a class="action-button" href="{{ urls.download }}">{{#local}}Download Dataset{{/local}}</a> + <a>{{#local}}Additional Files{{/local}}</a> + {{#each urls.meta_download}} + <a class="action-button" href="{{ url }}">{{#local}}Download{{/local}} {{ file_type }}</a> + {{/each}} +</div> +<div style="float:left;" class="menubutton split popup" id="dataset-{{ id }}-popup"> + <a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a> +</div> +{{else}} +{{! otherwise a simple icon button }} +<a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a> +{{/if}} +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-tagArea"> +{{! TODO: move to mvc/tag.js templates }} +<div class="tag-area" style="display: none;"> + <strong>{{#local}}Tags{{/local}}:</strong> + <div class="tag-elt"> + </div> +</div> +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-annotationArea"> +{{! TODO: move to mvc/annotations.js templates, editable-text }} +<div id="{{ id }}-annotation-area" class="annotation-area" style="display: none;"> + <strong>{{#local}}Annotation{{/local}}:</strong> + <div id="{{ id }}-anotation-elt" class="annotation-elt tooltip editable-text" + style="margin: 1px 0px 1px 0px" title="{{#local}}Edit dataset annotation{{/local}}"> + </div> +</div> +</script> + + + +<script type="text/template" class="template-hda" id="template-hda-displayApps"> +{{#each displayApps}} + {{label}} + {{#each links}} + <a target="{{target}}" href="{{href}}">{{#local}}{{text}}{{/local}}</a> + {{/each}} + <br /> +{{/each}} +</script> diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -1,115 +1,11 @@ -<script type="text/template" class="template-history" id="template-history-warning-messages"> -{{#if deleted}}{{#unless purged}} -{{#warningmessagesmall}} - {{#local}}This dataset has been deleted.{{/local}} - {{#if urls.undelete}} - {{! how in the hell would you localize this? }} - Click <a href="{{ urls.undelete }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" - target="galaxy_history">here</a> to undelete it - {{#if urls.purge}} - or <a href="{{ urls.purge }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" - target="galaxy_history">here</a> to immediately remove it from disk - {{/if}} - {{/if}} -{{/warningmessagesmall}} -{{/unless}}{{/if}} - -{{#if purged}}{{#warningmessagesmall}} - {{#local}}This dataset has been deleted and removed from disk.{{/local}} -{{/warningmessagesmall}}{{/if}} - -{{#unless visible}}{{#warningmessagesmall}} - {{#local}}This dataset has been hidden.{{/local}} - {{#if urls.unhide}} - Click <a href="{{ urls.unhide }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" - target="galaxy_history">here</a> to unhide it - {{/if}} -{{/warningmessagesmall}}{{/unless}} -</script> - -<script type="text/template" class="template-history" id="template-history-titleLink"> -<a href="javascript:void(0);"><span class="historyItemTitle">{{ hid }}: {{ name }}</span></a> -</script> - -<script type="text/template" class="template-history" id="template-history-hdaSummary"> -<div class="hda-summary"> - {{ misc_blurb }}<br /> - format: <span class="{{ data_type }}">{{ data_type }}</span>, - database: - {{#if dbkey_unknown_and_editable }} - <a href="{{ urls.edit }}" target="galaxy_main">{{ metadata_dbkey }}</a> - {{else}} - <span class="{{ metadata_dbkey }}">{{ metadata_dbkey }}</span> - {{/if}} -</div> -{{#if misc_info}} -<div class="hda-info">{{ misc_info }}</div> -{{/if}} -</script> - -<script type="text/template" class="template-history" id="template-history-failedMetaData"> -{{#warningmessagesmall}} -{{#local}}An error occurred setting the metadata for this dataset.{{/local}} -You may be able to <a href="{{ urls.edit }}" target="galaxy_main">set it manually or retry auto-detection</a>. -{{/warningmessagesmall}} -</script> - -<script type="text/template" class="template-history" id="template-history-downloadLinks"> -{{#if urls.meta_download}} -{{! this will be built using a popupmenu }} -<div popupmenu="dataset-{{ id }}-popup"> - <a class="action-button" href="{{ urls.download }}">{{#local}}Download Dataset{{/local}}</a> - <a>{{#local}}Additional Files{{/local}}</a> - {{#each urls.meta_download}} - <a class="action-button" href="{{ url }}">{{#local}}Download{{/local}} {{ file_type }}</a> - {{/each}} -</div> -<div style="float:left;" class="menubutton split popup" id="dataset-{{ id }}-popup"> - <a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a> -</div> -{{else}} -{{! otherwise a simple icon button }} -<a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a> -{{/if}} -</script> - -<script type="text/template" class="template-history" id="template-history-tagArea"> -{{! TODO: move to mvc/tag.js templates }} -<div class="tag-area" style="display: none;"> - <strong>{{#local}}Tags{{/local}}:</strong> - <div class="tag-elt"> - </div> -</div> -</script> - -<script type="text/template" class="template-history" id="template-history-annotationArea"> -{{! TODO: move to mvc/annotations.js templates, editable-text }} -<div id="{{ id }}-annotation-area" class="annotation-area" style="display: none;"> - <strong>{{#local}}Annotation{{/local}}:</strong> - <div id="{{ id }}-anotation-elt" class="annotation-elt tooltip editable-text" - style="margin: 1px 0px 1px 0px" title="{{#local}}Edit dataset annotation{{/local}}"> - </div> -</div> -</script> - -<script type="text/template" class="template-history" id="template-history-displayApps"> -{{#each displayApps}} - {{label}} - {{#each links}} - <a target="{{target}}" href="{{href}}">{{#local}}{{text}}{{/local}}</a> - {{/each}} - <br /> -{{/each}} -</script> - <script type="text/template" class="template-history" id="template-history-historyPanel"> -{{! history name (if any) }} <div id="history-controls"><div id="history-title-area" class="historyLinks"> + {{! history name (if any) }} <div id="history-name-container" style="float: left;"> {{! TODO: factor out conditional css }} {{#if user.email}} diff -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 -r d30d2888780f44d815d4463e337bf0f62996e2df templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -233,27 +233,33 @@ "helpers-common-templates", "template-warningmessagesmall", - "template-history-warning-messages", - "template-history-titleLink", - "template-history-failedMetadata", - "template-history-hdaSummary", - "template-history-downloadLinks", - "template-history-tagArea", - "template-history-annotationArea", - "template-history-displayApps", - "template-history-historyPanel", + "template-hda-warning-messages", + "template-hda-titleLink", + "template-hda-failedMetadata", + "template-hda-hdaSummary", + "template-hda-downloadLinks", + "template-hda-tagArea", + "template-hda-annotationArea", + "template-hda-displayApps", + "template-user-quotaMeter-quota", "template-user-quotaMeter-usage" )} ##TODO: fix: curr hasta be _after_ h.templates bc these use those templates - move somehow ${h.js( - "mvc/dataset/hda-model", "mvc/dataset/hda-edit", - "mvc/history/history-model", "mvc/history/history-panel", - ##"mvc/tags", "mvc/annotations", - "mvc/user/user-model", "mvc/user/user-quotameter" + "mvc/user/user-model", "mvc/user/user-quotameter", + + "mvc/dataset/hda-model", + "mvc/dataset/hda-base", + "mvc/dataset/hda-edit", + ##"mvc/dataset/hda-readonly", + + ##"mvc/tags", "mvc/annotations" + + "mvc/history/history-model", "mvc/history/history-panel" )} <script type="text/javascript"> @@ -417,6 +423,7 @@ width: 90%; margin: -2px 0px -3px -4px; font-weight: bold; + font-size: 110%; color: black; } @@ -439,6 +446,17 @@ margin: 10px 0px 10px 0px; } + .historyItemTitle { + text-decoration: none; + cursor: pointer; + -webkit-user-select: none; + -moz-user-select: none; + -khtml-user-select: none; + } + .historyItemTitle:hover { + text-decoration: underline; + } + </style><noscript> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: (alt)history: standardize custom broadcasted events, localize all strings; base-mvc, GalaxyLocalization: add (commented-out) code to store non-localized strings that are attempting to be localized; pack scripts;
by Bitbucket 09 Nov '12

09 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/65fddffc937d/ changeset: 65fddffc937d user: carlfeberhard date: 2012-11-09 17:01:48 summary: (alt)history: standardize custom broadcasted events, localize all strings; base-mvc, GalaxyLocalization: add (commented-out) code to store non-localized strings that are attempting to be localized; pack scripts; affected #: 33 files diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -79,15 +79,17 @@ * GalaxyLocalization.setLocalizedString( original, localized ) * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) * get with either: - * _l( original ) + * GalaxyLocalization.localize( string ) + * _l( string ) */ //TODO: move to Galaxy.Localization (maybe galaxy.base.js) var GalaxyLocalization = jQuery.extend( {}, { ALIAS_NAME : '_l', localizedStrings : {}, - + + // Set a single English string -> localized string association, or set an entire map of those associations + // Pass in either two strings (english, localized) or just an obj (map) of english : localized setLocalizedString : function( str_or_obj, localizedString ){ - // pass in either two strings (english, translated) or an obj (map) of english : translated attributes //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); var self = this; @@ -115,16 +117,19 @@ } }, + // Attempt to get a localized string for strToLocalize. If not found, return the original strToLocalize localize : function( strToLocalize ){ //console.debug( this + '.localize:', strToLocalize ); + + //// uncomment this section to cache strings that need to be localized but haven't been + //if( !_.has( this.localizedStrings, strToLocalize ) ){ + // //console.debug( 'localization NOT found:', strToLocalize ); + // if( !this.nonLocalized ){ this.nonLocalized = {}; } + // this.nonLocalized[ strToLocalize ] = false; + //} + // return the localized version if it's there, the strToLocalize if not - var retStr = strToLocalize; - if( _.has( this.localizedStrings, strToLocalize ) ){ - //console.debug( 'found' ); - retStr = this.localizedStrings[ strToLocalize ]; - } - //console.debug( 'returning:', retStr ); - return retStr; + return this.localizedStrings[ strToLocalize ] || strToLocalize; }, toString : function(){ return 'GalaxyLocalization'; } @@ -247,4 +252,3 @@ return returnedStorage; }; - diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -68,6 +68,7 @@ }, // ................................................................................ RENDER MAIN + // events: rendered, rendered:ready, rendered:initial, rendered:ready:initial render : function(){ var view = this, id = this.model.get( 'id' ), @@ -101,8 +102,8 @@ view.$el.children().remove(); view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ view.log( view + ' rendered:', view.$el ); + var renderedEventName = 'rendered'; - if( initialRender ){ renderedEventName += ':initial'; } else if( view.model.inReadyState() ){ @@ -179,10 +180,10 @@ // show a disabled display if the data's been purged if( this.model.get( 'purged' ) ){ displayBtnData.enabled = false; - displayBtnData.title = 'Cannot display datasets removed from disk'; + displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); } else { - displayBtnData.title = 'Display data in browser'; + displayBtnData.title = _l( 'Display data in browser' ); displayBtnData.href = this.urls.display; } @@ -208,7 +209,7 @@ var purged = this.model.get( 'purged' ), deleted = this.model.get( 'deleted' ), editBtnData = { - title : 'Edit attributes', + title : _l( 'Edit Attributes' ), href : this.urls.edit, target : 'galaxy_main', icon_class : 'edit' @@ -219,9 +220,9 @@ if( deleted || purged ){ editBtnData.enabled = false; if( purged ){ - editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + editBtnData.title = _l( 'Cannot edit attributes of datasets removed from disk' ); } else if( deleted ){ - editBtnData.title = 'Undelete dataset to edit attributes'; + editBtnData.title = _l( 'Undelete dataset to edit attributes' ); } } @@ -239,14 +240,14 @@ } var deleteBtnData = { - title : 'Delete', + title : _l( 'Delete' ), href : this.urls[ 'delete' ], id : 'historyItemDeleter-' + this.model.get( 'id' ), icon_class : 'delete' }; if( this.model.get( 'deleted' ) || this.model.get( 'purged' ) ){ deleteBtnData = { - title : 'Dataset is already deleted', + title : _l( 'Dataset is already deleted' ), icon_class : 'delete', enabled : false }; @@ -306,7 +307,7 @@ || ( !this.model.get( 'for_editing' ) ) ){ return null; } this.errButton = new IconButtonView({ model : new IconButton({ - title : 'View or report this error', + title : _l( 'View or report this error' ), href : this.urls.report_error, target : 'galaxy_main', icon_class : 'bug' @@ -318,7 +319,7 @@ _render_showParamsButton : function(){ // gen. safe to show in all cases this.showParamsButton = new IconButtonView({ model : new IconButton({ - title : 'View details', + title : _l( 'View details' ), href : this.urls.show_params, target : 'galaxy_main', icon_class : 'information' @@ -330,7 +331,7 @@ _render_rerunButton : function(){ if( !this.model.get( 'for_editing' ) ){ return null; } this.rerunButton = new IconButtonView({ model : new IconButton({ - title : 'Run this job again', + title : _l( 'Run this job again' ), href : this.urls.rerun, target : 'galaxy_main', icon_class : 'arrow-circle' @@ -360,7 +361,7 @@ // render the icon from template this.visualizationsButton = new IconButtonView({ model : new IconButton({ - title : 'Visualize', + title : _l( 'Visualize' ), href : visualization_url, icon_class : 'chart_curve' })}); @@ -395,7 +396,7 @@ _.each( visualizations, function( visualization ) { //TODO: move to utils var titleCaseVisualization = visualization.charAt( 0 ).toUpperCase() + visualization.slice( 1 ); - popup_menu_dict[ titleCaseVisualization ] = create_viz_action( visualization ); + popup_menu_dict[ _l( titleCaseVisualization ) ] = create_viz_action( visualization ); }); make_popupmenu( $icon, popup_menu_dict ); } @@ -426,7 +427,7 @@ || ( !this.urls.tags.get ) ){ return null; } this.tagButton = new IconButtonView({ model : new IconButton({ - title : 'Edit dataset tags', + title : _l( 'Edit dataset tags' ), target : 'galaxy_main', href : this.urls.tags.get, icon_class : 'tags' @@ -442,7 +443,7 @@ || ( !this.urls.annotation.get ) ){ return null; } this.annotateButton = new IconButtonView({ model : new IconButton({ - title : 'Edit dataset annotation', + title : _l( 'Edit dataset annotation' ), target : 'galaxy_main', icon_class : 'annotate' })}); @@ -509,15 +510,15 @@ //TODO: only render these on expansion (or already expanded) _render_body_not_viewable : function( parent ){ //TODO: revisit - still showing display, edit, delete (as common) - that CAN'T be right - parent.append( $( '<div>You do not have permission to view dataset.</div>' ) ); + parent.append( $( '<div>' + _l( 'You do not have permission to view dataset' ) + '.</div>' ) ); }, _render_body_uploading : function( parent ){ - parent.append( $( '<div>Dataset is uploading</div>' ) ); + parent.append( $( '<div>' + _l( 'Dataset is uploading' ) + '</div>' ) ); }, _render_body_queued : function( parent ){ - parent.append( $( '<div>Job is waiting to run.</div>' ) ); + parent.append( $( '<div>' + _l( 'Job is waiting to run' ) + '.</div>' ) ); parent.append( this._render_primaryActionButtons([ this._render_showParamsButton, this._render_rerunButton @@ -525,7 +526,7 @@ }, _render_body_running : function( parent ){ - parent.append( '<div>Job is currently running.</div>' ); + parent.append( '<div>' + _l( 'Job is currently running' ) + '.</div>' ); parent.append( this._render_primaryActionButtons([ this._render_showParamsButton, this._render_rerunButton @@ -536,7 +537,7 @@ if( !this.model.get( 'purged' ) ){ parent.append( $( '<div>' + this.model.get( 'misc_blurb' ) + '</div>' ) ); } - parent.append( ( 'An error occurred running this job: ' + parent.append( ( _l( 'An error occurred running this job' ) + ': ' + '<i>' + $.trim( this.model.get( 'misc_info' ) ) + '</i>' ) ); parent.append( this._render_primaryActionButtons([ this._render_downloadButton, @@ -547,7 +548,7 @@ }, _render_body_discarded : function( parent ){ - parent.append( '<div>The job creating this dataset was cancelled before completion.</div>' ); + parent.append( '<div>' + _l( 'The job creating this dataset was cancelled before completion' ) + '.</div>' ); parent.append( this._render_primaryActionButtons([ this._render_showParamsButton, this._render_rerunButton @@ -555,13 +556,13 @@ }, _render_body_setting_metadata : function( parent ){ - parent.append( $( '<div>Metadata is being auto-detected.</div>' ) ); + parent.append( $( '<div>' + _l( 'Metadata is being auto-detected' ) + '.</div>' ) ); }, _render_body_empty : function( parent ){ //TODO: replace i with dataset-misc-info class //?? why are we showing the file size when we know it's zero?? - parent.append( $( '<div>No data: <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); + parent.append( $( '<div>' + _l( 'No data' ) + ': <i>' + this.model.get( 'misc_blurb' ) + '</i></div>' ) ); parent.append( this._render_primaryActionButtons([ this._render_showParamsButton, this._render_rerunButton @@ -700,7 +701,7 @@ $.ajax({ //TODO: the html from this breaks a couple of times url: this.urls.tags.get, - error: function() { alert( "Tagging failed" ); }, + error: function() { alert( _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); tagElt.find(".tooltip").tooltip(); @@ -733,10 +734,10 @@ // Need to fill annotation element. $.ajax({ url: this.urls.annotation.get, - error: function(){ alert( "Annotations failed" ); }, + error: function(){ alert( _l( "Annotations failed" ) ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ - htmlFromAjax = "<em>Describe or add notes to dataset</em>"; + htmlFromAjax = "<em>" + _l( "Describe or add notes to dataset" ) + "</em>"; } annotationElem.html( htmlFromAjax ); annotationArea.find(".tooltip").tooltip(); @@ -761,18 +762,22 @@ }, // expand/collapse body - //side effect: trigger event + // event: body-visible, body-hidden toggleBodyVisibility : function( event, expanded ){ - var $body = this.$el.find( '.historyItemBody' ); + var hdaView = this, + $body = this.$el.find( '.historyItemBody' ); expanded = ( expanded === undefined )?( !$body.is( ':visible' ) ):( expanded ); //this.log( 'toggleBodyVisibility, expanded:', expanded, '$body:', $body ); if( expanded ){ - $body.slideDown( 'fast' ); + $body.slideDown( 'fast', function(){ + hdaView.trigger( 'body-visible', hdaView.model.get( 'id' ) ); + }); } else { - $body.slideUp( 'fast' ); + $body.slideUp( 'fast', function(){ + hdaView.trigger( 'body-hidden', hdaView.model.get( 'id' ) ); + }); } - this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), expanded ); }, // ................................................................................ UTILTIY @@ -823,17 +828,17 @@ $.ajax({ url: vis_url + '/list_tracks?f-' + $.param(params), dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, + error: function() { alert( _l( "Could not add this dataset to browser" ) + '.' ); }, success: function(table_html) { var parent = window.parent; - parent.show_modal("View Data in a New or Saved Visualization", "", { + parent.show_modal( _l( "View Data in a New or Saved Visualization" ), "", { "Cancel": function() { parent.hide_modal(); }, "View in saved visualization": function() { // Show new modal with saved visualizations. - parent.show_modal("Add Data to Saved Visualization", table_html, { + parent.show_modal( _l( "Add Data to Saved Visualization" ), table_html, { "Cancel": function() { parent.hide_modal(); }, diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -9,7 +9,7 @@ //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages - logger : console, + //logger : console, // values from api (may need more) defaults : { @@ -47,14 +47,15 @@ //this.on( 'change', function( currModel, changedList ){ // this.log( this + ' has changed:', currModel, changedList ); //}); - this.bind( 'all', function( event ){ - //this.log( this + '', arguments ); - console.info( this + '', arguments ); - }); + //this.bind( 'all', function( event ){ + // //this.log( this + '', arguments ); + // console.info( this + '', arguments ); + //}); }, // get data via the api (alternative to sending options,hdas to initialize) //TODO: this needs work - move to more straightforward deferred + // events: loaded, loaded:user, loaded:hdas loadFromApi : function( historyId, success ){ var history = this; @@ -66,11 +67,12 @@ history.fetch() ).then( function( userResponse, historyResponse ){ - console.warn( 'fetched user: ', userResponse[0] ); - console.warn( 'fetched history: ', historyResponse[0] ); + //console.warn( 'fetched user: ', userResponse[0] ); + //console.warn( 'fetched history: ', historyResponse[0] ); history.attributes.user = userResponse[0]; //? meh. - history.trigger( 'loaded', historyResponse ); - history.log( history ); + + history.trigger( 'loaded:user', userResponse[0] ); + history.trigger( 'loaded', historyResponse[0] ); }).then( function(){ // ...then the hdas (using contents?ids=...) @@ -82,6 +84,7 @@ //console.warn( 'fetched hdas', hdas ); history.hdas.reset( hdas ); history.checkForUpdates(); + history.trigger( 'loaded:hdas', hdas ); if( success ){ callback( history ); } }); @@ -98,17 +101,22 @@ }, // get the history's state from it's cummulative ds states, delay + update if needed + // events: ready checkForUpdates : function( datasets ){ // get overall History state from collection, run updater if History has running/queued hdas // boiling it down on the client to running/not if( this.hdas.running().length ){ this.stateUpdater(); + + } else { + this.trigger( 'ready' ); } return this; }, // update this history, find any hda's running/queued, update ONLY those that have changed states, // set up to run this again in some interval of time + // events: ready stateUpdater : function(){ var history = this, oldState = this.get( 'state' ), @@ -148,13 +156,17 @@ setTimeout( function(){ history.stateUpdater(); }, 4000 ); + + // otherwise, we're now in a 'ready' state (no hdas running) + } else { + history.trigger( 'ready' ); } }).error( function( xhr, status, error ){ if( console && console.warn ){ console.warn( 'Error getting history updates from the server:', xhr, status, error ); } - alert( 'Error getting history updates from the server.\n' + error ); + alert( _l( 'Error getting history updates from the server.' ) + '\n' + error ); }); }, @@ -172,7 +184,7 @@ var HistoryCollection = Backbone.Collection.extend( LoggableMixin ).extend({ model : History, urlRoot : 'api/histories', - logger : console + //logger : console }); //============================================================================== diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -7,14 +7,15 @@ TODO: anon user, mako template init: bug: rename url seems to be wrong url - BUG: shouldn't have tag/anno buttons (on hdas) + Check for user in hdaView somehow logged in, mako template: + BUG: quotaMsg not showing when 100% (on load) + bug: rename not being changed locally - render() shows old name, refresh: new name BUG: meter is not updating RELIABLY on change:nice_size BUG: am able to start upload even if over quota - 'runs' forever bug: quotaMeter bar rendering square in chrome - BUG: quotaMsg not showing when 100% (on load) BUG: imported, shared history with unaccessible dataset errs in historycontents when getting history (entire history is inaccessible) ??: still happening? @@ -199,6 +200,7 @@ }, // render urls, historyView body, and hdas (if any are shown), fade out, swap, fade in, set up behaviours + // events: rendered, rendered:initial render : function(){ var historyView = this, setUpQueueName = historyView.toString() + '.set-up', @@ -298,7 +300,6 @@ // set up HistoryView->HDAView listeners setUpHdaListeners : function( hdaView ){ var historyView = this; - // use storage to maintain a list of hdas whose bodies are expanded hdaView.bind( 'toggleBodyVisibility', function( id, visible ){ if( visible ){ @@ -307,9 +308,6 @@ historyView.storage.get( 'expandedHdas' ).deleteKey( id ); } }); - - // rendering listeners - hdaView.bind( 'rendered:ready', function(){ historyView.trigger( 'hda:rendered:ready' ); }); }, // set up js/widget behaviours: tooltips, @@ -336,8 +334,6 @@ async_save_text( "history-annotation-container", "history-annotation", this.urls.annotate, "new_annotation", 18, true, 4 ); - - //this.$( 'button' ).button(); }, // update the history size display (curr. upper right of panel) @@ -397,7 +393,7 @@ $.ajax({ //TODO: the html from this breaks a couple of times url: view.urls.tag, - error: function() { alert( "Tagging failed" ); }, + error: function() { alert( _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { //view.log( view + ' tag elt html (ajax)', tag_elt_html ); tagElt.html(tag_elt_html); diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/user/user-model.js --- a/static/scripts/mvc/user/user-model.js +++ b/static/scripts/mvc/user/user-model.js @@ -1,9 +1,10 @@ var User = BaseModel.extend( LoggableMixin ).extend({ //logger : console, + urlRoot : 'api/users', defaults : { id : null, - username : "(anonymous user)", + username : '(' + _l( "anonymous user" ) + ')', email : "", total_disk_usage : 0, nice_total_disk_usage : "0 bytes" @@ -16,7 +17,7 @@ this.on( 'change', function( model, data ){ this.log( this + ' has changed:', model, data.changes ); }); }, - urlRoot : 'api/users', + // events: loaded loadFromApi : function( idOrCurrent, options ){ idOrCurrent = idOrCurrent || User.CURRENT_ID_STR; options = options || {}; @@ -26,6 +27,8 @@ model.trigger( 'loaded', newModel, response ); if( userFn ){ userFn( newModel, response ); } }; + + // requests for the current user must have a sep. constructed url (fetch don't work, ma) if( idOrCurrent === User.CURRENT_ID_STR ){ options.url = this.urlRoot + '/' + User.CURRENT_ID_STR; } @@ -55,6 +58,6 @@ // (stub) collection for users (shouldn't be common unless admin UI) var UserCollection = Backbone.Collection.extend( LoggableMixin ).extend({ model : User, - logger : console, urlRoot : 'api/users' + //logger : console, }); diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/mvc/user/user-quotameter.js --- a/static/scripts/mvc/user/user-quotameter.js +++ b/static/scripts/mvc/user/user-quotameter.js @@ -9,31 +9,11 @@ options : { warnAtPercent : 85, - errorAtPercent : 100, - - // the quota/usage bar is in the masthead - meterDocument : window.top.document, - containerSelector : '.quota-meter-container', - meterSelector : '#quota-meter', - barSelector : '#quota-meter-bar', - textSelector : '#quota-meter-text', - - // the quota message currently displays in the history panel - msgDocument : ( top.frames.galaxy_history )?( top.frames.galaxy_history.document ) - :( top.document ), - msgSelector : '#quota-message-container', - - warnClass : 'quota-meter-bar-warn', - errorClass : 'quota-meter-bar-error', - usageTemplate : 'Using <%= nice_total_disk_usage %>', - quotaTemplate : 'Using <%= quota_percent %>%', - meterTemplate : '', // see where I'm going? - animationSpeed : 'fast' + errorAtPercent : 100 }, initialize : function( options ){ this.log( this + '.initialize:', options ); - _.extend( this.options, options ); //this.bind( 'all', function( event, data ){ this.log( this + ' event:', event, data ); }, this ); @@ -51,6 +31,7 @@ && this.model.get( 'quota_percent' ) >= this.options.errorAtPercent ); }, + // events: quota:over, quota:under, quota:under:approaching, quota:under:ok _render_quota : function(){ var modelJson = this.model.toJSON(), //prevPercent = this.model.previous( 'quota_percent' ), diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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 BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){var a=b;if(_.has(this.localizedStrings,b)){a=this.localizedStrings[b]}return a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;var e=function(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this.save();return this},deleteKey:function(j){delete i[j];this.save();return this},save:function(){return h.save()},toString:function(){return("StorageRecursionHelper("+i+")")}}};var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);f.save=function(h){c(g,f.get())};f.destroy=function(){a(g)};f.toString=function(){return"PersistantStorage("+data+")"};return f}; \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;var e=function(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this.save();return this},deleteKey:function(j){delete i[j];this.save();return this},save:function(){return h.save()},toString:function(){return("StorageRecursionHelper("+i+")")}}};var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);f.save=function(h){c(g,f.get())};f.destroy=function(){a(g)};f.toString=function(){return"PersistantStorage("+data+")"};return f}; \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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 @@ -var HDAView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this._clearReferences();this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title="Cannot display datasets removed from disk"}else{a.title="Display data in browser";a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title="Cannot edit attributes of datasets removed from disk"}else{if(a){b.title="Undelete dataset to edit attributes"}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:"Delete",href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:"Visualize",href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[h]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b,a){var c=this.$el.find(".historyItemBody");a=(a===undefined)?(!c.is(":visible")):(a);if(a){c.slideDown("fast")}else{c.slideUp("fast")}this.trigger("toggleBodyVisibility",this.model.get("id"),a)},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(e){var f=window.parent;f.show_modal("View Data in a New or Saved Visualization","",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal("Add Data to Saved Visualization",e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this._clearReferences();this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-visible",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-hidden",b.model.get("id"))})}},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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 @@ -var History=BaseModel.extend(LoggableMixin).extend({logger:console,defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}this.bind("all",function(c){console.info(this+"",arguments)})},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){console.warn("fetched user: ",e[0]);console.warn("fetched history: ",d[0]);b.attributes.user=e[0];b.trigger("loaded",d);b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}else{c.trigger("ready")}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert(_l("Error getting history updates from the server.")+"\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",}); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,username:"(anonymous user)",email:"",total_disk_usage:0,nice_total_disk_usage:"0 bytes"},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)})},urlRoot:"api/users",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 BaseModel.prototype.fetch.call(this,b)},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,logger:console,urlRoot:"api/users"}); \ No newline at end of file +var User=BaseModel.extend(LoggableMixin).extend({urlRoot:"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"0 bytes"},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)})},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 BaseModel.prototype.fetch.call(this,b)},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:"api/users"}); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 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=BaseView.extend(LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100,meterDocument:window.top.document,containerSelector:".quota-meter-container",meterSelector:"#quota-meter",barSelector:"#quota-meter-bar",textSelector:"#quota-meter-text",msgDocument:(top.frames.galaxy_history)?(top.frames.galaxy_history.document):(top.document),msgSelector:"#quota-message-container",warnClass:"quota-meter-bar-warn",errorClass:"quota-meter-bar-error",usageTemplate:"Using <%= nice_total_disk_usage %>",quotaTemplate:"Using <%= quota_percent %>%",meterTemplate:"",animationSpeed:"fast"},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(),b=a.quota_percent,c=$(UserQuotaMeter.templates.quota(a));if(this.isOverQuota()){c.addClass("progress-danger");c.find("#quota-meter-text").css("color","white");this.trigger("quota:over",a)}else{if(b>=this.options.warnAtPercent){c.addClass("progress-warning");this.trigger("quota:under quota:under:approaching",a)}else{c.addClass("progress-success");this.trigger("quota:under quota:under:ok",a)}}return c},_render_usage:function(){var a=$(UserQuotaMeter.templates.usage(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.$el.html(a);return this},toString:function(){return"UserQuotaMeter("+this.model+")"}});UserQuotaMeter.templates={quota:Handlebars.templates["template-user-quotaMeter-quota"],usage:Handlebars.templates["template-user-quotaMeter-usage"]}; \ No newline at end of file +var UserQuotaMeter=BaseView.extend(LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100},initialize:function(a){this.log(this+".initialize:",a);_.extend(this.options,a);this.model.bind("change:quota_percent change:total_disk_usage",this.render,this)},update:function(a){this.log(this+" updating user data...",a);this.model.loadFromApi(this.model.get("id"),a);return this},isOverQuota:function(){return(this.model.get("quota_percent")!==null&&this.model.get("quota_percent")>=this.options.errorAtPercent)},_render_quota:function(){var a=this.model.toJSON(),b=a.quota_percent,c=$(UserQuotaMeter.templates.quota(a));if(this.isOverQuota()){c.addClass("progress-danger");c.find("#quota-meter-text").css("color","white");this.trigger("quota:over",a)}else{if(b>=this.options.warnAtPercent){c.addClass("progress-warning");this.trigger("quota:under quota:under:approaching",a)}else{c.addClass("progress-success");this.trigger("quota:under quota:under:ok",a)}}return c},_render_usage:function(){var a=$(UserQuotaMeter.templates.usage(this.model.toJSON()));this.log(this+".rendering usage:",a);return a},render:function(){var a=null;this.log(this+".model.quota_percent:",this.model.get("quota_percent"));if((this.model.get("quota_percent")===null)||(this.model.get("quota_percent")===undefined)){a=this._render_usage()}else{a=this._render_quota()}this.$el.html(a);return this},toString:function(){return"UserQuotaMeter("+this.model+")"}});UserQuotaMeter.templates={quota:Handlebars.templates["template-user-quotaMeter-quota"],usage:Handlebars.templates["template-user-quotaMeter-usage"]}; \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-annotationArea.js --- a/static/scripts/packed/templates/compiled/template-history-annotationArea.js +++ b/static/scripts/packed/templates/compiled/template-history-annotationArea.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-annotationArea"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='\n<div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>Annotation:</strong>\n <div id="';g=d.id;if(g){c=g.call(l,{hash:{}})}else{c=l.id;c=typeof c===f?c():c}h+=i(c)+'-anotation-elt" class="annotation-elt tooltip editable-text"\n style="margin: 1px 0px 1px 0px" title="Edit dataset annotation">\n </div>\n</div>';return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-annotationArea"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this,o=f.blockHelperMissing;function e(r,q){return"Annotation"}function c(r,q){return"Edit dataset annotation"}j+='\n<div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-annotation-area" class="annotation-area" style="display: none;">\n <strong>';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)})}if(d||d===0){j+=d}j+=':</strong>\n <div id="';i=f.id;if(i){d=i.call(n,{hash:{}})}else{d=n.id;d=typeof d===h?d():d}j+=k(d)+'-anotation-elt" class="annotation-elt tooltip editable-text"\n style="margin: 1px 0px 1px 0px" title="';i=f.local;if(i){d=i.call(n,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}else{d=n.local;d=typeof d===h?d():d}if(!f.local){d=o.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)})}if(d||d===0){j+=d}j+='">\n </div>\n</div>';return j})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-displayApps.js --- a/static/scripts/packed/templates/compiled/template-history-displayApps.js +++ b/static/scripts/packed/templates/compiled/template-history-displayApps.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-displayApps"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(r,q){var o="",p,n;o+="\n ";n=f.label;if(n){p=n.call(r,{hash:{}})}else{p=r.label;p=typeof p===h?p():p}o+=i(p)+"\n ";p=r.links;p=f.each.call(r,p,{hash:{},inverse:m.noop,fn:m.program(2,d,q)});if(p||p===0){o+=p}o+="\n <br />\n";return o}function d(r,q){var o="",p,n;o+='\n <a target="';n=f.target;if(n){p=n.call(r,{hash:{}})}else{p=r.target;p=typeof p===h?p():p}o+=i(p)+'" href="';n=f.href;if(n){p=n.call(r,{hash:{}})}else{p=r.href;p=typeof p===h?p():p}o+=i(p)+'">';n=f.text;if(n){p=n.call(r,{hash:{}})}else{p=r.text;p=typeof p===h?p():p}o+=i(p)+"</a>\n ";return o}c=l.displayApps;c=f.each.call(l,c,{hash:{},inverse:m.noop,fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-displayApps"]=b(function(h,m,g,l,k){g=g||h.helpers;var d,i="function",j=this.escapeExpression,o=this,n=g.blockHelperMissing;function f(t,s){var q="",r,p;q+="\n ";p=g.label;if(p){r=p.call(t,{hash:{}})}else{r=t.label;r=typeof r===i?r():r}q+=j(r)+"\n ";r=t.links;r=g.each.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,e,s)});if(r||r===0){q+=r}q+="\n <br />\n";return q}function e(t,s){var q="",r,p;q+='\n <a target="';p=g.target;if(p){r=p.call(t,{hash:{}})}else{r=t.target;r=typeof r===i?r():r}q+=j(r)+'" href="';p=g.href;if(p){r=p.call(t,{hash:{}})}else{r=t.href;r=typeof r===i?r():r}q+=j(r)+'">';p=g.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}else{r=t.local;r=typeof r===i?r():r}if(!g.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(3,c,s)})}if(r||r===0){q+=r}q+="</a>\n ";return q}function c(s,r){var q,p;p=g.text;if(p){q=p.call(s,{hash:{}})}else{q=s.text;q=typeof q===i?q():q}return j(q)}d=m.displayApps;d=g.each.call(m,d,{hash:{},inverse:o.noop,fn:o.program(1,f,k)});if(d||d===0){return d}else{return""}})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/packed/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/packed/templates/compiled/template-history-downloadLinks.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,l,f,k,j){f=f||g.helpers;var c,h="function",i=this.escapeExpression,m=this;function e(s,r){var p="",q,o;p+="\n";p+='\n<div popupmenu="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a class="action-button" href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'">Download Dataset</a>\n <a>Additional Files</a>\n ';q=s.urls;q=q==null||q===false?q:q.meta_download;q=f.each.call(s,q,{hash:{},inverse:m.noop,fn:m.program(2,d,r)});if(q||q===0){p+=q}p+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';o=f.id;if(o){q=o.call(s,{hash:{}})}else{q=s.id;q=typeof q===h?q():q}p+=i(q)+'-popup">\n <a href="';q=s.urls;q=q==null||q===false?q:q.download;q=typeof q===h?q():q;p+=i(q)+'" title="Download" class="icon-button disk tooltip"></a>\n</div>\n';return p}function d(s,r){var p="",q,o;p+='\n <a class="action-button" href="';o=f.url;if(o){q=o.call(s,{hash:{}})}else{q=s.url;q=typeof q===h?q():q}p+=i(q)+'">Download ';o=f.file_type;if(o){q=o.call(s,{hash:{}})}else{q=s.file_type;q=typeof q===h?q():q}p+=i(q)+"</a>\n ";return p}function n(r,q){var o="",p;o+="\n";o+='\n<a href="';p=r.urls;p=p==null||p===false?p:p.download;p=typeof p===h?p():p;o+=i(p)+'" title="Download" class="icon-button disk tooltip"></a>\n';return o}c=l.urls;c=c==null||c===false?c:c.meta_download;c=f["if"].call(l,c,{hash:{},inverse:m.program(4,n,j),fn:m.program(1,e,j)});if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-downloadLinks"]=b(function(g,q,p,k,t){p=p||g.helpers;var h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(y,x){var v="",w,u;v+="\n";v+='\n<div popupmenu="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a class="action-button" href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(2,m,x)})}if(w||w===0){v+=w}v+="</a>\n <a>";u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(4,l,x)})}if(w||w===0){v+=w}v+="</a>\n ";w=y.urls;w=w==null||w===false?w:w.meta_download;w=p.each.call(y,w,{hash:{},inverse:o.noop,fn:o.program(6,j,x)});if(w||w===0){v+=w}v+='\n</div>\n<div style="float:left;" class="menubutton split popup" id="dataset-';u=p.id;if(u){w=u.call(y,{hash:{}})}else{w=y.id;w=typeof w===e?w():w}v+=d(w)+'-popup">\n <a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(9,f,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n</div>\n';return v}function m(v,u){return"Download Dataset"}function l(v,u){return"Additional Files"}function j(y,x){var v="",w,u;v+='\n <a class="action-button" href="';u=p.url;if(u){w=u.call(y,{hash:{}})}else{w=y.url;w=typeof w===e?w():w}v+=d(w)+'">';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(7,i,x)})}if(w||w===0){v+=w}v+=" ";u=p.file_type;if(u){w=u.call(y,{hash:{}})}else{w=y.file_type;w=typeof w===e?w():w}v+=d(w)+"</a>\n ";return v}function i(v,u){return"Download"}function f(v,u){return"Download"}function s(y,x){var v="",w,u;v+="\n";v+='\n<a href="';w=y.urls;w=w==null||w===false?w:w.download;w=typeof w===e?w():w;v+=d(w)+'" title="';u=p.local;if(u){w=u.call(y,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}else{w=y.local;w=typeof w===e?w():w}if(!p.local){w=c.call(y,w,{hash:{},inverse:o.noop,fn:o.program(12,r,x)})}if(w||w===0){v+=w}v+='" class="icon-button disk tooltip"></a>\n';return v}function r(v,u){return"Download"}h=q.urls;h=h==null||h===false?h:h.meta_download;h=p["if"].call(q,h,{hash:{},inverse:o.program(11,s,t),fn:o.program(1,n,t)});if(h||h===0){return h}else{return""}})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/packed/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/packed/templates/compiled/template-history-failedMetaData.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(f,l,e,k,j){e=e||f.helpers;var c,h,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(r,q){var o="",p;o+='\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href="';p=r.urls;p=p==null||p===false?p:p.edit;p=typeof p===g?p():p;o+=i(p)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return o}h=e.warningmessagesmall;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.warningmessagesmall;c=typeof c===g?c():c}if(!e.warningmessagesmall){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-failedMetaData"]=b(function(g,m,f,l,k){f=f||g.helpers;var c,i,o=this,h="function",n=f.blockHelperMissing,j=this.escapeExpression;function e(t,s){var q="",r,p;q+="\n";p=f.local;if(p){r=p.call(t,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}else{r=t.local;r=typeof r===h?r():r}if(!f.local){r=n.call(t,r,{hash:{},inverse:o.noop,fn:o.program(2,d,s)})}if(r||r===0){q+=r}q+='\nYou may be able to <a href="';r=t.urls;r=r==null||r===false?r:r.edit;r=typeof r===h?r():r;q+=j(r)+'" target="galaxy_main">set it manually or retry auto-detection</a>.\n';return q}function d(q,p){return"An error occurred setting the metadata for this dataset."}i=f.warningmessagesmall;if(i){c=i.call(m,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}else{c=m.warningmessagesmall;c=typeof c===h?c():c}if(!f.warningmessagesmall){c=n.call(m,c,{hash:{},inverse:o.noop,fn:o.program(1,e,k)})}if(c||c===0){return c}else{return""}})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,t,r,n,B){r=r||g.helpers;var s="",k,j,e="function",d=this.escapeExpression,q=this,c=r.blockHelperMissing;function p(G,F){var D="",E,C;D+='\n <div id="history-name" class="tooltip editable-text"\n title="Click to rename history">';C=r.name;if(C){E=C.call(G,{hash:{}})}else{E=G.name;E=typeof E===e?E():E}D+=d(E)+"</div>\n ";return D}function o(G,F){var D="",E,C;D+='\n <div id="history-name" class="tooltip"\n title="You must be logged in to edit your history name">';C=r.name;if(C){E=C.call(G,{hash:{}})}else{E=G.name;E=typeof E===e?E():E}D+=d(E)+"</div>\n ";return D}function m(D,C){return"Click to see more actions"}function l(G,F){var D="",E,C;D+='\n <div id="history-secondary-links" style="float: right;">\n <a id="history-tag" title="';C=r.local;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(8,i,F)})}else{E=G.local;E=typeof E===e?E():E}if(!r.local){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(8,i,F)})}if(E||E===0){D+=E}D+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';C=r.local;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(10,A,F)})}else{E=G.local;E=typeof E===e?E():E}if(!r.local){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(10,A,F)})}if(E||E===0){D+=E}D+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return D}function i(D,C){return"Edit history tags"}function A(D,C){return"Edit history annotation"}function z(G,F){var D="",E,C;D+="\n ";C=r.warningmessagesmall;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(13,y,F)})}else{E=G.warningmessagesmall;E=typeof E===e?E():E}if(!r.warningmessagesmall){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(13,y,F)})}if(E||E===0){D+=E}D+="\n ";return D}function y(F,E){var D,C;C=r.local;if(C){D=C.call(F,{hash:{},inverse:q.noop,fn:q.program(14,x,E)})}else{D=F.local;D=typeof D===e?D():D}if(!r.local){D=c.call(F,D,{hash:{},inverse:q.noop,fn:q.program(14,x,E)})}if(D||D===0){return D}else{return""}}function x(D,C){return"You are currently viewing a deleted history!"}function w(F,E){var C="",D;C+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';D=F.annotation;D=r["if"].call(F,D,{hash:{},inverse:q.program(19,u,E),fn:q.program(17,v,E)});if(D||D===0){C+=D}C+="\n </div>\n </div>\n </div>\n </div>\n ";return C}function v(G,F){var D="",E,C;D+="\n ";C=r.annotation;if(C){E=C.call(G,{hash:{}})}else{E=G.annotation;E=typeof E===e?E():E}D+=d(E)+"\n ";return D}function u(D,C){return"\n <em>Describe or add notes to history</em>\n "}function h(G,F){var D="",E,C;D+='\n <div id="message-container">\n <div class="';C=r.status;if(C){E=C.call(G,{hash:{}})}else{E=G.status;E=typeof 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Click 'Get Data' on the left pane to start"}s+='\n<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n <div id="history-name-container" style="float: left;">\n ';s+="\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.program(3,o,B),fn:q.program(1,p,B)});if(k||k===0){s+=k}s+='\n </div>\n\n <a id="history-action-popup" class="tooltip" title="';j=r.local;if(j){k=j.call(t,{hash:{},inverse:q.noop,fn:q.program(5,m,B)})}else{k=t.local;k=typeof k===e?k():k}if(!r.local){k=c.call(t,k,{hash:{},inverse:q.noop,fn:q.program(5,m,B)})}if(k||k===0){s+=k}s+='"\n href="javascript:void(0);" style="float: right;">\n <span class="ficon cog large"></span>\n </a>\n <div style="clear: both;"></div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';j=r.nice_size;if(j){k=j.call(t,{hash:{}})}else{k=t.nice_size;k=typeof k===e?k():k}s+=d(k)+"</div>\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(7,l,B)});if(k||k===0){s+=k}s+='\n <div style="clear: both;"></div>\n </div>\n\n ';k=t.deleted;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(12,z,B)});if(k||k===0){s+=k}s+="\n\n ";s+="\n ";s+="\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(16,w,B)});if(k||k===0){s+=k}s+="\n\n ";k=t.message;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(21,h,B)});if(k||k===0){s+=k}s+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id="';j=r.id;if(j){k=j.call(t,{hash:{}})}else{k=t.id;k=typeof k===e?k():k}s+=d(k)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';j=r.local;if(j){k=j.call(t,{hash:{},inverse:q.noop,fn:q.program(23,f,B)})}else{k=t.local;k=typeof k===e?k():k}if(!r.local){k=c.call(t,k,{hash:{},inverse:q.noop,fn:q.program(23,f,B)})}if(k||k===0){s+=k}s+="\n</div>";return s})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,A,y,q,I){y=y||k.helpers;var z="",n,m,v=this,e="function",c=y.blockHelperMissing,d=this.escapeExpression;function t(N,M){var K="",L,J;K+='\n <div id="history-name" class="tooltip editable-text"\n title="';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(2,s,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(2,s,M)})}if(L||L===0){K+=L}K+='">';J=y.name;if(J){L=J.call(N,{hash:{}})}else{L=N.name;L=typeof L===e?L():L}K+=d(L)+"</div>\n ";return K}function s(K,J){return"Click to rename history"}function r(N,M){var K="",L,J;K+='\n <div id="history-name" class="tooltip"\n title="';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(5,p,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(5,p,M)})}if(L||L===0){K+=L}K+='">';J=y.name;if(J){L=J.call(N,{hash:{}})}else{L=N.name;L=typeof L===e?L():L}K+=d(L)+"</div>\n ";return K}function p(K,J){return"You must be logged in to edit your history name"}function o(K,J){return"Click to see more actions"}function j(N,M){var K="",L,J;K+='\n <div id="history-secondary-links" style="float: right;">\n <a id="history-tag" title="';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(10,H,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(10,H,M)})}if(L||L===0){K+=L}K+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(12,G,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(12,G,M)})}if(L||L===0){K+=L}K+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return K}function H(K,J){return"Edit history tags"}function G(K,J){return"Edit history annotation"}function F(N,M){var K="",L,J;K+="\n ";J=y.warningmessagesmall;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(15,E,M)})}else{L=N.warningmessagesmall;L=typeof L===e?L():L}if(!y.warningmessagesmall){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(15,E,M)})}if(L||L===0){K+=L}K+="\n ";return K}function E(M,L){var K,J;J=y.local;if(J){K=J.call(M,{hash:{},inverse:v.noop,fn:v.program(16,D,L)})}else{K=M.local;K=typeof K===e?K():K}if(!y.local){K=c.call(M,K,{hash:{},inverse:v.noop,fn:v.program(16,D,L)})}if(K||K===0){return K}else{return""}}function D(K,J){return"You are currently viewing a deleted history!"}function C(N,M){var K="",L,J;K+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(19,B,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(19,B,M)})}if(L||L===0){K+=L}K+=':</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(21,l,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(21,l,M)})}if(L||L===0){K+=L}K+=':</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text"\n title="';J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(23,i,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(23,i,M)})}if(L||L===0){K+=L}K+='">\n ';L=N.annotation;L=y["if"].call(N,L,{hash:{},inverse:v.program(27,g,M),fn:v.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n </div>\n ";return K}function B(K,J){return"Tags"}function l(K,J){return"Annotation"}function i(K,J){return"Click to edit annotation"}function h(N,M){var K="",L,J;K+="\n ";J=y.annotation;if(J){L=J.call(N,{hash:{}})}else{L=N.annotation;L=typeof L===e?L():L}K+=d(L)+"\n ";return K}function g(N,M){var K="",L,J;K+="\n <em>";J=y.local;if(J){L=J.call(N,{hash:{},inverse:v.noop,fn:v.program(28,f,M)})}else{L=N.local;L=typeof L===e?L():L}if(!y.local){L=c.call(N,L,{hash:{},inverse:v.noop,fn:v.program(28,f,M)})}if(L||L===0){K+=L}K+="</em>\n ";return K}function f(K,J){return"Describe or add notes to history"}function x(N,M){var K="",L,J;K+='\n <div id="message-container">\n <div class="';J=y.status;if(J){L=J.call(N,{hash:{}})}else{L=N.status;L=typeof L===e?L():L}K+=d(L)+'message">\n ';J=y.message;if(J){L=J.call(N,{hash:{}})}else{L=N.message;L=typeof L===e?L():L}K+=d(L)+"\n </div><br />\n </div>\n ";return K}function w(K,J){return"You are over your disk quota.\n Tool execution is on hold until your disk usage drops below your allocated quota."}function u(K,J){return"Your history is empty. Click 'Get Data' on the left pane to start"}z+='\n<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n <div id="history-name-container" style="float: left;">\n ';z+="\n ";n=A.user;n=n==null||n===false?n:n.email;n=y["if"].call(A,n,{hash:{},inverse:v.program(4,r,I),fn:v.program(1,t,I)});if(n||n===0){z+=n}z+='\n </div>\n\n <a id="history-action-popup" class="tooltip" title="';m=y.local;if(m){n=m.call(A,{hash:{},inverse:v.noop,fn:v.program(7,o,I)})}else{n=A.local;n=typeof n===e?n():n}if(!y.local){n=c.call(A,n,{hash:{},inverse:v.noop,fn:v.program(7,o,I)})}if(n||n===0){z+=n}z+='"\n href="javascript:void(0);" style="float: right;">\n <span class="ficon cog large"></span>\n </a>\n <div style="clear: both;"></div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';m=y.nice_size;if(m){n=m.call(A,{hash:{}})}else{n=A.nice_size;n=typeof n===e?n():n}z+=d(n)+"</div>\n ";n=A.user;n=n==null||n===false?n:n.email;n=y["if"].call(A,n,{hash:{},inverse:v.noop,fn:v.program(9,j,I)});if(n||n===0){z+=n}z+='\n <div style="clear: both;"></div>\n </div>\n\n ';n=A.deleted;n=y["if"].call(A,n,{hash:{},inverse:v.noop,fn:v.program(14,F,I)});if(n||n===0){z+=n}z+="\n\n ";z+="\n ";z+="\n ";n=A.user;n=n==null||n===false?n:n.email;n=y["if"].call(A,n,{hash:{},inverse:v.noop,fn:v.program(18,C,I)});if(n||n===0){z+=n}z+="\n\n ";n=A.message;n=y["if"].call(A,n,{hash:{},inverse:v.noop,fn:v.program(30,x,I)});if(n||n===0){z+=n}z+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n ';m=y.local;if(m){n=m.call(A,{hash:{},inverse:v.noop,fn:v.program(32,w,I)})}else{n=A.local;n=typeof n===e?n():n}if(!y.local){n=c.call(A,n,{hash:{},inverse:v.noop,fn:v.program(32,w,I)})}if(n||n===0){z+=n}z+='\n </div>\n </div>\n</div>\n\n<div id="';m=y.id;if(m){n=m.call(A,{hash:{}})}else{n=A.id;n=typeof n===e?n():n}z+=d(n)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';m=y.local;if(m){n=m.call(A,{hash:{},inverse:v.noop,fn:v.program(34,u,I)})}else{n=A.local;n=typeof n===e?n():n}if(!y.local){n=c.call(A,n,{hash:{},inverse:v.noop,fn:v.program(34,u,I)})}if(n||n===0){z+=n}z+="\n</div>";return z})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-tagArea.js --- a/static/scripts/packed/templates/compiled/template-history-tagArea.js +++ b/static/scripts/packed/templates/compiled/template-history-tagArea.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-tagArea"]=b(function(g,h,e,d,f){e=e||g.helpers;var c="";c+='\n<div class="tag-area" style="display: none;">\n <strong>Tags:</strong>\n <div class="tag-elt">\n </div>\n</div>';return c})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-tagArea"]=b(function(f,l,e,k,j){e=e||f.helpers;var i="",c,h,n=this,g="function",m=e.blockHelperMissing;function d(p,o){return"Tags"}i+='\n<div class="tag-area" style="display: none;">\n <strong>';h=e.local;if(h){c=h.call(l,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}else{c=l.local;c=typeof c===g?c():c}if(!e.local){c=m.call(l,c,{hash:{},inverse:n.noop,fn:n.program(1,d,j)})}if(c||c===0){i+=c}i+=':</strong>\n <div class="tag-elt">\n </div>\n</div>';return i})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-history-warning-messages.js --- a/static/scripts/packed/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/packed/templates/compiled/template-history-warning-messages.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(f,s,q,k,w){q=q||f.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(z,y){var x;x=z.purged;x=q.unless.call(z,x,{hash:{},inverse:p.noop,fn:p.program(2,n,y)});if(x||x===0){return x}else{return""}}function n(B,A){var y="",z,x;y+="\n";x=q.warningmessagesmall;if(x){z=x.call(B,{hash:{},inverse:p.noop,fn:p.program(3,m,A)})}else{z=B.warningmessagesmall;z=typeof z===e?z():z}if(!q.warningmessagesmall){z=c.call(B,z,{hash:{},inverse:p.noop,fn:p.program(3,m,A)})}if(z||z===0){y+=z}y+="\n";return y}function m(A,z){var x="",y;x+="\n This dataset has been deleted.\n ";y=A.urls;y=y==null||y===false?y:y.undelete;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(4,l,z)});if(y||y===0){x+=y}x+="\n";return x}function l(B,A){var y="",z,x;y+='\n Click <a href="';z=B.urls;z=z==null||z===false?z:z.undelete;z=typeof z===e?z():z;y+=d(z)+'" class="historyItemUndelete" id="historyItemUndeleter-';x=q.id;if(x){z=x.call(B,{hash:{}})}else{z=B.id;z=typeof z===e?z():z}y+=d(z)+'"\n target="galaxy_history">here</a> to undelete it\n ';z=B.urls;z=z==null||z===false?z:z.purge;z=q["if"].call(B,z,{hash:{},inverse:p.noop,fn:p.program(5,j,A)});if(z||z===0){y+=z}y+="\n ";return y}function j(B,A){var y="",z,x;y+='\n or <a href="';z=B.urls;z=z==null||z===false?z:z.purge;z=typeof z===e?z():z;y+=d(z)+'" class="historyItemPurge" id="historyItemPurger-';x=q.id;if(x){z=x.call(B,{hash:{}})}else{z=B.id;z=typeof z===e?z():z}y+=d(z)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return y}function i(A,z){var y,x;x=q.warningmessagesmall;if(x){y=x.call(A,{hash:{},inverse:p.noop,fn:p.program(8,g,z)})}else{y=A.warningmessagesmall;y=typeof y===e?y():y}if(!q.warningmessagesmall){y=c.call(A,y,{hash:{},inverse:p.noop,fn:p.program(8,g,z)})}if(y||y===0){return y}else{return""}}function g(y,x){return"\n This dataset has been deleted and removed from disk.\n"}function v(A,z){var y,x;x=q.warningmessagesmall;if(x){y=x.call(A,{hash:{},inverse:p.noop,fn:p.program(11,u,z)})}else{y=A.warningmessagesmall;y=typeof y===e?y():y}if(!q.warningmessagesmall){y=c.call(A,y,{hash:{},inverse:p.noop,fn:p.program(11,u,z)})}if(y||y===0){return y}else{return""}}function u(A,z){var x="",y;x+="\n This dataset has been hidden.\n ";y=A.urls;y=y==null||y===false?y:y.unhide;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(12,t,z)});if(y||y===0){x+=y}x+="\n";return x}function t(B,A){var y="",z,x;y+='\n Click <a href="';z=B.urls;z=z==null||z===false?z:z.unhide;z=typeof z===e?z():z;y+=d(z)+'" class="historyItemUnhide" id="historyItemUnhider-';x=q.id;if(x){z=x.call(B,{hash:{}})}else{z=B.id;z=typeof z===e?z():z}y+=d(z)+'"\n target="galaxy_history">here</a> to unhide it\n ';return y}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,w)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(7,i,w)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(10,v,w)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,z){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(C,B){var A;A=C.purged;A=q.unless.call(C,A,{hash:{},inverse:p.noop,fn:p.program(2,n,B)});if(A||A===0){return A}else{return""}}function n(E,D){var B="",C,A;B+="\n";A=q.warningmessagesmall;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}else{C=E.warningmessagesmall;C=typeof C===e?C():C}if(!q.warningmessagesmall){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(3,m,D)})}if(C||C===0){B+=C}B+="\n";return B}function m(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(4,l,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.undelete;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(6,j,D)});if(C||C===0){B+=C}B+="\n";return B}function l(B,A){return"This dataset has been deleted."}function j(E,D){var B="",C,A;B+="\n ";B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.undelete;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUndelete" id="historyItemUndeleter-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to undelete it\n ';C=E.urls;C=C==null||C===false?C:C.purge;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(7,i,D)});if(C||C===0){B+=C}B+="\n ";return B}function i(E,D){var B="",C,A;B+='\n or <a href="';C=E.urls;C=C==null||C===false?C:C.purge;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemPurge" id="historyItemPurger-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return B}function f(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(10,y,C)})}if(B||B===0){return B}else{return""}}function y(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(11,x,D)})}if(C||C===0){B+=C}B+="\n";return B}function x(B,A){return"This dataset has been deleted and removed from disk."}function w(D,C){var B,A;A=q.warningmessagesmall;if(A){B=A.call(D,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}else{B=D.warningmessagesmall;B=typeof B===e?B():B}if(!q.warningmessagesmall){B=c.call(D,B,{hash:{},inverse:p.noop,fn:p.program(14,v,C)})}if(B||B===0){return B}else{return""}}function v(E,D){var B="",C,A;B+="\n ";A=q.local;if(A){C=A.call(E,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(15,u,D)})}if(C||C===0){B+=C}B+="\n ";C=E.urls;C=C==null||C===false?C:C.unhide;C=q["if"].call(E,C,{hash:{},inverse:p.noop,fn:p.program(17,t,D)});if(C||C===0){B+=C}B+="\n";return B}function u(B,A){return"This dataset has been hidden."}function t(E,D){var B="",C,A;B+='\n Click <a href="';C=E.urls;C=C==null||C===false?C:C.unhide;C=typeof C===e?C():C;B+=d(C)+'" class="historyItemUnhide" id="historyItemUnhider-';A=q.id;if(A){C=A.call(E,{hash:{}})}else{C=E.id;C=typeof C===e?C():C}B+=d(C)+'"\n target="galaxy_history">here</a> to unhide it\n ';return B}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,z)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,z)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(13,w,z)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js --- a/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js +++ b/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-quota"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<div id="quota-meter" class="quota-meter progress">\n <div id="quota-meter-bar" class="quota-meter-bar bar" style="width: ';g=d.quota_percent;if(g){c=g.call(l,{hash:{}})}else{c=l.quota_percent;c=typeof c===f?c():c}h+=i(c)+'%"></div>\n ';h+='\n <div id="quota-meter-text" class="quota-meter-text"style="top: 6px">\n Using ';g=d.quota_percent;if(g){c=g.call(l,{hash:{}})}else{c=l.quota_percent;c=typeof c===f?c():c}h+=i(c)+"%\n </div>\n</div>";return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-quota"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,o=this,n=e.blockHelperMissing;function d(q,p){return"Using"}i+='<div id="quota-meter" class="quota-meter progress">\n <div id="quota-meter-bar" class="quota-meter-bar bar" style="width: ';h=e.quota_percent;if(h){c=h.call(m,{hash:{}})}else{c=m.quota_percent;c=typeof c===g?c():c}i+=j(c)+'%"></div>\n ';i+='\n <div id="quota-meter-text" class="quota-meter-text"style="top: 6px">\n ';h=e.local;if(h){c=h.call(m,{hash:{},inverse:o.noop,fn:o.program(1,d,k)})}else{c=m.local;c=typeof c===g?c():c}if(!e.local){c=n.call(m,c,{hash:{},inverse:o.noop,fn:o.program(1,d,k)})}if(c||c===0){i+=c}i+=" ";h=e.quota_percent;if(h){c=h.call(m,{hash:{}})}else{c=m.quota_percent;c=typeof c===g?c():c}i+=j(c)+"%\n </div>\n</div>";return i})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js --- a/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js +++ b/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-usage"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='\n<div id="quota-meter" class="quota-meter" style="background-color: transparent">\n <div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white">\n Using ';g=d.nice_total_disk_usage;if(g){c=g.call(l,{hash:{}})}else{c=l.nice_total_disk_usage;c=typeof c===f?c():c}h+=i(c)+"\n </div>\n</div>";return h})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-usage"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,o=this,g="function",n=e.blockHelperMissing,j=this.escapeExpression;function d(q,p){return"Using"}i+='\n<div id="quota-meter" class="quota-meter" style="background-color: transparent">\n <div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white">\n ';h=e.local;if(h){c=h.call(m,{hash:{},inverse:o.noop,fn:o.program(1,d,k)})}else{c=m.local;c=typeof c===g?c():c}if(!e.local){c=n.call(m,c,{hash:{},inverse:o.noop,fn:o.program(1,d,k)})}if(c||c===0){i+=c}i+=" ";h=e.nice_total_disk_usage;if(h){c=h.call(m,{hash:{}})}else{c=m.nice_total_disk_usage;c=typeof c===g?c():c}i+=j(c)+"\n </div>\n</div>";return i})})(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-annotationArea.js --- a/static/scripts/templates/compiled/template-history-annotationArea.js +++ b/static/scripts/templates/compiled/template-history-annotationArea.js @@ -2,17 +2,38 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-annotationArea'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; +function program1(depth0,data) { + + + return "Annotation";} + +function program3(depth0,data) { + + + return "Edit dataset annotation";} buffer += "\n<div id=\""; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-annotation-area\" class=\"annotation-area\" style=\"display: none;\">\n <strong>Annotation:</strong>\n <div id=\""; + buffer += escapeExpression(stack1) + "-annotation-area\" class=\"annotation-area\" style=\"display: none;\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div id=\""; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "-anotation-elt\" class=\"annotation-elt tooltip editable-text\"\n style=\"margin: 1px 0px 1px 0px\" title=\"Edit dataset annotation\">\n </div>\n</div>"; + buffer += escapeExpression(stack1) + "-anotation-elt\" class=\"annotation-elt tooltip editable-text\"\n style=\"margin: 1px 0px 1px 0px\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">\n </div>\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-displayApps.js --- a/static/scripts/templates/compiled/template-history-displayApps.js +++ b/static/scripts/templates/compiled/template-history-displayApps.js @@ -2,7 +2,7 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-displayApps'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { @@ -29,11 +29,20 @@ if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n "; + return buffer;} +function program3(depth0,data) { + + var stack1, foundHelper; foundHelper = helpers.text; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</a>\n "; - return buffer;} + return escapeExpression(stack1);} stack1 = depth0.displayApps; stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-downloadLinks.js --- a/static/scripts/templates/compiled/template-history-downloadLinks.js +++ b/static/scripts/templates/compiled/template-history-downloadLinks.js @@ -2,7 +2,7 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-downloadLinks'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + var stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { @@ -16,10 +16,22 @@ stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">Download Dataset</a>\n <a>Additional Files</a>\n "; + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n <a>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a>\n "; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>\n<div style=\"float:left;\" class=\"menubutton split popup\" id=\"dataset-"; foundHelper = helpers.id; @@ -29,36 +41,77 @@ stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; + buffer += escapeExpression(stack1) + "\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button disk tooltip\"></a>\n</div>\n"; return buffer;} function program2(depth0,data) { + + return "Download Dataset";} + +function program4(depth0,data) { + + + return "Additional Files";} + +function program6(depth0,data) { + var buffer = "", stack1, foundHelper; buffer += "\n <a class=\"action-button\" href=\""; foundHelper = helpers.url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\">Download "; + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " "; foundHelper = helpers.file_type; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.file_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</a>\n "; return buffer;} +function program7(depth0,data) { + + + return "Download";} -function program4(depth0,data) { +function program9(depth0,data) { - var buffer = "", stack1; + + return "Download";} + +function program11(depth0,data) { + + var buffer = "", stack1, foundHelper; buffer += "\n"; buffer += "\n<a href=\""; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.download; stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\" title=\"Download\" class=\"icon-button disk tooltip\"></a>\n"; + buffer += escapeExpression(stack1) + "\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" class=\"icon-button disk tooltip\"></a>\n"; return buffer;} +function program12(depth0,data) { + + + return "Download";} stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.meta_download; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(11, program11, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { return stack1; } else { return ''; }}); })(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-failedMetaData.js --- a/static/scripts/templates/compiled/template-history-failedMetaData.js +++ b/static/scripts/templates/compiled/template-history-failedMetaData.js @@ -2,17 +2,27 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-failedMetaData'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + var stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; function program1(depth0,data) { - var buffer = "", stack1; - buffer += "\nAn error occurred setting the metadata for this dataset.\nYou may be able to <a href=\""; + var buffer = "", stack1, foundHelper; + buffer += "\n"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\nYou may be able to <a href=\""; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.edit; stack1 = typeof stack1 === functionType ? stack1() : stack1; buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">set it manually or retry auto-detection</a>.\n"; return buffer;} +function program2(depth0,data) { + + + return "An error occurred setting the metadata for this dataset.";} foundHelper = helpers.warningmessagesmall; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -2,95 +2,148 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; function program1(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip editable-text\"\n title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} +function program2(depth0,data) { + + + return "Click to rename history";} -function program3(depth0,data) { +function program4(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip\"\n title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} +function program5(depth0,data) { + + + return "You must be logged in to edit your history name";} -function program5(depth0,data) { +function program7(depth0,data) { return "Click to see more actions";} -function program7(depth0,data) { +function program9(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <div id=\"history-secondary-links\" style=\"float: right;\">\n <a id=\"history-tag\" title=\""; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; - foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; return buffer;} -function program8(depth0,data) { +function program10(depth0,data) { return "Edit history tags";} -function program10(depth0,data) { +function program12(depth0,data) { return "Edit history annotation";} -function program12(depth0,data) { +function program14(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program13(depth0,data) { +function program15(depth0,data) { var stack1, foundHelper; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program14(depth0,data) { +function program16(depth0,data) { return "You are currently viewing a deleted history!";} -function program16(depth0,data) { +function program18(depth0,data) { - var buffer = "", stack1; - buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\"\n title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\">\n "; stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(19, program19, data),fn:self.program(17, program17, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n </div>\n </div>\n </div>\n "; return buffer;} -function program17(depth0,data) { +function program19(depth0,data) { + + + return "Tags";} + +function program21(depth0,data) { + + + return "Annotation";} + +function program23(depth0,data) { + + + return "Click to edit annotation";} + +function program25(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -100,12 +153,23 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program19(depth0,data) { +function program27(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <em>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(28, program28, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(28, program28, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</em>\n "; + return buffer;} +function program28(depth0,data) { - return "\n <em>Describe or add notes to history</em>\n ";} + + return "Describe or add notes to history";} -function program21(depth0,data) { +function program30(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <div id=\"message-container\">\n <div class=\""; @@ -119,7 +183,12 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n </div>\n "; return buffer;} -function program23(depth0,data) { +function program32(depth0,data) { + + + return "You are over your disk quota.\n Tool execution is on hold until your disk usage drops below your allocated quota.";} + +function program34(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} @@ -128,13 +197,13 @@ buffer += "\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(4, program4, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n\n <a id=\"history-action-popup\" class=\"tooltip\" title=\""; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\"\n href=\"javascript:void(0);\" style=\"float: right;\">\n <span class=\"ficon cog large\"></span>\n </a>\n <div style=\"clear: both;\"></div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; foundHelper = helpers.nice_size; @@ -143,32 +212,38 @@ buffer += escapeExpression(stack1) + "</div>\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n <div style=\"clear: both;\"></div>\n </div>\n\n "; stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; buffer += "\n "; buffer += "\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(30, program30, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id=\""; + buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(32, program32, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(32, program32, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n </div>\n</div>\n\n<div id=\""; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(34, program34, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(34, program34, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>"; return buffer;}); diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-tagArea.js --- a/static/scripts/templates/compiled/template-history-tagArea.js +++ b/static/scripts/templates/compiled/template-history-tagArea.js @@ -2,9 +2,19 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-tagArea'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = ""; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing; +function program1(depth0,data) { + + + return "Tags";} - buffer += "\n<div class=\"tag-area\" style=\"display: none;\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\">\n </div>\n</div>"; + buffer += "\n<div class=\"tag-area\" style=\"display: none;\">\n <strong>"; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div class=\"tag-elt\">\n </div>\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-history-warning-messages.js --- a/static/scripts/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -24,17 +24,29 @@ return buffer;} function program3(depth0,data) { - var buffer = "", stack1; - buffer += "\n This dataset has been deleted.\n "; + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} function program4(depth0,data) { + + return "This dataset has been deleted.";} + +function program6(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n "; buffer += "\n Click <a href=\""; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.undelete; @@ -46,11 +58,11 @@ buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.purge; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program5(depth0,data) { +function program7(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n or <a href=\""; @@ -64,40 +76,62 @@ buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; return buffer;} -function program7(depth0,data) { +function program9(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program8(depth0,data) { +function program10(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program11(depth0,data) { - return "\n This dataset has been deleted and removed from disk.\n";} + + return "This dataset has been deleted and removed from disk.";} -function program10(depth0,data) { +function program13(depth0,data) { var stack1, foundHelper; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program11(depth0,data) { +function program14(depth0,data) { - var buffer = "", stack1; - buffer += "\n This dataset has been hidden.\n "; + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; stack1 = depth0.urls; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.unhide; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n"; return buffer;} -function program12(depth0,data) { +function program15(depth0,data) { + + + return "This dataset has been hidden.";} + +function program17(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n Click <a href=\""; @@ -116,11 +150,11 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.purged; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.visible; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer;}); })(); \ No newline at end of file diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-user-quotaMeter-quota.js --- a/static/scripts/templates/compiled/template-user-quotaMeter-quota.js +++ b/static/scripts/templates/compiled/template-user-quotaMeter-quota.js @@ -2,15 +2,25 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-user-quotaMeter-quota'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; +function program1(depth0,data) { + + + return "Using";} buffer += "<div id=\"quota-meter\" class=\"quota-meter progress\">\n <div id=\"quota-meter-bar\" class=\"quota-meter-bar bar\" style=\"width: "; foundHelper = helpers.quota_percent; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.quota_percent; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "%\"></div>\n "; - buffer += "\n <div id=\"quota-meter-text\" class=\"quota-meter-text\"style=\"top: 6px\">\n Using "; + buffer += "\n <div id=\"quota-meter-text\" class=\"quota-meter-text\"style=\"top: 6px\">\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " "; foundHelper = helpers.quota_percent; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.quota_percent; stack1 = typeof stack1 === functionType ? stack1() : stack1; } diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/compiled/template-user-quotaMeter-usage.js --- a/static/scripts/templates/compiled/template-user-quotaMeter-usage.js +++ b/static/scripts/templates/compiled/template-user-quotaMeter-usage.js @@ -2,10 +2,20 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-user-quotaMeter-usage'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; +function program1(depth0,data) { + + + return "Using";} - buffer += "\n<div id=\"quota-meter\" class=\"quota-meter\" style=\"background-color: transparent\">\n <div id=\"quota-meter-text\" class=\"quota-meter-text\" style=\"top: 6px; color: white\">\n Using "; + buffer += "\n<div id=\"quota-meter\" class=\"quota-meter\" style=\"background-color: transparent\">\n <div id=\"quota-meter-text\" class=\"quota-meter-text\" style=\"top: 6px; color: white\">\n "; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " "; foundHelper = helpers.nice_total_disk_usage; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.nice_total_disk_usage; stack1 = typeof stack1 === functionType ? stack1() : stack1; } diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -1,8 +1,9 @@ <script type="text/template" class="template-history" id="template-history-warning-messages"> {{#if deleted}}{{#unless purged}} {{#warningmessagesmall}} - This dataset has been deleted. + {{#local}}This dataset has been deleted.{{/local}} {{#if urls.undelete}} + {{! how in the hell would you localize this? }} Click <a href="{{ urls.undelete }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" target="galaxy_history">here</a> to undelete it {{#if urls.purge}} @@ -14,11 +15,11 @@ {{/unless}}{{/if}} {{#if purged}}{{#warningmessagesmall}} - This dataset has been deleted and removed from disk. + {{#local}}This dataset has been deleted and removed from disk.{{/local}} {{/warningmessagesmall}}{{/if}} {{#unless visible}}{{#warningmessagesmall}} - This dataset has been hidden. + {{#local}}This dataset has been hidden.{{/local}} {{#if urls.unhide}} Click <a href="{{ urls.unhide }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" target="galaxy_history">here</a> to unhide it @@ -48,7 +49,7 @@ <script type="text/template" class="template-history" id="template-history-failedMetaData"> {{#warningmessagesmall}} -An error occurred setting the metadata for this dataset. +{{#local}}An error occurred setting the metadata for this dataset.{{/local}} You may be able to <a href="{{ urls.edit }}" target="galaxy_main">set it manually or retry auto-detection</a>. {{/warningmessagesmall}} </script> @@ -57,25 +58,25 @@ {{#if urls.meta_download}} {{! this will be built using a popupmenu }} <div popupmenu="dataset-{{ id }}-popup"> - <a class="action-button" href="{{ urls.download }}">Download Dataset</a> - <a>Additional Files</a> + <a class="action-button" href="{{ urls.download }}">{{#local}}Download Dataset{{/local}}</a> + <a>{{#local}}Additional Files{{/local}}</a> {{#each urls.meta_download}} - <a class="action-button" href="{{ url }}">Download {{ file_type }}</a> + <a class="action-button" href="{{ url }}">{{#local}}Download{{/local}} {{ file_type }}</a> {{/each}} </div><div style="float:left;" class="menubutton split popup" id="dataset-{{ id }}-popup"> - <a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a> + <a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a></div> {{else}} {{! otherwise a simple icon button }} -<a href="{{ urls.download }}" title="Download" class="icon-button disk tooltip"></a> +<a href="{{ urls.download }}" title="{{#local}}Download{{/local}}" class="icon-button disk tooltip"></a> {{/if}} </script><script type="text/template" class="template-history" id="template-history-tagArea"> {{! TODO: move to mvc/tag.js templates }} <div class="tag-area" style="display: none;"> - <strong>Tags:</strong> + <strong>{{#local}}Tags{{/local}}:</strong><div class="tag-elt"></div></div> @@ -84,9 +85,9 @@ <script type="text/template" class="template-history" id="template-history-annotationArea"> {{! TODO: move to mvc/annotations.js templates, editable-text }} <div id="{{ id }}-annotation-area" class="annotation-area" style="display: none;"> - <strong>Annotation:</strong> + <strong>{{#local}}Annotation{{/local}}:</strong><div id="{{ id }}-anotation-elt" class="annotation-elt tooltip editable-text" - style="margin: 1px 0px 1px 0px" title="Edit dataset annotation"> + style="margin: 1px 0px 1px 0px" title="{{#local}}Edit dataset annotation{{/local}}"></div></div></script> @@ -95,7 +96,7 @@ {{#each displayApps}} {{label}} {{#each links}} - <a target="{{target}}" href="{{href}}">{{text}}</a> + <a target="{{target}}" href="{{href}}">{{#local}}{{text}}{{/local}}</a> {{/each}} <br /> {{/each}} @@ -113,10 +114,10 @@ {{! TODO: factor out conditional css }} {{#if user.email}} <div id="history-name" class="tooltip editable-text" - title="Click to rename history">{{name}}</div> + title="{{#local}}Click to rename history{{/local}}">{{name}}</div> {{else}} <div id="history-name" class="tooltip" - title="You must be logged in to edit your history name">{{name}}</div> + title="{{#local}}You must be logged in to edit your history name{{/local}}">{{name}}</div> {{/if}} </div> @@ -150,18 +151,19 @@ <div id="history-tag-annotation"><div id="history-tag-area" style="display: none"> - <strong>Tags:</strong> + <strong>{{#local}}Tags{{/local}}:</strong><div class="tag-elt"></div></div><div id="history-annotation-area" style="display: none"> - <strong>Annotation / Notes:</strong> + <strong>{{#local}}Annotation{{/local}}:</strong><div id="history-annotation-container"> - <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + <div id="history-annotation" class="tooltip editable-text" + title="{{#local}}Click to edit annotation{{/local}}"> {{#if annotation}} {{annotation}} {{else}} - <em>Describe or add notes to history</em> + <em>{{#local}}Describe or add notes to history{{/local}}</em> {{/if}} </div></div> @@ -179,7 +181,8 @@ <div id="quota-message-container" style="display: none"><div id="quota-message" class="errormessage"> - You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + {{#local}}You are over your disk quota. + Tool execution is on hold until your disk usage drops below your allocated quota.{{/local}} </div></div></div> diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 static/scripts/templates/ui-templates.html --- a/static/scripts/templates/ui-templates.html +++ b/static/scripts/templates/ui-templates.html @@ -3,7 +3,7 @@ <div id="quota-meter-bar" class="quota-meter-bar bar" style="width: {{quota_percent}}%"></div> {{! TODO: remove the hardcoded style }} <div id="quota-meter-text" class="quota-meter-text"style="top: 6px"> - Using {{ quota_percent }}% + {{#local}}Using{{/local}} {{ quota_percent }}% </div></div></script> @@ -12,7 +12,7 @@ {{! TODO: remove the hardcoded styles }} <div id="quota-meter" class="quota-meter" style="background-color: transparent"><div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white"> - Using {{ nice_total_disk_usage }} + {{#local}}Using{{/local}} {{ nice_total_disk_usage }} </div></div></script> diff -r 29d47f28af664cf58941085332666de032a7e7d5 -r 65fddffc937dec062dcf4044cd9d1cd4be2f83e7 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -15,6 +15,37 @@ ## a list of localized strings used in the backbone views, etc. (to be loaded and cached) ##! change on per page basis <% + ## havent been localized + ##[ + ## "anonymous user", + ## "Click to rename history", + ## "Click to see more actions", + ## "Edit history tags", + ## "Edit history annotation", + ## "Tags", + ## "Annotation", + ## "Click to edit annotation", + ## "You are over your disk ...w your allocated quota.", + ## "Show deleted", + ## "Show hidden", + ## "Display data in browser", + ## "Edit Attributes", + ## "Download", + ## "View details", + ## "Run this job again", + ## "Visualize", + ## "Edit dataset tags", + ## "Edit dataset annotation", + ## "Trackster", + ## "Circster", + ## "Scatterplot", + ## "GeneTrack", + ## "Local", + ## "Web", + ## "Current", + ## "main", + ## "Using" + ##] strings_to_localize = [ # from history.mako @@ -193,6 +224,7 @@ "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", "libs/json2", + ##"libs/bootstrap", "libs/backbone/backbone-relational", "mvc/base-mvc", "mvc/ui" )} @@ -220,7 +252,6 @@ ${h.js( "mvc/dataset/hda-model", "mvc/dataset/hda-edit", "mvc/history/history-model", "mvc/history/history-panel", - ##"mvc/tags", "mvc/annotations", "mvc/user/user-model", "mvc/user/user-quotameter" )} @@ -251,6 +282,7 @@ top.Galaxy.paths = galaxy_paths; + top.Galaxy.localization = GalaxyLocalization; window.Galaxy = top.Galaxy; } @@ -289,30 +321,27 @@ // i don't like this history+user relationship, but user authentication changes views/behaviour history.user = user; - //var historyPanel = new HistoryPanel({ - // model : new History( history, hdas ), + var historyPanel = new HistoryPanel({ + model : new History( history, hdas ), + urlTemplates : galaxy_paths.attributes, + logger : console, + // is page sending in show settings? if so override history's + 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' ) } + }); + historyPanel.render(); + + // ...or LOAD FROM THE API + //historyPanel = new HistoryPanel({ + // model: new History(), // urlTemplates : galaxy_paths.attributes, // logger : console, // // is page sending in show settings? if so override history's // 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' ) } //}); - //historyPanel.render(); + //historyPanel.model.loadFromApi( history.id ); - // ...or LOAD FROM THE API - historyPanel = new HistoryPanel({ - model: new History(), - urlTemplates : galaxy_paths.attributes, - logger : console, - // is page sending in show settings? if so override history's - 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' ) } - }); - historyPanel.model.loadFromApi( history.id, historyPanel.show_deleted ); - - if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } - if( !( historyPanel in Galaxy.historyPanels ) ){ Galaxy.historyPanels.unshift( historyPanel ); } - // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) @@ -331,7 +360,7 @@ quotaMeter.bind( 'quota:over', historyPanel.showQuotaMessage, historyPanel ); quotaMeter.bind( 'quota:under', historyPanel.hideQuotaMessage, historyPanel ); // having to add this to handle re-render of hview while overquota (the above do not fire) - historyPanel.on( 'rendered', function(){ + historyPanel.on( 'rendered rendered:initial', function(){ if( quotaMeter.isOverQuota() ){ historyPanel.showQuotaMessage(); } @@ -344,6 +373,9 @@ }, quotaMeter ); + if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } + if( !( historyPanel in Galaxy.historyPanels ) ){ Galaxy.historyPanels.unshift( historyPanel ); } + return; }); </script> @@ -388,6 +420,13 @@ color: black; } + #quota-message-container { + margin: 8px 0px 5px 0px; + } + #quota-message { + margin: 0px; + } + #history-subtitle-area { /*border: 1px solid green;*/ } @@ -397,7 +436,7 @@ } #history-tag-area, #history-annotation-area { - margin-top: 10px; + margin: 10px 0px 10px 0px; } </style> 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 Bitbucket 08 Nov '12

08 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f548b977ce33/ changeset: f548b977ce33 user: carlfeberhard date: 2012-11-08 22:14:15 summary: api/histories, show: state_ids now returns all ids (incl. deleted hdas); (alt)history: minor changes affected #: 6 files diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -80,7 +80,8 @@ if not dataset_dict['deleted']: state_counts[ item_state ] = state_counts[ item_state ] + 1 - state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) ) + + state_ids[ item_state ].append( trans.security.encode_id( dataset_dict[ 'id' ] ) ) return ( state_counts, state_ids ) @@ -114,7 +115,6 @@ state = states.NEW else: - if( ( state_counts[ states.RUNNING ] > 0 ) or ( state_counts[ states.SETTING_METADATA ] > 0 ) or ( state_counts[ states.UPLOAD ] > 0 ) ): @@ -131,13 +131,10 @@ state = states.OK history_data[ 'state' ] = state - history_data[ 'state_details' ] = state_counts history_data[ 'state_ids' ] = state_ids - history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) - except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) log.error( msg, exc_info=True ) diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -9,7 +9,7 @@ //TODO: bind change events from items and collection to this (itemLengths, states) // uncomment this out see log messages - //logger : console, + logger : console, // values from api (may need more) defaults : { @@ -17,19 +17,14 @@ name : '', state : '', - ////TODO: wire these to items (or this) - //show_deleted : false, - //show_hidden : false, - // diskSize : 0, deleted : false, - tags : [], + //tags : [], annotation : null, - //TODO: quota msg and message? how to get those over the api? - message : null, - quotaMsg : false + //TODO: message? how to get over the api? + message : null }, url : function(){ @@ -52,36 +47,43 @@ //this.on( 'change', function( currModel, changedList ){ // this.log( this + ' has changed:', currModel, changedList ); //}); - //this.bind( 'all', function( event ){ - // this.log( this + '', arguments ); - //}); + this.bind( 'all', function( event ){ + //this.log( this + '', arguments ); + console.info( this + '', arguments ); + }); }, // get data via the api (alternative to sending options,hdas to initialize) - loadFromApi : function( historyId, callback ){ + //TODO: this needs work - move to more straightforward deferred + loadFromApi : function( historyId, success ){ var history = this; // fetch the history AND the user (mainly to see if they're logged in at this point) history.attributes.id = historyId; //TODO:?? really? fetch user here? - jQuery.when( jQuery.ajax( 'api/users/current' ), history.fetch() + jQuery.when( + jQuery.ajax( 'api/users/current' ), + history.fetch() ).then( function( userResponse, historyResponse ){ - //console.warn( 'fetched user, history: ', userResponse, historyResponse ); + console.warn( 'fetched user: ', userResponse[0] ); + console.warn( 'fetched history: ', historyResponse[0] ); history.attributes.user = userResponse[0]; //? meh. + history.trigger( 'loaded', historyResponse ); history.log( history ); }).then( function(){ // ...then the hdas (using contents?ids=...) jQuery.ajax( history.url() + '/contents?' + jQuery.param({ - ids : history.itemIdsFromStateIds().join( ',' ) + ids : history.hdaIdsFromStateIds().join( ',' ) // reset the collection to the hdas returned })).success( function( hdas ){ - //console.warn( 'fetched hdas' ); + //console.warn( 'fetched hdas', hdas ); history.hdas.reset( hdas ); history.checkForUpdates(); - callback(); + history.trigger( 'loaded:hdas', hdas ); + if( success ){ callback( history ); } }); }); }, diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -20,7 +20,8 @@ ??: still happening? from loadFromApi: - BUG: not showing previous annotations + BUG: not loading deleted datasets + FIXED: history_contents, show: state_ids returns all ids now (incl. deleted) fixed: BUG: upload, history size, doesn't change @@ -217,6 +218,7 @@ this.setUpActionButton( newRender.find( '#history-action-popup' ) ); // render hda views (if any and any shown (show_deleted/hidden) + //TODO: this seems too elaborate if( !this.model.hdas.length || !this.renderItems( newRender.find( '#' + this.model.get( 'id' ) + '-datasets' ) ) ){ // if history is empty or no hdas would be rendered, show the empty message @@ -268,24 +270,27 @@ renderItems : function( $whereTo ){ this.hdaViews = {}; var historyView = this, + // only render the shown hdas + //TODO: switch to more general filtered pattern visibleHdas = this.model.hdas.getVisible( this.storage.get( 'show_deleted' ), this.storage.get( 'show_hidden' ) ); - // only render the shown hdas _.each( visibleHdas, function( hda ){ var hdaId = hda.get( 'id' ), expanded = historyView.storage.get( 'expandedHdas' ).get( hdaId ); + historyView.hdaViews[ hdaId ] = new HDAView({ model : hda, expanded : expanded, urlTemplates : historyView.hdaUrlTemplates }); historyView.setUpHdaListeners( historyView.hdaViews[ hdaId ] ); + // render it (NOTE: reverse order, newest on top (prepend)) //TODO: by default send a reverse order list (although this may be more efficient - it's more confusing) - $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); + $whereTo.prepend( historyView.hdaViews[ hdaId ].render().$el ); }); return visibleHdas.length; }, diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -26,66 +26,71 @@ function program5(depth0,data) { + + return "Click to see more actions";} + +function program7(depth0,data) { + var buffer = "", stack1, foundHelper; buffer += "\n <div id=\"history-secondary-links\" style=\"float: right;\">\n <a id=\"history-tag\" title=\""; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; - foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; return buffer;} -function program6(depth0,data) { +function program8(depth0,data) { return "Edit history tags";} -function program8(depth0,data) { +function program10(depth0,data) { return "Edit history annotation";} -function program10(depth0,data) { +function program12(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program11(depth0,data) { +function program13(depth0,data) { var stack1, foundHelper; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } if(stack1 || stack1 === 0) { return stack1; } else { return ''; }} -function program12(depth0,data) { +function program14(depth0,data) { return "You are currently viewing a deleted history!";} -function program14(depth0,data) { +function program16(depth0,data) { var buffer = "", stack1; buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(17, program17, data),fn:self.program(15, program15, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(19, program19, data),fn:self.program(17, program17, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n </div>\n </div>\n </div>\n "; return buffer;} -function program15(depth0,data) { +function program17(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -95,12 +100,12 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program17(depth0,data) { +function program19(depth0,data) { return "\n <em>Describe or add notes to history</em>\n ";} -function program19(depth0,data) { +function program21(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <div id=\"message-container\">\n <div class=\""; @@ -114,7 +119,7 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n </div>\n "; return buffer;} -function program21(depth0,data) { +function program23(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} @@ -125,29 +130,35 @@ stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <a id=\"history-action-popup\" href=\"javascript:void(0);\" style=\"float: right;\">\n <span class=\"ficon cog large\"></span>\n </a>\n <div style=\"clear: both;\"></div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; + buffer += "\n </div>\n\n <a id=\"history-action-popup\" class=\"tooltip\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n href=\"javascript:void(0);\" style=\"float: right;\">\n <span class=\"ficon cog large\"></span>\n </a>\n <div style=\"clear: both;\"></div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; foundHelper = helpers.nice_size; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n <div style=\"clear: both;\"></div>\n </div>\n\n "; stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; buffer += "\n "; buffer += "\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id=\""; foundHelper = helpers.id; @@ -155,9 +166,9 @@ else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>"; return buffer;}); diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -120,7 +120,8 @@ {{/if}} </div> - <a id="history-action-popup" href="javascript:void(0);" style="float: right;"> + <a id="history-action-popup" class="tooltip" title="{{#local}}Click to see more actions{{/local}}" + href="javascript:void(0);" style="float: right;"><span class="ficon cog large"></span></a><div style="clear: both;"></div> diff -r 6344832c535aab0a8cc4a57be1414fc179e8540b -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -289,24 +289,31 @@ // i don't like this history+user relationship, but user authentication changes views/behaviour history.user = user; - var historyPanel = new HistoryPanel({ - model : new History( history, hdas ), + //var historyPanel = new HistoryPanel({ + // model : new History( history, hdas ), + // urlTemplates : galaxy_paths.attributes, + // logger : console, + // // is page sending in show settings? if so override history's + // 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' ) } + //}); + //historyPanel.render(); + + // ...or LOAD FROM THE API + historyPanel = new HistoryPanel({ + model: new History(), urlTemplates : galaxy_paths.attributes, logger : console, // is page sending in show settings? if so override history's 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' ) } }); - historyPanel.render(); + historyPanel.model.loadFromApi( history.id, historyPanel.show_deleted ); + if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } if( !( historyPanel in Galaxy.historyPanels ) ){ Galaxy.historyPanels.unshift( historyPanel ); } + - - // ...or LOAD FROM THE API - //historyPanel = new HistoryView({ model: new History().setPaths( galaxy_paths ) }); - //historyPanel.loadFromApi( pageData.history.id ); - - // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) //TODO: this really belongs in the masthead @@ -389,6 +396,10 @@ #history-secondary-links { } + #history-tag-area, #history-annotation-area { + margin-top: 10px; + } + </style><noscript> https://bitbucket.org/galaxy/galaxy-central/changeset/29d47f28af66/ changeset: 29d47f28af66 user: carlfeberhard date: 2012-11-08 22:15:03 summary: pack scripts affected #: 2 files diff -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f -r 29d47f28af664cf58941085332666de032a7e7d5 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 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({logger:console,defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}this.bind("all",function(c){console.info(this+"",arguments)})},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){console.warn("fetched user: ",e[0]);console.warn("fetched history: ",d[0]);b.attributes.user=e[0];b.trigger("loaded",d);b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file diff -r f548b977ce33c8e0ba59a2d1586d0122cd9b963f -r 29d47f28af664cf58941085332666de032a7e7d5 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(f,s,q,m,A){q=q||f.helpers;var r="",j,i,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(F,E){var C="",D,B;C+='\n <div id="history-name" class="tooltip editable-text"\n title="Click to rename history">';B=q.name;if(B){D=B.call(F,{hash:{}})}else{D=F.name;D=typeof D===e?D():D}C+=d(D)+"</div>\n ";return C}function n(F,E){var C="",D,B;C+='\n <div id="history-name" class="tooltip"\n title="You must be logged in to edit your history name">';B=q.name;if(B){D=B.call(F,{hash:{}})}else{D=F.name;D=typeof D===e?D():D}C+=d(D)+"</div>\n ";return C}function l(F,E){var C="",D,B;C+='\n <div id="history-secondary-links" style="float: right;">\n <a id="history-tag" title="';B=q.local;if(B){D=B.call(F,{hash:{},inverse:p.noop,fn:p.program(6,k,E)})}else{D=F.local;D=typeof D===e?D():D}if(!q.local){D=c.call(F,D,{hash:{},inverse:p.noop,fn:p.program(6,k,E)})}if(D||D===0){C+=D}C+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';B=q.local;if(B){D=B.call(F,{hash:{},inverse:p.noop,fn:p.program(8,h,E)})}else{D=F.local;D=typeof D===e?D():D}if(!q.local){D=c.call(F,D,{hash:{},inverse:p.noop,fn:p.program(8,h,E)})}if(D||D===0){C+=D}C+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return C}function k(C,B){return"Edit history tags"}function h(C,B){return"Edit history annotation"}function z(F,E){var C="",D,B;C+="\n ";B=q.warningmessagesmall;if(B){D=B.call(F,{hash:{},inverse:p.noop,fn:p.program(11,y,E)})}else{D=F.warningmessagesmall;D=typeof D===e?D():D}if(!q.warningmessagesmall){D=c.call(F,D,{hash:{},inverse:p.noop,fn:p.program(11,y,E)})}if(D||D===0){C+=D}C+="\n ";return C}function y(E,D){var C,B;B=q.local;if(B){C=B.call(E,{hash:{},inverse:p.noop,fn:p.program(12,x,D)})}else{C=E.local;C=typeof C===e?C():C}if(!q.local){C=c.call(E,C,{hash:{},inverse:p.noop,fn:p.program(12,x,D)})}if(C||C===0){return C}else{return""}}function x(C,B){return"You are currently viewing a deleted history!"}function w(E,D){var B="",C;B+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';C=E.annotation;C=q["if"].call(E,C,{hash:{},inverse:p.program(17,u,D),fn:p.program(15,v,D)});if(C||C===0){B+=C}B+="\n </div>\n </div>\n </div>\n </div>\n ";return B}function v(F,E){var C="",D,B;C+="\n ";B=q.annotation;if(B){D=B.call(F,{hash:{}})}else{D=F.annotation;D=typeof D===e?D():D}C+=d(D)+"\n ";return C}function u(C,B){return"\n <em>Describe or add notes to history</em>\n "}function t(F,E){var C="",D,B;C+='\n <div id="message-container">\n <div class="';B=q.status;if(B){D=B.call(F,{hash:{}})}else{D=F.status;D=typeof D===e?D():D}C+=d(D)+'message">\n ';B=q.message;if(B){D=B.call(F,{hash:{}})}else{D=F.message;D=typeof D===e?D():D}C+=d(D)+"\n </div><br />\n </div>\n ";return C}function g(C,B){return"Your history is empty. Click 'Get Data' on the left pane to start"}r+='\n<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n <div id="history-name-container" style="float: left;">\n ';r+="\n ";j=s.user;j=j==null||j===false?j:j.email;j=q["if"].call(s,j,{hash:{},inverse:p.program(3,n,A),fn:p.program(1,o,A)});if(j||j===0){r+=j}r+='\n </div>\n\n <a id="history-action-popup" href="javascript:void(0);" style="float: right;">\n <span class="ficon cog large"></span>\n </a>\n <div style="clear: both;"></div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';i=q.nice_size;if(i){j=i.call(s,{hash:{}})}else{j=s.nice_size;j=typeof j===e?j():j}r+=d(j)+"</div>\n ";j=s.user;j=j==null||j===false?j:j.email;j=q["if"].call(s,j,{hash:{},inverse:p.noop,fn:p.program(5,l,A)});if(j||j===0){r+=j}r+='\n <div style="clear: both;"></div>\n </div>\n\n ';j=s.deleted;j=q["if"].call(s,j,{hash:{},inverse:p.noop,fn:p.program(10,z,A)});if(j||j===0){r+=j}r+="\n\n ";r+="\n ";r+="\n ";j=s.user;j=j==null||j===false?j:j.email;j=q["if"].call(s,j,{hash:{},inverse:p.noop,fn:p.program(14,w,A)});if(j||j===0){r+=j}r+="\n\n ";j=s.message;j=q["if"].call(s,j,{hash:{},inverse:p.noop,fn:p.program(19,t,A)});if(j||j===0){r+=j}r+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id="';i=q.id;if(i){j=i.call(s,{hash:{}})}else{j=s.id;j=typeof j===e?j():j}r+=d(j)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';i=q.local;if(i){j=i.call(s,{hash:{},inverse:p.noop,fn:p.program(21,g,A)})}else{j=s.local;j=typeof j===e?j():j}if(!q.local){j=c.call(s,j,{hash:{},inverse:p.noop,fn:p.program(21,g,A)})}if(j||j===0){r+=j}r+="\n</div>";return r})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(g,t,r,n,B){r=r||g.helpers;var s="",k,j,e="function",d=this.escapeExpression,q=this,c=r.blockHelperMissing;function p(G,F){var D="",E,C;D+='\n <div id="history-name" class="tooltip editable-text"\n title="Click to rename history">';C=r.name;if(C){E=C.call(G,{hash:{}})}else{E=G.name;E=typeof E===e?E():E}D+=d(E)+"</div>\n ";return D}function o(G,F){var D="",E,C;D+='\n <div id="history-name" class="tooltip"\n title="You must be logged in to edit your history name">';C=r.name;if(C){E=C.call(G,{hash:{}})}else{E=G.name;E=typeof E===e?E():E}D+=d(E)+"</div>\n ";return D}function m(D,C){return"Click to see more actions"}function l(G,F){var D="",E,C;D+='\n <div id="history-secondary-links" style="float: right;">\n <a id="history-tag" title="';C=r.local;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(8,i,F)})}else{E=G.local;E=typeof E===e?E():E}if(!r.local){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(8,i,F)})}if(E||E===0){D+=E}D+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';C=r.local;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(10,A,F)})}else{E=G.local;E=typeof E===e?E():E}if(!r.local){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(10,A,F)})}if(E||E===0){D+=E}D+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return D}function i(D,C){return"Edit history tags"}function A(D,C){return"Edit history annotation"}function z(G,F){var D="",E,C;D+="\n ";C=r.warningmessagesmall;if(C){E=C.call(G,{hash:{},inverse:q.noop,fn:q.program(13,y,F)})}else{E=G.warningmessagesmall;E=typeof E===e?E():E}if(!r.warningmessagesmall){E=c.call(G,E,{hash:{},inverse:q.noop,fn:q.program(13,y,F)})}if(E||E===0){D+=E}D+="\n ";return D}function y(F,E){var D,C;C=r.local;if(C){D=C.call(F,{hash:{},inverse:q.noop,fn:q.program(14,x,E)})}else{D=F.local;D=typeof D===e?D():D}if(!r.local){D=c.call(F,D,{hash:{},inverse:q.noop,fn:q.program(14,x,E)})}if(D||D===0){return D}else{return""}}function x(D,C){return"You are currently viewing a deleted history!"}function w(F,E){var C="",D;C+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';D=F.annotation;D=r["if"].call(F,D,{hash:{},inverse:q.program(19,u,E),fn:q.program(17,v,E)});if(D||D===0){C+=D}C+="\n </div>\n </div>\n </div>\n </div>\n ";return C}function v(G,F){var D="",E,C;D+="\n ";C=r.annotation;if(C){E=C.call(G,{hash:{}})}else{E=G.annotation;E=typeof E===e?E():E}D+=d(E)+"\n ";return D}function u(D,C){return"\n <em>Describe or add notes to history</em>\n "}function h(G,F){var D="",E,C;D+='\n <div id="message-container">\n <div class="';C=r.status;if(C){E=C.call(G,{hash:{}})}else{E=G.status;E=typeof E===e?E():E}D+=d(E)+'message">\n ';C=r.message;if(C){E=C.call(G,{hash:{}})}else{E=G.message;E=typeof E===e?E():E}D+=d(E)+"\n </div><br />\n </div>\n ";return D}function f(D,C){return"Your history is empty. Click 'Get Data' on the left pane to start"}s+='\n<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n <div id="history-name-container" style="float: left;">\n ';s+="\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.program(3,o,B),fn:q.program(1,p,B)});if(k||k===0){s+=k}s+='\n </div>\n\n <a id="history-action-popup" class="tooltip" title="';j=r.local;if(j){k=j.call(t,{hash:{},inverse:q.noop,fn:q.program(5,m,B)})}else{k=t.local;k=typeof k===e?k():k}if(!r.local){k=c.call(t,k,{hash:{},inverse:q.noop,fn:q.program(5,m,B)})}if(k||k===0){s+=k}s+='"\n href="javascript:void(0);" style="float: right;">\n <span class="ficon cog large"></span>\n </a>\n <div style="clear: both;"></div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';j=r.nice_size;if(j){k=j.call(t,{hash:{}})}else{k=t.nice_size;k=typeof k===e?k():k}s+=d(k)+"</div>\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(7,l,B)});if(k||k===0){s+=k}s+='\n <div style="clear: both;"></div>\n </div>\n\n ';k=t.deleted;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(12,z,B)});if(k||k===0){s+=k}s+="\n\n ";s+="\n ";s+="\n ";k=t.user;k=k==null||k===false?k:k.email;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(16,w,B)});if(k||k===0){s+=k}s+="\n\n ";k=t.message;k=r["if"].call(t,k,{hash:{},inverse:q.noop,fn:q.program(21,h,B)});if(k||k===0){s+=k}s+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id="';j=r.id;if(j){k=j.call(t,{hash:{}})}else{k=t.id;k=typeof k===e?k():k}s+=d(k)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';j=r.local;if(j){k=j.call(t,{hash:{},inverse:q.noop,fn:q.program(23,f,B)})}else{k=t.local;k=typeof k===e?k():k}if(!r.local){k=c.call(t,k,{hash:{},inverse:q.noop,fn:q.program(23,f,B)})}if(k||k===0){s+=k}s+="\n</div>";return s})})(); \ 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: 2 new changesets
by Bitbucket 08 Nov '12

08 Nov '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c2e7520982ef/ changeset: c2e7520982ef user: carlfeberhard date: 2012-11-08 20:42:26 summary: (alt)history: move show_deleted, show_hidden to the client. galaxy.util: added string_as_bool_or_none which parses True/False/None values from controller args. affected #: 11 files diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -339,6 +339,24 @@ else: return False +def string_as_bool_or_none( string ): + """ + Returns True, None or False based on the argument: + True if passed True, 'True', 'Yes', or 'On' + None if passed None or 'None' + False otherwise + + Note: string comparison is case-insensitive so lowecase versions of those + function equivalently. + """ + string = str( string ).lower() + if string in ( 'true', 'yes', 'on' ): + return True + elif string == 'none': + return None + else: + return False + def listify( item ): """ Make a single item a single item list, or return a list if passed a diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -98,7 +98,8 @@ return trans.fill_template_mako( "/my_data.mako" ) @web.expose - def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ): + #def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ): + def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): """ Display the current history, creating a new history if necessary. NOTE: No longer accepts "id" or "template" options for security reasons. @@ -116,9 +117,9 @@ show_deleted=util.string_as_bool( show_deleted ), show_hidden=util.string_as_bool( show_hidden ) ) else: - show_deleted = util.string_as_bool( show_deleted ) - show_hidden = util.string_as_bool( show_hidden ) - show_purged = util.string_as_bool( show_deleted ) + show_deleted = util.string_as_bool_or_none( show_deleted ) + show_purged = show_deleted + show_hidden = util.string_as_bool_or_none( show_hidden ) datasets = [] history_panel_template = "root/history.mako" @@ -128,6 +129,7 @@ if 'USE_ALTERNATE' in locals(): datasets = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) + #datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden, show_purged ) history_panel_template = "root/alternate_history.mako" else: diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -17,10 +17,10 @@ name : '', state : '', - //TODO: wire these to items (or this) - show_deleted : false, - show_hidden : false, - + ////TODO: wire these to items (or this) + //show_deleted : false, + //show_hidden : false, + // diskSize : 0, deleted : false, diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -8,6 +8,8 @@ anon user, mako template init: bug: rename url seems to be wrong url + BUG: shouldn't have tag/anno buttons (on hdas) + logged in, mako template: BUG: meter is not updating RELIABLY on change:nice_size BUG: am able to start upload even if over quota - 'runs' forever @@ -54,6 +56,8 @@ show_deleted/hidden: use storage on/off ui + need urls + change template move histview fadein/out in render to app? don't draw body until it's first expand event localize all @@ -124,10 +128,30 @@ // data that needs to be persistant over page refreshes // (note the key function which uses the history id as well) - this.storage = new PersistantStorage( - 'HistoryView.' + this.model.get( 'id' ), - { expandedHdas : {} } - ); + this.storage = new PersistantStorage( 'HistoryView.' + this.model.get( 'id' ), { + expandedHdas : {}, + show_deleted : false, + show_hidden : false + }); + this.log( 'this.storage:', this.storage.get() ); + + // get the show_deleted/hidden settings giving priority to values passed into initialize, but + // using web storage otherwise + this.log( 'show_deleted:', attributes.show_deleted, 'show_hidden', attributes.show_hidden ); + // if the page has specifically requested show_deleted/hidden, these will be either true or false + // (as opposed to undefined, null) - and we give priority to that setting + if( ( attributes.show_deleted === true ) || ( attributes.show_deleted === false ) ){ + // save them to web storage + this.storage.set( 'show_deleted', attributes.show_deleted ); + } + if( ( attributes.show_hidden === true ) || ( attributes.show_hidden === false ) ){ + this.storage.set( 'show_hidden', attributes.show_hidden ); + } + // pull show_deleted/hidden from the web storage if the page hasn't specified whether to show_deleted/hidden, + this.show_deleted = this.storage.get( 'show_deleted' ); + this.show_hidden = this.storage.get( 'show_hidden' ); + this.log( 'this.show_deleted:', this.show_deleted, 'show_hidden', this.show_hidden ); + this.log( '(now) this.storage:', this.storage.get() ); // bind events from the model's hda collection //this.model.bind( 'change', this.render, this ); @@ -189,7 +213,8 @@ // render the main template, tooltips //NOTE: this is done before the items, since item views should handle theirs themselves newRender.append( HistoryPanel.templates.historyPanel( modelJson ) ); - newRender.find( '.tooltip' ).tooltip(); + newRender.find( '.tooltip' ).tooltip({ placement: 'bottom' }); + this.setUpActionButton( newRender.find( '#history-action-popup' ) ); // render hda views (if any and any shown (show_deleted/hidden) if( !this.model.hdas.length @@ -227,13 +252,26 @@ return this; }, + setUpActionButton : function( $button ){ + var historyPanel = this, + show_deletedText = ( this.storage.get( 'show_deleted' ) )?( 'Hide deleted' ):( 'Show deleted' ), + show_hiddenText = ( this.storage.get( 'show_hidden' ) )?( 'Hide hidden' ):( 'Show hidden' ), + menuActions = {}; + menuActions[ _l( 'refresh' ) ] = function(){ window.location.reload(); }; + menuActions[ _l( 'collapse all' ) ] = function(){ historyPanel.hideAllHdaBodies(); }; + menuActions[ _l( show_deletedText ) ] = function(){ historyPanel.toggleShowDeleted(); }; + menuActions[ _l( show_hiddenText ) ] = function(){ historyPanel.toggleShowHidden(); }; + make_popupmenu( $button, menuActions ); + }, + // set up a view for each item to be shown, init with model and listeners, cache to map ( model.id : view ) renderItems : function( $whereTo ){ this.hdaViews = {}; var historyView = this, - show_deleted = this.model.get( 'show_deleted' ), - show_hidden = this.model.get( 'show_hidden' ), - visibleHdas = this.model.hdas.getVisible( show_deleted, show_hidden ); + visibleHdas = this.model.hdas.getVisible( + this.storage.get( 'show_deleted' ), + this.storage.get( 'show_hidden' ) + ); // only render the shown hdas _.each( visibleHdas, function( hda ){ @@ -293,6 +331,8 @@ async_save_text( "history-annotation-container", "history-annotation", this.urls.annotate, "new_annotation", 18, true, 4 ); + + //this.$( 'button' ).button(); }, // update the history size display (curr. upper right of panel) @@ -300,6 +340,10 @@ this.$el.find( '#history-size' ).text( this.model.get( 'nice_size' ) ); }, + events : { + 'click #history-tag' : 'loadAndDisplayTags' + }, + //TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here showQuotaMessage : function( userData ){ var msg = this.$el.find( '#quota-message-container' ); @@ -314,9 +358,14 @@ if( !msg.is( ':hidden' ) ){ msg.slideUp( 'fast' ); } }, - events : { - 'click #history-collapse-all' : 'hideAllHdaBodies', - 'click #history-tag' : 'loadAndDisplayTags' + toggleShowDeleted : function( x, y, z ){ + this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) ); + this.render(); + }, + + toggleShowHidden : function(){ + this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) ); + this.render(); }, // collapse all hda bodies diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/dataset/hda-edit.js --- /dev/null +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -0,0 +1,1 @@ +var HDAView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this.renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b.renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b.renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this._clearReferences();this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null;this.showParamsButton=null;this.rerunButton=null;this.visualizationsButton=null;this.tagButton=null;this.annotateButton=null},_render_warnings:function(){return $(jQuery.trim(HDAView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={icon_class:"display"};if(this.model.get("purged")){a.enabled=false;a.title="Cannot display datasets removed from disk"}else{a.title="Display data in browser";a.href=this.urls.display}if(this.model.get("for_editing")){a.target="galaxy_main"}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title="Cannot edit attributes of datasets removed from disk"}else{if(a){b.title="Undelete dataset to edit attributes"}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((!this.model.get("for_editing"))||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var a={title:"Delete",href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDAView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDAView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HDAView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a&&a.length)||!(f)){return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:"Visualize",href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[h]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.tags.get)){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.urls.annotation.get)){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDAView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HDAView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b,a){var c=this.$el.find(".historyItemBody");a=(a===undefined)?(!c.is(":visible")):(a);if(a){c.slideDown("fast")}else{c.slideUp("fast")}this.trigger("toggleBodyVisibility",this.model.get("id"),a)},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(e){var f=window.parent;f.show_modal("View Data in a New or Saved Visualization","",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal("Add Data to Saved Visualization",e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/dataset/hda-model.js --- /dev/null +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -0,0 +1,1 @@ +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false,for_editing:true},url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",OK:"ok",EMPTY:"empty",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}}); \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/history/history-model.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-model.js @@ -0,0 +1,1 @@ +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/packed/mvc/history/history-panel.js --- /dev/null +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -0,0 +1,1 @@ +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);_.each(d,function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -7,232 +7,157 @@ function program1(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip editable-text\"\n title=\"Click to rename history\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; + buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} function program3(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-name\" style=\"margin-right: 50px;\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; + buffer += "\n <div id=\"history-name\" class=\"tooltip\"\n title=\"You must be logged in to edit your history name\">"; foundHelper = helpers.name; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n "; + buffer += escapeExpression(stack1) + "</div>\n "; return buffer;} function program5(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n <div id=\"history-secondary-links\" style=\"float: right;\">\n <a id=\"history-tag\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; + return buffer;} +function program6(depth0,data) { - return "refresh";} + + return "Edit history tags";} -function program7(depth0,data) { +function program8(depth0,data) { - return "collapse all";} + return "Edit history annotation";} -function program9(depth0,data) { +function program10(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n <a id=\"history-tag\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + buffer += "\n "; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\n "; + return buffer;} +function program11(depth0,data) { + + var stack1, foundHelper; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; - return buffer;} -function program10(depth0,data) { - - - return "Edit history tags";} - + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} function program12(depth0,data) { - return "Edit history annotation";} + return "You are currently viewing a deleted history!";} function program14(depth0,data) { - var buffer = "", stack1, foundHelper; - buffer += "\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_deleted; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); } + var buffer = "", stack1; + buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + stack1 = depth0.annotation; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(17, program17, data),fn:self.program(15, program15, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; + buffer += "\n </div>\n </div>\n </div>\n </div>\n "; return buffer;} function program15(depth0,data) { - - return "hide deleted";} + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.annotation; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\n "; + return buffer;} function program17(depth0,data) { - var buffer = "", stack1, foundHelper; - buffer += "\n <a href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.hide_hidden; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\">"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</a>\n "; - return buffer;} -function program18(depth0,data) { - - return "hide hidden";} + return "\n <em>Describe or add notes to history</em>\n ";} -function program20(depth0,data) { +function program19(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n"; - foundHelper = helpers.warningmessagesmall; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n"; - return buffer;} -function program21(depth0,data) { - - var stack1, foundHelper; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(22, program22, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program22(depth0,data) { - - - return "You are currently viewing a deleted history!";} - -function program24(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; - stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n </div>\n </div>\n "; - return buffer;} -function program25(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.annotation; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\n "; - return buffer;} - -function program27(depth0,data) { - - - return "\n <em>Describe or add notes to history</em>\n ";} - -function program29(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n<div id=\"message-container\">\n <div class=\""; + buffer += "\n <div id=\"message-container\">\n <div class=\""; foundHelper = helpers.status; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "message\">\n "; + buffer += escapeExpression(stack1) + "message\">\n "; foundHelper = helpers.message; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\n </div><br />\n</div>\n"; + buffer += escapeExpression(stack1) + "\n </div><br />\n </div>\n "; return buffer;} -function program31(depth0,data) { +function program21(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} - buffer += "\n<div id=\"history-name-area\" class=\"historyLinks\">\n <div id=\"history-name-container\" style=\"position: relative;\">\n "; - buffer += "\n <div id=\"history-size\" style=\"position: absolute; top: 3px; right: 0px;\">"; + buffer += "\n<div id=\"history-controls\">\n <div id=\"history-title-area\" class=\"historyLinks\">\n\n <div id=\"history-name-container\" style=\"float: left;\">\n "; + buffer += "\n "; + stack1 = depth0.user; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </div>\n\n <a id=\"history-action-popup\" href=\"javascript:void(0);\" style=\"float: right;\">\n <span class=\"ficon cog large\"></span>\n </a>\n <div style=\"clear: both;\"></div>\n </div>\n\n <div id=\"history-subtitle-area\">\n <div id=\"history-size\" style=\"float:left;\">"; foundHelper = helpers.nice_size; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "</div>\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div> \n</div>\n<div style=\"clear: both;\"></div>\n\n<div id=\"top-links\" class=\"historyLinks\">\n <a title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); } + buffer += "\n <div style=\"clear: both;\"></div>\n </div>\n\n "; + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\" class=\"icon-button arrow-circle tooltip\" href=\""; - stack1 = depth0.urls; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.base; - stack1 = typeof stack1 === functionType ? stack1() : stack1; - buffer += escapeExpression(stack1) + "\"></a>\n <a title='"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n <div style=\"width: 40px; float: right; white-space: nowrap;\">\n "; + buffer += "\n\n "; + buffer += "\n "; + buffer += "\n "; stack1 = depth0.user; stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n</div>\n<div style=\"clear: both;\"></div>\n\n"; - buffer += "\n<div class=\"historyLinks\">\n "; - stack1 = depth0.show_deleted; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - stack1 = depth0.show_hidden; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); + buffer += "\n\n "; + stack1 = depth0.message; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.deleted; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n"; - buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n "; - stack1 = depth0.user; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</div>\n\n"; - stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(29, program29, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n<div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n</div>\n\n<div id=\""; + buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n </div>\n</div>\n\n<div id=\""; foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(31, program31, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>"; return buffer;}); diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -106,86 +106,80 @@ --><script type="text/template" class="template-history" id="template-history-historyPanel"> {{! history name (if any) }} -<div id="history-name-area" class="historyLinks"> - <div id="history-name-container" style="position: relative;"> - {{! TODO: factor out conditional css }} - <div id="history-size" style="position: absolute; top: 3px; right: 0px;">{{nice_size}}</div> - {{#if user.email}} - <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" +<div id="history-controls"> + <div id="history-title-area" class="historyLinks"> + + <div id="history-name-container" style="float: left;"> + {{! TODO: factor out conditional css }} + {{#if user.email}} + <div id="history-name" class="tooltip editable-text" title="Click to rename history">{{name}}</div> - {{else}} - <div id="history-name" style="margin-right: 50px;" class="tooltip" + {{else}} + <div id="history-name" class="tooltip" title="You must be logged in to edit your history name">{{name}}</div> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> + {{/if}} + </div> -<div id="top-links" class="historyLinks"> - <a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{urls.base}}"></a> - <a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" - class='icon-button toggle tooltip' href='javascript:void(0);'></a> - <div style="width: 40px; float: right; white-space: nowrap;"> - {{#if user.email}} - <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" - class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a> - <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" - class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a> - {{/if}} - </div> -</div> -<div style="clear: both;"></div> - -{{! TODO: move to js with no reload - use each with historyLinks }} -<div class="historyLinks"> - {{#if show_deleted}} - <a href="{{urls.hide_deleted}}">{{#local}}hide deleted{{/local}}</a> - {{/if}} - {{#if show_hidden}} - <a href="{{urls.hide_hidden}}">{{#local}}hide hidden{{/local}}</a> - {{/if}} -</div> - -{{#if deleted}} -{{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} -{{/if}} - -{{! tags and annotations }} -{{! TODO: move inline styles out }} -<div style="margin: 0px 5px 10px 5px"> - - {{#if user.email}} - <div id="history-tag-area" style="display: none"> - <strong>Tags:</strong> - <div class="tag-elt"></div> + <a id="history-action-popup" href="javascript:void(0);" style="float: right;"> + <span class="ficon cog large"></span> + </a> + <div style="clear: both;"></div></div> - <div id="history-annotation-area" style="display: none"> - <strong>Annotation / Notes:</strong> - <div id="history-annotation-container"> - <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> - {{#if annotation}} - {{annotation}} - {{else}} - <em>Describe or add notes to history</em> - {{/if}} + <div id="history-subtitle-area"> + <div id="history-size" style="float:left;">{{nice_size}}</div> + {{#if user.email}} + <div id="history-secondary-links" style="float: right;"> + <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" + class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a> + <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" + class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a></div> + {{/if}} + <div style="clear: both;"></div> + </div> + + {{#if deleted}} + {{#warningmessagesmall}}{{#local}}You are currently viewing a deleted history!{{/local}}{{/warningmessagesmall}} + {{/if}} + + {{! tags and annotations }} + {{! TODO: move inline styles out }} + {{#if user.email}} + <div id="history-tag-annotation"> + + <div id="history-tag-area" style="display: none"> + <strong>Tags:</strong> + <div class="tag-elt"></div> + </div> + + <div id="history-annotation-area" style="display: none"> + <strong>Annotation / Notes:</strong> + <div id="history-annotation-container"> + <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> + {{#if annotation}} + {{annotation}} + {{else}} + <em>Describe or add notes to history</em> + {{/if}} + </div> + </div></div></div> {{/if}} -</div> -{{#if message}} -<div id="message-container"> - <div class="{{status}}message"> - {{message}} - </div><br /> -</div> -{{/if}} + {{#if message}} + <div id="message-container"> + <div class="{{status}}message"> + {{message}} + </div><br /> + </div> + {{/if}} -<div id="quota-message-container" style="display: none"> - <div id="quota-message" class="errormessage"> - You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + <div id="quota-message-container" style="display: none"> + <div id="quota-message" class="errormessage"> + You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. + </div></div></div> diff -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -42,9 +42,9 @@ 'No data: ', 'format: ', 'database: ', - # localized data.dbkey?? - localize in the datasetup above + #TODO localized data.dbkey?? 'Info: ', - # localized display_app.display_name?? - localize above + #TODO localized display_app.display_name?? # _( link_app.name ) # localized peek...ugh 'Error: unknown dataset state', @@ -63,12 +63,6 @@ encoded_id_template = '<%= id %>' url_dict = { - # TODO:?? next 3 needed? - 'base' : h.url_for( controller="/history" ), - ##TODO: move these into the historyMV - 'hide_deleted' : h.url_for( controller="/history", show_deleted=False ), - 'hide_hidden' : h.url_for( controller="/history", show_hidden=False ), - ##TODO: into their own MVs 'rename' : h.url_for( controller="/history", action="rename_async", id=encoded_id_template ), @@ -294,15 +288,14 @@ // add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour history.user = user; - // is page sending in show settings? if so override history's - //TODO: move into historyPanel - history.show_deleted = ${ 'true' if show_deleted else 'false' }; - history.show_hidden = ${ 'true' if show_hidden else 'false' }; var historyPanel = new HistoryPanel({ - model : new History( history, hdas ), - urlTemplates: galaxy_paths.attributes, - logger : console + model : new History( history, hdas ), + urlTemplates : galaxy_paths.attributes, + logger : console, + // is page sending in show settings? if so override history's + 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' ) } }); historyPanel.render(); if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } @@ -317,6 +310,7 @@ // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) //TODO: this really belongs in the masthead + //TODO: and the quota message (curr. in the history panel) belongs somewhere else //window.currUser.logger = console; var quotaMeter = new UserQuotaMeter({ @@ -351,30 +345,50 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css("base", "history", "autocomplete_tagging" )} + ${h.css( + "base", + "history", + "autocomplete_tagging" + )} <style> ## TODO: move to base.less .historyItemBody { display: none; } - div.form-row { - padding: 5px 5px 5px 0px; + + #history-controls { + /*border: 1px solid white;*/ + margin-bottom: 5px; + padding: 5px; } - #top-links { - margin-bottom: 15px; - } - #history-name-container { - color: gray; - font-weight: bold; + + #history-title-area { + margin: 0px 0px 5px 0px; + /*border: 1px solid red;*/ } #history-name { word-wrap: break-word; + font-weight: bold; + color: black; } .editable-text { border: solid transparent 1px; - padding: 3px; - margin: -4px; } + #history-name-container input { + width: 90%; + margin: -2px 0px -3px -4px; + font-weight: bold; + color: black; + } + + #history-subtitle-area { + /*border: 1px solid green;*/ + } + #history-size { + } + #history-secondary-links { + } + </style><noscript> https://bitbucket.org/galaxy/galaxy-central/changeset/6344832c535a/ changeset: 6344832c535a user: carlfeberhard date: 2012-11-08 20:43:26 summary: pack scripts affected #: 4 files diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b 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 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",show_deleted:false,show_hidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false},url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.log(b)}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.itemIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();c()})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}}).error(function(f,d,e){if(console&&console.warn){console.warn("Error getting history updates from the server:",f,d,e)}alert("Error getting history updates from the server.\n"+e)})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories",logger:console}); \ No newline at end of file diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{}});this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip();if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},renderItems:function(c){this.hdaViews={};var b=this,a=this.model.get("show_deleted"),e=this.model.get("show_hidden"),d=this.model.hdas.getVisible(a,e);_.each(d,function(h){var g=h.get("id"),f=b.storage.get("expandedHdas").get(g);b.hdaViews[g]=new HDAView({model:h,expanded:f,urlTemplates:b.hdaUrlTemplates});b.setUpHdaListeners(b.hdaViews[g]);c.prepend(b.hdaViews[g].render().$el)});return d.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},events:{"click #history-collapse-all":"hideAllHdaBodies","click #history-tag":"loadAndDisplayTags"},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw ("HDAView needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw ("HDAView needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());this.log("show_deleted:",a.show_deleted,"show_hidden",a.show_hidden);if((a.show_deleted===true)||(a.show_deleted===false)){this.storage.set("show_deleted",a.show_deleted)}if((a.show_hidden===true)||(a.show_hidden===false)){this.storage.set("show_hidden",a.show_hidden)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("this.show_deleted:",this.show_deleted,"show_hidden",this.show_hidden);this.log("(now) this.storage:",this.storage.get());this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("all",this.all,this);this.hdaViews={};this.urls={}},add:function(a){},addAll:function(){this.render()},all:function(a){},renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this.renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this.setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b.setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("refresh")]=function(){window.location.reload()};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a.setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},setUpHdaListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("expandedHdas").set(d,true)}else{a.storage.get("expandedHdas").deleteKey(d)}});b.bind("rendered:ready",function(){a.trigger("hda:rendered:ready")})},setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},events:{"click #history-tag":"loadAndDisplayTags"},showQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(b.is(":hidden")){b.slideDown("fast")}},hideQuotaMessage:function(a){var b=this.$el.find("#quota-message-container");if(!b.is(":hidden")){b.slideUp("fast")}},toggleShowDeleted:function(a,c,b){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert("Tagging failed")},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r c2e7520982ef42400a93f97654ad55ce7d6d1a30 -r 6344832c535aab0a8cc4a57be1414fc179e8540b static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(l,z,x,s,G){x=x||l.helpers;var y="",o,n,f="function",e=this.escapeExpression,v=this,c=x.blockHelperMissing;function u(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text"\n title="Click to rename history">';H=x.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function t(L,K){var I="",J,H;I+='\n <div id="history-name" style="margin-right: 50px;" class="tooltip"\n title="You must be logged in to edit your history name">';H=x.name;if(H){J=H.call(L,{hash:{}})}else{J=L.name;J=typeof J===f?J():J}I+=e(J)+"</div>\n ";return I}function r(I,H){return"refresh"}function q(I,H){return"collapse all"}function k(L,K){var I="",J,H;I+='\n <a id="history-tag" title="';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(10,F,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(10,F,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(12,E,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(12,E,K)})}if(J||J===0){I+=J}I+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return I}function F(I,H){return"Edit history tags"}function E(I,H){return"Edit history annotation"}function D(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_deleted;J=typeof J===f?J():J;I+=e(J)+'">';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(15,C,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(15,C,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function C(I,H){return"hide deleted"}function B(L,K){var I="",J,H;I+='\n <a href="';J=L.urls;J=J==null||J===false?J:J.hide_hidden;J=typeof J===f?J():J;I+=e(J)+'">';H=x.local;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(18,A,K)})}else{J=L.local;J=typeof J===f?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(18,A,K)})}if(J||J===0){I+=J}I+="</a>\n ";return I}function A(I,H){return"hide hidden"}function p(L,K){var I="",J,H;I+="\n";H=x.warningmessagesmall;if(H){J=H.call(L,{hash:{},inverse:v.noop,fn:v.program(21,m,K)})}else{J=L.warningmessagesmall;J=typeof J===f?J():J}if(!x.warningmessagesmall){J=c.call(L,J,{hash:{},inverse:v.noop,fn:v.program(21,m,K)})}if(J||J===0){I+=J}I+="\n";return I}function m(K,J){var I,H;H=x.local;if(H){I=H.call(K,{hash:{},inverse:v.noop,fn:v.program(22,j,J)})}else{I=K.local;I=typeof I===f?I():I}if(!x.local){I=c.call(K,I,{hash:{},inverse:v.noop,fn:v.program(22,j,J)})}if(I||I===0){return I}else{return""}}function j(I,H){return"You are currently viewing a deleted history!"}function i(K,J){var H="",I;H+='\n <div id="history-tag-area" style="display: none">\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';I=K.annotation;I=x["if"].call(K,I,{hash:{},inverse:v.program(27,g,J),fn:v.program(25,h,J)});if(I||I===0){H+=I}H+="\n </div>\n </div>\n </div>\n ";return H}function h(L,K){var I="",J,H;I+="\n ";H=x.annotation;if(H){J=H.call(L,{hash:{}})}else{J=L.annotation;J=typeof J===f?J():J}I+=e(J)+"\n ";return I}function g(I,H){return"\n <em>Describe or add notes to history</em>\n "}function d(L,K){var I="",J,H;I+='\n<div id="message-container">\n <div class="';H=x.status;if(H){J=H.call(L,{hash:{}})}else{J=L.status;J=typeof J===f?J():J}I+=e(J)+'message">\n ';H=x.message;if(H){J=H.call(L,{hash:{}})}else{J=L.message;J=typeof J===f?J():J}I+=e(J)+"\n </div><br />\n</div>\n";return I}function w(I,H){return"Your history is empty. 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o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") 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j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(v,w){v.update_radius_bounds(r[w])});g.each(this.chords_views,function(v){v.update_radius_bounds(r[0])});var q=this.circular_views.length,u=(t.get("track_type")==="LineTrack"?d:e),n=new u({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var e=f.extend({get_data_bounds:function(o){var n=g.map(o,function(p){if(typeof p==="string"||!p.max){return 0}return p.max});return[0,(n&&typeof n!=="string"?this._quantile(values,0.98):0)]}});var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var A=(y.get("track_type")==="LineTrack"?d:e),x=new A({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(v,w){v.update_radius_bounds(r[w])});g.each(this.chords_views,function(v){v.update_radius_bounds(r[0])});var q=this.circular_views.length,u=(t.get("track_type")==="LineTrack"?d:e),n=new u({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var e=f.extend({get_data_bounds:function(o){var n=g.map(o,function(p){if(typeof p==="string"||!p.max){return 0}return p.max});return[0,(n&&typeof n!=="string"?this._quantile(values,0.98):0)]}});var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});return{CircsterView:a}}); \ 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: greg: Add the shed_tool_data_table_config to the functional test's app.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/86fbf6e15f79/ changeset: 86fbf6e15f79 user: greg date: 2012-11-08 17:41:21 summary: Add the shed_tool_data_table_config to the functional test's app. affected #: 1 file diff -r 762d4010a9a534ce5237d7a0bb6d317a9d9501ac -r 86fbf6e15f791d62f7a2472d9987577011aa9a8c scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -169,6 +169,7 @@ tool_data_table_config_path = 'tool_data_table_conf.test.xml' else: tool_data_table_config_path = 'tool_data_table_conf.xml' + shed_tool_data_table_config = 'shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) @@ -266,6 +267,7 @@ tool_parse_help = False, test_conf = "test.conf", tool_data_table_config_path = tool_data_table_config_path, + shed_tool_data_table_config = shed_tool_data_table_config, log_destination = "stdout", use_heartbeat = False, allow_user_creation = True, 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: dan: Provide a warning message when uploading files to a toolshed repository and a tool_dependencies.xml has been provided, but tool_dependencies metadata has not been generated.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/762d4010a9a5/ changeset: 762d4010a9a5 user: dan date: 2012-11-08 16:52:45 summary: Provide a warning message when uploading files to a toolshed repository and a tool_dependencies.xml has been provided, but tool_dependencies metadata has not been generated. affected #: 1 file diff -r d3054b066218eacd366e618cc97535d059d8bf6a -r 762d4010a9a534ce5237d7a0bb6d317a9d9501ac lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -160,6 +160,7 @@ # Get the new repository tip. if tip == repository.tip: message = 'No changes to repository. ' + status = 'warning' else: if ( isgzip or isbz2 ) and uncompress_file: uncompress_str = ' uncompressed and ' @@ -182,6 +183,16 @@ message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) + #provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to e.g. a requirement tag mismatch + if get_config_from_disk( 'tool_dependencies.xml', repo_dir ): + if repository.metadata_revisions: + metadata_dict = repository.metadata_revisions[0].metadata + else: + metadata_dict = {} + if 'tool_dependencies' not in metadata_dict: + message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml". ' + status = 'warning' + log.debug( 'Error in tool dependencies for repository %s: %s.' % ( repository.id, repository.name ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', 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: greg: Add the new ched_tool_data_table_config setting to the tool shed's config object.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d3054b066218/ changeset: d3054b066218 user: greg date: 2012-11-08 16:32:30 summary: Add the new ched_tool_data_table_config setting to the tool shed's config object. affected #: 1 file diff -r b5ce9451c5d190f0507f3b2c484afe937f12a045 -r d3054b066218eacd366e618cc97535d059d8bf6a lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -48,6 +48,7 @@ self.tool_secret = kwargs.get( "tool_secret", "" ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) # Location for dependencies if 'tool_dependency_dir' in kwargs: 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: greg: Attempt to make sure .sample files included in an installed tool shed repository are only copied to ~/tool-data if they are sample data index files.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b5ce9451c5d1/ changeset: b5ce9451c5d1 user: greg date: 2012-11-08 16:01:08 summary: Attempt to make sure .sample files included in an installed tool shed repository are only copied to ~/tool-data if they are sample data index files. affected #: 1 file diff -r 5ff899b77dffce59580991a4b1d4dfbcdc091090 -r b5ce9451c5d190f0507f3b2c484afe937f12a045 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -7,6 +7,7 @@ from galaxy.web.form_builder import SelectField from galaxy.tools import parameters from galaxy.datatypes.checkers import * +from galaxy.datatypes.sniff import is_column_based from galaxy.util.json import * from galaxy.util import inflector from galaxy.tools.search import ToolBoxSearch @@ -546,15 +547,20 @@ shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) ) def copy_sample_files( app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None ): """ - Copy all files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied - are contained in sample_files_copied. The default value for dest_path is ~/tool-data. + Copy all appropriate files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied + are contained in sample_files_copied. The default value for dest_path is ~/tool-data. We need to be careful to copy only appropriate + files here because tool shed repositories can contain files ending in .sample that should not be copied to the ~/tool-data directory. """ + filenames_not_to_copy = [ 'tool_data_table_conf.xml.sample' ] sample_files_copied = util.listify( sample_files_copied ) for filename in sample_files: - if filename not in sample_files_copied: + filename_sans_path = os.path.split( filename )[ 1 ] + if filename_sans_path not in filenames_not_to_copy and filename not in sample_files_copied: if tool_path: filename=os.path.join( tool_path, filename ) - copy_sample_file( app, filename, dest_path=dest_path ) + # Attempt to ensure we're copying an appropriate file. + if is_data_index_sample_file( filename ): + copy_sample_file( app, filename, dest_path=dest_path ) def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ): repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, @@ -1539,9 +1545,11 @@ if shed_tool_conf == file_name: return index, shed_tool_conf_dict def get_tool_index_sample_files( sample_files ): + """Try to return the list of all appropriate tool data sample files included in the repository.""" tool_index_sample_files = [] for s in sample_files: - if s.endswith( '.loc.sample' ): + # The problem with this is that Galaxy does not follow a standard naming convention for file names. + if s.endswith( '.loc.sample' ) or s.endswith( '.xml.sample' ) or s.endswith( '.txt.sample' ): tool_index_sample_files.append( s ) return tool_index_sample_files def get_tool_dependency( trans, id ): @@ -1846,6 +1854,29 @@ parent_id=tool_version_using_parent_id.id ) sa_session.add( tool_version_association ) sa_session.flush() +def is_data_index_sample_file( file_path ): + """ + Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when a tool shed repository is being installed + into a Galaxy instance. + """ + # Currently most data index files are tabular, so check that first. We'll assume that if the file is tabular, it's ok to copy. + if is_column_based( file_path ): + return True + # If the file is any of the following, don't copy it. + if check_html( file_path ): + return False + if check_image( file_path ): + return False + if check_binary( name=file_path ): + return False + if is_bz2( file_path ): + return False + if is_gzip( file_path ): + return False + if check_zip( file_path ): + return False + # Default to copying the file if none of the above are true. + return True def is_downloadable( metadata_dict ): return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): 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: dan: Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5ff899b77dff/ changeset: 5ff899b77dff user: dan date: 2012-11-08 03:16:17 summary: Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh. affected #: 1 file diff -r 982b9522efca2abf46637870e06c7abf1204be6d -r 5ff899b77dffce59580991a4b1d4dfbcdc091090 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -68,6 +68,7 @@ datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample +shed_tool_data_table_conf.xml.sample migrated_tools_conf.xml.sample tool-data/shared/ensembl/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample 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: dan: Fix for params_to_incoming.
by Bitbucket 08 Nov '12

08 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/982b9522efca/ changeset: 982b9522efca user: dan date: 2012-11-08 03:06:54 summary: Fix for params_to_incoming. affected #: 2 files diff -r ec51a727a497d5912fdd4269571d7c26d7523436 -r 982b9522efca2abf46637870e06c7abf1204be6d lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -115,5 +115,5 @@ incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ] params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) else: - incoming[ name_prefix + input.name ] = input.to_string( input_values.get( input.name ), app ) + incoming[ name_prefix + input.name ] = input.to_html_value( input_values.get( input.name ), app ) diff -r ec51a727a497d5912fdd4269571d7c26d7523436 -r 982b9522efca2abf46637870e06c7abf1204be6d lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -106,6 +106,10 @@ """ return value + def to_html_value( self, value, app ): + """Convert an object value to the value expected from an html post""" + return self.to_string( value, app ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" return str( value ) @@ -370,6 +374,11 @@ return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) + def to_html_value( self, value, app ): + if value: + return [ 'true', 'true' ] + else: + return [ 'true' ] def to_python( self, value, app ): return ( value == 'True' ) def get_initial_value( self, trans, context ): 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: clements: Modified docstrings so that Sphinx would not complain about them. However, I couldn't get Sphinx to be happy with all docstrings, so we are still getting 10 warnings (down from over 70 though).
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ec51a727a497/ changeset: ec51a727a497 user: clements date: 2012-11-02 07:25:39 summary: Modified docstrings so that Sphinx would not complain about them. However, I couldn't get Sphinx to be happy with all docstrings, so we are still getting 10 warnings (down from over 70 though). affected #: 25 files diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/fastq_to_fqtoc.py --- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py @@ -6,11 +6,13 @@ def main(): """ - The format of the file is JSON: - { "sections" : [ - { "start" : "x", "end" : "y", "sequences" : "z" }, - ... - ]} + The format of the file is JSON:: + + { "sections" : [ + { "start" : "x", "end" : "y", "sequences" : "z" }, + ... + ]} + This works only for UNCOMPRESSED fastq files. The Python GzipFile does not provide seekable offsets via tell(), so clients just have to split the slow way """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/interval_to_fli.py --- a/lib/galaxy/datatypes/converters/interval_to_fli.py +++ b/lib/galaxy/datatypes/converters/interval_to_fli.py @@ -1,12 +1,16 @@ ''' Creates a feature location index (FLI) for a given BED/GFF file. -FLI index has the form: +FLI index has the form:: + [line_length] <symbol1_in_lowercase><tab><symbol1><tab><location><symbol2_in_lowercase><tab><symbol2><tab><location> ... + where location is formatted as: + contig:start-end + and symbols are sorted in lexigraphical order. ''' @@ -94,4 +98,4 @@ out.close() if __name__ == '__main__': - main() \ No newline at end of file + main() diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py --- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py +++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py @@ -78,10 +78,14 @@ """ need to work with rgenetics composite datatypes so in and out are html files with data in extrafiles path - <command interpreter="python"> - pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' - '$output1' '$output1.files_path' 'plink' - </command> + + .. raw:: xml + + <command interpreter="python"> + pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh' + '$output1' '$output1.files_path' 'plink' + </command> + """ nparm = 7 if len(sys.argv) < nparm: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -800,11 +800,12 @@ def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ): """ - Returns the first LINE_COUNT lines wrapped to WIDTH:: + Returns the first LINE_COUNT lines wrapped to WIDTH - ## >>> fname = get_test_fname('4.bed') - ## >>> get_file_peek(fname) - ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' + ## >>> fname = get_test_fname('4.bed') + ## >>> get_file_peek(fname) + ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' + """ # Set size for file.readline() to a negative number to force it to # read until either a newline or EOF. Needed for datasets with very diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -46,6 +46,7 @@ process all data lines. Items of interest: + 1. We treat 'overwrite' as always True (we always want to set tabular metadata when called). 2. If a tabular file has no data, it will have one column of type 'str'. 3. We used to check only the first 100 lines when setting metadata and this class's @@ -356,15 +357,18 @@ Determines whether the file is in SAM format A file in SAM format consists of lines of tab-separated data. - The following header line may be the first line: - @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL - or - @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT + The following header line may be the first line:: + + @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL + or + @QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT + Data in the OPT column is optional and can consist of tab-separated data For complete details see http://samtools.sourceforge.net/SAM1.pdf - Rules for sniffing as True: + Rules for sniffing as True:: + There must be 11 or more columns of data on each line Columns 2 (FLAG), 4(POS), 5 (MAPQ), 8 (MPOS), and 9 (ISIZE) must be numbers (9 can be negative) We will only check that up to the first 5 alignments are correctly formatted. @@ -579,10 +583,11 @@ A file in ELAND export format consists of lines of tab-separated data. There is no header. - Rules for sniffing as True: - There must be 22 columns on each line - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct - We will only check that up to the first 5 alignments are correctly formatted. + Rules for sniffing as True:: + + - There must be 22 columns on each line + - LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct + - We will only check that up to the first 5 alignments are correctly formatted. """ import gzip try: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -51,6 +51,7 @@ store, False otherwise. FIELD DESCRIPTIONS (these apply to all the methods in this class): + :type obj: object :param obj: A Galaxy object with an assigned database ID accessible via the .id attribute. @@ -118,6 +119,7 @@ """ Deletes the object identified by `obj`. See `exists` method for the description of other fields. + :type entire_dir: bool :param entire_dir: If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/quota/__init__.py --- a/lib/galaxy/quota/__init__.py +++ b/lib/galaxy/quota/__init__.py @@ -41,6 +41,7 @@ def get_quota( self, user, nice_size=False ): """ Calculated like so: + 1. Anonymous users get the default quota. 2. Logged in users start with the highest of their associated '=' quotas or the default quota, if there are no associated '=' diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -173,17 +173,21 @@ which the request is sent. We cannot use trans.user_is_admin() because the controller is what is important since admin users do not necessarily have permission to do things on items outside of the admin view. + If cntrller is from the admin side ( e.g., library_admin ): - -if item is public, all roles, including private roles, are legitimate. - -if item is restricted, legitimate roles are derived from the users and groups associated - with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or - LIBRARY_MANAGE ) on item. Legitimate roles will include private roles. + + - if item is public, all roles, including private roles, are legitimate. + - if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or + LIBRARY_MANAGE ) on item. Legitimate roles will include private roles. + If cntrller is not from the admin side ( e.g., root, library ): - -if item is public, all non-private roles, except for the current user's private role, - are legitimate. - -if item is restricted, legitimate roles are derived from the users and groups associated - with each role that is associated with the access permission on item. Private roles, except - for the current user's private role, will be excluded. + + - if item is public, all non-private roles, except for the current user's private role, + are legitimate. + - if item is restricted, legitimate roles are derived from the users and groups associated + with each role that is associated with the access permission on item. Private roles, except + for the current user's private role, will be excluded. """ admin_controller = cntrller in [ 'library_admin' ] roles = set() @@ -1063,9 +1067,10 @@ comma-separated string of folder ids. This method works with the show_library_item() method below, and it returns libraries for which the received user has permission to perform the received actions. Here is an example call to this method to return all - libraries for which the received user has LIBRARY_ADD permission: - libraries = trans.app.security_agent.get_permitted_libraries( trans, user, - [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries for which the received user has LIBRARY_ADD permission:: + + libraries = trans.app.security_agent.get_permitted_libraries( trans, user, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) """ all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted == False ) \ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -250,10 +250,11 @@ def set_environment( app, elem, tool_shed_repository ): """ Create a ToolDependency to set an environment variable. This is different from the process used to set an environment variable that is associated - with a package. An example entry in a tool_dependencies.xml file is: - <set_environment version="1.0"> - <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> + with a package. An example entry in a tool_dependencies.xml file is:: + + <set_environment version="1.0"> + <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> """ sa_session = app.model.context.current tool_dependency = None diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -112,16 +112,20 @@ def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: - <toolbox> - <tool file="data_source/upload.xml"/> # tools outside sections - <label text="Basic Tools" id="basic_tools" /> # labels outside sections - <workflow id="529fd61ab1c6cc36" /> # workflows outside sections - <section name="Get Data" id="getext"> # sections - <tool file="data_source/biomart.xml" /> # tools inside sections - <label text="In Section" id="in_section" /> # labels inside sections - <workflow id="adb5f5c93f827949" /> # workflows inside sections - </section> - </toolbox> + + .. raw:: xml + + <toolbox> + <tool file="data_source/upload.xml"/> # tools outside sections + <label text="Basic Tools" id="basic_tools" /> # labels outside sections + <workflow id="529fd61ab1c6cc36" /> # workflows outside sections + <section name="Get Data" id="getext"> # sections + <tool file="data_source/biomart.xml" /> # tools inside sections + <label text="In Section" id="in_section" /> # labels inside sections + <workflow id="adb5f5c93f827949" /> # workflows inside sections + </section> + </toolbox> + """ if self.app.config.get_bool( 'enable_tool_tags', False ): log.info("removing all tool tag associations (" + str( self.sa_session.query( self.app.model.ToolTagAssociation ).count() ) + ")" ) @@ -740,7 +744,8 @@ class ToolOutput( object ): """ Represents an output datasets produced by a tool. For backward - compatibility this behaves as if it were the tuple: + compatibility this behaves as if it were the tuple:: + (format, metadata_source, parent) """ @@ -1079,7 +1084,7 @@ else: self.trackster_conf = None def parse_inputs( self, root ): - """ + r""" Parse the "<inputs>" element and create appropriate `ToolParameter`s. This implementation supports multiple pages and grouping constructs. """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -31,10 +31,11 @@ def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: - 1) When the ToolDataTableManager is initialized (see __init__ above). - 2) Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml + + 1. When the ToolDataTableManager is initialized (see __init__ above). + 2. Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml are being loaded into the ToolDataTableManager.data_tables. - 3) When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local + 3. When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example: """ tree = util.parse_xml( config_filename ) @@ -57,20 +58,24 @@ def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being - installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: - <tables> + installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example:: + + <tables> +  + <table name="tmap_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/tmap_index.loc" /> + </table> + </tables> + + and files whose root tag is <table>, for example:: + <table name="tmap_indexes" comment_char="#"><columns>value, dbkey, name, path</columns><file path="tool-data/tmap_index.loc" /></table> - </tables> - and files whose root tag is <table>, for example: -  - <table name="tmap_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/tmap_index.loc" /> - </table> + """ tree = util.parse_xml( config_filename ) root = tree.getroot() @@ -119,13 +124,14 @@ class TabularToolDataTable( ToolDataTable ): """ Data stored in a tabular / separated value format on disk, allows multiple - files to be merged but all must have the same column definitions. + files to be merged but all must have the same column definitions:: - <table type="tabular" name="test"> - <column name='...' index = '...' /> - <file path="..." /> - <file path="..." /> - </table> + <table type="tabular" name="test"> + <column name='...' index = '...' /> + <file path="..." /> + <file path="..." /> + </table> + """ type_key = 'tabular' diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -64,16 +64,20 @@ Type: data_meta - When no 'from_' source has been specified in the <options> tag, this will populate the options list with (meta_value, meta_value, False). + When no 'from' source has been specified in the <options> tag, this will populate the options list with (meta_value, meta_value, False). Otherwise, options which do not match the metadata value in the column are discarded. Required Attributes: - ref: Name of input dataset - key: Metadata key to use for comparison - column: column in options to compare with (not required when not associated with input options) + + - ref: Name of input dataset + - key: Metadata key to use for comparison + - column: column in options to compare with (not required when not associated with input options) + Optional Attributes: - multiple: Option values are multiple, split column by separator (True) - separator: When multiple split by this (,) + + - multiple: Option values are multiple, split column by separator (True) + - separator: When multiple split by this (,) + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) @@ -132,12 +136,16 @@ Type: param_value Required Attributes: - ref: Name of input value - column: column in options to compare with + + - ref: Name of input value + - column: column in options to compare with + Optional Attributes: - keep: Keep columns matching value (True) - Discard columns matching value (False) - ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter + + - keep: Keep columns matching value (True) + Discard columns matching value (False) + - ref_attribute: Period (.) separated attribute chain of input (ref) to use as value for filter + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) @@ -294,13 +302,15 @@ Type: remove_value - Required Attributes: + Required Attributes:: + value: value to remove from select list or ref: param to refer to or meta_ref: dataset to refer to key: metadata key to compare to + """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/heartbeat.py --- a/lib/galaxy/util/heartbeat.py +++ b/lib/galaxy/util/heartbeat.py @@ -134,7 +134,9 @@ Scans a given backtrace stack frames, returns a single quadraple of [filename, line, function-name, text] of the single, deepest, most interesting frame. - Interesting being: + + Interesting being:: + inside the galaxy source code ("/lib/galaxy"), prefreably not an egg. """ diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2397,11 +2397,13 @@ def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates - to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is: - {"name": "bwa", - "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", - "type": "package", - "version": "0.6.2"} + to an installed tool shed repository. The original_dependency_dict is a single tool dependency definition, an example of which is:: + + {"name": "bwa", + "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", + "type": "package", + "version": "0.6.2"} + The new_dependencies_dict is the dictionary generated by the generate_tool_dependency_metadata method. """ new_tool_dependency = None diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/util/topsort.py --- a/lib/galaxy/util/topsort.py +++ b/lib/galaxy/util/topsort.py @@ -9,18 +9,24 @@ value is a list, representing a total ordering that respects all the input constraints. E.g., + topsort( [(1,2), (3,3)] ) + may return any of (but nothing other than) + [3, 1, 2] [1, 3, 2] [1, 2, 3] + because those are the permutations of the input elements that respect the "1 precedes 2" and "3 precedes 3" input constraints. Note that a constraint of the form (x, x) is really just a trick to make sure x appears *somewhere* in the output list. If there's a cycle in the constraints, say + topsort( [(1,2), (2,1)] ) + then CycleError is raised, and the exception object supports many methods to help analyze and break the cycles. This requires a good deal more code than topsort itself! diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -610,11 +610,16 @@ def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ - Returns a dict with the following attributes: + Returns a dict with the following attributes:: + data - a list of variants with the format + + .. raw:: text + [<guid>, <start>, <end>, <name>, cigar, seq] message - error/informative message + """ rval = [] message = None @@ -893,13 +898,17 @@ def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): """ - Returns a dict with the following attributes: + Returns a dict with the following attributes:: + data - a list of reads with the format - [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] + [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>] + where <read_1> has the format [<start>, <end>, <cigar>, <strand>, <read_seq>] + and <read_2> has the format [<start>, <end>, <cigar>, <strand>, <read_seq>] + Field 7 is empty so that mapq scores' location matches that in single-end reads. For single-end reads, read has format: [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>, <mapq_score>] @@ -910,6 +919,7 @@ max_low - lowest coordinate for the returned reads max_high - highest coordinate for the returned reads message - error/informative message + """ # No iterator indicates no reads. if iterator is None: diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/visualization/data_providers/phyloviz/newickparser.py --- a/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py +++ b/lib/galaxy/visualization/data_providers/phyloviz/newickparser.py @@ -112,9 +112,12 @@ def parseNode(self, string, depth): """ Recursive method for parsing newick string, works by stripping down the string into substring of newick contained with brackers, which is used to call itself. - Eg ... ( A, B, (D, E)C, F, G ) ... + + Eg ... ( A, B, (D, E)C, F, G ) ... + We will make the preceeding nodes first A, B, then the internal node C, its children D, E, - and finally the succeeding nodes F, G""" + and finally the succeeding nodes F, G + """ # Base case where there is only an empty string if string == "": diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -708,9 +708,12 @@ selected_value='none', refresh_on_change=False, multiple=False, display=None, size=None ): """ Build a SelectField given a set of objects. The received params are: + - objs: the set of objects used to populate the option list - label_attr: the attribute of each obj (e.g., name, email, etc ) whose value is used to populate each option label. + - If the string 'self' is passed as label_attr, each obj in objs is assumed to be a string, so the obj itself is used + - select_field_name: the name of the SelectField - initial_value: the value of the first option in the SelectField - allows for an option telling the user to select something - selected_value: the value of the currently selected option diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -624,6 +624,7 @@ def handle_user_login( self, user ): """ Login a new user (possibly newly created) + - create a new session - associate new session with user - if old session had a history and it was not associated with a user, associate it with the new session, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -140,7 +140,7 @@ def get_database_engine_options( kwargs ): """ Allow options for the SQLAlchemy database engine to be passed by using - the prefix "database_engine_option_". + the prefix "database_engine_option". """ conversions = { 'convert_unicode': string_as_bool, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -48,25 +48,25 @@ POST /api/genomes Download and/or index a genome. - Parameters: + Parameters:: - dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source - ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source - ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source - url_dbkey DB key to use for this build, ignored unless URL is specified as the source - source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL - indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) - func Allowed values: - 'download' Download and index - 'index' Index only - - Returns: + dbkey DB key of the build to download, ignored unless 'UCSC' is specified as the source + ncbi_name NCBI's genome identifier, ignored unless NCBI is specified as the source + ensembl_dbkey Ensembl's genome identifier, ignored unless Ensembl is specified as the source + url_dbkey DB key to use for this build, ignored unless URL is specified as the source + source Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + indexers POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + func Allowed values: + 'download' Download and index + 'index' Index only + + Returns:: - If no error: - dict( status: 'ok', job: <job ID> ) + If no error: + dict( status: 'ok', job: <job ID> ) - If error: - dict( status: 'error', error: <error message> ) + If error: + dict( status: 'error', error: <error message> ) """ params = util.Params( payload ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -13,12 +13,15 @@ @web.expose_api def index( self, trans, **kwds ): """ - GET /api/tools: returns a list of tools defined by parameters + GET /api/tools: returns a list of tools defined by parameters:: + parameters: + in_panel - if true, tools are returned in panel structure, including sections and labels trackster - if true, only tools that are compatible with Trackster are returned + """ # Read params. diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1980,8 +1980,8 @@ def edgelist_for_workflow_steps( steps ): """ - Create a list of tuples representing edges between `WorkflowSteps` based - on associated `WorkflowStepConnection`s + Create a list of tuples representing edges between ``WorkflowSteps`` based + on associated ``WorkflowStepConnection``s """ edges = [] steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -56,7 +56,7 @@ def get_database_engine_options( kwargs ): """ Allow options for the SQLAlchemy database engine to be passed by using - the prefix "database_engine_option_". + the prefix "database_engine_option". """ conversions = { 'convert_unicode': string_as_bool, diff -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 -r ec51a727a497d5912fdd4269571d7c26d7523436 lib/mimeparse.py --- a/lib/mimeparse.py +++ b/lib/mimeparse.py @@ -39,18 +39,21 @@ return (type.strip(), subtype.strip(), params) def parse_media_range(range): - """Carves up a media range and returns a tuple of the - (type, subtype, params) where 'params' is a dictionary - of all the parameters for the media range. - For example, the media range 'application/*;q=0.5' would - get parsed into: + r""" + Carves up a media range and returns a tuple of the + (type, subtype, params) where 'params' is a dictionary + of all the parameters for the media range. + For example, the media range 'application/*;q=0.5' would + get parsed into: - ('application', '*', {'q', '0.5'}) + .. raw:: text - In addition this function also guarantees that there - is a value for 'q' in the params dictionary, filling it - in with a proper default if necessary. - """ + ('application', '*', {'q', '0.5'}) + + In addition this function also guarantees that there + is a value for 'q' in the params dictionary, filling it + in with a proper default if necessary. + """ (type, subtype, params) = parse_mime_type(range) if not params.has_key('q') or not params['q'] or \ not float(params['q']) or float(params['q']) > 1\ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTab
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bc5fa254bafc/ changeset: bc5fa254bafc user: greg date: 2012-11-07 22:36:28 summary: Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly. affected #: 11 files diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -76,8 +76,13 @@ self.genomes = Genomes( self ) # Data providers registry. self.data_provider_registry = DataProviderRegistry() - # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=True ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -66,6 +66,7 @@ tcf = 'tool_conf.xml' self.tool_configs = [ resolve_path( p, self.root ) for p in listify( tcf ) ] self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) try: self.hours_between_check = int( kwargs.get( 'hours_between_check', 12 ) ) diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -184,7 +184,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -41,8 +41,13 @@ self.datatypes_registry = galaxy.datatypes.registry.Registry() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) - # Tool data tables - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path, self.config.tool_data_table_config_path ) + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=True ) # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -15,17 +15,28 @@ """Manages a collection of tool data tables""" def __init__( self, tool_data_path, config_filename=None ): self.tool_data_path = tool_data_path - self.data_tables = {} - # Store config elements for on-the-fly persistence. - self.data_table_elems = [] + # This stores all defined data table entries from both the tool_data_table_conf.xml file and the shed_tool_data_table_conf.xml file + # at server startup. If tool shed repositories are installed that contain a valid file named tool_data_table_conf.xml.sample, entries + # from that file are inserted into this dict at the time of installation. + self.data_tables = {} + # Store config elements for on-the-fly persistence to the defined shed_tool_data_table_config file name. + self.shed_data_table_elems = [] self.data_table_elem_names = [] if config_filename: - self.load_from_config_file( config_filename, self.tool_data_path ) + self.load_from_config_file( config_filename, self.tool_data_path, from_shed_config=False ) def __getitem__( self, key ): return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) - def load_from_config_file( self, config_filename, tool_data_path ): + def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): + """ + This method is called under 3 conditions: + 1) When the ToolDataTableManager is initialized (see __init__ above). + 2) Just after the ToolDataTableManager is initialized and the additional entries defined by shed_tool_data_table_conf.xml + are being loaded into the ToolDataTableManager.data_tables. + 3) When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local + Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example: + """ tree = util.parse_xml( config_filename ) root = tree.getroot() table_elems = [] @@ -36,13 +47,14 @@ table_elem_name = table_elem.get( 'name', None ) if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) - self.data_table_elems.append( table_elem ) + if from_shed_config: + self.shed_data_table_elems.append( table_elem ) table = tool_data_table_types[ type ]( table_elem, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) return table_elems - def add_new_entries_from_config_file( self, config_filename, tool_data_path, tool_data_table_config_path, persist=False ): + def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: @@ -65,7 +77,9 @@ # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': - table_elems = self.load_from_config_file( config_filename, tool_data_path ) + table_elems = self.load_from_config_file( config_filename=config_filename, + tool_data_path=tool_data_path, + from_shed_config=True ) else: table_elems = [] type = root.get( 'type', 'tabular' ) @@ -74,23 +88,22 @@ table_elem_name = root.get( 'name', None ) if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) - self.data_table_elems.append( root ) + self.shed_data_table_elems.append( root ) table = tool_data_table_types[ type ]( root, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Added new tool data table '%s'", table.name ) if persist and self.data_table_elem_names != original_data_table_elem_names: # Persist Galaxy's version of the changed tool_data_table_conf.xml file. - self.to_xml_file( tool_data_table_config_path ) + self.to_xml_file( shed_tool_data_table_config ) return table_elems - def to_xml_file( self, tool_data_table_config_path ): - """Write the current in-memory version of the tool_data-table_conf.xml file to disk.""" - full_path = os.path.abspath( tool_data_table_config_path ) + def to_xml_file( self, shed_tool_data_table_config ): + """Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.""" + full_path = os.path.abspath( shed_tool_data_table_config ) fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, "\n" ) os.write( fd, '<tables>\n' ) - for elem in self.data_table_elems: + for elem in self.shed_data_table_elems: os.write( fd, '%s' % util.xml_to_string( elem ) ) os.write( fd, '</tables>\n' ) os.close( fd ) diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -753,12 +753,15 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict={}, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be an absolute path to a temporary directory containing a clone). If it is an absolute path, the value of relative_install_dir must contain repository.repo_path. + + The value of persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries + should ultimately be persisted to the file referred to by app.config.shed_tool_data_table_config. """ if updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository installed into a local Galaxy instance for which @@ -810,9 +813,9 @@ relative_path, filename = os.path.split( sample_file ) if filename == 'tool_data_table_conf.xml.sample': new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, - tool_data_path=app.config.tool_data_path, - tool_data_table_config_path=app.config.tool_data_table_config_path, - persist=False ) + tool_data_path=original_tool_data_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, + persist=persist ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -1768,15 +1771,15 @@ return tool, message, sample_files def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ - Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) - if call is from the Galaxy side (not the tool shed), the new entries will be appended to Galaxy's tool_data_table_conf.xml file on disk. + Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur + if call is from the Galaxy side, not the tool shed), the new entries will be appended to Galaxy's shed_tool_data_table_conf.xml file on disk. """ error = False message = '' try: new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, tool_data_path=app.config.tool_data_path, - tool_data_table_config_path=app.config.tool_data_table_config_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, persist=persist ) except Exception, e: message = str( e ) @@ -2143,7 +2146,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: update_in_shed_tool_config( trans.app, repository ) @@ -2221,7 +2225,8 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -10,9 +10,8 @@ from galaxy.util.shed_util import generate_clone_url_for_repository_in_tool_shed, generate_message_for_invalid_tools, generate_metadata_for_changeset_revision from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx from galaxy.util.shed_util import get_parent_id, get_repository_in_tool_shed, get_repository_metadata_by_changeset_revision -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config -from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, is_downloadable, load_tool_from_config, remove_dir -from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import is_downloadable, load_tool_from_config, remove_dir, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.web.base.controllers.admin import * from galaxy.webapps.community import model @@ -640,7 +639,8 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -447,6 +447,12 @@ @web.expose @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): + """ + Handle all changes when a tool shed repository is being deactivated or uninstalled. Notice that if the repository contents include + a file named tool_data_table_conf.xml.sample, it's entries are not removed from the defined config.shed_tool_data_table_config. This + is because it becomes a bit complex to determine if other installed repositories include tools that require the same entry. For now + we'll never delete entries from config.shed_tool_data_table_config, but we may choose to do so in the future if it becomes necessary. + """ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -753,7 +759,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -1491,7 +1498,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False ) + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: update_in_shed_tool_config( trans.app, repository ) @@ -1675,7 +1683,8 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=True ) + updating_installed_repository=True, + persist=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 run.sh --- a/run.sh +++ b/run.sh @@ -13,6 +13,7 @@ reports_wsgi.ini.sample shed_tool_conf.xml.sample tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample tool_sheds_conf.xml.sample openid_conf.xml.sample diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 shed_tool_data_table_conf.xml.sample --- /dev/null +++ b/shed_tool_data_table_conf.xml.sample @@ -0,0 +1,3 @@ +<?xml version="1.0"?> +<tables> +</tables> diff -r dbff28bde968a05b787dd53cfca182c53a81eeb7 -r bc5fa254bafc981c70bdffd394e9c44c8dda4ab8 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -149,6 +149,16 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# XML config file that contains data table entries for the ToolDataTableManager. This file is manually +# maintained by the Galaxy administrator. +#tool_data_table_config_path = tool_data_table_conf.xml + +# XML config file that contains additional data table entries for the ToolDataTableManager. This file +# is automatically generated based on the current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically +# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +#shed_tool_data_table_config = shed_tool_data_table_conf.xml + # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration 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: dan: Allow unhiding all datasets in the current history.
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dbff28bde968/ changeset: dbff28bde968 user: dan date: 2012-11-07 19:50:06 summary: Allow unhiding all datasets in the current history. affected #: 3 files diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -694,6 +694,9 @@ @property def get_disk_size_bytes( self ): return self.get_disk_size( nice_size=False ) + def unhide_datasets( self ): + for dataset in self.datasets: + dataset.mark_unhidden() def get_disk_size( self, nice_size=False ): # unique datasets only db_session = object_session( self ) diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -550,6 +550,20 @@ return trans.show_ok_message( "History deleted, a new history is active", refresh_frames=['history'] ) @web.expose + def unhide_datasets( self, trans, current=False, ids=None ): + """Unhide the datasets in the active history -- this does not require a logged in user.""" + if not ids and util.string_as_bool( current ): + histories = [ trans.get_history() ] + refresh_frames = ['history'] + else: + raise NotImplementedError( "You can currently only unhide all the datasets of the current history." ) + for history in histories: + history.unhide_datasets() + trans.sa_session.add( history ) + trans.sa_session.flush() + return trans.show_ok_message( "Your datasets have been unhidden.", refresh_frames=refresh_frames ) + + @web.expose @web.require_login( "rate items" ) @web.json def rate_async( self, trans, id, rating ): diff -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 -r dbff28bde968a05b787dd53cfca182c53a81eeb7 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -43,6 +43,11 @@ "${_("Show Hidden Datasets")}": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; }, + "${_("Unhide Hidden Datasets")}": function() { + if ( confirm( "Really unhide all hidden datasets?" ) ) { + galaxy_main.location = "${h.url_for( controller='history', action='unhide_datasets', current=True )}"; + } + }, "${_("Purge Deleted Datasets")}": function() { if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}"; 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: jgoecks: Circster: do not transition labels if there are no data bounds (and hence nothing to transition).
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/932585f1dd8d/ changeset: 932585f1dd8d user: jgoecks date: 2012-11-07 19:16:07 summary: Circster: do not transition labels if there are no data bounds (and hence nothing to transition). affected #: 1 file diff -r 7bd34ce09e9fd795df2088be9c13c695b00424cd -r 932585f1dd8d67c28d2c22003af0d9ae318ef947 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -803,6 +803,9 @@ // FIXME: (a) pull out function for getting labeled chroms? and (b) function used in transition below // is copied from UseTicks mixin, so pull out and make generally available. + // If there are no data bounds, nothing to transition. + if (this.data_bounds.length === 0) { return; } + // Transition labels to new radius bounds. var self = this, visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }), 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: dannon: Move doc/build to an appropriate location in .hgignore
by Bitbucket 07 Nov '12

07 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7bd34ce09e9f/ changeset: 7bd34ce09e9f user: dannon date: 2012-11-07 17:02:43 summary: Move doc/build to an appropriate location in .hgignore affected #: 1 file diff -r 0a20563f9d46749d041c079907492bf9d4866628 -r 7bd34ce09e9fd795df2088be9c13c695b00424cd .hgignore --- a/.hgignore +++ b/.hgignore @@ -41,8 +41,6 @@ static/welcome.html.* static/welcome.html -doc/build - # Tool data. tool-data/annotation_profiler_options.xml tool-data/annotation_profiler_valid_builds.txt @@ -74,6 +72,9 @@ */variables.less static/june_2007_style/blue/base_sprites.less +# Documentation build files. +doc/build + # Misc *.orig .DS_Store 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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