- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: davebgx: Add check to ensure that repositories cannot be created unless at least one category has been defined.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66c738595730/ Changeset: 66c738595730 User: davebgx Date: 2014-03-26 15:11:54 Summary: Add check to ensure that repositories cannot be created unless at least one category has been defined. Affected #: 1 file diff -r 561929fb2d7e827f20ea078904aeebe35173f3f9 -r 66c7385957303447c8f5bb96731945bba179c83a test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -2,6 +2,8 @@ repository_name = 'filtering_0000' repository_description = "Galaxy's filtering tool for test 0000" repository_long_description = "Long description of Galaxy's filtering tool for test 0000" +import logging +log = logging.getLogger( __name__ ) class TestBasicRepositoryFeatures( ShedTwillTestCase ): '''Test core repository features.''' @@ -24,12 +26,18 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) - def test_0005_create_categories( self ): + def test_0005_create_repository_without_categories( self ): + '''Verify that a repository cannot be created unless at least one category has been defined.''' + strings_displayed = [ 'No categories have been configured in this instance of the Galaxy Tool Shed' ] + self.visit_url( '/repository/create_repository' ) + self.check_for_strings( strings_displayed=strings_displayed, strings_not_displayed=[] ) + + def test_0010_create_categories( self ): """Create categories for this test suite""" self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' ) - def test_0010_create_repository( self ): + def test_0015_create_repository( self ): """Create the filtering repository""" self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) @@ -43,7 +51,7 @@ category_id=self.security.encode_id( category.id ), strings_displayed=strings_displayed ) - def test_0015_edit_repository( self ): + def test_0020_edit_repository( self ): """Edit the repository name, description, and long description""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) new_name = "renamed_filtering" @@ -51,20 +59,20 @@ new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) - def test_0020_change_repository_category( self ): + def test_0025_change_repository_category( self ): """Change the categories associated with the filtering repository""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.edit_repository_categories( repository, categories_to_add=[ "Test 0000 Basic Repository Features 2" ], categories_to_remove=[ "Test 0000 Basic Repository Features 1" ] ) - def test_0025_grant_write_access( self ): + def test_0030_grant_write_access( self ): '''Grant write access to another user''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.grant_write_access( repository, usernames=[ common.test_user_2_name ] ) self.revoke_write_access( repository, common.test_user_2_name ) - def test_0030_upload_filtering_1_1_0( self ): + def test_0035_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -77,7 +85,7 @@ strings_displayed=[], strings_not_displayed=[] ) - def test_0035_verify_repository( self ): + def test_0040_verify_repository( self ): '''Display basic repository pages''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) latest_changeset_revision = self.get_repository_tip( repository ) @@ -101,7 +109,7 @@ repository_name, strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) - def test_0040_alter_repository_states( self ): + def test_0045_alter_repository_states( self ): '''Test toggling the malicious and deprecated repository flags.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.logout() @@ -127,7 +135,7 @@ strings_displayed = [ 'Mark repository as deprecated', 'Upload files', 'Reset all repository metadata' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) - def test_0045_display_repository_tip_file( self ): + def test_0050_display_repository_tip_file( self ): '''Display the contents of filtering.xml in the repository tip revision''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_repository_file_contents( repository=repository, @@ -136,7 +144,7 @@ strings_displayed=[ '1.1.0' ], strings_not_displayed=[] ) - def test_0050_upload_filtering_txt_file( self ): + def test_0055_upload_filtering_txt_file( self ): '''Upload filtering.txt file associated with tool version 1.1.0.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -150,7 +158,7 @@ strings_not_displayed=[] ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) - def test_0055_upload_filtering_test_data( self ): + def test_0060_upload_filtering_test_data( self ): '''Upload filtering test data.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -169,7 +177,7 @@ strings_not_displayed=[] ) self.check_repository_metadata( repository, tip_only=True ) - def test_0060_upload_filtering_2_2_0( self ): + def test_0065_upload_filtering_2_2_0( self ): '''Upload filtering version 2.2.0''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -182,7 +190,7 @@ strings_displayed=[], strings_not_displayed=[] ) - def test_0065_verify_filtering_repository( self ): + def test_0070_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) category = self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) @@ -204,7 +212,7 @@ tool_page_strings_displayed=tool_page_strings_displayed ) self.check_repository_metadata( repository, tip_only=False ) - def test_0070_upload_readme_txt_file( self ): + def test_0075_upload_readme_txt_file( self ): '''Upload readme.txt file associated with tool version 2.2.0.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, @@ -223,26 +231,26 @@ strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] ) - def test_0075_delete_readme_txt_file( self ): + def test_0080_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) - def test_0080_search_for_valid_filter_tool( self ): + def test_0085_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) tip_changeset = self.get_repository_tip( repository ) search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' ) self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] ) - def test_0085_verify_repository_metadata( self ): + def test_0090_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.verify_unchanged_repository_metadata( repository ) - def test_0090_verify_reserved_repository_name_handling( self ): + def test_0095_verify_reserved_repository_name_handling( self ): '''Check that reserved repository names are handled correctly.''' category = self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) error_message = 'The term <b>repos</b> is a reserved word in the tool shed, so it cannot be used as a repository name.' 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: 3 new changesets
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4950bc66225/ Changeset: c4950bc66225 User: carlfeberhard Date: 2014-03-25 20:30:51 Summary: History API: show: add importable, username_and_slug to returned attributes, update: 1) allow setting importable and published, 2) published automatically makes a history importable, 3) in both cases slug is automatically set set_as_current: now correctly uses the HTTP method PUT (not POST), HDA API: all: histories that are importable and/or published now allow GET'ing the contents properly, create: you can now copy HDAs into your histories if the HDA and it's history are accessible Affected #: 7 files diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -773,7 +773,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ): dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged' ) + dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug' ) default_name = 'Unnamed history' def __init__( self, id=None, name=None, user=None ): diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -187,8 +187,11 @@ def validate_and_sanitize_basestring_list( self, key, val ): if not isinstance( val, list ): - raise ValueError( '%s must be a list: %s' %( key, str( type( val ) ) ) ) - return [ unicode( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ] + raise ValueError( '%s must be a list of strings: %s' %( key, str( type( val ) ) ) ) + try: + return [ unicode( sanitize_html( t, 'utf-8', 'text/html' ), 'utf-8' ) for t in val ] + except TypeError, type_err: + raise ValueError( '%s must be a list of strings: %s' %( key, str( type_err ) ) ) def validate_boolean( self, key, val ): if not isinstance( val, bool ): @@ -527,6 +530,10 @@ if not history_dict[ 'annotation' ]: history_dict[ 'annotation' ] = '' #TODO: item_slug url + if history_dict[ 'importable' ] and history_dict[ 'slug' ]: + #TODO: this should be in History (or a superclass of) + username_and_slug = ( '/' ).join(( 'u', history.user.username, 'h', history_dict[ 'slug' ] )) + history_dict[ 'username_and_slug' ] = username_and_slug hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history ) #TODO remove the following in v2 @@ -541,26 +548,69 @@ """ Changes history data using the given dictionary new_data. """ - # precondition: access of the history has already been checked + #precondition: ownership of the history has already been checked + #precondition: user is not None (many of these attributes require a user to set properly) + user = trans.get_user() + # published histories should always be importable + if 'published' in new_data and new_data[ 'published' ] and not history.importable: + new_data[ 'importable' ] = True # send what we can down into the model changed = history.set_from_dict( new_data ) + # the rest (often involving the trans) - do here - if 'annotation' in new_data.keys() and trans.get_user(): - history.add_item_annotation( trans.sa_session, trans.get_user(), history, new_data[ 'annotation' ] ) + #TODO: the next two could be an aspect/mixin + #TODO: also need a way to check whether they've changed - assume they have for now + if 'annotation' in new_data: + history.add_item_annotation( trans.sa_session, user, history, new_data[ 'annotation' ] ) changed[ 'annotation' ] = new_data[ 'annotation' ] - if 'tags' in new_data.keys() and trans.get_user(): - self.set_tags_from_list( trans, history, new_data[ 'tags' ], user=trans.user ) - # importable (ctrl.history.set_accessible_async) - # sharing/permissions? - # slugs? - # purged - duh duh duhhhhhhnnnnnnnnnn + + if 'tags' in new_data: + self.set_tags_from_list( trans, history, new_data[ 'tags' ], user=user ) + changed[ 'tags' ] = new_data[ 'tags' ] + + #TODO: sharing with user/permissions? if changed.keys(): trans.sa_session.flush() + # create a slug if none exists (setting importable to false should not remove the slug) + if 'importable' in changed and changed[ 'importable' ] and not history.slug: + self._create_history_slug( trans, history ) + return changed + def _create_history_slug( self, trans, history ): + #TODO: mixins need to die a quick, horrible death + # (this is duplicate from SharableMixin which can't be added to UsesHistory without exposing various urls) + cur_slug = history.slug + + # Setup slug base. + if cur_slug is None or cur_slug == "": + # Item can have either a name or a title. + item_name = history.name + slug_base = util.ready_name_for_url( item_name.lower() ) + 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 ( trans.sa_session.query( trans.app.model.History ) + .filter_by( user=history.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. + trans.sa_session.add( history ) + history.slug = new_slug + trans.sa_session.flush() + return history.slug == cur_slug + class ExportsHistoryMixin: @@ -685,9 +735,9 @@ else: #TODO: do we really need the history? history = self.get_history( trans, history_id, - check_ownership=True, check_accessible=True, deleted=False ) + check_ownership=False, check_accessible=True, deleted=False ) hda = self.get_history_dataset_association( trans, history, id, - check_ownership=True, check_accessible=True ) + check_ownership=False, check_accessible=True ) return hda def get_hda_list( self, trans, hda_ids, check_ownership=True, check_accessible=False, check_state=True ): diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -6,20 +6,26 @@ import pkg_resources pkg_resources.require( "Paste" ) -from paste.httpexceptions import HTTPBadRequest, HTTPForbidden, HTTPInternalServerError, HTTPException + +from paste.httpexceptions import HTTPBadRequest +from paste.httpexceptions import HTTPForbidden +from paste.httpexceptions import HTTPInternalServerError +from paste.httpexceptions import HTTPException from galaxy import exceptions from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw as expose_api_raw -from galaxy.util import string_as_bool -from galaxy.util import restore_text + from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.base.controller import UsesTagsMixin from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin + +from galaxy.util import string_as_bool +from galaxy.util import restore_text from galaxy.web import url_for import logging @@ -48,27 +54,22 @@ #TODO: query (by name, date, etc.) rval = [] deleted = string_as_bool( deleted ) - try: - if trans.user: - histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) - #for history in query: - for history in histories: - item = history.to_dict(value_mapper={'id': trans.security.encode_id}) - item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - rval.append( item ) - elif trans.galaxy_session.current_history: - #No user, this must be session authentication with an anonymous user. - history = trans.galaxy_session.current_history + if trans.user: + histories = self.get_user_histories( trans, user=trans.user, only_deleted=deleted ) + + for history in histories: item = history.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) - rval.append(item) + rval.append( item ) - except Exception, e: - raise - rval = "Error in history API" - log.error( rval + ": %s" % str(e) ) - trans.response.status = 500 + elif trans.galaxy_session.current_history: + #No user, this must be session authentication with an anonymous user. + history = trans.galaxy_session.current_history + item = history.to_dict(value_mapper={'id': trans.security.encode_id}) + item['url'] = url_for( 'history', id=trans.security.encode_id( history.id ) ) + rval.append(item) + return rval @web.expose_api_anonymous @@ -92,7 +93,6 @@ :returns: detailed history information from :func:`galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin.get_history_dict` """ - #TODO: GET /api/histories/{encoded_history_id}?as_archive=True #TODO: GET /api/histories/s/{username}/{slug} history_id = id deleted = string_as_bool( deleted ) @@ -116,7 +116,7 @@ except HTTPBadRequest, bad_req: trans.response.status = 400 - return str( bad_req ) + raise exceptions.MessageException( bad_req.detail ) except Exception, e: msg = "Error in history API at showing history detail: %s" % ( str( e ) ) @@ -444,7 +444,7 @@ continue if key in ( 'name', 'genome_build', 'annotation' ): validated_payload[ key ] = self.validate_and_sanitize_basestring( key, val ) - if key in ( 'deleted', 'published' ): + if key in ( 'deleted', 'published', 'importable' ): validated_payload[ key ] = self.validate_boolean( key, val ) elif key == 'tags': validated_payload[ key ] = self.validate_and_sanitize_basestring_list( key, val ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -2,20 +2,32 @@ API operations on the contents of a history. """ -import logging -from galaxy import exceptions, util, web -from galaxy.web.base.controller import ( BaseAPIController, url_for, - UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, - UsesLibraryMixinItems, UsesTagsMixin ) +from galaxy import exceptions +from galaxy import util +from galaxy import web + +from galaxy.web import _future_expose_api as expose_api +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.web import _future_expose_api_raw as expose_api_raw + +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin +from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import UsesLibraryMixin +from galaxy.web.base.controller import UsesLibraryMixinItems +from galaxy.web.base.controller import UsesTagsMixin + +from galaxy.web.base.controller import url_for from galaxy.util.sanitize_html import sanitize_html +import logging log = logging.getLogger( __name__ ) class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems, UsesTagsMixin ): - @web.expose_api_anonymous + @expose_api_anonymous def index( self, trans, history_id, ids=None, **kwd ): """ index( self, trans, history_id, ids=None, **kwd ) @@ -52,7 +64,7 @@ history = trans.history # otherwise, check permissions for the history first else: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) + history = self.get_history( trans, history_id, check_ownership=False, check_accessible=True ) # Allow passing in type or types - for continuity rest of methods # take in type - but this one can be passed multiple types and @@ -134,7 +146,7 @@ hda.history_id, hda.id, type( exc ), str( exc ) ) return self.get_hda_dict_with_error( trans, hda=hda, error_msg=str( exc ) ) - @web.expose_api_anonymous + @expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ show( self, trans, id, history_id, **kwd ) @@ -170,7 +182,7 @@ trans.response.status = 500 return msg - @web.expose_api + @expose_api def create( self, trans, history_id, payload, **kwd ): """ create( self, trans, history_id, payload, **kwd ) @@ -201,6 +213,8 @@ # retrieve history try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) + except exceptions.httpexceptions.HTTPException: + raise except Exception, e: # no way to tell if it failed bc of perms or other (all MessageExceptions) trans.response.status = 500 @@ -236,7 +250,8 @@ elif source == 'hda': try: #NOTE: user currently only capable of copying one of their own datasets - hda = self.get_dataset( trans, content ) + hda = self.get_dataset( trans, content, check_ownership=False, check_accessible=True ) + self.security_check( trans, hda.history, check_ownership=False, check_accessible=True ) except ( exceptions.httpexceptions.HTTPRequestRangeNotSatisfiable, exceptions.httpexceptions.HTTPBadRequest ), id_exc: # wot... @@ -259,7 +274,7 @@ trans.response.status = 501 return - @web.expose_api_anonymous + @expose_api_anonymous def update( self, trans, history_id, id, payload, **kwd ): """ update( self, trans, history_id, id, payload, **kwd ) @@ -306,6 +321,7 @@ if hda.history != trans.history: trans.response.status = 401 return { 'error': 'Anonymous users cannot edit datasets outside their current history' } + else: payload = self._validate_and_parse_update_payload( payload ) # only check_state if not deleting, otherwise cannot delete uploading files @@ -316,6 +332,7 @@ changed = self.set_hda_from_dict( trans, hda, payload ) if payload.get( 'deleted', False ): self.stop_hda_creating_job( hda ) + except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -330,7 +347,7 @@ return changed #TODO: allow anonymous del/purge and test security on this - @web.expose_api + @expose_api def delete( self, trans, history_id, id, purge=False, **kwd ): """ delete( self, trans, history_id, id, **kwd ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -165,8 +165,9 @@ parent_resources=dict( member_name='page', collection_name='pages' ) ) # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource + #webapp.mapper.connect( "set_as_current", "/api/histories/set_as_current/{id}", webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", - controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) + controller="histories", action="set_as_current", conditions=dict( method=["PUT"] ) ) webapp.mapper.connect( "history_archive_export", "/api/histories/{id}/exports", controller="histories", action="archive_export", conditions=dict( method=[ "PUT" ] ) ) diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -84,7 +84,10 @@ var panel = this, historyFn = function(){ // make this current and get history data with one call - return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); + return jQuery.ajax({ + url : galaxy_config.root + 'api/histories/' + historyId + '/set_as_current', + method : 'PUT' + }); }; return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) .then(function( historyData, hdaData ){ diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r c4950bc662256f013916b0aaabb73a47508213c5 static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel","mvc/base-mvc"],function(b,f,c){var d=c.SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});d.storageKey=function e(){return("history-panel")};var a=f.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(g){g=g||{};this.preferences=new d(_.extend({id:d.storageKey()},_.pick(g,_.keys(d.prototype.defaults))));f.HistoryPanel.prototype.initialize.call(this,g)},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories/"+j+"/set_as_current")};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},setModel:function(h,g,i){f.HistoryPanel.prototype.setModel.call(this,h,g,i);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){f.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children());g.renderBasedOnPrefs()}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(i){var h=this,g=h.$emptyMessage(i),j=$(".toolMenuContainer");if((_.isEmpty(h.hdaViews)&&!h.searchFor)&&(Galaxy&&Galaxy.upload&&j.size())){g.empty();g.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));g.find(".uploader-link").click(function(k){Galaxy.upload._eventShow(k)});g.find(".get-data-link").click(function(k){j.parent().scrollTop(0);j.find('span:contains("Get Data")').click()});g.show()}else{f.HistoryPanel.prototype._renderEmptyMsg.call(this,i)}return this},toggleSearchControls:function(h,g){var i=f.HistoryPanel.prototype.toggleSearchControls.call(this,h,g);this.preferences.set("searching",i)},_renderTags:function(g){var h=this;f.HistoryPanel.prototype._renderTags.call(this,g);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("tagsEditorShown",i.hidden)})},_renderAnnotation:function(g){var h=this;f.HistoryPanel.prototype._renderAnnotation.call(this,g);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("annotationEditorShown",i.hidden)})},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel","mvc/base-mvc"],function(b,f,c){var d=c.SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});d.storageKey=function e(){return("history-panel")};var a=f.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(g){g=g||{};this.preferences=new d(_.extend({id:d.storageKey()},_.pick(g,_.keys(d.prototype.defaults))));f.HistoryPanel.prototype.initialize.call(this,g)},loadCurrentHistory:function(h){var g=this;return this.loadHistoryWithHDADetails("current",h).then(function(j,i){g.trigger("current-history",g)})},switchToHistory:function(j,i){var g=this,h=function(){return jQuery.ajax({url:galaxy_config.root+"api/histories/"+j+"/set_as_current",method:"PUT"})};return this.loadHistoryWithHDADetails(j,i,h).then(function(l,k){g.trigger("switched-history",g)})},createNewHistory:function(i){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var g=this,h=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,i,h).then(function(k,j){g.trigger("new-history",g)})},setModel:function(h,g,i){f.HistoryPanel.prototype.setModel.call(this,h,g,i);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpModelEventHandlers:function(){f.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(h,i,g){if((!h.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[h.id])}},this)},render:function(i,j){i=(i===undefined)?(this.fxSpeed):(i);var g=this,h;if(this.model){h=this.renderModel()}else{h=this.renderWithoutModel()}$(g).queue("fx",[function(k){if(i&&g.$el.is(":visible")){g.$el.fadeOut(i,k)}else{k()}},function(k){g.$el.empty();if(h){g.$el.append(h.children());g.renderBasedOnPrefs()}k()},function(k){if(i&&!g.$el.is(":visible")){g.$el.fadeIn(i,k)}else{k()}},function(k){if(j){j.call(this)}g.trigger("rendered",this);k()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.toggleSearchControls(0,true)}},_renderEmptyMsg:function(i){var h=this,g=h.$emptyMessage(i),j=$(".toolMenuContainer");if((_.isEmpty(h.hdaViews)&&!h.searchFor)&&(Galaxy&&Galaxy.upload&&j.size())){g.empty();g.html([_l("This history is empty. "),_l("You can "),'<a class="uploader-link" href="javascript:void(0)">',_l("load your own data"),"</a>",_l(" or "),'<a class="get-data-link" href="javascript:void(0)">',_l("get data from an external source"),"</a>"].join(""));g.find(".uploader-link").click(function(k){Galaxy.upload._eventShow(k)});g.find(".get-data-link").click(function(k){j.parent().scrollTop(0);j.find('span:contains("Get Data")').click()});g.show()}else{f.HistoryPanel.prototype._renderEmptyMsg.call(this,i)}return this},toggleSearchControls:function(h,g){var i=f.HistoryPanel.prototype.toggleSearchControls.call(this,h,g);this.preferences.set("searching",i)},_renderTags:function(g){var h=this;f.HistoryPanel.prototype._renderTags.call(this,g);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("tagsEditorShown",i.hidden)})},_renderAnnotation:function(g){var h=this;f.HistoryPanel.prototype._renderAnnotation.call(this,g);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(i){h.preferences.set("annotationEditorShown",i.hidden)})},connectToQuotaMeter:function(g){if(!g){return this}this.listenTo(g,"quota:over",this.showQuotaMessage);this.listenTo(g,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(g&&g.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var g=this.$el.find(".quota-message");if(g.is(":hidden")){g.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var g=this.$el.find(".quota-message");if(!g.is(":hidden")){g.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(g){if(!g){return this}this.on("new-storage",function(i,h){if(g&&i){g.findItemByHtml(_l("Include Deleted Datasets")).checked=i.get("show_deleted");g.findItemByHtml(_l("Include Hidden Datasets")).checked=i.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/79ab14af25e4/ Changeset: 79ab14af25e4 User: carlfeberhard Date: 2014-03-25 21:59:27 Summary: History/HDA API: begin normalizing exceptions and return codes; Browser testing: update and expand history/hda testing, add importable/published permissions testing, transfer upload functions to api module Affected #: 8 files diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -97,32 +97,32 @@ history_id = id deleted = string_as_bool( deleted ) - try: - if history_id == "most_recently_used": - if not trans.user or len( trans.user.galaxy_sessions ) <= 0: - return None - # Most recent active history for user sessions, not deleted - history = trans.user.galaxy_sessions[0].histories[-1].history + #try: + if history_id == "most_recently_used": + if not trans.user or len( trans.user.galaxy_sessions ) <= 0: + return None + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history - elif history_id == "current": - history = trans.get_history( create=True ) + elif history_id == "current": + history = trans.get_history( create=True ) - else: - history = self.get_history( trans, history_id, check_ownership=False, - check_accessible=True, deleted=deleted ) + else: + history = self.get_history( trans, history_id, check_ownership=False, + check_accessible=True, deleted=deleted ) - history_data = self.get_history_dict( trans, history ) - history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) + history_data = self.get_history_dict( trans, history ) + history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) - except HTTPBadRequest, bad_req: - trans.response.status = 400 - raise exceptions.MessageException( bad_req.detail ) - - except Exception, e: - msg = "Error in history API at showing history detail: %s" % ( str( e ) ) - log.exception( msg ) - trans.response.status = 500 - return msg + #except HTTPBadRequest, bad_req: + # trans.response.status = 400 + # raise exceptions.MessageException( bad_req.detail ) + # + #except Exception, e: + # msg = "Error in history API at showing history detail: %s" % ( str( e ) ) + # log.exception( msg ) + # trans.response.status = 500 + # return msg return history_data diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-hda-tests.js --- a/test/casperjs/api-hda-tests.js +++ b/test/casperjs/api-hda-tests.js @@ -32,33 +32,12 @@ } spaceghost.user.loginOrRegisterUser( email, password ); -var uploadFilename = '1.sam', - uploadFilepath = '../../test-data/' + uploadFilename, - upload = {}; -spaceghost.thenOpen( spaceghost.baseUrl ).tools.uploadFile( uploadFilepath, function( uploadInfo ){ - upload = uploadInfo; +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.api.tools.thenUpload( spaceghost.api.histories.show( 'current' ).id, { + filepath: this.options.scriptDir + '/../../test-data/1.sam' + }); }); -function hasKeys( object, keysArray ){ - if( !utils.isObject( object ) ){ return false; } - for( var i=0; i<keysArray.length; i += 1 ){ - if( !object.hasOwnProperty( keysArray[i] ) ){ - spaceghost.debug( 'object missing key: ' + keysArray[i] ); - return false; - } - } - return true; -} - -function countKeys( object ){ - if( !utils.isObject( object ) ){ return 0; } - var count = 0; - for( var key in object ){ - if( object.hasOwnProperty( key ) ){ count += 1; } - } - return count; -} - // =================================================================== TESTS var summaryKeys = [ 'id', 'name', 'type', 'url' ], detailKeys = [ @@ -76,11 +55,8 @@ 'metadata_comment_lines', 'metadata_data_lines' ]; -spaceghost.historypanel.waitForHdas().then( function(){ +spaceghost.then( function(){ - var uploaded = this.historypanel.hdaElementInfoByTitle( uploadFilename ); - this.info( 'found uploaded hda: ' + uploaded.attributes.id ); - this.debug( 'uploaded hda: ' + this.jsonStr( uploaded ) ); // ------------------------------------------------------------------------------------------- INDEX this.test.comment( 'index should return a list of summary data for each hda' ); var histories = this.api.histories.index(), @@ -92,18 +68,17 @@ this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); var firstHda = hdaIndex[0]; - this.test.assert( hasKeys( firstHda, summaryKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHda, summaryKeys ), 'Has the proper keys' ); this.test.assert( this.api.isEncodedId( firstHda.id ), 'Id appears well-formed: ' + firstHda.id ); - this.test.assert( uploaded.text.indexOf( firstHda.name ) !== -1, 'Title matches: ' + firstHda.name ); - // not caring about type or url here + this.test.assert( firstHda.name === '1.sam', 'Title matches: ' + firstHda.name ); // ------------------------------------------------------------------------------------------- SHOW this.test.comment( 'show should get an HDA details object' ); var hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); //this.debug( this.jsonStr( hdaShow ) ); - this.test.assert( hasKeys( hdaShow, detailKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( hdaShow, detailKeys ), 'Has the proper keys' ); //TODO: validate data in each hdaShow attribute... @@ -117,7 +92,7 @@ this.test.assert( hdaIndex.length >= 1, 'Has at least one hda' ); firstHda = hdaIndex[0]; - this.test.assert( hasKeys( firstHda, detailKeys ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHda, detailKeys ), 'Has the proper keys' ); //TODO??: validate data in firstHda attribute? we ASSUME it's from a common method as show... @@ -133,29 +108,21 @@ var returned = this.api.hdas.update( lastHistory.id, firstHda.id, { name : hdaShow.name }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); this.test.comment( 'updating using a nonsense key should NOT fail with an error' ); returned = this.api.hdas.update( lastHistory.id, firstHda.id, { konamiCode : 'uuddlrlrba' }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); this.test.comment( 'updating by attempting to change type should cause an error' ); - err = {}; - try { + this.api.assertRaises( function(){ returned = this.api.hdas.update( lastHistory.id, firstHda.id, { //name : false deleted : 'sure why not' }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( !!err.message, "Error occurred: " + err.message ); - this.test.assert( err.status === 400, "Error status is 400: " + err.status ); - //TODO??: other type checks? - + }, 400, 'deleted must be a boolean', 'changing deleted type failed' ); // ........................................................................................... name this.test.comment( 'update should allow changing the name' ); @@ -330,25 +297,68 @@ // ------------------------------------------------------------------------------------------- ERRORS this.test.comment( 'create should error with "Please define the source" when the param "from_ld_id" is not used' ); - var errored = false; - try { - // sending an empty object won't work - var created = this.api.hdas.create( lastHistory.id, { bler: 'bler' } ); + this.api.assertRaises( function(){ + this.api.hdas.create( lastHistory.id, { bler: 'bler' } ); + }, 400, 'Please define the source', 'create with no source failed' ); - } catch( err ){ - errored = true; - this.test.assert( err.message.indexOf( 'Please define the source' ) !== -1, - 'Error has the proper message: ' + err.message ); - this.test.assert( err.status === 400, 'Error has the proper status code: ' + err.status ); - } - if( !errored ){ - this.test.fail( 'create without "from_ld_id" did not cause error' ); - } + this.test.comment( 'updating using a nonsense key should fail silently' ); + returned = this.api.hdas.update( lastHistory.id, hdaShow.id, { + konamiCode : 'uuddlrlrba' + }); + this.test.assert( returned.konamiCode === undefined, 'key was not set: ' + returned.konamiCode ); - //var returned = this.api.hdas.update( lastHistory.id, hdaIndex[0].id, { deleted: true, blerp: 'blerp' }); - //var returned = this.api.hdas.update( lastHistory.id, { deleted: true, blerp: 'blerp' }); - //this.debug( 'returned:' + this.jsonStr( returned ) ); - //this.debug( 'page:' + this.jsonStr( this.page ) ); + spaceghost.test.comment( 'A bad id should throw an error when using show' ); + this.api.assertRaises( function(){ + this.api.hdas.show( lastHistory.id, '1234123412341234' ); + }, 500, 'unable to decode', 'Bad Request with invalid id: show' ); + spaceghost.test.comment( 'A bad id should throw an error when using update' ); + this.api.assertRaises( function(){ + this.api.hdas.update( lastHistory.id, '1234123412341234', {} ); + }, 400, 'invalid literal for int', 'Bad Request with invalid id: update' ); + spaceghost.test.comment( 'A bad id should throw an error when using delete' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( lastHistory.id, '1234123412341234' ); + }, 500, 'invalid literal for int', 'Bad Request with invalid id: delete' ); + spaceghost.test.comment( 'A bad id should throw an error when using undelete' ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + [ 'name', 'annotation', 'genome_build', 'misc_info' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = false; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs ); + }, 400, key + ' must be a string or unicode', 'type validation error' ); + }); + [ 'deleted', 'visible' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = 'straaang'; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, updatedAttrs ); + }, 400, key + ' must be a boolean', 'type validation error' ); + }); + [ 'you\'re it', [ true ] ].forEach( function( badVal ){ + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.hdas.update( hdaShow.history_id, hdaShow.id, { tags: badVal }); + }, 400, 'tags must be a list', 'type validation error' ); + }); + + // ------------------------------------------------------------------------------------------- DELETE + this.test.comment( 'calling delete on an hda should mark it as deleted but not change the history size' ); + lastHistory = this.api.histories.show( lastHistory.id ); + var sizeBeforeDelete = lastHistory.nice_size; + + returned = this.api.hdas.delete_( lastHistory.id, firstHda.id ); + //this.debug( this.jsonStr( returned ) ); + + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.deleted, 'hda is marked deleted' ); + lastHistory = this.api.histories.show( lastHistory.id ); + this.test.assert( lastHistory.nice_size === sizeBeforeDelete, 'history size has not changed' ); + + // by default, purging fails bc uni.ini:allow_user_dataset_purge=False + this.api.assertRaises( function(){ + returned = this.api.hdas.delete_( lastHistory.id, firstHda.id, { purge : true }); + }, 403, 'This instance does not allow user dataset purging', 'Purge failed' ); /* */ }); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-history-permission-tests.js --- /dev/null +++ b/test/casperjs/api-history-permission-tests.js @@ -0,0 +1,303 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +var email2 = spaceghost.user.getRandomEmail(), + password2 = '123456'; +if( spaceghost.fixtureData.testUser2 ){ + email2 = spaceghost.fixtureData.testUser2.email; + password2 = spaceghost.fixtureData.testUser2.password; +} + +var inaccessibleHistory, accessibleHistory, publishedHistory, + inaccessibleHdas, accessibleHdas, publishedHdas, + accessibleLink; + +// =================================================================== TESTS +//// ------------------------------------------------------------------------------------------- create 3 histories +spaceghost.user.loginOrRegisterUser( email, password ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + // create three histories: make the 2nd importable (via the API), and the third published + + this.test.comment( 'importable, slug, and published should all be returned by show and initially off' ); + // make the current the inaccessible one + inaccessibleHistory = this.api.histories.show( 'current' ); + this.test.assert( this.hasKeys( inaccessibleHistory, [ 'id', 'name', 'slug', 'importable', 'published' ] ), + 'Has the proper keys' ); + this.test.assert( inaccessibleHistory.slug === null, + 'initial slug is null: ' + inaccessibleHistory.slug ); + this.test.assert( inaccessibleHistory.importable === false, + 'initial importable is false: ' + inaccessibleHistory.importable ); + this.test.assert( inaccessibleHistory.published === false, + 'initial published is false: ' + inaccessibleHistory.published ); + this.api.histories.update( inaccessibleHistory.id, { name: 'inaccessible' }); + + this.test.comment( 'Setting importable to true should create a slug, username_and_slug, and importable === true' ); + accessibleHistory = this.api.histories.create({ name: 'accessible' }); + var returned = this.api.histories.update( accessibleHistory.id, { + importable : true + }); + this.debug( this.jsonStr( returned ) ); + accessibleHistory = this.api.histories.show( accessibleHistory.id ); + this.test.assert( this.hasKeys( accessibleHistory, [ 'username_and_slug' ] ), + 'Has the proper keys' ); + this.test.assert( accessibleHistory.slug === 'accessible', + 'slug is not null: ' + accessibleHistory.slug ); + this.test.assert( accessibleHistory.importable, + 'importable is true: ' + accessibleHistory.importable ); + accessibleLink = 'u/' + email.replace( '@test.test', '' ) + '/h/accessible'; + this.test.assert( accessibleHistory.username_and_slug === accessibleLink, + 'username_and_slug is proper: ' + accessibleHistory.username_and_slug ); + + this.test.comment( 'Setting published to true should create make accessible and published === true' ); + publishedHistory = this.api.histories.create({ name: 'published' }); + returned = this.api.histories.update( publishedHistory.id, { + published : true + }); + this.debug( this.jsonStr( returned ) ); + publishedHistory = this.api.histories.show( publishedHistory.id ); + this.test.assert( this.hasKeys( publishedHistory, [ 'username_and_slug' ] ), + 'Has the proper keys' ); + this.test.assert( publishedHistory.published, + 'published is true: ' + publishedHistory.published ); + this.test.assert( publishedHistory.importable, + 'importable is true: ' + publishedHistory.importable ); + this.test.assert( publishedHistory.slug === 'published', + 'slug is not null: ' + publishedHistory.slug ); + accessibleLink = 'u/' + email.replace( '@test.test', '' ) + '/h/published'; + this.test.assert( publishedHistory.username_and_slug === accessibleLink, + 'username_and_slug is proper: ' + publishedHistory.username_and_slug ); + +}); + +//// ------------------------------------------------------------------------------------------- upload some files +spaceghost.then( function(){ + this.api.tools.thenUpload( inaccessibleHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); + this.api.tools.thenUpload( accessibleHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); + this.api.tools.thenUpload( publishedHistory.id, { filepath: this.options.scriptDir + '/../../test-data/1.bed' }); +}); +spaceghost.then( function(){ + // check that they're there + inaccessibleHdas = this.api.hdas.index( inaccessibleHistory.id ), + accessibleHdas = this.api.hdas.index( accessibleHistory.id ), + publishedHdas = this.api.hdas.index( publishedHistory.id ); + this.test.assert( inaccessibleHdas.length === 1, + 'uploaded file to inaccessible: ' + inaccessibleHdas.length ); + this.test.assert( accessibleHdas.length === 1, + 'uploaded file to accessible: ' + accessibleHdas.length ); + this.test.assert( publishedHdas.length === 1, + 'uploaded file to published: ' + publishedHdas.length ); +}); +spaceghost.user.logout(); + +//// ------------------------------------------------------------------------------------------- log in user2 +function ensureInaccessibility( history, hdas ){ + + this.test.comment( 'all four CRUD API calls should fail for user2 with history: ' + history.name ); + this.api.assertRaises( function(){ + this.api.histories.show( history.id ); + }, 400, 'History is not accessible to the current user', 'show failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.create({ history_id : history.id }); + }, 403, 'History is not accessible to the current user', 'copy failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.update( history.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( history.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'all four HDA CRUD API calls should fail for user2 with history: ' + history.name ); + this.api.assertRaises( function(){ + this.api.hdas.index( history.id ); + }, 500, 'History is not accessible to the current user', 'index failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.show( history.id, hdas[0].id ); + }, 500, 'History is not accessible to the current user', 'show failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.update( history.id, hdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( history.id, hdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + + this.test.comment( 'Attempting to copy an accessible hda (default is accessible)' + + 'from an inaccessible history should fail' ); + this.api.assertRaises( function(){ + var returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : hdas[0].id + }); + this.debug( this.jsonStr( returned ) ); + }, 403, 'History is not accessible to the current user', 'copy failed with error' ); + +} +spaceghost.user.loginOrRegisterUser( email2, password2 ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ----------------------------------------------------------------------------------------- user2 + inaccessible + ensureInaccessibility.call( spaceghost, inaccessibleHistory, inaccessibleHdas ); + + // ----------------------------------------------------------------------------------------- user2 + accessible + this.test.comment( 'show should work for the importable history' ); + this.test.assert( this.api.histories.show( accessibleHistory.id ).id === accessibleHistory.id, + 'show worked' ); + + this.test.comment( 'create/copy should work for the importable history' ); + var returned = this.api.histories.create({ history_id : accessibleHistory.id }); + this.test.assert( returned.name === "Copy of '" + accessibleHistory.name + "'", + 'copied name matches: ' + returned.name ); + + this.test.comment( 'update should fail for the importable history' ); + this.api.assertRaises( function(){ + this.api.histories.update( accessibleHistory.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.test.comment( 'delete should fail for the importable history' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( accessibleHistory.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'indexing should work for the contents of the importable history' ); + this.test.assert( this.api.hdas.index( accessibleHistory.id ).length === 1, + 'index worked' ); + this.test.comment( 'showing should work for the contents of the importable history' ); + this.test.assert( this.api.hdas.show( accessibleHistory.id, accessibleHdas[0].id ).id === accessibleHdas[0].id, + 'show worked' ); + this.test.comment( 'updating should fail for the contents of the importable history' ); + this.api.assertRaises( function(){ + this.api.hdas.update( accessibleHistory.id, accessibleHdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.test.comment( 'deleting should fail for the contents of the importable history' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( accessibleHistory.id, accessibleHdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + this.test.comment( 'copying a dataset from the importable history should work' ); + returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : accessibleHdas[0].id + }); + this.test.assert( returned.name === accessibleHdas[0].name, 'successful copy from: ' + returned.name ); + + this.test.comment( 'copying a dataset into the importable history should fail' ); + this.api.assertRaises( function(){ + this.api.hdas.create( accessibleHistory.id, { + source : 'hda', + // should error before it checks the id + content : 'bler' + }); + }, 400, 'History is not owned by the current user', 'copy to failed' ); + + //// ----------------------------------------------------------------------------------------- user2 + published + this.test.comment( 'show should work for the published history' ); + this.test.assert( this.api.histories.show( publishedHistory.id ).id === publishedHistory.id, + 'show worked' ); + this.test.comment( 'create/copy should work for the published history' ); + returned = this.api.histories.create({ history_id : publishedHistory.id }); + this.test.assert( returned.name === "Copy of '" + publishedHistory.name + "'", + 'copied name matches: ' + returned.name ); + this.test.comment( 'update should fail for the published history' ); + this.api.assertRaises( function(){ + this.api.histories.update( publishedHistory.id, { deleted: true }); + }, 500, 'History is not owned by the current user', 'update failed with error' ); + this.test.comment( 'delete should fail for the published history' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( publishedHistory.id ); + }, 400, 'History is not owned by the current user', 'delete failed with error' ); + + this.test.comment( 'indexing should work for the contents of the published history' ); + this.test.assert( this.api.hdas.index( publishedHistory.id ).length === 1, + 'index worked' ); + this.test.comment( 'showing should work for the contents of the published history' ); + this.test.assert( this.api.hdas.show( publishedHistory.id, publishedHdas[0].id ).id === publishedHdas[0].id, + 'show worked' ); + this.test.comment( 'updating should fail for the contents of the published history' ); + this.api.assertRaises( function(){ + this.api.hdas.update( publishedHistory.id, publishedHdas[0].id, { deleted: true }); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'update failed with error' ); + this.test.comment( 'deleting should fail for the contents of the published history' ); + this.api.assertRaises( function(){ + this.api.hdas.delete_( publishedHistory.id, publishedHdas[0].id ); + }, 500, 'HistoryDatasetAssociation is not owned by current user', 'delete failed with error' ); + + this.test.comment( 'copying a dataset from the published history should work' ); + returned = this.api.hdas.create( this.api.histories.show( 'current' ).id, { + source : 'hda', + content : publishedHdas[0].id + }); + this.test.assert( returned.name === publishedHdas[0].name, 'successful copy from: ' + returned.name ); + + this.test.comment( 'copying a dataset into the published history should fail' ); + this.api.assertRaises( function(){ + this.api.hdas.create( publishedHistory.id, { + source : 'hda', + // should error before it checks the id + content : 'bler' + }); + }, 400, 'History is not owned by the current user', 'copy to failed' ); +}); +spaceghost.user.logout(); + + +//// ------------------------------------------------------------------------------------------- user1 revoke perms +spaceghost.user.loginOrRegisterUser( email, password ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( 'revoking perms should prevent access' ); + this.api.histories.update( accessibleHistory.id, { + importable : false + }); + var returned = this.api.histories.show( accessibleHistory.id ); + this.test.assert( !returned.importable, 'now not importable' ); + this.test.assert( !returned.published, '(still not published)' ); + this.test.assert( !!returned.slug, '(slug still set) ' + returned.slug ); + + this.api.histories.update( publishedHistory.id, { + importable : false, + published : false + }); + returned = this.api.histories.show( publishedHistory.id ); + this.test.assert( !returned.importable, 'now not importable' ); + this.test.assert( !returned.published, 'now not published' ); + this.test.assert( !!returned.slug, '(slug still set) ' + returned.slug ); +}); +spaceghost.user.logout(); + + +//// ------------------------------------------------------------------------------------------- user2 retry perms +spaceghost.user.loginOrRegisterUser( email2, password2 ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + ensureInaccessibility.call( spaceghost, accessibleHistory, accessibleHdas ); + ensureInaccessibility.call( spaceghost, publishedHistory, publishedHdas ); +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -33,25 +33,6 @@ } spaceghost.user.loginOrRegisterUser( email, password ); -function hasKeys( object, keysArray ){ - if( !utils.isObject( object ) ){ return false; } - for( var i=0; i<keysArray.length; i += 1 ){ - if( !object.hasOwnProperty( keysArray[i] ) ){ - spaceghost.debug( 'object missing key: ' + keysArray[i] ); - return false; - } - } - return true; -} - -function countKeys( object ){ - if( !utils.isObject( object ) ){ return 0; } - var count = 0; - for( var key in object ){ - if( object.hasOwnProperty( key ) ){ count += 1; } - } - return count; -} // =================================================================== TESTS spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ @@ -64,7 +45,7 @@ this.test.assert( historyIndex.length >= 1, 'Has at least one history' ); var firstHistory = historyIndex[0]; - this.test.assert( hasKeys( firstHistory, [ 'id', 'name', 'url' ] ), 'Has the proper keys' ); + this.test.assert( this.hasKeys( firstHistory, [ 'id', 'name', 'url' ] ), 'Has the proper keys' ); this.test.assert( this.api.isEncodedId( firstHistory.id ), 'Id appears well-formed' ); @@ -72,7 +53,7 @@ this.test.comment( 'show should get a history details object' ); var historyShow = this.api.histories.show( firstHistory.id ); //this.debug( this.jsonStr( historyShow ) ); - this.test.assert( hasKeys( historyShow, [ + this.test.assert( this.hasKeys( historyShow, [ 'id', 'name', 'annotation', 'nice_size', 'contents_url', 'state', 'state_details', 'state_ids' ]), 'Has the proper keys' ); @@ -83,8 +64,8 @@ 'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload' ], state_details = historyShow.state_details, state_ids = historyShow.state_ids; - this.test.assert( hasKeys( state_details, states ), 'state_details has the proper keys' ); - this.test.assert( hasKeys( state_ids, states ), 'state_ids has the proper keys' ); + this.test.assert( this.hasKeys( state_details, states ), 'state_details has the proper keys' ); + this.test.assert( this.hasKeys( state_ids, states ), 'state_ids has the proper keys' ); var state_detailsAreNumbers = true; state_idsAreArrays = true; states.forEach( function( state ){ @@ -103,20 +84,19 @@ this.test.assert( this.api.histories.show( this.api.histories.index()[0].id ).id === firstHistory.id, 'combining function calls works' ); - // test server bad id protection - this.test.comment( 'A bad id to show should throw an error' ); - this.assertRaises( function(){ - this.api.histories.show( '1234123412341234' ); - }, '400 Bad Request', 'Raises an exception' ); + this.test.comment( 'Calling show with "current" should return the current history' ); + this.test.assert( this.api.histories.show( 'current' ).id === historyShow.id, 'current returned same id' ); // ------------------------------------------------------------------------------------------- CREATE - this.test.comment( 'Calling create should create a new history and allow setting the name' ); + this.test.comment( 'Calling create should create a new history and allow setting the name and making it current' ); var newHistoryName = 'Created History', - createdHistory = this.api.histories.create({ name: newHistoryName }); + createdHistory = this.api.histories.create({ name: newHistoryName, current: true }); //this.debug( 'returned from create:\n' + this.jsonStr( createdHistory ) ); this.test.assert( createdHistory.name === newHistoryName, "Name of created history (from create) is correct: " + createdHistory.name ); + this.test.assert( this.api.histories.show( 'current' ).id === createdHistory.id, + "was made current" ); // check the index var newFirstHistory = this.api.histories.index()[0]; @@ -156,50 +136,25 @@ "Undeletion returned 'OK' - even though that's not a great, informative response: " + undeletedHistory ); newFirstHistory = this.api.histories.index()[0]; - this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); + //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); this.test.assert( newFirstHistory.id === createdHistory.id, "Id of last history (from index) DOES appear after undeletion: " + newFirstHistory.id ); //TODO: show, deleted flag //TODO: delete, purge flag + + + // ------------------------------------------------------------------------------------------- set_as_current + this.test.comment( 'calling set_as_current on a non-current history will make it current' ); + this.test.assert( this.api.histories.show( 'current' ).id !== historyShow.id, historyShow.id + ' is not current' ); + var returned = this.api.histories.set_as_current( historyShow.id ); + this.debug( this.jsonStr( returned ) ); + this.test.assert( this.api.histories.show( 'current' ).id === historyShow.id, 'made current' ); + this.api.histories.set_as_current( newFirstHistory.id ); + + // ------------------------------------------------------------------------------------------- UPDATE - // ........................................................................................... idiot proofing - this.test.comment( 'updating to the current value should return no value (no change)' ); - historyShow = this.api.histories.show( newFirstHistory.id ); - var returned = this.api.histories.update( newFirstHistory.id, { - name : historyShow.name - }); - this.test.assert( countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); - - this.test.comment( 'updating using a nonsense key should fail silently' ); - var err = null; - try { - returned = this.api.histories.update( newFirstHistory.id, { - konamiCode : 'uuddlrlrba' - }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( err === null, "No error occurred: " + this.jsonStr( err ) ); - - this.test.comment( 'updating by attempting to change type should cause an error' ); - err = {}; - try { - returned = this.api.histories.update( newFirstHistory.id, { - //name : false - deleted : 'sure why not' - }); - } catch( error ){ - err = error; - //this.debug( this.jsonStr( err ) ); - } - this.test.assert( !!err.message, "Error occurred: " + err.message ); - this.test.assert( err.status === 400, "Error status is 400: " + err.status ); - //TODO??: other type checks? - - // ........................................................................................... name this.test.comment( 'update should allow changing the name' ); returned = this.api.histories.update( newFirstHistory.id, { @@ -339,8 +294,58 @@ // ------------------------------------------------------------------------------------------- ERRORS - //TODO: make sure expected errors are being passed back (but no permissions checks here - different suite) - // bad ids: index, show, update, delete, undelete + // ........................................................................................... idiot proofing + this.test.comment( 'updating to the current value should return no value (no change)' ); + historyShow = this.api.histories.show( newFirstHistory.id ); + returned = this.api.histories.update( newFirstHistory.id, { + name : historyShow.name + }); + this.test.assert( this.countKeys( returned ) === 0, "No changed returned: " + this.jsonStr( returned ) ); + + this.test.comment( 'updating using a nonsense key should fail silently' ); + returned = this.api.histories.update( newFirstHistory.id, { + konamiCode : 'uuddlrlrba' + }); + this.test.assert( returned.konamiCode === undefined, 'key was not set: ' + returned.konamiCode ); + + // test server bad id protection + spaceghost.test.comment( 'A bad id should throw an error' ); + this.api.assertRaises( function(){ + this.api.histories.show( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: show' ); + spaceghost.test.comment( 'A bad id should throw an error when using update' ); + this.api.assertRaises( function(){ + this.api.histories.update( '1234123412341234', {} ); + }, 500, 'unable to decode', 'Bad Request with invalid id: update' ); + spaceghost.test.comment( 'A bad id should throw an error when using delete' ); + this.api.assertRaises( function(){ + this.api.histories.delete_( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: delete' ); + spaceghost.test.comment( 'A bad id should throw an error when using undelete' ); + this.api.assertRaises( function(){ + this.api.histories.undelete( '1234123412341234' ); + }, 400, 'unable to decode', 'Bad Request with invalid id: undelete' ); + + this.test.comment( 'updating by attempting to change type should cause an error' ); + [ 'name', 'annotation' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = false; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, updatedAttrs ); + }, 400, key + ' must be a string or unicode', 'type validation error' ); + }); + [ 'deleted', 'importable', 'published' ].forEach( function( key ){ + var updatedAttrs = {}; + updatedAttrs[ key ] = 'straaang'; + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, updatedAttrs ); + }, 400, key + ' must be a boolean', 'type validation error' ); + }); + [ 'you\'re it', [ true ] ].forEach( function( badVal ){ + spaceghost.api.assertRaises( function(){ + returned = spaceghost.api.histories.update( newFirstHistory.id, { tags: badVal }); + }, 400, 'tags must be a list', 'type validation error' ); + }); /* */ //this.debug( this.jsonStr( historyShow ) ); diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -81,6 +81,7 @@ """ # debugging flag - set to true to have casperjs tests output with --verbose=true and --logLevel=debug + #debug = True debug = False # bit of a hack - this is the beginning of the last string when capserjs --verbose=true --logLevel=debug # use this to get subprocess to stop waiting for output @@ -191,6 +192,7 @@ except ValueError, val_err: if str( val_err ) == 'No JSON object could be decoded': log.debug( '(error parsing returned JSON from casperjs, dumping stdout...)\n:%s', stdout_output ) + return HeadlessJSJavascriptError( 'see log for details' ) else: raise @@ -375,19 +377,29 @@ class Test_04_HDAs( CasperJSTestCase ): """Tests for HistoryDatasetAssociation fetching, rendering, and modeling. """ - def test_00_HDA_states( self ): - """Test structure rendering of HDAs in all the possible HDA states - """ - self.run_js_script( 'hda-state-tests.js' ) + #def test_00_HDA_states( self ): + # """Test structure rendering of HDAs in all the possible HDA states + # """ + # self.run_js_script( 'hda-state-tests.js' ) class Test_05_API( CasperJSTestCase ): """Tests for API functionality and security. """ - def test_00_history_api( self ): - """Test history API. + #def test_00_history_api( self ): + # """Test history API. + # """ + # self.run_js_script( 'api-history-tests.js' ) + + def test_01_hda_api( self ): + """Test HDA API. """ - self.run_js_script( 'api-history-tests.js' ) + self.run_js_script( 'api-hda-tests.js' ) + + def test_02_history_permissions_api( self ): + """Test API permissions for importable, published histories. + """ + self.run_js_script( 'api-history-permission-tests.js' ) # ==================================================================== MAIN diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -75,12 +75,63 @@ if( resp.status !== 200 ){ // grrr... this doesn't lose the \n\r\t //throw new APIError( resp.responseText.replace( /[\s\n\r\t]+/gm, ' ' ).replace( /"/, '' ) ); - this.spaceghost.debug( 'api error response status code: ' + resp.status ); + this.spaceghost.debug( 'API error: code: ' + resp.status + ', responseText: ' + resp.responseText ); + this.spaceghost.debug( '\t responseJSON: ' + this.spaceghost.jsonStr( resp.responseJSON ) ); throw new APIError( resp.responseText, resp.status ); } return JSON.parse( resp.responseText ); }; +// =================================================================== TESTING +/** Checks whether fn raises an error with a message that contains a status and given string. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @private + */ +API.prototype._APIRaises = function _APIRaises( testFn, statusExpected, errMsgContains ){ + var failed = false; + try { + testFn.call( this.spaceghost ); + } catch( err ){ + this.spaceghost.debug( err.name + ': ' + err.status ); + this.spaceghost.debug( err.message ); + if( ( err.name === 'APIError' ) + && ( err.status && err.status === statusExpected ) + && ( err.message.indexOf( errMsgContains ) !== -1 ) ){ + failed = true; + + // re-raise other, non-searched-for errors + } else { + throw err; + } + } + return failed; +}; + +/** Simple assert raises. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @param {String} msg assertion message to display + */ +API.prototype.assertRaises = function assertRaises( testFn, statusExpected, errMsgContains, msg ){ + return this.spaceghost.test.assert( this._APIRaises( testFn, statusExpected, errMsgContains ), msg ); +}; + +/** Simple assert does not raise. + * NOTE: DOES NOT work with steps. @see SpaceGhost#assertStepsRaise + * @param {Function} testFn a function that may throw an error + * @param {Integer} statusExpected the HTTP status code expected + * @param {String} errMsgContains some portion of the correct error msg + * @param {String} msg assertion message to display + */ +API.prototype.assertDoesntRaise = function assertDoesntRaise( testFn, statusExpected, errMsgContains, msg ){ + return this.spaceghost.test.assert( !this._APIRaises( testFn, statusExpected, errMsgContains ), msg ); +}; + // =================================================================== MISC API.prototype.isEncodedId = function isEncodedId( id ){ if( typeof id !== 'string' ){ return false; } @@ -164,7 +215,8 @@ create : 'api/histories', delete_ : 'api/histories/%s', undelete: 'api/histories/deleted/%s/undelete', - update : 'api/histories/%s' + update : 'api/histories/%s', + set_as_current : 'api/histories/%s/set_as_current' }; HistoriesAPI.prototype.index = function index( deleted ){ @@ -179,7 +231,7 @@ HistoriesAPI.prototype.show = function show( id, deleted ){ this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); - id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + id = ( id === 'most_recently_used' || id === 'current' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; return this.api._ajax( utils.format( this.urlTpls.show, id ), { data : { deleted: deleted } @@ -217,7 +269,7 @@ }); }; -HistoriesAPI.prototype.update = function create( id, payload ){ +HistoriesAPI.prototype.update = function update( id, payload ){ this.api.spaceghost.info( 'histories.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data @@ -231,6 +283,15 @@ }); }; +HistoriesAPI.prototype.set_as_current = function set_as_current( id ){ + this.api.spaceghost.info( 'histories.set_as_current: ' + id ); + id = this.api.ensureId( id ); + + return this.api._ajax( utils.format( this.urlTpls.set_as_current, id ), { + type : 'PUT' + }); +}; + // =================================================================== HDAS var HDAAPI = function HDAAPI( api ){ @@ -297,6 +358,23 @@ }); }; +HDAAPI.prototype.delete_ = function create( historyId, id, purge ){ + this.api.spaceghost.info( 'hdas.delete_: ' + [ historyId, id ] ); + historyId = this.api.ensureId( historyId ); + id = this.api.ensureId( id ); + + // have to attach like GET param - due to body loss in jq + url = utils.format( this.urlTpls.update, historyId, id ); + if( purge ){ + url += '?purge=True'; + } + return this.api._ajax( url, { + type : 'DELETE' + }); +}; + +//TODO: delete_ + // =================================================================== TOOLS var ToolsAPI = function HDAAPI( api ){ @@ -350,6 +428,218 @@ }); }; +//ToolsAPI.prototype.uploadByForm = function upload( historyId, options ){ +// this.api.spaceghost.debug( '-------------------------------------------------' ); +// this.api.spaceghost.info( 'tools.upload: ' + [ historyId, '(contents)', this.api.spaceghost.jsonStr( options ) ] ); +// this.api.ensureId( historyId ); +// options = options || {}; +// +// this.api.spaceghost.evaluate( function( url ){ +// var html = [ +// '<form action="', url, '" method="post" enctype="multipart/form-data">', +// '<input type="file" name="files_0|file_data">', +// '<input type="hidden" name="tool_id" />', +// '<input type="hidden" name="history_id" />', +// '<input type="hidden" name="inputs" />', +// '<button type="submit">Submit</button>', +// '</form>' +// ]; +// document.write( html.join('') ); +// //document.getElementsByTagName( 'body' )[0].innerHTML = html.join(''); +// }, utils.format( this.urlTpls.create ) ); +// +// this.api.spaceghost.fill( 'form', { +// 'files_0|file_data' : '1.txt', +// 'tool_id' : 'upload1', +// 'history_id' : historyId, +// 'inputs' : JSON.stringify({ +// 'file_type' : 'auto', +// 'files_0|type' : 'upload_dataset', +// 'to_posix_lines' : true, +// 'space_to_tabs' : false, +// 'dbkey' : '?' +// }) +// }, true ); +// // this causes the page to switch...I think +//}; + +/** paste a file - either from a string (options.paste) or from a filesystem file (options.filepath) */ +ToolsAPI.prototype.uploadByPaste = function upload( historyId, options ){ + this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.ensureId( historyId ); + options = options || {}; + + var inputs = { + 'files_0|NAME' : options.name || 'Test Dataset', + 'dbkey' : options.dbkey || '?', + 'file_type' : options.ext || 'auto' + }; + if( options.filepath ){ + var fs = require( 'fs' ); + inputs[ 'files_0|url_paste' ] = fs.read( options.filepath ); + + } else if( options.paste ){ + inputs[ 'files_0|url_paste' ] = options.paste; + } + if( options.posix ){ + inputs[ 'files_0|to_posix_lines' ] = 'Yes'; + } + if( options.tabs ){ + inputs[ 'files_0|space_to_tab' ] = 'Yes'; + } + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : { + tool_id : 'upload1', + upload_type : 'upload_dataset', + history_id : historyId, + inputs : inputs + } + }); +}; + +/** post a file to the upload1 tool over ajax */ +ToolsAPI.prototype.upload = function upload( historyId, options ){ + this.api.spaceghost.info( 'tools.upload: ' + [ historyId, this.api.spaceghost.jsonStr( options ) ] ); + this.api.ensureId( historyId ); + options = options || {}; + + // We can post an upload using jquery and formdata (see below), the more + // difficult part is attaching the file without user intervention. + // To do this we need to (unfortunately) create a form phantom can attach the file to first. + this.api.spaceghost.evaluate( function(){ + $( 'body' ).append( '<input type="file" name="casperjs-upload-file" />' ); + }); + this.api.spaceghost.page.uploadFile( 'input[name="casperjs-upload-file"]', options.filepath ); + + var inputs = { + 'file_type' : options.ext || 'auto', + 'files_0|type' : 'upload_dataset', + 'dbkey' : options.dbkey || '?' + }; + if( options.posix ){ + inputs[ 'files_0|to_posix_lines' ] = 'Yes'; + } + if( options.tabs ){ + inputs[ 'files_0|space_to_tab' ] = 'Yes'; + } + var response = this.api.spaceghost.evaluate( function( url, historyId, inputs ){ + var file = $( 'input[name="casperjs-upload-file"]' )[0].files[0], + formData = new FormData(), + response; + + formData.append( 'files_0|file_data', file ); + formData.append( 'history_id', historyId ); + formData.append( 'tool_id', 'upload1' ); + formData.append( 'inputs', JSON.stringify( inputs ) ); + $.ajax({ + url : url, + async : false, + type : 'POST', + data : formData, + // when sending FormData don't have jq process or cache the data + cache : false, + contentType : false, + processData : false, + // if we don't add this, payload isn't processed as JSON + headers : { 'Accept': 'application/json' } + }).done(function( resp ){ + response = resp; + }); + // this works only bc jq is async + return response; + }, utils.format( this.urlTpls.create ), historyId, inputs ); + + if( !response ){ + throw new APIError( 'Failed to upload: ' + options.filepath, 0 ); + } + + return response; +}; + +/** amount of time allowed to upload a file (before erroring) */ +ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000; + +/** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */ +ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){ + var spaceghost = this.api.spaceghost, + uploadedId; + + spaceghost.then( function(){ + var returned = this.api.tools.upload( historyId, options ); + this.debug( 'returned: ' + this.jsonStr( returned ) ); + uploadedId = returned.outputs[0].id; + this.debug( 'uploadedId: ' + uploadedId ); + }); + + spaceghost.then( function(){ + this.waitFor( + function testHdaState(){ + var hda = spaceghost.api.hdas.show( historyId, uploadedId ); + spaceghost.debug( spaceghost.jsonStr( hda.state ) ); + return !( hda.state === 'upload' || hda.state === 'queued' || hda.state === 'running' ); + }, + function _then(){ + spaceghost.info( 'upload finished: ' + uploadedId ); + if( then ){ + then.call( spaceghost, uploadedId ); + } + //var hda = spaceghost.api.hdas.show( historyId, uploadedId ); + //spaceghost.debug( spaceghost.jsonStr( hda ) ); + }, + function timeout(){ + throw new APIError( 'timeout uploading file', 408 ); + }, + options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT + ); + }); + return spaceghost; +}; + +/** add two casperjs steps - upload multiple files (described in optionsArray) and wait for all jobs to complete */ +ToolsAPI.prototype.thenUploadMultiple = function thenUploadMultiple( historyId, optionsArray, then ){ + var spaceghost = this.api.spaceghost, + uploadedIds = []; + + this.api.spaceghost.then( function(){ + var spaceghost = this; + optionsArray.forEach( function( options ){ + var returned = spaceghost.api.tools.upload( historyId, options ); + spaceghost.debug( 'uploaded:' + spaceghost.jsonStr( returned ) ); + uploadedIds.push( returned.outputs[0].id ); + }); + }); + + // wait for every hda to finish running - IOW, don't use uploadedIds + this.api.spaceghost.then( function(){ + this.debug( this.jsonStr( uploadedIds ) ); + this.waitFor( + function testHdaStates(){ + var hdas = spaceghost.api.hdas.index( historyId ), + running = hdas.filter( function( hda ){ + return ( hda.state === 'upload' || hda.state === 'queued' || hda.state === 'running' ); + }).map( function( hda ){ + return hda.id; + }); + //spaceghost.debug( 'still uploading: ' + spaceghost.jsonStr( running ) ); + return running.length === 0; + }, + function _then(){ + var hdas = spaceghost.api.hdas.index( historyId ); + spaceghost.debug( spaceghost.jsonStr( hdas ) ); + if( then ){ + then.call( spaceghost, uploadedIds ); + } + }, + function timeout(){ + throw new APIError( 'timeout uploading files', 408 ); + }, + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) * optionsArray.length + ); + }); + return spaceghost; +}; + // =================================================================== WORKFLOWS var WorkflowsAPI = function WorkflowsAPI( api ){ @@ -495,7 +785,7 @@ }; -// =================================================================== HISTORIES +// =================================================================== VISUALIZATIONS var VisualizationsAPI = function VisualizationsAPI( api ){ this.api = api; }; diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -280,6 +280,9 @@ User.prototype.getRandomEmail = function getRandomEmail( username, domain ){ username = username || 'test'; domain = domain || 'test.test'; - return username + Date.now() + '@' + domain; + var number = Math.ceil( Math.random() * 10000000000000 ); + // doesn't work so well when creating two users at once + //var number = Date.now(); + return username + number + '@' + domain; }; diff -r c4950bc662256f013916b0aaabb73a47508213c5 -r 79ab14af25e4182dac99ecad3918ed653c50f272 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -886,6 +886,30 @@ this.test.assert( classes.indexOf( className ) === -1, msg ); }; +/** Return true if object has all keys in keysArray (useful in API testing of return values). + * @param {Object} object the object to test + * @param {String[]} keysArray an array of expected keys + */ +SpaceGhost.prototype.hasKeys = function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + return false; + } + } + return true; +}; + +/** Returns count of keys in object. */ +SpaceGhost.prototype.countKeys = function countKeys( object ){ + if( !utils.isObject( object ) ){ return 0; } + var count = 0; + for( var key in object ){ + if( object.hasOwnProperty( key ) ){ count += 1; } + } + return count; +}; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. https://bitbucket.org/galaxy/galaxy-central/commits/561929fb2d7e/ Changeset: 561929fb2d7e User: carlfeberhard Date: 2014-03-25 22:00:03 Summary: merge Affected #: 3 files diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1106,6 +1106,10 @@ }); // For vertical alignment, track mouse with simple line. + // Fixes needed for this to work: + // (a) make work with embedded visualizations; + // (b) seems to get stuck on tile overlaps. + /* var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element); // Show tracker only when hovering over view. @@ -1125,6 +1129,7 @@ mouse_tracker_div.hide(); } ); + */ this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); @@ -3053,14 +3058,21 @@ var tile_drawn = $.Deferred(); track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { - // If deferred objects ever show up in tile data, that is likely because a - // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset - // was returned but then couldn't be used). It's not clear whether this will happen - // in practice, and currently the code doesn't handle it. It could probably handle it - // by recursively calling draw_helper. var tile_data = get_tile_data(), tracks_data = tile_data, seq_data; + + // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk + // that cannot be subsetted. This may occur if the superset has a message. If there is a + // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the + // GenomeDataManager in visualization module. + if (_.find(tile_data, function(d) { return util.is_deferred(d); })) { + track.tile_cache.set_elt(key, undefined); + $.when(track.draw_helper(region, w_scale, options)).then(function(tile) { + tile_drawn.resolve(tile); + }); + return; + } // If sequence data is available, subset to get only data in region. if (view.reference_track) { diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,6 +1,13 @@ define(function(){ /** + * Helper to determine if object is jQuery deferred. + */ +var is_deferred = function ( d ) { + return ('promise' in d); +}; + +/** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ @@ -109,6 +116,7 @@ }; return { + is_deferred: is_deferred, ServerStateDeferred : ServerStateDeferred, get_random_color : get_random_color }; diff -r 79ab14af25e4182dac99ecad3918ed653c50f272 -r 561929fb2d7e827f20ea078904aeebe35173f3f9 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -86,14 +86,6 @@ }); }; - -/** - * Helper to determine if object is jQuery deferred. - */ -var is_deferred = function ( d ) { - return ('promise' in d); -}; - // --------- Models --------- /** @@ -380,11 +372,10 @@ * Get data from dataset. */ get_data: function(region, mode, resolution, extra_params) { - // Look for entry and return if it's a deferred or if data available is compatible with mode. var entry = this.get_elt(region); if ( entry && - ( is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { + ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { return entry; } @@ -405,12 +396,12 @@ // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[entry_region.toString()]; - if ( is_deferred(entry) || + if ( util_mod.is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(entry_region, i); // If there's data, subset it. - if ( !is_deferred(entry) ) { + if ( !util_mod.is_deferred(entry) ) { var subset_entry = this.subset_entry(entry, region); this.set(region, subset_entry); entry = subset_entry; 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: Jeremy Goecks: Trackster: (a) fix bug when trying to subset from supersets with messages; (b) display vertical placeholder until bugs are resolved.
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47211cedc8d0/ Changeset: 47211cedc8d0 User: Jeremy Goecks Date: 2014-03-25 20:41:40 Summary: Trackster: (a) fix bug when trying to subset from supersets with messages; (b) display vertical placeholder until bugs are resolved. Affected #: 3 files diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1106,6 +1106,10 @@ }); // For vertical alignment, track mouse with simple line. + // Fixes needed for this to work: + // (a) make work with embedded visualizations; + // (b) seems to get stuck on tile overlaps. + /* var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element); // Show tracker only when hovering over view. @@ -1125,6 +1129,7 @@ mouse_tracker_div.hide(); } ); + */ this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); @@ -3053,14 +3058,21 @@ var tile_drawn = $.Deferred(); track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { - // If deferred objects ever show up in tile data, that is likely because a - // Deferred-subsetting interaction failed. Specifically, a Deferred for a superset - // was returned but then couldn't be used). It's not clear whether this will happen - // in practice, and currently the code doesn't handle it. It could probably handle it - // by recursively calling draw_helper. var tile_data = get_tile_data(), tracks_data = tile_data, seq_data; + + // Deferreds may show up here if trying to fetch a subset of data from a superset data chunk + // that cannot be subsetted. This may occur if the superset has a message. If there is a + // Deferred, try again from the top. NOTE: this condition could (should?) be handled by the + // GenomeDataManager in visualization module. + if (_.find(tile_data, function(d) { return util.is_deferred(d); })) { + track.tile_cache.set_elt(key, undefined); + $.when(track.draw_helper(region, w_scale, options)).then(function(tile) { + tile_drawn.resolve(tile); + }); + return; + } // If sequence data is available, subset to get only data in region. if (view.reference_track) { diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -1,6 +1,13 @@ define(function(){ /** + * Helper to determine if object is jQuery deferred. + */ +var is_deferred = function ( d ) { + return ('promise' in d); +}; + +/** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. */ @@ -109,6 +116,7 @@ }; return { + is_deferred: is_deferred, ServerStateDeferred : ServerStateDeferred, get_random_color : get_random_color }; diff -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 -r 47211cedc8d0db9a3d9189bc2d3bfa7e3fe11b86 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -86,14 +86,6 @@ }); }; - -/** - * Helper to determine if object is jQuery deferred. - */ -var is_deferred = function ( d ) { - return ('promise' in d); -}; - // --------- Models --------- /** @@ -380,11 +372,10 @@ * Get data from dataset. */ get_data: function(region, mode, resolution, extra_params) { - // Look for entry and return if it's a deferred or if data available is compatible with mode. var entry = this.get_elt(region); if ( entry && - ( is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { + ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { return entry; } @@ -405,12 +396,12 @@ // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[entry_region.toString()]; - if ( is_deferred(entry) || + if ( util_mod.is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(entry_region, i); // If there's data, subset it. - if ( !is_deferred(entry) ) { + if ( !util_mod.is_deferred(entry) ) { var subset_entry = this.subset_entry(entry, region); this.set(region, subset_entry); entry = subset_entry; 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: guerler: Ui/Upload: Close modal on escape
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d2f3398ad6d/ Changeset: 4d2f3398ad6d User: guerler Date: 2014-03-25 19:01:26 Summary: Ui/Upload: Close modal on escape Affected #: 2 files diff -r 208533b58c7e135e99a74e7cf5183a63020b3341 -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 static/scripts/mvc/ui/ui-modal.js --- a/static/scripts/mvc/ui/ui-modal.js +++ b/static/scripts/mvc/ui/ui-modal.js @@ -115,7 +115,7 @@ this.$el.remove(); // remove escape event - $(document).off('keyup'); + $(document).off('keyup.ui-modal'); } // create new element @@ -157,13 +157,11 @@ // bind additional closing events if (this.options.closing_events) { // bind the ESC key to hide() function - if (!this.options.buttons.Pause){ // don't bind for the upload modal because of the side effects with system modal for file choosing - $(document).on('keyup', function(e) { - if (e.keyCode == 27) { - self.hide(); - } - }); - } + $(document).on('keyup.ui-modal', function(e) { + if (e.keyCode == 27) { + self.hide(); + } + }); // hide modal if background is clicked this.$el.find('.modal-backdrop').on('click', function() { self.hide(); }); diff -r 208533b58c7e135e99a74e7cf5183a63020b3341 -r 4d2f3398ad6d6eebfe084a184bf860dd7c6f9071 static/scripts/packed/mvc/ui/ui-modal.js --- a/static/scripts/packed/mvc/ui/ui-modal.js +++ b/static/scripts/packed/mvc/ui/ui-modal.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:true,height:null,width:null,closing_events:false},buttonList:{},initialize:function(c){if(c){this._create(c)}},show:function(c){this.initialize(c);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.visible=false;this.$el.fadeOut("fast")},enableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",false)},disableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",true)},showButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).show()},hideButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).hide()},getButton:function(c){var d=this.buttonList[c];return this.$buttons.find("#"+d)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var d=this;this.options=_.defaults(e,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove();$(document).off("keyup")}this.setElement(this._template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){this.buttonList={};var c=0;$.each(this.options.buttons,function(f,h){var g="button-"+c++;d.$buttons.append($('<button id="'+g+'"></button>').text(f).click(h)).append(" ");d.buttonList[f]=g})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.closing_events){if(!this.options.buttons.Pause){$(document).on("keyup",function(f){if(f.keyCode==27){d.hide()}})}this.$el.find(".modal-backdrop").on("click",function(){d.hide()})}},_template:function(c){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+c+'</h4></div><div class="modal-body" style="position: static;"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:true,height:null,width:null,closing_events:false},buttonList:{},initialize:function(c){if(c){this._create(c)}},show:function(c){this.initialize(c);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.visible=false;this.$el.fadeOut("fast")},enableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",false)},disableButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).prop("disabled",true)},showButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).show()},hideButton:function(c){var d=this.buttonList[c];this.$buttons.find("#"+d).hide()},getButton:function(c){var d=this.buttonList[c];return this.$buttons.find("#"+d)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var d=this;this.options=_.defaults(e,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove();$(document).off("keyup.ui-modal")}this.setElement(this._template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){this.buttonList={};var c=0;$.each(this.options.buttons,function(f,h){var g="button-"+c++;d.$buttons.append($('<button id="'+g+'"></button>').text(f).click(h)).append(" ");d.buttonList[f]=g})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.closing_events){$(document).on("keyup.ui-modal",function(f){if(f.keyCode==27){d.hide()}});this.$el.find(".modal-backdrop").on("click",function(){d.hide()})}},_template:function(c){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+c+'</h4></div><div class="modal-body" style="position: static;"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: davebgx: Fix server error when attempting to create a repository before any categories have been created.
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/208533b58c7e/ Changeset: 208533b58c7e User: davebgx Date: 2014-03-25 18:25:19 Summary: Fix server error when attempting to create a repository before any categories have been created. Affected #: 1 file diff -r cab5878ce755b1736d09a9a74e419eddb12c0f2d -r 208533b58c7e135e99a74e7cf5183a63020b3341 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -950,7 +950,7 @@ categories = suc.get_categories( trans ) if not categories: message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' - message += 'An administrator needs to create some via the Administrator control panel before creating repositories.', + message += 'An administrator needs to create some via the Administrator control panel before creating repositories.' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', 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: guerler: Charts: Improve fit and chart state handling, recalculate chart only if neccessary
by commits-noreply＠bitbucket.org 25 Mar '14

25 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cab5878ce755/ Changeset: cab5878ce755 User: guerler Date: 2014-03-25 13:35:20 Summary: Charts: Improve fit and chart state handling, recalculate chart only if neccessary Affected #: 9 files diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof module!="undefined"&&module.exports&&(exports=module.exports=x),exports._=x):e._=x,x.VERSION="1.4.4";var T=x.each=x.forEach=function(e,t,r){if(e==null)return;if(c&&e.forEach===c)e.forEach(t,r);else if(e.length===+e.length){for(var i=0,s=e.length;i<s;i++)if(t.call(r,e[i],i,e)===n)return}else for(var o in e)if(x.has(e,o)&&t.call(r,e[o],o,e)===n)return};x.map=x.collect=function(e,t,n){var r=[];return e==null?r:h&&e.map===h?e.map(t,n):(T(e,function(e,i,s){r.push(t.call(n,e,i,s))}),r)};var N="Reduce of empty array with no initial value";x.reduce=x.foldl=x.inject=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(p&&e.reduce===p)return r&&(t=x.bind(t,r)),i?e.reduce(t,n):e.reduce(t);T(e,function(e,s,o){i?n=t.call(r,n,e,s,o):(n=e,i=!0)});if(!i)throw new TypeError(N);return n},x.reduceRight=x.foldr=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(d&&e.reduceRight===d)return r&&(t=x.bind(t,r)),i?e.reduceRight(t,n):e.reduceRight(t);var s=e.length;if(s!==+s){var o=x.keys(e);s=o.length}T(e,function(u,a,f){a=o?o[--s]:--s,i?n=t.call(r,n,e[a],a,f):(n=e[a],i=!0)});if(!i)throw new TypeError(N);return n},x.find=x.detect=function(e,t,n){var r;return C(e,function(e,i,s){if(t.call(n,e,i,s))return r=e,!0}),r},x.filter=x.select=function(e,t,n){var r=[];return e==null?r:v&&e.filter===v?e.filter(t,n):(T(e,function(e,i,s){t.call(n,e,i,s)&&r.push(e)}),r)},x.reject=function(e,t,n){return x.filter(e,function(e,r,i){return!t.call(n,e,r,i)},n)},x.every=x.all=function(e,t,r){t||(t=x.identity);var i=!0;return e==null?i:m&&e.every===m?e.every(t,r):(T(e,function(e,s,o){if(!(i=i&&t.call(r,e,s,o)))return n}),!!i)};var C=x.some=x.any=function(e,t,r){t||(t=x.identity);var i=!1;return e==null?i:g&&e.some===g?e.some(t,r):(T(e,function(e,s,o){if(i||(i=t.call(r,e,s,o)))return n}),!!i)};x.contains=x.include=function(e,t){return e==null?!1:y&&e.indexOf===y?e.indexOf(t)!=-1:C(e,function(e){return e===t})},x.invoke=function(e,t){var n=u.call(arguments,2),r=x.isFunction(t);return x.map(e,function(e){return(r?t:e[t]).apply(e,n)})},x.pluck=function(e,t){return x.map(e,function(e){return e[t]})},x.where=function(e,t,n){return x.isEmpty(t)?n?void 0:[]:x[n?"find":"filter"](e,function(e){for(var n in t)if(t[n]!==e[n])return!1;return!0})},x.findWhere=function(e,t){return x.where(e,t,!0)},x.max=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.max.apply(Math,e);if(!t&&x.isEmpty(e))return-Infinity;var r={computed:-Infinity,value:-Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o>=r.computed&&(r={value:e,computed:o})}),r.value},x.min=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.min.apply(Math,e);if(!t&&x.isEmpty(e))return Infinity;var r={computed:Infinity,value:Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o<r.computed&&(r={value:e,computed:o})}),r.value},x.shuffle=function(e){var t,n=0,r=[];return T(e,function(e){t=x.random(n++),r[n-1]=r[t],r[t]=e}),r};var k=function(e){return x.isFunction(e)?e:function(t){return t[e]}};x.sortBy=function(e,t,n){var r=k(t);return x.pluck(x.map(e,function(e,t,i){return{value:e,index:t,criteria:r.call(n,e,t,i)}}).sort(function(e,t){var n=e.criteria,r=t.criteria;if(n!==r){if(n>r||n===void 0)return 1;if(n<r||r===void 0)return-1}return e.index<t.index?-1:1}),"value")};var L=function(e,t,n,r){var i={},s=k(t==null?x.identity:t);return T(e,function(t,o){var u=s.call(n,t,o,e);r(i,u,t)}),i};x.groupBy=function(e,t,n){return L(e,t,n,function(e,t,n){(x.has(e,t)?e[t]:e[t]=[]).push(n)})},x.countBy=function(e,t,n){return L(e,t,n,function(e,t){x.has(e,t)||(e[t]=0),e[t]++})},x.sortedIndex=function(e,t,n,r){n=n==null?x.identity:k(n);var i=n.call(r,t),s=0,o=e.length;while(s<o){var u=s+o>>>1;n.call(r,e[u])<i?s=u+1:o=u}return s},x.toArray=function(e){return e?x.isArray(e)?u.call(e):e.length===+e.length?x.map(e,x.identity):x.values(e):[]},x.size=function(e){return e==null?0:e.length===+e.length?e.length:x.keys(e).length},x.first=x.head=x.take=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,0,t):e[0]},x.initial=function(e,t,n){return u.call(e,0,e.length-(t==null||n?1:t))},x.last=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,Math.max(e.length-t,0)):e[e.length-1]},x.rest=x.tail=x.drop=function(e,t,n){return u.call(e,t==null||n?1:t)},x.compact=function(e){return x.filter(e,x.identity)};var A=function(e,t,n){return T(e,function(e){x.isArray(e)?t?o.apply(n,e):A(e,t,n):n.push(e)}),n};x.flatten=function(e,t){return A(e,t,[])},x.without=function(e){return x.difference(e,u.call(arguments,1))},x.uniq=x.unique=function(e,t,n,r){x.isFunction(t)&&(r=n,n=t,t=!1);var i=n?x.map(e,n,r):e,s=[],o=[];return T(i,function(n,r){if(t?!r||o[o.length-1]!==n:!x.contains(o,n))o.push(n),s.push(e[r])}),s},x.union=function(){return x.uniq(a.apply(r,arguments))},x.intersection=function(e){var t=u.call(arguments,1);return x.filter(x.uniq(e),function(e){return x.every(t,function(t){return x.indexOf(t,e)>=0})})},x.difference=function(e){var t=a.apply(r,u.call(arguments,1));return x.filter(e,function(e){return!x.contains(t,e)})},x.zip=function(){var e=u.call(arguments),t=x.max(x.pluck(e,"length")),n=new Array(t);for(var r=0;r<t;r++)n[r]=x.pluck(e,""+r);return n},x.unzip=function(e){var t=[];return x.each(e,function(e,n){x.each(e,function(e,r){t.length<=r&&(t[r]=[]),t[r][n]=e})}),t},x.object=function(e,t){if(e==null)return{};var n={};for(var r=0,i=e.length;r<i;r++)t?n[e[r]]=t[r]:n[e[r][0]]=e[r][1];return n},x.indexOf=function(e,t,n){if(e==null)return-1;var r=0,i=e.length;if(n){if(typeof n!="number")return r=x.sortedIndex(e,t),e[r]===t?r:-1;r=n<0?Math.max(0,i+n):n}if(y&&e.indexOf===y)return e.indexOf(t,n);for(;r<i;r++)if(e[r]===t)return r;return-1},x.lastIndexOf=function(e,t,n){if(e==null)return-1;var r=n!=null;if(b&&e.lastIndexOf===b)return r?e.lastIndexOf(t,n):e.lastIndexOf(t);var i=r?n:e.length;while(i--)if(e[i]===t)return i;return-1},x.range=function(e,t,n){arguments.length<=1&&(t=e||0,e=0),n=arguments[2]||1;var r=Math.max(Math.ceil((t-e)/n),0),i=0,s=new Array(r);while(i<r)s[i++]=e,e+=n;return s};var O=function(){};x.bind=function(e,t){var n,r;if(e.bind===S&&S)return S.apply(e,u.call(arguments,1));if(!x.isFunction(e))throw new TypeError;return n=u.call(arguments,2),r=function(){if(this instanceof r){O.prototype=e.prototype;var i=new O;O.prototype=null;var s=e.apply(i,n.concat(u.call(arguments)));return Object(s)===s?s:i}return e.apply(t,n.concat(u.call(arguments)))}},x.partial=function(e){var t=u.call(arguments,1);return function(){return e.apply(this,t.concat(u.call(arguments)))}},x.bindAll=function(e){var t=u.call(arguments,1);if(t.length===0)throw new Error("bindAll must be passed function names");return T(t,function(t){e[t]=x.bind(e[t],e)}),e},x.memoize=function(e,t){var n={};return t||(t=x.identity),function(){var r=t.apply(this,arguments);return x.has(n,r)?n[r]:n[r]=e.apply(this,arguments)}},x.delay=function(e,t){var n=u.call(arguments,2);return setTimeout(function(){return e.apply(null,n)},t)},x.defer=function(e){return x.delay.apply(x,[e,1].concat(u.call(arguments,1)))},x.throttle=function(e,t,n){var r,i,s,o,u=0,a=function(){u=new Date,s=null,o=e.apply(r,i)};return function(){var f=new Date;!u&&n===!1&&(u=f);var l=t-(f-u);return r=this,i=arguments,l<=0?(clearTimeout(s),s=null,u=f,o=e.apply(r,i)):s||(s=setTimeout(a,l)),o}},x.debounce=function(e,t,n){var r,i;return function(){var s=this,o=arguments,u=function(){r=null,n||(i=e.apply(s,o))},a=n&&!r;return clearTimeout(r),r=setTimeout(u,t),a&&(i=e.apply(s,o)),i}},x.once=function(e){var t=!1,n;return function(){return t?n:(t=!0,n=e.apply(this,arguments),e=null,n)}},x.wrap=function(e,t){return function(){var n=[e];return o.apply(n,arguments),t.apply(this,n)}},x.compose=function(){var e=arguments;return function(){var t=arguments;for(var n=e.length-1;n>=0;n--)t=[e[n].apply(this,t)];return t[0]}},x.after=function(e,t){return e<=0?t():function(){if(--e<1)return t.apply(this,arguments)}},x.keys=E||function(e){if(e!==Object(e))throw new TypeError("Invalid object");var t=[];for(var n in e)x.has(e,n)&&t.push(n);return t},x.values=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push(e[n]);return t},x.pairs=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push([n,e[n]]);return t},x.invert=function(e){var t={};for(var n in e)x.has(e,n)&&(t[e[n]]=n);return t},x.functions=x.methods=function(e){var t=[];for(var n in e)x.isFunction(e[n])&&t.push(n);return t.sort()},x.extend=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]=t[n]}),e},x.pick=function(e){var t={},n=a.apply(r,u.call(arguments,1));return T(n,function(n){n in e&&(t[n]=e[n])}),t},x.omit=function(e){var t={},n=a.apply(r,u.call(arguments,1));for(var i in e)x.contains(n,i)||(t[i]=e[i]);return t},x.defaults=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]===void 0&&(e[n]=t[n])}),e},x.clone=function(e){return x.isObject(e)?x.isArray(e)?e.slice():x.extend({},e):e},x.tap=function(e,t){return t(e),e};var M=function(e,t,n,r){if(e===t)return e!==0||1/e==1/t;if(e==null||t==null)return e===t;e instanceof x&&(e=e._wrapped),t instanceof x&&(t=t._wrapped);var i=f.call(e);if(i!=f.call(t))return!1;switch(i){case"[object String]":return e==String(t);case"[object Number]":return e!=+e?t!=+t:e==0?1/e==1/t:e==+t;case"[object Date]":case"[object Boolean]":return+e==+t;case"[object RegExp]":return e.source==t.source&&e.global==t.global&&e.multiline==t.multiline&&e.ignoreCase==t.ignoreCase}if(typeof e!="object"||typeof t!="object")return!1;var s=n.length;while(s--)if(n[s]==e)return r[s]==t;n.push(e),r.push(t);var o=0,u=!0;if(i=="[object Array]"){o=e.length,u=o==t.length;if(u)while(o--)if(!(u=M(e[o],t[o],n,r)))break}else{var a=e.constructor,l=t.constructor;if(a!==l&&!(x.isFunction(a)&&a instanceof a&&x.isFunction(l)&&l instanceof l))return!1;for(var c in e)if(x.has(e,c)){o++;if(!(u=x.has(t,c)&&M(e[c],t[c],n,r)))break}if(u){for(c in t)if(x.has(t,c)&&!(o--))break;u=!o}}return n.pop(),r.pop(),u};x.isEqual=function(e,t){return M(e,t,[],[])},x.isEmpty=function(e){if(e==null)return!0;if(x.isArray(e)||x.isString(e))return e.length===0;for(var t in e)if(x.has(e,t))return!1;return!0},x.isElement=function(e){return!!e&&e.nodeType===1},x.isArray=w||function(e){return f.call(e)=="[object Array]"},x.isObject=function(e){return e===Object(e)},T(["Arguments","Function","String","Number","Date","RegExp"],function(e){x["is"+e]=function(t){return f.call(t)=="[object "+e+"]"}}),x.isArguments(arguments)||(x.isArguments=function(e){return!!e&&!!x.has(e,"callee")}),typeof /./!="function"&&(x.isFunction=function(e){return typeof e=="function"}),x.isFinite=function(e){return isFinite(e)&&!isNaN(parseFloat(e))},x.isNaN=function(e){return x.isNumber(e)&&e!=+e},x.isBoolean=function(e){return e===!0||e===!1||f.call(e)=="[object Boolean]"},x.isNull=function(e){return e===null},x.isUndefined=function(e){return e===void 0},x.has=function(e,t){return l.call(e,t)},x.noConflict=function(){return e._=t,this},x.identity=function(e){return e},x.times=function(e,t,n){var r=Array(e);for(var i=0;i<e;i++)r[i]=t.call(n,i);return r},x.random=function(e,t){return t==null&&(t=e,e=0),e+Math.floor(Math.random()*(t-e+1))};var _={escape:{"&":"&","<":"<",">":">",'"':""","'":"'","/":"/"}};_.unescape=x.invert(_.escape);var D={escape:new RegExp("["+x.keys(_.escape).join("")+"]","g"),unescape:new RegExp("("+x.keys(_.unescape).join("|")+")","g")};x.each(["escape","unescape"],function(e){x[e]=function(t){return t==null?"":(""+t).replace(D[e],function(t){return _[e][t]})}}),x.result=function(e,t){if(e==null)return void 0;var n=e[t];return x.isFunction(n)?n.call(e):n},x.mixin=function(e){T(x.functions(e),function(t){var n=x[t]=e[t];x.prototype[t]=function(){var e=[this._wrapped];return o.apply(e,arguments),F.call(this,n.apply(x,e))}})};var P=0;x.uniqueId=function(e){var t=++P+"";return e?e+t:t},x.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var H=/(.)^/,B={"'":"'","\\":"\\","\r":"r","\n":"n"," ":"t","\u2028":"u2028","\u2029":"u2029"},j=/\\|'|\r|\n|\t|\u2028|\u2029/g;x.template=function(e,t,n){var r;n=x.defaults({},n,x.templateSettings);var i=new RegExp([(n.escape||H).source,(n.interpolate||H).source,(n.evaluate||H).source].join("|")+"|$","g"),s=0,o="__p+='";e.replace(i,function(t,n,r,i,u){return o+=e.slice(s,u).replace(j,function(e){return"\\"+B[e]}),n&&(o+="'+\n((__t=("+n+"))==null?'':_.escape(__t))+\n'"),r&&(o+="'+\n((__t=("+r+"))==null?'':__t)+\n'"),i&&(o+="';\n"+i+"\n__p+='"),s=u+t.length,t}),o+="';\n",n.variable||(o="with(obj||{}){\n"+o+"}\n"),o="var __t,__p='',__j=Array.prototype.join,print=function(){__p+=__j.call(arguments,'');};\n"+o+"return __p;\n";try{r=new Function(n.variable||"obj","_",o)}catch(u){throw u.source=o,u}if(t)return r(t,x);var a=function(e){return r.call(this,e,x)};return a.source="function("+(n.variable||"obj")+"){\n"+o+"}",a},x.chain=function(e){return x(e).chain()};var F=function(e){return this._chain?x(e).chain():e};x.mixin(x),T(["pop","push","reverse","shift","sort","splice","unshift"],function(e){var t=r[e];x.prototype[e]=function(){var n=this._wrapped;return t.apply(n,arguments),(e=="shift"||e=="splice")&&n.length===0&&delete n[0],F.call(this,n)}}),T(["concat","join","slice"],function(e){var t=r[e];x.prototype[e]=function(){return F.call(this,t.apply(this._wrapped,arguments))}}),x.extend(x.prototype,{chain:function(){return this._chain=!0,this},value:function(){return this._wrapped}})}).call(this),define("libs/underscore",function(e){return function(){var t,n;return t||e._}}(this)),define("utils/utils",["libs/underscore"],function(e){function t(e,t,r){n("GET",e,{},t,r)}function n(e,t,n,r,i){if(e=="GET"||e=="DELETE")t.indexOf("?")==-1?t+="?":t+="&",t+=$.param(n);var s=new XMLHttpRequest;s.open(e,t,!0),s.setRequestHeader("Accept","application/json"),s.setRequestHeader("Cache-Control","no-cache"),s.setRequestHeader("X-Requested-With","XMLHttpRequest"),s.setRequestHeader("Content-Type","application/json"),s.onloadend=function(){var e=s.status;try{response=jQuery.parseJSON(s.responseText)}catch(t){response=s.responseText}e==200?r&&r(response):i&&i(response)},e=="GET"||e=="DELETE"?s.send():s.send(JSON.stringify(n))}function r(e,t){var n=$('<div class="'+e+'"></div>');n.appendTo(":eq(0)");var r=n.css(t);return n.remove(),r}function i(e){$('link[href^="'+e+'"]').length||$('<link href="'+galaxy_config.root+e+'" rel="stylesheet">').appendTo("head")}function s(t,n){return t?e.defaults(t,n):n}function o(e,t){var n="";if(e>=1e11)e/=1e11,n="TB";else if(e>=1e8)e/=1e8,n="GB";else if(e>=1e5)e/=1e5,n="MB";else if(e>=100)e/=100,n="KB";else{if(!(e>0))return"<strong>-</strong>";e*=10,n="b"}var r=Math.round(e)/10;return t?r+" "+n:"<strong>"+r+"</strong> "+n}function u(){return(new Date).getTime().toString(36)}function a(e){var t=$("<p></p>");return t.append(e),t}function f(){var e=new Date,t=(e.getHours()<10?"0":"")+e.getHours(),n=(e.getMinutes()<10?"0":"")+e.getMinutes(),r=e.getDate()+"/"+(e.getMonth()+1)+"/"+e.getFullYear()+", "+t+":"+n;return r}return{cssLoadFile:i,cssGetAttribute:r,get:t,merge:s,bytesToString:o,uuid:u,time:f,wrap:a,request:n}}),define("mvc/ui/ui-modal",["utils/utils"],function(e){var t=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast")},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({height:300,initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template()));var r=this;this.chart.on("redraw",function(){r._draw(r.chart)})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_draw:function(e){var t=this;if(!e.ready()){this.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}this.svg&&this.svg.remove(),this.svg=document.createElementNS("http://www.w3.org/2000/svg","svg"),this.svg.setAttribute("height",this.height),this.$el.append(this.svg),this.svg=d3.select(this.$el.find("svg")[0]),e.off("change:state"),e.on("change:state",function(){var n=t.$el.find("#info"),r=n.find("#icon");r.removeClass(),n.show(),n.find("#text").html(e.get("state_info"));var i=e.get("state");switch(i){case"ok":n.hide();break;case"failed":r.addClass("fa fa-warning");break;default:r.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n),t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e))})},_template:function(){return'<div><div id="info" style="text-align: center; margin-top: 20px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize",onclick:function(){s._wait(s.app.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait...",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}});var u=this;this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.app.config.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.storage.load()?(this.go("viewer"),this.chart.trigger("redraw")):this.go("editor")},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file +(function(){var e=this,t=e._,n={},r=Array.prototype,i=Object.prototype,s=Function.prototype,o=r.push,u=r.slice,a=r.concat,f=i.toString,l=i.hasOwnProperty,c=r.forEach,h=r.map,p=r.reduce,d=r.reduceRight,v=r.filter,m=r.every,g=r.some,y=r.indexOf,b=r.lastIndexOf,w=Array.isArray,E=Object.keys,S=s.bind,x=function(e){if(e instanceof x)return e;if(!(this instanceof x))return new x(e);this._wrapped=e};typeof exports!="undefined"?(typeof module!="undefined"&&module.exports&&(exports=module.exports=x),exports._=x):e._=x,x.VERSION="1.4.4";var T=x.each=x.forEach=function(e,t,r){if(e==null)return;if(c&&e.forEach===c)e.forEach(t,r);else if(e.length===+e.length){for(var i=0,s=e.length;i<s;i++)if(t.call(r,e[i],i,e)===n)return}else for(var o in e)if(x.has(e,o)&&t.call(r,e[o],o,e)===n)return};x.map=x.collect=function(e,t,n){var r=[];return e==null?r:h&&e.map===h?e.map(t,n):(T(e,function(e,i,s){r.push(t.call(n,e,i,s))}),r)};var N="Reduce of empty array with no initial value";x.reduce=x.foldl=x.inject=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(p&&e.reduce===p)return r&&(t=x.bind(t,r)),i?e.reduce(t,n):e.reduce(t);T(e,function(e,s,o){i?n=t.call(r,n,e,s,o):(n=e,i=!0)});if(!i)throw new TypeError(N);return n},x.reduceRight=x.foldr=function(e,t,n,r){var i=arguments.length>2;e==null&&(e=[]);if(d&&e.reduceRight===d)return r&&(t=x.bind(t,r)),i?e.reduceRight(t,n):e.reduceRight(t);var s=e.length;if(s!==+s){var o=x.keys(e);s=o.length}T(e,function(u,a,f){a=o?o[--s]:--s,i?n=t.call(r,n,e[a],a,f):(n=e[a],i=!0)});if(!i)throw new TypeError(N);return n},x.find=x.detect=function(e,t,n){var r;return C(e,function(e,i,s){if(t.call(n,e,i,s))return r=e,!0}),r},x.filter=x.select=function(e,t,n){var r=[];return e==null?r:v&&e.filter===v?e.filter(t,n):(T(e,function(e,i,s){t.call(n,e,i,s)&&r.push(e)}),r)},x.reject=function(e,t,n){return x.filter(e,function(e,r,i){return!t.call(n,e,r,i)},n)},x.every=x.all=function(e,t,r){t||(t=x.identity);var i=!0;return e==null?i:m&&e.every===m?e.every(t,r):(T(e,function(e,s,o){if(!(i=i&&t.call(r,e,s,o)))return n}),!!i)};var C=x.some=x.any=function(e,t,r){t||(t=x.identity);var i=!1;return e==null?i:g&&e.some===g?e.some(t,r):(T(e,function(e,s,o){if(i||(i=t.call(r,e,s,o)))return n}),!!i)};x.contains=x.include=function(e,t){return e==null?!1:y&&e.indexOf===y?e.indexOf(t)!=-1:C(e,function(e){return e===t})},x.invoke=function(e,t){var n=u.call(arguments,2),r=x.isFunction(t);return x.map(e,function(e){return(r?t:e[t]).apply(e,n)})},x.pluck=function(e,t){return x.map(e,function(e){return e[t]})},x.where=function(e,t,n){return x.isEmpty(t)?n?void 0:[]:x[n?"find":"filter"](e,function(e){for(var n in t)if(t[n]!==e[n])return!1;return!0})},x.findWhere=function(e,t){return x.where(e,t,!0)},x.max=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.max.apply(Math,e);if(!t&&x.isEmpty(e))return-Infinity;var r={computed:-Infinity,value:-Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o>=r.computed&&(r={value:e,computed:o})}),r.value},x.min=function(e,t,n){if(!t&&x.isArray(e)&&e[0]===+e[0]&&e.length<65535)return Math.min.apply(Math,e);if(!t&&x.isEmpty(e))return Infinity;var r={computed:Infinity,value:Infinity};return T(e,function(e,i,s){var o=t?t.call(n,e,i,s):e;o<r.computed&&(r={value:e,computed:o})}),r.value},x.shuffle=function(e){var t,n=0,r=[];return T(e,function(e){t=x.random(n++),r[n-1]=r[t],r[t]=e}),r};var k=function(e){return x.isFunction(e)?e:function(t){return t[e]}};x.sortBy=function(e,t,n){var r=k(t);return x.pluck(x.map(e,function(e,t,i){return{value:e,index:t,criteria:r.call(n,e,t,i)}}).sort(function(e,t){var n=e.criteria,r=t.criteria;if(n!==r){if(n>r||n===void 0)return 1;if(n<r||r===void 0)return-1}return e.index<t.index?-1:1}),"value")};var L=function(e,t,n,r){var i={},s=k(t==null?x.identity:t);return T(e,function(t,o){var u=s.call(n,t,o,e);r(i,u,t)}),i};x.groupBy=function(e,t,n){return L(e,t,n,function(e,t,n){(x.has(e,t)?e[t]:e[t]=[]).push(n)})},x.countBy=function(e,t,n){return L(e,t,n,function(e,t){x.has(e,t)||(e[t]=0),e[t]++})},x.sortedIndex=function(e,t,n,r){n=n==null?x.identity:k(n);var i=n.call(r,t),s=0,o=e.length;while(s<o){var u=s+o>>>1;n.call(r,e[u])<i?s=u+1:o=u}return s},x.toArray=function(e){return e?x.isArray(e)?u.call(e):e.length===+e.length?x.map(e,x.identity):x.values(e):[]},x.size=function(e){return e==null?0:e.length===+e.length?e.length:x.keys(e).length},x.first=x.head=x.take=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,0,t):e[0]},x.initial=function(e,t,n){return u.call(e,0,e.length-(t==null||n?1:t))},x.last=function(e,t,n){return e==null?void 0:t!=null&&!n?u.call(e,Math.max(e.length-t,0)):e[e.length-1]},x.rest=x.tail=x.drop=function(e,t,n){return u.call(e,t==null||n?1:t)},x.compact=function(e){return x.filter(e,x.identity)};var A=function(e,t,n){return T(e,function(e){x.isArray(e)?t?o.apply(n,e):A(e,t,n):n.push(e)}),n};x.flatten=function(e,t){return A(e,t,[])},x.without=function(e){return x.difference(e,u.call(arguments,1))},x.uniq=x.unique=function(e,t,n,r){x.isFunction(t)&&(r=n,n=t,t=!1);var i=n?x.map(e,n,r):e,s=[],o=[];return T(i,function(n,r){if(t?!r||o[o.length-1]!==n:!x.contains(o,n))o.push(n),s.push(e[r])}),s},x.union=function(){return x.uniq(a.apply(r,arguments))},x.intersection=function(e){var t=u.call(arguments,1);return x.filter(x.uniq(e),function(e){return x.every(t,function(t){return x.indexOf(t,e)>=0})})},x.difference=function(e){var t=a.apply(r,u.call(arguments,1));return x.filter(e,function(e){return!x.contains(t,e)})},x.zip=function(){var e=u.call(arguments),t=x.max(x.pluck(e,"length")),n=new Array(t);for(var r=0;r<t;r++)n[r]=x.pluck(e,""+r);return n},x.unzip=function(e){var t=[];return x.each(e,function(e,n){x.each(e,function(e,r){t.length<=r&&(t[r]=[]),t[r][n]=e})}),t},x.object=function(e,t){if(e==null)return{};var n={};for(var r=0,i=e.length;r<i;r++)t?n[e[r]]=t[r]:n[e[r][0]]=e[r][1];return n},x.indexOf=function(e,t,n){if(e==null)return-1;var r=0,i=e.length;if(n){if(typeof n!="number")return r=x.sortedIndex(e,t),e[r]===t?r:-1;r=n<0?Math.max(0,i+n):n}if(y&&e.indexOf===y)return e.indexOf(t,n);for(;r<i;r++)if(e[r]===t)return r;return-1},x.lastIndexOf=function(e,t,n){if(e==null)return-1;var r=n!=null;if(b&&e.lastIndexOf===b)return r?e.lastIndexOf(t,n):e.lastIndexOf(t);var i=r?n:e.length;while(i--)if(e[i]===t)return i;return-1},x.range=function(e,t,n){arguments.length<=1&&(t=e||0,e=0),n=arguments[2]||1;var r=Math.max(Math.ceil((t-e)/n),0),i=0,s=new Array(r);while(i<r)s[i++]=e,e+=n;return s};var O=function(){};x.bind=function(e,t){var n,r;if(e.bind===S&&S)return S.apply(e,u.call(arguments,1));if(!x.isFunction(e))throw new TypeError;return n=u.call(arguments,2),r=function(){if(this instanceof r){O.prototype=e.prototype;var i=new O;O.prototype=null;var s=e.apply(i,n.concat(u.call(arguments)));return Object(s)===s?s:i}return e.apply(t,n.concat(u.call(arguments)))}},x.partial=function(e){var t=u.call(arguments,1);return function(){return e.apply(this,t.concat(u.call(arguments)))}},x.bindAll=function(e){var t=u.call(arguments,1);if(t.length===0)throw new Error("bindAll must be passed function names");return T(t,function(t){e[t]=x.bind(e[t],e)}),e},x.memoize=function(e,t){var n={};return t||(t=x.identity),function(){var r=t.apply(this,arguments);return x.has(n,r)?n[r]:n[r]=e.apply(this,arguments)}},x.delay=function(e,t){var n=u.call(arguments,2);return setTimeout(function(){return e.apply(null,n)},t)},x.defer=function(e){return x.delay.apply(x,[e,1].concat(u.call(arguments,1)))},x.throttle=function(e,t,n){var r,i,s,o,u=0,a=function(){u=new Date,s=null,o=e.apply(r,i)};return function(){var f=new Date;!u&&n===!1&&(u=f);var l=t-(f-u);return r=this,i=arguments,l<=0?(clearTimeout(s),s=null,u=f,o=e.apply(r,i)):s||(s=setTimeout(a,l)),o}},x.debounce=function(e,t,n){var r,i;return function(){var s=this,o=arguments,u=function(){r=null,n||(i=e.apply(s,o))},a=n&&!r;return clearTimeout(r),r=setTimeout(u,t),a&&(i=e.apply(s,o)),i}},x.once=function(e){var t=!1,n;return function(){return t?n:(t=!0,n=e.apply(this,arguments),e=null,n)}},x.wrap=function(e,t){return function(){var n=[e];return o.apply(n,arguments),t.apply(this,n)}},x.compose=function(){var e=arguments;return function(){var t=arguments;for(var n=e.length-1;n>=0;n--)t=[e[n].apply(this,t)];return t[0]}},x.after=function(e,t){return e<=0?t():function(){if(--e<1)return t.apply(this,arguments)}},x.keys=E||function(e){if(e!==Object(e))throw new TypeError("Invalid object");var t=[];for(var n in e)x.has(e,n)&&t.push(n);return t},x.values=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push(e[n]);return t},x.pairs=function(e){var t=[];for(var n in e)x.has(e,n)&&t.push([n,e[n]]);return t},x.invert=function(e){var t={};for(var n in e)x.has(e,n)&&(t[e[n]]=n);return t},x.functions=x.methods=function(e){var t=[];for(var n in e)x.isFunction(e[n])&&t.push(n);return t.sort()},x.extend=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]=t[n]}),e},x.pick=function(e){var t={},n=a.apply(r,u.call(arguments,1));return T(n,function(n){n in e&&(t[n]=e[n])}),t},x.omit=function(e){var t={},n=a.apply(r,u.call(arguments,1));for(var i in e)x.contains(n,i)||(t[i]=e[i]);return t},x.defaults=function(e){return T(u.call(arguments,1),function(t){if(t)for(var n in t)e[n]===void 0&&(e[n]=t[n])}),e},x.clone=function(e){return x.isObject(e)?x.isArray(e)?e.slice():x.extend({},e):e},x.tap=function(e,t){return t(e),e};var M=function(e,t,n,r){if(e===t)return e!==0||1/e==1/t;if(e==null||t==null)return e===t;e instanceof x&&(e=e._wrapped),t instanceof x&&(t=t._wrapped);var i=f.call(e);if(i!=f.call(t))return!1;switch(i){case"[object String]":return e==String(t);case"[object Number]":return e!=+e?t!=+t:e==0?1/e==1/t:e==+t;case"[object Date]":case"[object Boolean]":return+e==+t;case"[object RegExp]":return e.source==t.source&&e.global==t.global&&e.multiline==t.multiline&&e.ignoreCase==t.ignoreCase}if(typeof e!="object"||typeof t!="object")return!1;var s=n.length;while(s--)if(n[s]==e)return r[s]==t;n.push(e),r.push(t);var o=0,u=!0;if(i=="[object Array]"){o=e.length,u=o==t.length;if(u)while(o--)if(!(u=M(e[o],t[o],n,r)))break}else{var a=e.constructor,l=t.constructor;if(a!==l&&!(x.isFunction(a)&&a instanceof a&&x.isFunction(l)&&l instanceof l))return!1;for(var c in e)if(x.has(e,c)){o++;if(!(u=x.has(t,c)&&M(e[c],t[c],n,r)))break}if(u){for(c in t)if(x.has(t,c)&&!(o--))break;u=!o}}return n.pop(),r.pop(),u};x.isEqual=function(e,t){return M(e,t,[],[])},x.isEmpty=function(e){if(e==null)return!0;if(x.isArray(e)||x.isString(e))return e.length===0;for(var t in e)if(x.has(e,t))return!1;return!0},x.isElement=function(e){return!!e&&e.nodeType===1},x.isArray=w||function(e){return f.call(e)=="[object Array]"},x.isObject=function(e){return e===Object(e)},T(["Arguments","Function","String","Number","Date","RegExp"],function(e){x["is"+e]=function(t){return f.call(t)=="[object "+e+"]"}}),x.isArguments(arguments)||(x.isArguments=function(e){return!!e&&!!x.has(e,"callee")}),typeof /./!="function"&&(x.isFunction=function(e){return typeof e=="function"}),x.isFinite=function(e){return isFinite(e)&&!isNaN(parseFloat(e))},x.isNaN=function(e){return x.isNumber(e)&&e!=+e},x.isBoolean=function(e){return e===!0||e===!1||f.call(e)=="[object Boolean]"},x.isNull=function(e){return e===null},x.isUndefined=function(e){return e===void 0},x.has=function(e,t){return l.call(e,t)},x.noConflict=function(){return e._=t,this},x.identity=function(e){return e},x.times=function(e,t,n){var r=Array(e);for(var i=0;i<e;i++)r[i]=t.call(n,i);return r},x.random=function(e,t){return t==null&&(t=e,e=0),e+Math.floor(Math.random()*(t-e+1))};var _={escape:{"&":"&","<":"<",">":">",'"':""","'":"'","/":"/"}};_.unescape=x.invert(_.escape);var D={escape:new RegExp("["+x.keys(_.escape).join("")+"]","g"),unescape:new RegExp("("+x.keys(_.unescape).join("|")+")","g")};x.each(["escape","unescape"],function(e){x[e]=function(t){return t==null?"":(""+t).replace(D[e],function(t){return _[e][t]})}}),x.result=function(e,t){if(e==null)return void 0;var n=e[t];return x.isFunction(n)?n.call(e):n},x.mixin=function(e){T(x.functions(e),function(t){var n=x[t]=e[t];x.prototype[t]=function(){var e=[this._wrapped];return o.apply(e,arguments),F.call(this,n.apply(x,e))}})};var P=0;x.uniqueId=function(e){var t=++P+"";return e?e+t:t},x.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var H=/(.)^/,B={"'":"'","\\":"\\","\r":"r","\n":"n"," ":"t","\u2028":"u2028","\u2029":"u2029"},j=/\\|'|\r|\n|\t|\u2028|\u2029/g;x.template=function(e,t,n){var r;n=x.defaults({},n,x.templateSettings);var i=new RegExp([(n.escape||H).source,(n.interpolate||H).source,(n.evaluate||H).source].join("|")+"|$","g"),s=0,o="__p+='";e.replace(i,function(t,n,r,i,u){return o+=e.slice(s,u).replace(j,function(e){return"\\"+B[e]}),n&&(o+="'+\n((__t=("+n+"))==null?'':_.escape(__t))+\n'"),r&&(o+="'+\n((__t=("+r+"))==null?'':__t)+\n'"),i&&(o+="';\n"+i+"\n__p+='"),s=u+t.length,t}),o+="';\n",n.variable||(o="with(obj||{}){\n"+o+"}\n"),o="var __t,__p='',__j=Array.prototype.join,print=function(){__p+=__j.call(arguments,'');};\n"+o+"return __p;\n";try{r=new Function(n.variable||"obj","_",o)}catch(u){throw u.source=o,u}if(t)return r(t,x);var a=function(e){return r.call(this,e,x)};return a.source="function("+(n.variable||"obj")+"){\n"+o+"}",a},x.chain=function(e){return x(e).chain()};var F=function(e){return this._chain?x(e).chain():e};x.mixin(x),T(["pop","push","reverse","shift","sort","splice","unshift"],function(e){var t=r[e];x.prototype[e]=function(){var n=this._wrapped;return t.apply(n,arguments),(e=="shift"||e=="splice")&&n.length===0&&delete n[0],F.call(this,n)}}),T(["concat","join","slice"],function(e){var t=r[e];x.prototype[e]=function(){return F.call(this,t.apply(this._wrapped,arguments))}}),x.extend(x.prototype,{chain:function(){return this._chain=!0,this},value:function(){return this._wrapped}})}).call(this),define("libs/underscore",function(e){return function(){var t,n;return t||e._}}(this)),define("utils/utils",["libs/underscore"],function(e){function t(e,t,r){n("GET",e,{},t,r)}function n(e,t,n,r,i){if(e=="GET"||e=="DELETE")t.indexOf("?")==-1?t+="?":t+="&",t+=$.param(n);var s=new XMLHttpRequest;s.open(e,t,!0),s.setRequestHeader("Accept","application/json"),s.setRequestHeader("Cache-Control","no-cache"),s.setRequestHeader("X-Requested-With","XMLHttpRequest"),s.setRequestHeader("Content-Type","application/json"),s.onloadend=function(){var e=s.status;try{response=jQuery.parseJSON(s.responseText)}catch(t){response=s.responseText}e==200?r&&r(response):i&&i(response)},e=="GET"||e=="DELETE"?s.send():s.send(JSON.stringify(n))}function r(e,t){var n=$('<div class="'+e+'"></div>');n.appendTo(":eq(0)");var r=n.css(t);return n.remove(),r}function i(e){$('link[href^="'+e+'"]').length||$('<link href="'+galaxy_config.root+e+'" rel="stylesheet">').appendTo("head")}function s(t,n){return t?e.defaults(t,n):n}function o(e,t){var n="";if(e>=1e11)e/=1e11,n="TB";else if(e>=1e8)e/=1e8,n="GB";else if(e>=1e5)e/=1e5,n="MB";else if(e>=100)e/=100,n="KB";else{if(!(e>0))return"<strong>-</strong>";e*=10,n="b"}var r=Math.round(e)/10;return t?r+" "+n:"<strong>"+r+"</strong> "+n}function u(){return(new Date).getTime().toString(36)}function a(e){var t=$("<p></p>");return t.append(e),t}function f(){var e=new Date,t=(e.getHours()<10?"0":"")+e.getHours(),n=(e.getMinutes()<10?"0":"")+e.getMinutes(),r=e.getDate()+"/"+(e.getMonth()+1)+"/"+e.getFullYear()+", "+t+":"+n;return r}return{cssLoadFile:i,cssGetAttribute:r,get:t,merge:s,bytesToString:o,uuid:u,time:f,wrap:a,request:n}}),define("mvc/ui/ui-modal",["utils/utils"],function(e){var t=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast")},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},drawable:function(){return this.get("state")=="ok"||this.get("state")=="failed"||this.get("state")=="initialized"},editable:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template()));var r=this;this.chart.on("redraw",function(){r._create_svg(),r._draw(r.chart)}),this.chart.on("change:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":r.chart.trigger("drawable"),e.hide();break;case"failed":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;case"initialized":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg=d3.select(this.$el.find("svg")[0])},_draw:function(e){var t=this;if(!e.drawable()){e.off("drawable"),e.on("drawable",function(){t.chart.off("drawable"),e.drawable()&&t._draw(e)});return}e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n);if(!r.execute||r.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){this.app.storage.save(),i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e)):i.draw(e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_svg:function(){return'<svg style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.editable())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata..."),this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("initialized","Metadata initialized...")})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}});var u=this;this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.app.config.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.storage.load()?(this.go("viewer"),this.chart.trigger("redraw")):this.go("editor")},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/charts/histogram/histogram.js --- a/config/plugins/visualizations/charts/static/charts/histogram/histogram.js +++ b/config/plugins/visualizations/charts/static/charts/histogram/histogram.js @@ -13,9 +13,6 @@ // render draw : function(chart, request_dictionary) { - // update request dataset id - request_dictionary.id = chart.get('dataset_id_job'); - // configure request var index = 0; for (var i in request_dictionary.groups) { diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/library/jobs.js --- a/config/plugins/visualizations/charts/static/library/jobs.js +++ b/config/plugins/visualizations/charts/static/library/jobs.js @@ -17,12 +17,15 @@ cleanup: function(chart) { // cleanup previous dataset file var previous = chart.get('dataset_id_job'); - if (previous) { + if (previous != '') { var self = this; Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() { // update galaxy history self._refreshHdas(); }); + + // reset id + chart.set('dataset_id_job', ''); } }, @@ -53,9 +56,6 @@ } } - // cleanup - self.cleanup(chart); - // set chart state chart.state('submit', 'Sending job request...'); diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/library/storage.js --- a/config/plugins/visualizations/charts/static/library/storage.js +++ b/config/plugins/visualizations/charts/static/library/storage.js @@ -77,7 +77,6 @@ this.vis.save() .fail(function(xhr, status, message) { console.error(xhr, status, message); - alert( 'Error loading data:\n' + xhr.responseText ); }) .then(function(response) { if (response && response.id) { @@ -110,6 +109,9 @@ // reset status this.chart.state('ok', 'Loaded previously saved visualization.'); + // reset modified flag + this.chart.set('modified', false); + // return return true; } diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/models/chart.js --- a/config/plugins/visualizations/charts/static/models/chart.js +++ b/config/plugins/visualizations/charts/static/models/chart.js @@ -7,12 +7,15 @@ { // defaults defaults : { - id : null, - title : '', - type : '', - date : null, - state : 'ok', - state_info : '' + id : null, + title : '', + type : '', + date : null, + state : '', + state_info : '', + modified : false, + dataset_id : '', + dataset_id_job : '' }, // initialize @@ -56,7 +59,11 @@ this.set('state', value); }, - ready: function() { + drawable: function() { + return (this.get('state') == 'ok') || (this.get('state') == 'failed') || (this.get('state') == 'initialized'); + }, + + editable: function() { return (this.get('state') == 'ok') || (this.get('state') == 'failed'); } }); diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/editor.js --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -222,10 +222,7 @@ // refresh title _refreshTitle: function() { var title = this.chart.get('title'); - if (title) { - title = ' - ' + title; - } - this.portlet.title('Charts' + title); + this.portlet.title(title); }, // update @@ -280,6 +277,9 @@ // update titles this._refreshGroupKey(); + + // reset + this.chart.set('modified', true); }, // remove group diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -98,6 +98,7 @@ gid : id, onchange : function(value) { self.group.set(this.gid, value); + self.chart.set('modified', true); }, value : value, wait : true @@ -112,6 +113,9 @@ list[id] = select; } + // loading + this.chart.state('wait', 'Loading metadata...'); + // get dataset this.app.datasets.request({id : dataset_id}, function(dataset) { // configure columns @@ -133,6 +137,9 @@ list[key].update(self.columns); list[key].show(); } + + // loading + self.chart.state('initialized', 'Metadata initialized...'); }); }, diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -32,7 +32,7 @@ title : 'Customize', onclick : function() { // attempt to load chart editor - self._wait (self.app.chart, function() { + self._wait (self.chart, function() { self.app.go('editor'); }); } @@ -41,7 +41,7 @@ } }); - // append view port + // append portlet this.portlet.append(this.viewport_view.$el); // set element @@ -71,23 +71,20 @@ // refresh title _refreshTitle: function() { var title = this.chart.get('title'); - if (title) { - title = ' - ' + title; - } - this.portlet.title('Charts' + title); + this.portlet.title(title); }, // wait for chart to be ready _wait: function(chart, callback) { // get chart - if (chart.ready()) { + if (chart.editable()) { callback(); } else { // show modal var self = this; this.app.modal.show({ title : 'Please wait!', - body : 'Your chart is currently being processed. Please wait...', + body : 'Your chart is currently being processed. Please wait and try again.', buttons : { 'Close' : function() {self.app.modal.hide();}, 'Retry' : function() { diff -r ec715604b476c47703b90385062a6ec482cfd302 -r cab5878ce755b1736d09a9a74e419eddb12c0f2d config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -5,9 +5,6 @@ // widget return Backbone.View.extend( { - // height - height : 300, - // initialize initialize: function(app, options) { @@ -26,8 +23,48 @@ // events var self = this; this.chart.on('redraw', function() { + // create svg element + self._create_svg(); + + // initialize self._draw(self.chart); }); + + // link status handler + this.chart.on('change:state', function() { + // get info element + var $info = self.$el.find('#info'); + + // get icon + var $icon = $info.find('#icon'); + + // remove icon + $icon.removeClass(); + + // show info + $info.show(); + $info.find('#text').html(self.chart.get('state_info')); + + // check status + var state = self.chart.get('state'); + switch (state) { + case 'ok': + self.chart.trigger('drawable'); + $info.hide(); + break; + case 'failed': + self.chart.trigger('drawable'); + $icon.addClass('fa fa-warning'); + break; + case 'initialized': + self.chart.trigger('drawable'); + $icon.addClass('fa fa-warning'); + break; + default: + $icon.addClass('fa fa-spinner fa-spin'); + break; + } + }); }, // show @@ -40,62 +77,36 @@ this.$el.hide(); }, - // add - _draw: function(chart) { - // link this - var self = this; - - // check - if (!chart.ready()) { - this.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.'); - return; - } - + // create + _create_svg: function() { // clear svg if (this.svg) { this.svg.remove(); } // create - this.svg = document.createElementNS('http://www.w3.org/2000/svg', 'svg'); - this.svg.setAttribute('height', this.height); - this.$el.append(this.svg); + this.$el.append($(this._template_svg())); // find svg element this.svg = d3.select(this.$el.find('svg')[0]); - - // clear all previous handlers (including redraw listeners) - chart.off('change:state'); + }, + + // add + _draw: function(chart) { + // link this + var self = this; - // link status handler - chart.on('change:state', function() { - // get info element - var $info = self.$el.find('#info'); - - // get icon - var $icon = $info.find('#icon'); - - // remove icon - $icon.removeClass(); - - // show info - $info.show(); - $info.find('#text').html(chart.get('state_info')); - - // check status - var state = chart.get('state'); - switch (state) { - case 'ok': - $info.hide(); - break; - case 'failed': - $icon.addClass('fa fa-warning'); - break; - default: - $icon.addClass('fa fa-spinner fa-spin'); - break; - } - }); + // proceed once chart is drawable + if (!chart.drawable()) { + chart.off('drawable'); + chart.on('drawable', function() { + self.chart.off('drawable'); + if (chart.drawable()) { + self._draw(chart); + } + }); + return; + } // set chart state chart.state('wait', 'Please wait...'); @@ -104,6 +115,16 @@ var chart_type = chart.get('type'); var chart_settings = this.app.types.get(chart_type); + // clean up data if there is any from previous jobs + if (!chart_settings.execute || + (chart_settings.execute && chart.get('modified'))) { + // reset jobs + this.app.jobs.cleanup(chart); + + // reset modified flag + chart.set('modified', false); + } + // create chart view var self = this; require(['plugin/charts/' + chart_type + '/' + chart_type], function(ChartView) { @@ -112,25 +133,26 @@ // request data if (chart_settings.execute) { - self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { + if (chart.get('dataset_id_job') == '') { + // submit job + self.app.jobs.submit(chart, self._defaultSettingsString(chart), self._defaultRequestString(chart), function() { + // save + this.app.storage.save(); + + // draw + view.draw(chart, self._defaultRequestDictionary(chart)); + }); + } else { + // load data into view view.draw(chart, self._defaultRequestDictionary(chart)); - }); + } } else { + // load data into view view.draw(chart, self._defaultRequestDictionary(chart)); } }); }, - // template - _template: function() { - return '<div>' + - '<div id="info" style="text-align: center; margin-top: 20px;">' + - '<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' + - '<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' + - '</div>' + - '</div>'; - }, - // create default chart request _defaultRequestString: function(chart) { @@ -175,10 +197,16 @@ // configure request var request_dictionary = { - id : chart.get('dataset_id'), - groups : [] + groups : [] }; + // update request dataset id + if (chart_settings.execute) { + request_dictionary.id = chart.get('dataset_id_job'); + } else { + request_dictionary.id = chart.get('dataset_id'); + } + // add groups to data request var group_index = 0; chart.groups.each(function(group) { @@ -198,7 +226,23 @@ // return return request_dictionary; - } + }, + + // template + _template: function() { + return '<div style="height: 100%; min-height: 50px;">' + + '<div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;">' + + '<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' + + '<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' + + '</div>' + + '</div>'; + }, + + // template svg element + _template_svg: function() { + return '<svg style="height: calc(100% - 80px)"/>'; + }, + }); }); \ 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: dan: Refactor tool error / bug reporting. Allow reporting errors via biostar in addition to existing email functionality.
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ec715604b476/ Changeset: ec715604b476 User: dan Date: 2014-03-24 21:19:35 Summary: Refactor tool error / bug reporting. Allow reporting errors via biostar in addition to existing email functionality. Affected #: 5 files diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/tools/errors.py --- /dev/null +++ b/lib/galaxy/tools/errors.py @@ -0,0 +1,121 @@ +""" +Functionality for dealing with tool errors. +""" +import string +from galaxy import model, util, web + +error_report_template = """ +GALAXY TOOL ERROR REPORT +------------------------ + +This error report was sent from the Galaxy instance hosted on the server +"${host}" +----------------------------------------------------------------------------- +This is in reference to dataset id ${dataset_id} from history id ${history_id} +----------------------------------------------------------------------------- +You should be able to view the history containing the related history item + +${hid}: ${history_item_name} + +by logging in as a Galaxy admin user to the Galaxy instance referenced above +and pointing your browser to the following link. + +${history_view_link} +----------------------------------------------------------------------------- +The user '${email}' provided the following information: + +${message} +----------------------------------------------------------------------------- +job id: ${job_id} +tool id: ${job_tool_id} +job pid or drm id: ${job_runner_external_id} +----------------------------------------------------------------------------- +job command line: +${job_command_line} +----------------------------------------------------------------------------- +job stderr: +${job_stderr} +----------------------------------------------------------------------------- +job stdout: +${job_stdout} +----------------------------------------------------------------------------- +job info: +${job_info} +----------------------------------------------------------------------------- +job traceback: +${job_traceback} +----------------------------------------------------------------------------- +(This is an automated message). +""" + +class ErrorReporter( object ): + def __init__( self, hda, app ): + # Get the dataset + sa_session = app.model.context + if not isinstance( hda, model.HistoryDatasetAssociation ): + try: + hda = sa_session.query( model.HistoryDatasetAssociation ).get( hda ) + except: + hda = sa_session.query( model.HistoryDatasetAssociation ).get( app.security.decode_id( hda ) ) + assert isinstance( hda, model.HistoryDatasetAssociation ), ValueError( "Bad value provided for HDA (%s)." % ( hda ) ) + self.hda = hda + # Get the associated job + self.job = hda.creating_job + self.app = app + self.tool_id = self.job.tool_id + self.report = None + def _can_access_dataset( self, user ): + if user: + roles = user.all_roles() + else: + roles = [] + return self.app.security_agent.can_access_dataset( roles, self.hda.dataset ) + def create_report( self, email='', message='', **kwd ): + hda = self.hda + job = self.job + host = web.url_for( '/', qualified=True ) + history_view_link = web.url_for( controller="history", action="view", id=self.app.security.encode_id( hda.history_id ), qualified=True ) + # Build the email message + self.report = string.Template( error_report_template ) \ + .safe_substitute( host=host, + dataset_id=hda.dataset_id, + history_id=hda.history_id, + hid=hda.hid, + history_item_name=hda.get_display_name(), + history_view_link=history_view_link, + job_id=job.id, + job_tool_id=job.tool_id, + job_runner_external_id=job.job_runner_external_id, + job_command_line=job.command_line, + job_stderr=util.unicodify( job.stderr ), + job_stdout=util.unicodify( job.stdout ), + job_info=util.unicodify( job.info ), + job_traceback=util.unicodify( job.traceback ), + email=email, + message=util.unicodify( message ) ) + def _send_report( self, user, email=None, message=None, **kwd ): + return self.report + def send_report( self, user, email=None, message=None, **kwd ): + if self.report is None: + self.create_report( email=email, message=message, **kwd ) + return self._send_report( user, email=email, message=message, **kwd ) + +class EmailErrorReporter( ErrorReporter ): + def _send_report( self, user, email=None, message=None, **kwd ): + smtp_server = self.app.config.smtp_server + assert smtp_server, ValueError( "Mail is not configured for this galaxy instance" ) + to_address = self.app.config.error_email_to + assert to_address, ValueError( "Error reporting has been disabled for this galaxy instance" ) + + frm = to_address + # Check email a bit + email = email or '' + email = email.strip() + parts = email.split() + if len( parts ) == 1 and len( email ) > 0 and self._can_access_dataset( user ): + to = to_address + ", " + email + else: + to = to_address + subject = "Galaxy tool error report from %s" % email + # Send it + return util.send_mail( frm, to, subject, self.report, self.app.config ) diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -7,6 +7,7 @@ import re from unicodedata import normalize from galaxy.web.base.controller import url_for +from galaxy.tools.errors import ErrorReporter _punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+') @@ -27,6 +28,8 @@ # Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/) def slugify(text, delim=u'-'): """Generates an slightly worse ASCII-only slug.""" + if not isinstance( text, unicode ): + text = unicode( text ) result = [] for word in _punct_re.split(text.lower()): word = normalize('NFKD', word).encode('ascii', 'ignore') @@ -63,7 +66,7 @@ Generate a reasonable biostar tag for a tool. """ #Biostar can now handle tags with spaces, do we want to generate tags differently now? - return slugify( unicode( tool.name ), delim='-' ) + return slugify( tool.name, delim='-' ) def populate_tag_payload( payload=None, tool=None ): if payload is None: @@ -119,3 +122,18 @@ delete_cookie( trans, trans.app.config.biostar_key_name ) return get_biostar_url( trans.app, biostar_action='log_out' ) return None + +class BiostarErrorReporter( ErrorReporter ): + def _send_report( self, user, email=None, message=None, **kwd ): + assert biostar_enabled( self.app ), ValueError( "Biostar is not configured for this galaxy instance" ) + assert self._can_access_dataset( user ), Exception( "You are not allowed to access this dataset." ) + tool_version_select_field, tools, tool = \ + self.app.toolbox.get_tool_components( self.tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) + payload = { 'title': 'Bug report on "%s" tool' % ( tool.name ), 'content': self.report.replace( '\n', '<br />' ), 'tag_val':slugify( 'bug report' ) } + #Get footer for email from here + payload2 = populate_tool_payload( tool=tool ) + if 'content' in payload2: + payload[ 'content' ] = "%s<br />%s" % ( payload['content'], payload2['content'] ) + if 'tag_val' in payload2: + payload[ 'tag_val' ] = ','.join( [ payload2[ 'tag_val' ], payload[ 'tag_val' ] ] ) + return payload diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -75,6 +75,19 @@ return self.biostar_question_redirect( trans, payload ) @web.expose + def biostar_tool_bug_report( self, trans, hda=None, email=None, message=None ): + """ + Generate a redirect to a Biostar site using external authentication to + pass Galaxy user information and information about a specific tool error. + """ + try: + error_reporter = biostar.BiostarErrorReporter( hda, trans.app ) + payload = error_reporter.send_report( trans.user, email=email, message=message ) + except Exception, e: + return error( str( e ) ) + return self.biostar_question_redirect( trans, payload=payload ) + + @web.expose def biostar_logout( self, trans ): """ Log out of biostar diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -1,6 +1,5 @@ import logging import os -import string import tempfile import urllib import zipfile @@ -14,6 +13,7 @@ from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesExtendedMetadataMixin from galaxy.web.framework.helpers import grids, iff, time_ago from galaxy.web.framework.helpers import to_unicode +from galaxy.tools.errors import EmailErrorReporter eggs.require( "Paste" ) import paste.httpexceptions @@ -27,51 +27,6 @@ except ImportError: pass - -error_report_template = """ -GALAXY TOOL ERROR REPORT ------------------------- - -This error report was sent from the Galaxy instance hosted on the server -"${host}" ------------------------------------------------------------------------------ -This is in reference to dataset id ${dataset_id} from history id ${history_id} ------------------------------------------------------------------------------ -You should be able to view the history containing the related history item - -${hid}: ${history_item_name} - -by logging in as a Galaxy admin user to the Galaxy instance referenced above -and pointing your browser to the following link. - -${history_view_link} ------------------------------------------------------------------------------ -The user '${email}' provided the following information: - -${message} ------------------------------------------------------------------------------ -job id: ${job_id} -tool id: ${job_tool_id} -job pid or drm id: ${job_runner_external_id} ------------------------------------------------------------------------------ -job command line: -${job_command_line} ------------------------------------------------------------------------------ -job stderr: -${job_stderr} ------------------------------------------------------------------------------ -job stdout: -${job_stdout} ------------------------------------------------------------------------------ -job info: -${job_info} ------------------------------------------------------------------------------ -job traceback: -${job_traceback} ------------------------------------------------------------------------------ -(This is an automated message). -""" - class HistoryDatasetAssociationListGrid( grids.Grid ): # Custom columns for grid. class HistoryColumn( grids.GridColumn ): @@ -197,50 +152,15 @@ except: exit_code = "Invalid dataset ID or you are not allowed to access this dataset" return exit_code + @web.expose def report_error( self, trans, id, email='', message="", **kwd ): - smtp_server = trans.app.config.smtp_server - if smtp_server is None: - return trans.show_error_message( "Mail is not configured for this galaxy instance" ) - to_address = trans.app.config.error_email_to - if to_address is None: - return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" ) - # Get the dataset and associated job - hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - job = hda.creating_job - # Get the name of the server hosting the Galaxy instance from which this report originated - host = trans.request.host - history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) ) - # Build the email message - body = string.Template( error_report_template ) \ - .safe_substitute( host=host, - dataset_id=hda.dataset_id, - history_id=hda.history_id, - hid=hda.hid, - history_item_name=hda.get_display_name(), - history_view_link=history_view_link, - job_id=job.id, - job_tool_id=job.tool_id, - job_runner_external_id=job.job_runner_external_id, - job_command_line=job.command_line, - job_stderr=util.unicodify( job.stderr ), - job_stdout=util.unicodify( job.stdout ), - job_info=util.unicodify( job.info ), - job_traceback=util.unicodify( job.traceback ), - email=email, - message=util.unicodify( message ) ) - frm = to_address - # Check email a bit - email = email.strip() - parts = email.split() - if len( parts ) == 1 and len( email ) > 0 and self._can_access_dataset( trans, hda ): - to = to_address + ", " + email - else: - to = to_address - subject = "Galaxy tool error report from %s" % email - # Send it + biostar_report = 'biostar' in str( kwd.get( 'submit_error_report') ).lower() + if biostar_report: + return trans.response.send_redirect( url_for( controller='biostar', action='biostar_tool_bug_report', hda=id, email=email, message=message ) ) try: - util.send_mail( frm, to, subject, body, trans.app.config ) + error_reporter = EmailErrorReporter( id, trans.app ) + error_reporter.send_report( user=trans.user, email=email, message=message ) return trans.show_ok_message( "Your error report has been sent" ) except Exception, e: return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) diff -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c -r ec715604b476c47703b90385062a6ec482cfd302 templates/webapps/galaxy/dataset/errors.mako --- a/templates/webapps/galaxy/dataset/errors.mako +++ b/templates/webapps/galaxy/dataset/errors.mako @@ -71,7 +71,10 @@ <textarea name="message" rows="10" cols="40"></textarea></div><div class="form-row"> - <input type="submit" name="submit_error_report" value="Report"/> + <input type="submit" name="submit_error_report" value="Report" onclick="form.setAttribute('target', '_self');"/> + %if trans.app.config.biostar_url: + <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="form.setAttribute('target', '_blank');"/> + %endif </div></form></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: correct for random error that happens during grunt build (this css modification is just randomly modified for some builds)
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e9354d1fbdf/ Changeset: 6e9354d1fbdf User: martenson Date: 2014-03-24 20:15:10 Summary: correct for random error that happens during grunt build (this css modification is just randomly modified for some builds) Affected #: 1 file diff -r 68d35caf407f367c3447a1a6675d6705c8daacf4 -r 6e9354d1fbdfd92ff316c52302945c02bbf13a0c static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -41,7 +41,7 @@ body{font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:1.428571429;color:#333;background-color:#fff} input,button,select,textarea{font-family:inherit;font-size:inherit;line-height:inherit} button,input,select[multiple],textarea{background-image:none} -a{color:#5f6990;text-decoration:none}a:hover,a:focus{color:#404862;text-decoration:underline} +a{color:#303030;text-decoration:none}a:hover,a:focus{color:#0a0a0a;text-decoration:underline} a:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} img{vertical-align:middle} .img-responsive{display:block;max-width:100%;height:auto} @@ -114,13 +114,13 @@ .col-xs-12{width:100%} @media (min-width:768px){.container{max-width:750px} .col-sm-1,.col-sm-2,.col-sm-3,.col-sm-4,.col-sm-5,.col-sm-6,.col-sm-7,.col-sm-8,.col-sm-9,.col-sm-10,.col-sm-11{float:left} .col-sm-1{width:8.333333333333332%} .col-sm-2{width:16.666666666666664%} .col-sm-3{width:25%} .col-sm-4{width:33.33333333333333%} .col-sm-5{width:41.66666666666667%} .col-sm-6{width:50%} .col-sm-7{width:58.333333333333336%} .col-sm-8{width:66.66666666666666%} .col-sm-9{width:75%} .col-sm-10{width:83.33333333333334%} .col-sm-11{width:91.66666666666666%} .col-sm-12{width:100%} .col-sm-push-1{left:8.333333333333332%} .col-sm-push-2{left:16.666666666666664%} .col-sm-push-3{left:25%} .col-sm-push-4{left:33.33333333333333%} .col-sm-push-5{left:41.66666666666667%} .col-sm-push-6{left:50%} .col-sm-push-7{left:58.333333333333336%} .col-sm-push-8{left:66.66666666666666%} .col-sm-push-9{left:75%} .col-sm-push-10{left:83.33333333333334%} .col-sm-push-11{left:91.66666666666666%} .col-sm-pull-1{right:8.333333333333332%} .col-sm-pull-2{right:16.666666666666664%} .col-sm-pull-3{right:25%} .col-sm-pull-4{right:33.33333333333333%} .col-sm-pull-5{right:41.66666666666667%} .col-sm-pull-6{right:50%} .col-sm-pull-7{right:58.333333333333336%} .col-sm-pull-8{right:66.66666666666666%} .col-sm-pull-9{right:75%} .col-sm-pull-10{right:83.33333333333334%} .col-sm-pull-11{right:91.66666666666666%} .col-sm-offset-1{margin-left:8.333333333333332%} .col-sm-offset-2{margin-left:16.666666666666664%} .col-sm-offset-3{margin-left:25%} .col-sm-offset-4{margin-left:33.33333333333333%} .col-sm-offset-5{margin-left:41.66666666666667%} .col-sm-offset-6{margin-left:50%} .col-sm-offset-7{margin-left:58.333333333333336%} .col-sm-offset-8{margin-left:66.66666666666666%} .col-sm-offset-9{margin-left:75%} .col-sm-offset-10{margin-left:83.33333333333334%} .col-sm-offset-11{margin-left:91.66666666666666%}}@media (min-width:992px){.container{max-width:970px} .col-md-1,.col-md-2,.col-md-3,.col-md-4,.col-md-5,.col-md-6,.col-md-7,.col-md-8,.col-md-9,.col-md-10,.col-md-11{float:left} .col-md-1{width:8.333333333333332%} .col-md-2{width:16.666666666666664%} .col-md-3{width:25%} .col-md-4{width:33.33333333333333%} .col-md-5{width:41.66666666666667%} .col-md-6{width:50%} .col-md-7{width:58.333333333333336%} .col-md-8{width:66.66666666666666%} .col-md-9{width:75%} .col-md-10{width:83.33333333333334%} .col-md-11{width:91.66666666666666%} .col-md-12{width:100%} .col-md-push-0{left:auto} .col-md-push-1{left:8.333333333333332%} .col-md-push-2{left:16.666666666666664%} .col-md-push-3{left:25%} .col-md-push-4{left:33.33333333333333%} .col-md-push-5{left:41.66666666666667%} .col-md-push-6{left:50%} .col-md-push-7{left:58.333333333333336%} .col-md-push-8{left:66.66666666666666%} .col-md-push-9{left:75%} .col-md-push-10{left:83.33333333333334%} .col-md-push-11{left:91.66666666666666%} .col-md-pull-0{right:auto} .col-md-pull-1{right:8.333333333333332%} .col-md-pull-2{right:16.666666666666664%} .col-md-pull-3{right:25%} .col-md-pull-4{right:33.33333333333333%} .col-md-pull-5{right:41.66666666666667%} .col-md-pull-6{right:50%} .col-md-pull-7{right:58.333333333333336%} .col-md-pull-8{right:66.66666666666666%} .col-md-pull-9{right:75%} .col-md-pull-10{right:83.33333333333334%} .col-md-pull-11{right:91.66666666666666%} .col-md-offset-0{margin-left:0} .col-md-offset-1{margin-left:8.333333333333332%} .col-md-offset-2{margin-left:16.666666666666664%} .col-md-offset-3{margin-left:25%} .col-md-offset-4{margin-left:33.33333333333333%} .col-md-offset-5{margin-left:41.66666666666667%} .col-md-offset-6{margin-left:50%} .col-md-offset-7{margin-left:58.333333333333336%} .col-md-offset-8{margin-left:66.66666666666666%} .col-md-offset-9{margin-left:75%} .col-md-offset-10{margin-left:83.33333333333334%} .col-md-offset-11{margin-left:91.66666666666666%}}@media (min-width:1200px){.container{max-width:1170px} .col-lg-1,.col-lg-2,.col-lg-3,.col-lg-4,.col-lg-5,.col-lg-6,.col-lg-7,.col-lg-8,.col-lg-9,.col-lg-10,.col-lg-11{float:left} .col-lg-1{width:8.333333333333332%} .col-lg-2{width:16.666666666666664%} .col-lg-3{width:25%} .col-lg-4{width:33.33333333333333%} .col-lg-5{width:41.66666666666667%} .col-lg-6{width:50%} .col-lg-7{width:58.333333333333336%} .col-lg-8{width:66.66666666666666%} .col-lg-9{width:75%} .col-lg-10{width:83.33333333333334%} .col-lg-11{width:91.66666666666666%} .col-lg-12{width:100%} .col-lg-push-0{left:auto} .col-lg-push-1{left:8.333333333333332%} .col-lg-push-2{left:16.666666666666664%} .col-lg-push-3{left:25%} .col-lg-push-4{left:33.33333333333333%} .col-lg-push-5{left:41.66666666666667%} .col-lg-push-6{left:50%} .col-lg-push-7{left:58.333333333333336%} .col-lg-push-8{left:66.66666666666666%} .col-lg-push-9{left:75%} .col-lg-push-10{left:83.33333333333334%} .col-lg-push-11{left:91.66666666666666%} .col-lg-pull-0{right:auto} .col-lg-pull-1{right:8.333333333333332%} .col-lg-pull-2{right:16.666666666666664%} .col-lg-pull-3{right:25%} .col-lg-pull-4{right:33.33333333333333%} .col-lg-pull-5{right:41.66666666666667%} .col-lg-pull-6{right:50%} .col-lg-pull-7{right:58.333333333333336%} .col-lg-pull-8{right:66.66666666666666%} .col-lg-pull-9{right:75%} .col-lg-pull-10{right:83.33333333333334%} .col-lg-pull-11{right:91.66666666666666%} .col-lg-offset-0{margin-left:0} .col-lg-offset-1{margin-left:8.333333333333332%} .col-lg-offset-2{margin-left:16.666666666666664%} .col-lg-offset-3{margin-left:25%} .col-lg-offset-4{margin-left:33.33333333333333%} .col-lg-offset-5{margin-left:41.66666666666667%} .col-lg-offset-6{margin-left:50%} .col-lg-offset-7{margin-left:58.333333333333336%} .col-lg-offset-8{margin-left:66.66666666666666%} .col-lg-offset-9{margin-left:75%} .col-lg-offset-10{margin-left:83.33333333333334%} .col-lg-offset-11{margin-left:91.66666666666666%}}table{max-width:100%;background-color:transparent} th{text-align:left} -.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #bfbfbf} -.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #bfbfbf} +.table{width:100%;margin-bottom:17px}.table thead>tr>th,.table tbody>tr>th,.table tfoot>tr>th,.table thead>tr>td,.table tbody>tr>td,.table tfoot>tr>td{padding:8px;line-height:1.428571429;vertical-align:top;border-top:1px solid #d6b161} +.table thead>tr>th{vertical-align:bottom;border-bottom:2px solid #d6b161} .table caption+thead tr:first-child th,.table colgroup+thead tr:first-child th,.table thead:first-child tr:first-child th,.table caption+thead tr:first-child td,.table colgroup+thead tr:first-child td,.table thead:first-child tr:first-child td{border-top:0} -.table tbody+tbody{border-top:2px solid #bfbfbf} +.table tbody+tbody{border-top:2px solid #d6b161} .table .table{background-color:#fff} .table-condensed thead>tr>th,.table-condensed tbody>tr>th,.table-condensed tfoot>tr>th,.table-condensed thead>tr>td,.table-condensed tbody>tr>td,.table-condensed tfoot>tr>td{padding:5px} -.table-bordered{border:1px solid #bfbfbf}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #bfbfbf} +.table-bordered{border:1px solid #d6b161}.table-bordered>thead>tr>th,.table-bordered>tbody>tr>th,.table-bordered>tfoot>tr>th,.table-bordered>thead>tr>td,.table-bordered>tbody>tr>td,.table-bordered>tfoot>tr>td{border:1px solid #d6b161} .table-bordered>thead>tr>th,.table-bordered>thead>tr>td{border-bottom-width:2px} .table-striped>tbody>tr:nth-child(odd)>td,.table-striped>tbody>tr:nth-child(odd)>th{background-color:#f9f9f9} .table-hover>tbody>tr:hover>td,.table-hover>tbody>tr:hover>th{background-color:#f5f5f5} @@ -133,7 +133,7 @@ .table-hover>tbody>tr>td.danger:hover,.table-hover>tbody>tr>th.danger:hover,.table-hover>tbody>tr.danger:hover>td,.table-hover>tbody>tr.danger:hover>th{background-color:#f7b0ae;border-color:#c61913} .table>thead>tr>td.warning,.table>tbody>tr>td.warning,.table>tfoot>tr>td.warning,.table>thead>tr>th.warning,.table>tbody>tr>th.warning,.table>tfoot>tr>th.warning,.table>thead>tr.warning>td,.table>tbody>tr.warning>td,.table>tfoot>tr.warning>td,.table>thead>tr.warning>th,.table>tbody>tr.warning>th,.table>tfoot>tr.warning>th{background-color:#fce1ba;border-color:#e28709} .table-hover>tbody>tr>td.warning:hover,.table-hover>tbody>tr>th.warning:hover,.table-hover>tbody>tr.warning:hover>td,.table-hover>tbody>tr.warning:hover>th{background-color:#fbd6a2;border-color:#c97908} -@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #bfbfbf;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0} +@media (max-width:768px){.table-responsive{width:100%;margin-bottom:15px;overflow-y:hidden;overflow-x:scroll;-ms-overflow-style:-ms-autohiding-scrollbar;border:1px solid #d6b161;-webkit-overflow-scrolling:touch}.table-responsive>.table{margin-bottom:0;background-color:#fff}.table-responsive>.table>thead>tr>th,.table-responsive>.table>tbody>tr>th,.table-responsive>.table>tfoot>tr>th,.table-responsive>.table>thead>tr>td,.table-responsive>.table>tbody>tr>td,.table-responsive>.table>tfoot>tr>td{white-space:nowrap} .table-responsive>.table-bordered{border:0}.table-responsive>.table-bordered>thead>tr>th:first-child,.table-responsive>.table-bordered>tbody>tr>th:first-child,.table-responsive>.table-bordered>tfoot>tr>th:first-child,.table-responsive>.table-bordered>thead>tr>td:first-child,.table-responsive>.table-bordered>tbody>tr>td:first-child,.table-responsive>.table-bordered>tfoot>tr>td:first-child{border-left:0} .table-responsive>.table-bordered>thead>tr>th:last-child,.table-responsive>.table-bordered>tbody>tr>th:last-child,.table-responsive>.table-bordered>tfoot>tr>th:last-child,.table-responsive>.table-bordered>thead>tr>td:last-child,.table-responsive>.table-bordered>tbody>tr>td:last-child,.table-responsive>.table-bordered>tfoot>tr>td:last-child{border-right:0} .table-responsive>.table-bordered>thead>tr:last-child>th,.table-responsive>.table-bordered>tbody>tr:last-child>th,.table-responsive>.table-bordered>tfoot>tr:last-child>th,.table-responsive>.table-bordered>thead>tr:last-child>td,.table-responsive>.table-bordered>tbody>tr:last-child>td,.table-responsive>.table-bordered>tfoot>tr:last-child>td{border-bottom:0}}fieldset{padding:0;margin:0;border:0} legend{display:block;width:100%;padding:0;margin-bottom:17px;font-size:18px;line-height:inherit;color:#333;border:0;border-bottom:1px solid #bfbfbf} label{display:inline-block;margin-bottom:5px;font-weight:bold} input[type="search"]{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box} @@ -148,7 +148,7 @@ .form-control::-moz-placeholder{color:#999} .form-control:-ms-input-placeholder{color:#999} .form-control::-webkit-input-placeholder{color:#999} -.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #bfbfbf;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} +.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)} .form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee} textarea.form-control{height:auto} .form-group{margin-bottom:15px} @@ -202,9 +202,9 @@ .btn-info{color:#fff;background-color:#3186a0;border-color:#010304}.btn-info:hover,.btn-info:focus,.btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{color:#fff;background-color:#276c81;border-color:#000} .btn-info:active,.btn-info.active,.open .dropdown-toggle.btn-info{background-image:none} .btn-info.disabled,.btn-info[disabled],fieldset[disabled] .btn-info,.btn-info.disabled:hover,.btn-info[disabled]:hover,fieldset[disabled] .btn-info:hover,.btn-info.disabled:focus,.btn-info[disabled]:focus,fieldset[disabled] .btn-info:focus,.btn-info.disabled:active,.btn-info[disabled]:active,fieldset[disabled] .btn-info:active,.btn-info.disabled.active,.btn-info[disabled].active,fieldset[disabled] .btn-info.active{background-color:#3186a0;border-color:#010304} -.btn-link{color:#5f6990;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none} +.btn-link{color:#303030;font-weight:normal;cursor:pointer;border-radius:0}.btn-link,.btn-link:active,.btn-link[disabled],fieldset[disabled] .btn-link{background-color:transparent;-webkit-box-shadow:none;box-shadow:none} .btn-link,.btn-link:hover,.btn-link:focus,.btn-link:active{border-color:transparent} -.btn-link:hover,.btn-link:focus{color:#404862;text-decoration:underline;background-color:transparent} +.btn-link:hover,.btn-link:focus{color:#0a0a0a;text-decoration:underline;background-color:transparent} .btn-link[disabled]:hover,fieldset[disabled] .btn-link:hover,.btn-link[disabled]:focus,fieldset[disabled] .btn-link:focus{color:#999;text-decoration:none} .btn-lg{padding:8px 14px;font-size:15px;line-height:1.33;border-radius:5px} .btn-sm,.btn-xs{padding:3px 8px;font-size:11px;line-height:1.5;border-radius:2px} @@ -486,7 +486,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon,textarea.input-group-sm>.input-group-btn>.btn{height:auto} .input-group-addon,.input-group-btn,.input-group .form-control{display:table-cell}.input-group-addon:not(:first-child):not(:last-child),.input-group-btn:not(:first-child):not(:last-child),.input-group .form-control:not(:first-child):not(:last-child){border-radius:0} .input-group-addon,.input-group-btn{width:1%;white-space:nowrap;vertical-align:middle} -.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #bfbfbf;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px} +.input-group-addon{padding:4px 10px;font-size:12px;font-weight:normal;line-height:1;text-align:center;background-color:#eee;border:1px solid #aaa;border-radius:3px}.input-group-addon.input-sm{padding:3px 8px;font-size:11px;border-radius:2px} .input-group-addon.input-lg{padding:8px 14px;font-size:15px;border-radius:5px} .input-group-addon input[type="radio"],.input-group-addon input[type="checkbox"]{margin-top:0} .input-group .form-control:first-child,.input-group-addon:first-child,.input-group-btn:first-child>.btn,.input-group-btn:first-child>.dropdown-toggle,.input-group-btn:last-child>.btn:not(:last-child):not(.dropdown-toggle){border-bottom-right-radius:0;border-top-right-radius:0} @@ -502,7 +502,7 @@ .nav:after{clear:both} .nav>li{position:relative;display:block}.nav>li>a{position:relative;display:block;padding:4px 10px}.nav>li>a:hover,.nav>li>a:focus{text-decoration:none;background-color:#eee} .nav>li.disabled>a{color:#999}.nav>li.disabled>a:hover,.nav>li.disabled>a:focus{color:#999;text-decoration:none;background-color:transparent;cursor:not-allowed} -.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#5f6990} +.nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#303030} .nav .nav-divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5} .nav>li>a>img{max-width:none} .nav-tabs{border-bottom:1px solid #bfbfbf}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf} @@ -526,8 +526,8 @@ .tabbable:after{clear:both} .tab-content>.tab-pane,.pill-content>.pill-pane{display:none} .tab-content>.active,.pill-content>.active{display:block} -.nav .caret{border-top-color:#5f6990;border-bottom-color:#5f6990} -.nav a:hover .caret{border-top-color:#404862;border-bottom-color:#404862} +.nav .caret{border-top-color:#303030;border-bottom-color:#303030} +.nav a:hover .caret{border-top-color:#0a0a0a;border-bottom-color:#0a0a0a} .nav-tabs .dropdown-menu{margin-top:-1px;border-top-right-radius:0;border-top-left-radius:0} .navbar{position:relative;z-index:1000;min-height:33px;margin-bottom:17px;border:1px solid transparent}.navbar:before,.navbar:after{content:" ";display:table;} .navbar:after{clear:both} @@ -617,7 +617,7 @@ .badge{display:inline-block;min-width:10px;padding:3px 7px;font-size:11px;font-weight:bold;color:#fff;line-height:1;vertical-align:baseline;white-space:nowrap;text-align:center;background-color:#999;border-radius:10px}.badge:empty{display:none} a.badge:hover,a.badge:focus{color:#fff;text-decoration:none;cursor:pointer} .btn .badge{position:relative;top:-1px} -a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#5f6990;background-color:#fff} +a.list-group-item.active>.badge,.nav-pills>.active>a>.badge{color:#303030;background-color:#fff} .nav-pills>li>a>.badge{margin-left:3px} .jumbotron{padding:30px;margin-bottom:30px;font-size:18px;font-weight:200;line-height:2.1428571435;color:inherit;background-color:#eee}.jumbotron h1{line-height:1;color:inherit} .jumbotron p{line-height:1.4} @@ -672,7 +672,7 @@ .panel>.list-group .list-group-item:last-child{border-bottom:0} .panel-heading+.list-group .list-group-item:first-child{border-top-width:0} .panel>.table{margin-bottom:0} -.panel>.panel-body+.table{border-top:1px solid #bfbfbf} +.panel>.panel-body+.table{border-top:1px solid #d6b161} .panel-heading{padding:10px 15px;border-bottom:1px solid transparent;border-top-right-radius:2px;border-top-left-radius:2px} .panel-title{margin-top:0;margin-bottom:0;font-size:14px}.panel-title>a{color:inherit} .panel-footer{padding:10px 15px;background-color:#f5f5f5;border-top:1px solid #bfbfbf;border-bottom-right-radius:2px;border-bottom-left-radius:2px} @@ -1454,7 +1454,7 @@ select{padding:2px;font-size:12px;line-height:1.428571429} select,input,textarea{font:inherit} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%} -textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #bfbfbf;padding:3px} +textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px} input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none} input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} @@ -1465,7 +1465,7 @@ input[type="submit"].btn-primary,button.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}input[type="submit"].btn-primary:hover,button.btn-primary:hover,input[type="submit"].btn-primary:focus,button.btn-primary:focus,input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{color:#fff;background-color:#4e5777;border-color:#000} input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{background-image:none} input[type="submit"].btn-primary.disabled,button.btn-primary.disabled,input[type="submit"].btn-primary[disabled],button.btn-primary[disabled],fieldset[disabled] input[type="submit"].btn-primary,fieldset[disabled] button.btn-primary,input[type="submit"].btn-primary.disabled:hover,button.btn-primary.disabled:hover,input[type="submit"].btn-primary[disabled]:hover,button.btn-primary[disabled]:hover,fieldset[disabled] input[type="submit"].btn-primary:hover,fieldset[disabled] button.btn-primary:hover,input[type="submit"].btn-primary.disabled:focus,button.btn-primary.disabled:focus,input[type="submit"].btn-primary[disabled]:focus,button.btn-primary[disabled]:focus,fieldset[disabled] input[type="submit"].btn-primary:focus,fieldset[disabled] button.btn-primary:focus,input[type="submit"].btn-primary.disabled:active,button.btn-primary.disabled:active,input[type="submit"].btn-primary[disabled]:active,button.btn-primary[disabled]:active,fieldset[disabled] input[type="submit"].btn-primary:active,fieldset[disabled] button.btn-primary:active,input[type="submit"].btn-primary.disabled.active,button.btn-primary.disabled.active,input[type="submit"].btn-primary[disabled].active,button.btn-primary[disabled].active,fieldset[disabled] input[type="submit"].btn-primary.active,fieldset[disabled] button.btn-primary.active{background-color:#5f6990;border-color:#0e0f15} -.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #bfbfbf;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} +.search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:6px;top:9px} #search-clear-btn{position:absolute;right:6px;top:5px;display:block;font-size:1.4em;text-decoration:none;color:#888;font-family:FontAwesome;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}#search-clear-btn:before{content:"\f057"} @@ -1506,9 +1506,9 @@ table.tabletip th{white-space:nowrap;border-bottom:1px solid #444;padding-right:3px} table.tabletip td{border-bottom:1px solid #ddd} table.tabletip tbody tr:hover td{background-color:#eee} -table.colored{border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px} +table.colored{border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px} table.colored td,table.colored th{text-align:left;padding:5px;line-height:1.428571429} -table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #bfbfbf 1px;font-weight:bold} +table.colored tr.header{background:#ebd9b2;color:#000;background-repeat:repeat-x;background-position:top;border-bottom:solid #d6b161 1px;font-weight:bold} table.colored tr{background:#fff} table.colored tr.odd_row{background:#f9f9f9} div.debug{margin:10px;padding:5px;background:#FFFF99;border:solid #FFFF33 1px;color:black} @@ -1519,7 +1519,7 @@ .grid tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid tbody td:empty{padding:0} .grid thead tr{height:2em} -.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #bfbfbf 1px;border-bottom:solid #bfbfbf 1px;padding:5px;text-align:left;white-space:nowrap} +.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap} .grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px} .grid .current{background-color:#EEEEFF} .count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block} @@ -1618,7 +1618,7 @@ .icon-btn-group .icon-btn:only-child{margin:0px;border-radius:3px} .search-input .search-query{width:100%;padding-right:24px} .search-input .search-clear,.search-input .search-loading{position:relative;display:inline-block;float:right;margin-top:-23px;margin-right:4px;font-size:1.4em;line-height:23px;color:grey} -.search-input .search-clear:hover{color:#5f6990} +.search-input .search-clear:hover{color:#303030} #history-refresh-button,#history-options-button{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;padding:0px} .history-panel .dataset{border:1px solid #bfbfbf}.history-panel .dataset .vertical-spacing{margin-bottom:8px} .history-panel .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: libraries: refactor into separate files for model/views/main+router, showing infoicon for public libraries
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/68d35caf407f/ Changeset: 68d35caf407f User: martenson Date: 2014-03-24 20:12:48 Summary: libraries: refactor into separate files for model/views/main+router, showing infoicon for public libraries Affected #: 12 files diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -55,10 +55,12 @@ libraries = [] for library in query: item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) + if trans.app.security_agent.library_is_public( library, contents=False ): + item[ 'public' ] = True libraries.append( item ) return libraries - @expose_api + @expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): """ show( self, trans, id, deleted='False', **kwd ) @@ -139,6 +141,9 @@ .. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`. + :param id: the encoded id of the library + :type id: an encoded id string + :param payload: (required) dictionary structure containing:: 'name': new library's name, cannot be empty 'description': new library's description @@ -192,7 +197,7 @@ .. note:: Currently, only admin users can un/delete libraries. :param id: the encoded id of the library to un/delete - :type id: str + :type id: an encoded id string :param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false: :type undelete: bool diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -1,1192 +1,26 @@ -// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM -// === GALAXY LIBRARY MODULE ==== -// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === MAIN GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM // global variables -var view = null; var library_router = null; -var responses = []; // dependencies define([ "galaxy.masthead", "utils/utils", - "libs/toastr"], function(mod_masthead, mod_utils, mod_toastr) { - -// MMMMMMMMMMMMMMM -// === Models ==== -// MMMMMMMMMMMMMMM - - // LIBRARY - var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries/' - }); - - // FOLDER AS MODEL - var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' - }); - - // LIBRARIES - var Libraries = Backbone.Collection.extend({ - url: '/api/libraries', - - model: Library, - - sort_key: 'name', // default - - sort_order: null, // default - - }); - - // ITEM - var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets' - }); - - // FOLDER AS COLLECTION - var Folder = Backbone.Collection.extend({ - model: Item - }); - - // CONTAINER for folder contents (folders, items and metadata). - var FolderContainer = Backbone.Model.extend({ - defaults : { - folder : new Folder(), - full_path : "unknown", - urlRoot : "/api/folders/", - id : "unknown" - }, - parse : function(obj) { - this.full_path = obj[0].full_path; - // update the inner collection - this.get("folder").reset(obj[1].folder_contents); - return obj; - } - }); - - // HISTORY ITEM - var HistoryItem = Backbone.Model.extend({ - urlRoot : '/api/histories/' - }); - - // HISTORY - var GalaxyHistory = Backbone.Model.extend({ - url : '/api/histories/' - }); - - // HISTORIES - var GalaxyHistories = Backbone.Collection.extend({ - url : '/api/histories', - model : GalaxyHistory - }); - -// MMMMMMMMMMMMMM -// === VIEWS ==== -// MMMMMMMMMMMMMM - -//main view for folder browsing -var FolderContentView = Backbone.View.extend({ - // main element definition - el : '#center', - // progress percentage - progress: 0, - // progress rate per one item - progressStep: 1, - // last selected history in modal for UX - lastSelectedHistory: '', - // self modal - modal : null, - // loaded folders - folders : null, - - // initialize - initialize : function(){ - this.folders = []; - this.queue = jQuery.Deferred(); - this.queue.resolve(); - }, - -// MMMMMMMMMMMMMMMMMM -// === TEMPLATES ==== -// MMMMMMMMMMMMMMMMMM - - // main template for folder browsing - templateFolder : function (){ - var tmpl_array = []; - - // CONTAINER - tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); - tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - - // TOOLBAR - tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); - tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>'); - tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); - tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); - tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); - tmpl_array.push(' </button>'); - tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); - tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); - tmpl_array.push(' </ul>'); - tmpl_array.push(' </div>'); - - tmpl_array.push('</div>'); - - // BREADCRUMBS - tmpl_array.push('<ol class="breadcrumb">'); - tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); - tmpl_array.push(' <% _.each(path, function(path_item) { %>'); - tmpl_array.push(' <% if (path_item[0] != id) { %>'); - tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); - tmpl_array.push( '<% } else { %>'); - tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</ol>'); - - - // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th class="button_heading"></th>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th>name</th>'); - tmpl_array.push(' <th>data type</th>'); - tmpl_array.push(' <th>size</th>'); - tmpl_array.push(' <th>date (UTC)</th>'); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody>'); - tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder - tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); - tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder - tmpl_array.push(' <span class="muted">(empty folder)</span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td>folder</td>'); - tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size - tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset - tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type - tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size - tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% } %> '); - tmpl_array.push(' <% }); %>'); - tmpl_array.push(' '); - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); - - tmpl_array.push('</div>'); - return tmpl_array.join(''); - }, - templateDatasetModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<div class="modal_table">'); - tmpl_array.push(' <table class="grid table table-striped table-condensed">'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Data type</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Genome build</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Size</th>'); - tmpl_array.push(' <td><%= _.escape(size) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Uploaded by</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr scope="row">'); - tmpl_array.push(' <th scope="row">Data Lines</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Comment Lines</th>'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td scope="row">unknown</td>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Number of Columns</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Column Types</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' </table>'); - tmpl_array.push(' <pre class="peek">'); - tmpl_array.push(' </pre>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); - }, - - templateHistorySelectInModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); - tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); - tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</select>'); - tmpl_array.push('</span>'); - - return tmpl_array.join(''); - }, - - templateBulkImportInModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); - tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); - tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</select>'); - tmpl_array.push('</span>'); - - return tmpl_array.join(''); - }, - - templateProgressBar : function (){ - var tmpl_array = []; - - tmpl_array.push('<div class="import_text">'); - tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); - tmpl_array.push('</div>'); - tmpl_array.push('<div class="progress">'); - tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); - tmpl_array.push(' <span class="completion_span">0% Complete</span>'); - tmpl_array.push(' </div>'); - tmpl_array.push('</div>'); - tmpl_array.push(''); - - return tmpl_array.join(''); - }, - - templateNewFolderInModal: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="new_folder_modal">'); - tmpl_array.push('<form>'); - tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); - tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); - tmpl_array.push('</form>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); - }, - -// MMMMMMMMMMMMMMM -// === EVENTS ==== -// MMMMMMMMMMMMMMM - - // event binding - events: { - 'click #select-all-checkboxes' : 'selectAll', - 'click #toolbtn_bulk_import' : 'modalBulkImport', - 'click #toolbtn_dl' : 'bulkDownload', - 'click #toolbtn_create_folder' : 'createFolderFromModal', - 'click .library-dataset' : 'showDatasetDetails', - 'click .dataset_row' : 'selectClickedRow' - }, - -// MMMMMMMMMMMMMMMMMM -// === FUNCTIONS ==== -// MMMMMMMMMMMMMMMMMM - - //render the folder view - render: function (options) { - //hack to show scrollbars - $("#center").css('overflow','auto'); - - view = this; - var that = this; - - var folderContainer = new FolderContainer({id: options.id}); - folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; - - folderContainer.fetch({ - success: function (container) { - - // prepare nice size strings - for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { - var model = folderContainer.attributes.folder.models[i] - if (model.get('type') === 'file'){ - model.set('readable_size', that.size_to_string(model.get('file_size'))) - } - }; - - // find the upper id - var path = folderContainer.full_path; - var upper_folder_id; - if (path.length === 1){ // library is above us - upper_folder_id = 0; - } else { - upper_folder_id = path[path.length-2][0]; - } - - var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); - // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); - that.$el.html(template); - - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }) - }, - - // convert size to nice string - size_to_string : function (size) - { - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, - - //show modal with current dataset info - showDatasetDetails : function(event){ - // prevent default - event.preventDefault(); - - //TODO check whether we already have the data - - //load the ID of the row - var id = $(event.target).parent().parent().parent().attr('id'); - if (typeof id === 'undefined'){ - id = $(event.target).parent().attr('id'); - } - if (typeof id === 'undefined'){ - id = $(event.target).parent().parent().attr('id') - } - - //create new item - var item = new Item(); - var histories = new GalaxyHistories(); - item.id = id; - var self = this; - - //fetch the dataset info - item.fetch({ - success: function (item) { - // TODO can render here already - //fetch user histories for import purposes - histories.fetch({ - success: function (histories){ - self.renderModalAfterFetch(item, histories) - }, - error: function(){ - mod_toastr.error('An error occured during fetching histories:('); - self.renderModalAfterFetch(item) - } - }); - }, - error: function(){ - mod_toastr.error('An error occured during loading dataset details :('); - } - }); - }, - - // show the current dataset in a modal - renderModalAfterFetch : function(item, histories){ - var size = this.size_to_string(item.get('file_size')); - var template = _.template(this.templateDatasetModal(), { item : item, size : size }); - // make modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Dataset Details', - body : template, - buttons : { - 'Import' : function() { self.importCurrentIntoHistory() }, - 'Download' : function() { self.downloadCurrent() }, - 'Close' : function() { self.modal.hide() } - } - }); - - $(".peek").html('Peek:' + item.get("peek")); - - // show the import-into-history footer only if the request for histories succeeded - if (typeof history.models !== undefined){ - var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - // preset last selected history if we know it - if (self.lastSelectedHistory.length > 0) { - $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); - } - } - }, - - // download dataset shown currently in modal - downloadCurrent : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); - - var library_dataset_id = []; - library_dataset_id.push($('#id_row').attr('data-id')); - var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : library_dataset_id}; - - // we assume the view is existent - folderContentView.processDownload(url, data); - this.modal.enableButton('Import'); - this.modal.enableButton('Download'); - }, - - // import dataset shown currently in modal into selected history - importCurrentIntoHistory : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); - - var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); - this.lastSelectedHistory = history_id; //save selected history for further use - - var library_dataset_id = $('#id_row').attr('data-id'); - var historyItem = new HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; - - // save the dataset into selected history - historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ - mod_toastr.success('Dataset imported'); - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - }, error : function(){ - mod_toastr.error('An error occured! Dataset not imported. Please try again.') - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - } - }); - }, - - // select all datasets - selectAll : function (event) { - var selected = event.target.checked; - that = this; - // Iterate each checkbox - $(':checkbox').each(function () { - this.checked = selected; - $row = $(this.parentElement.parentElement); - // Change color of selected/unselected - (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); - }); - // Show the tools in menu - this.checkTools(); - }, - - // Check checkbox on row itself or row checkbox click - selectClickedRow : function (event) { - var checkbox = ''; - var $row; - var source; - if (event.target.localName === 'input'){ - checkbox = event.target; - $row = $(event.target.parentElement.parentElement); - source = 'input'; - } else if (event.target.localName === 'td') { - checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; - $row = $(event.target.parentElement); - source = 'td'; - } - - if (checkbox.checked){ - if (source==='td'){ - checkbox.checked = ''; - this.makeWhiteRow($row); - } else if (source==='input') { - this.makeDarkRow($row); - } - } else { - if (source==='td'){ - checkbox.checked = 'selected'; - this.makeDarkRow($row); - } else if (source==='input') { - this.makeWhiteRow($row); - } - } - this.checkTools(); - }, - - makeDarkRow: function($row){ - $row.removeClass('light'); - $row.find('a').removeClass('light'); - $row.addClass('dark'); - $row.find('a').addClass('dark'); - $row.find('span').removeClass('fa-file-o'); - $row.find('span').addClass('fa-file'); - - }, - - makeWhiteRow: function($row){ - $row.removeClass('dark'); - $row.find('a').removeClass('dark'); - $row.addClass('light'); - $row.find('a').addClass('light'); - $row.find('span').addClass('fa-file-o'); - $row.find('span').removeClass('fa-file'); - }, - - // show toolbar in case something is selected - checkTools : function(){ - var checkedValues = $('#folder_table').find(':checked'); - if(checkedValues.length > 0){ - $('#toolbtn_bulk_import').show(); - $('#toolbtn_dl').show(); - } else { - $('#toolbtn_bulk_import').hide(); - $('#toolbtn_dl').hide(); - } - }, - - // show bulk import modal - modalBulkImport : function(){ - var self = this; - // fetch histories - var histories = new GalaxyHistories(); - histories.fetch({ - success: function (histories){ - // make modal - var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); - self.modal = Galaxy.modal; - self.modal.show({ - closing_events : true, - title : 'Import into History', - body : history_modal_tmpl, - buttons : { - 'Import' : function() {self.importAllIntoHistory()}, - 'Close' : function() {self.modal.hide();} - } - }); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - }, - - // import all selected datasets into history - importAllIntoHistory : function (){ - //disable the button to prevent multiple submission - this.modal.disableButton('Import'); - - var history_id = $("select[name=dataset_import_bulk] option:selected").val(); - var history_name = $("select[name=dataset_import_bulk] option:selected").text(); - - var dataset_ids = []; - $('#folder_table').find(':checked').each(function(){ - if (this.parentElement.parentElement.id != '') { - dataset_ids.push(this.parentElement.parentElement.id); - } - }); - var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); - $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); - - // init the progress bar - var progressStep = 100 / dataset_ids.length; - this.initProgress(progressStep); - - // prepare the dataset objects to be imported - var datasets_to_import = []; - for (var i = dataset_ids.length - 1; i >= 0; i--) { - library_dataset_id = dataset_ids[i]; - var historyItem = new HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; - historyItem.content = library_dataset_id; - historyItem.source = 'library'; - datasets_to_import.push(historyItem); - }; - - // call the recursive function to call ajax one after each other (request FIFO queue) - this.chainCall(datasets_to_import); - }, - - chainCall: function(history_item_set){ - var self = this; - var popped_item = history_item_set.pop(); - if (typeof popped_item === "undefined") { - mod_toastr.success('All datasets imported'); - this.modal.hide(); - return - } - var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ - self.updateProgress(); - responses.push(a1); - self.chainCall(history_item_set); - }); - }, - - initProgress: function(progressStep){ - this.progress = 0; - this.progressStep = progressStep; - }, - updateProgress: function(){ - this.progress += this.progressStep; - $('.progress-bar-import').width(Math.round(this.progress) + '%'); - txt_representation = Math.round(this.progress) + '% Complete'; - $('.completion_span').text(txt_representation); - }, - - - - // download selected datasets - download : function(folder_id, format){ - var dataset_ids = []; - $('#folder_table').find(':checked').each(function(){ - if (this.parentElement.parentElement.id != '') { - dataset_ids.push(this.parentElement.parentElement.id); - } - }); - - var url = '/api/libraries/datasets/download/' + format; - var data = {'ldda_ids' : dataset_ids}; - this.processDownload(url, data, 'get'); - }, - - // create hidden form and submit through POST to initialize download - processDownload: function(url, data, method){ - //url and data options required - if( url && data ){ - //data can be string of parameters or array/object - data = typeof data == 'string' ? data : $.param(data); - //split params into form inputs - var inputs = ''; - $.each(data.split('&'), function(){ - var pair = this.split('='); - inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; - }); - //send request - $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') - .appendTo('body').submit().remove(); - - mod_toastr.info('Your download will begin soon'); - }; - }, - - // shows modal for creating folder - createFolderFromModal: function(){ - event.preventDefault(); - event.stopPropagation(); - - // create modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Create New Folder', - body : this.templateNewFolderInModal(), - buttons : { - 'Create' : function() {self.create_new_folder_event()}, - 'Close' : function() {self.modal.hide(); self.modal = null;} - } - }); - }, - - // create the new folder from modal - create_new_folder_event: function(){ - var folderDetails = this.serialize_new_folder(); - if (this.validate_new_folder(folderDetails)){ - var folder = new FolderAsModel(); - - url_items = Backbone.history.fragment.split('/'); - current_folder_id = url_items[url_items.length-1]; - folder.url = folder.urlRoot + '/' + current_folder_id ; - - var self = this; - folder.save(folderDetails, { - success: function (folder) { - self.modal.hide(); - mod_toastr.success('Folder created'); - self.render({id: current_folder_id}); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - } else { - mod_toastr.error('Folder\'s name is missing'); - } - return false; - }, - - // serialize data from the form - serialize_new_folder : function(){ - return { - name: $("input[name='Name']").val(), - description: $("input[name='Description']").val() - }; - }, - - // validate new library info - validate_new_folder: function(folderDetails){ - return folderDetails.name !== ''; - } - - }); - -// galaxy library view -var GalaxyLibraryview = Backbone.View.extend({ - el: '#libraries_element', - - events: { - 'click .edit_library_btn' : 'edit_button_event', - 'click .save_library_btn' : 'save_library_modification', - 'click .cancel_library_btn' : 'cancel_library_modification', - 'click .delete_library_btn' : 'delete_library', - 'click .undelete_library_btn' : 'undelete_library' - }, - - modal: null, - - collection: null, - - // initialize - initialize : function(){ - var viewContext = this; - this.collection = new Libraries(); - - this.collection.fetch({ - success: function(libraries){ - viewContext.render(); - // initialize the library tooltips - $("#center [data-toggle]").tooltip(); - // modification of upper DOM element to show scrollbars due to the #center element inheritance - $("#center").css('overflow','auto'); - }, - error: function(model, response){ - mod_toastr.error('An error occured. Please try again.'); - } - }) - }, - - /** Renders the libraries table either from the object's own collection, - or from a given array of library models, - or renders an empty list in case no data is given. */ - render: function (options) { - var template = this.templateLibraryList(); - var libraries_to_render = null; - var include_deleted = false; - var models = null - if (typeof options !== 'undefined'){ - include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false; - models = typeof options.models !== 'undefined' ? options.models : null; - } - - if (this.collection !== null && models === null){ - if (include_deleted){ // show all the libraries - libraries_to_render = this.collection.models; - } else{ // show only undeleted libraries - libraries_to_render = this.collection.where({deleted: false});; - } - } else if (models !== null){ - libraries_to_render = models; - } else { - libraries_to_render = []; - } - - this.$el.html(template({libraries: libraries_to_render, order: this.collection.sort_order})); - }, - - /** Sorts the underlying collection according to the parameters received through URL. - Currently supports only sorting by name. */ - sortLibraries: function(sort_by, order){ - if (sort_by === 'name'){ - if (order === 'asc'){ - this.collection.sort_order = 'asc'; - this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return 1; // after - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return -1; // before - return 0; // equal - } - } else if (order === 'desc'){ - this.collection.sort_order = 'desc'; - this.collection.comparator = function(libraryA, libraryB){ - if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return -1; // before - if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return 1; // after - return 0; // equal - } - } - this.collection.sort(); - } - - }, - -// MMMMMMMMMMMMMMMMMM -// === TEMPLATES ==== -// MMMMMMMMMMMMMMMMMM - - templateLibraryList: function(){ - tmpl_array = []; - - tmpl_array.push('<div class="library_container table-responsive">'); - tmpl_array.push('<% if(libraries.length === 0) { %>'); - tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>"); - tmpl_array.push('<% } else{ %>'); - tmpl_array.push('<table class="grid table table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); - tmpl_array.push(' <th style="width:22%;">description</th>'); - tmpl_array.push(' <th style="width:22%;">synopsis</th> '); - tmpl_array.push(' <th style="width:26%;"></th> '); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody>'); - tmpl_array.push(' <% _.each(libraries, function(library) { %>'); - tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">'); - tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); - tmpl_array.push(' <td class="right-center">'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); - tmpl_array.push('<% }%>'); - tmpl_array.push('</div>'); - - return _.template(tmpl_array.join('')); - }, - - templateNewLibraryInModal: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="new_library_modal">'); - tmpl_array.push(' <form>'); - tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">'); - tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">'); - tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">'); - tmpl_array.push(' </form>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); - }, - - save_library_modification: function(event){ - var $library_row = $(event.target).closest('tr'); - var library = this.collection.get($library_row.data('id')); - - var is_changed = false; - - var new_name = $library_row.find('.input_library_name').val(); - if (typeof new_name !== 'undefined' && new_name !== library.get('name') ){ - if (new_name.length > 2){ - library.set("name", new_name); - is_changed = true; - } else{ - mod_toastr.warning('Library name has to be at least 3 characters long'); - return - } - } - - var new_description = $library_row.find('.input_library_description').val(); - if (typeof new_description !== 'undefined' && new_description !== library.get('description') ){ - library.set("description", new_description); - is_changed = true; - } - - var new_synopsis = $library_row.find('.input_library_synopsis').val(); - if (typeof new_synopsis !== 'undefined' && new_synopsis !== library.get('synopsis') ){ - library.set("synopsis", new_synopsis); - is_changed = true; - } - - if (is_changed){ - library.save(null, { - patch: true, - success: function(library) { - mod_toastr.success('Changes to library saved'); - galaxyLibraryview.toggle_library_modification($library_row); - }, - error: function(model, response){ - mod_toastr.error('An error occured during updating the library :('); - } - }); - } - }, - - edit_button_event: function(event){ - this.toggle_library_modification($(event.target).closest('tr')); - }, - - toggle_library_modification: function($library_row){ - var library = this.collection.get($library_row.data('id')); - - $library_row.find('.edit_library_btn').toggle(); - $library_row.find('.save_library_btn').toggle(); - $library_row.find('.cancel_library_btn').toggle(); - if (library.get('deleted')){ - $library_row.find('.undelete_library_btn').toggle(); - } else { - $library_row.find('.delete_library_btn').toggle(); - } - - if ($library_row.find('.edit_library_btn').is(':hidden')){ - // library name - var current_library_name = library.get('name'); - var new_html = '<input type="text" class="form-control input_library_name" placeholder="name">'; - $library_row.children('td').eq(0).html(new_html); - if (typeof current_library_name !== undefined){ - $library_row.find('.input_library_name').val(current_library_name); - } - // library description - var current_library_description = library.get('description'); - var new_html = '<input type="text" class="form-control input_library_description" placeholder="description">'; - $library_row.children('td').eq(1).html(new_html); - if (typeof current_library_description !== undefined){ - $library_row.find('.input_library_description').val(current_library_description); - } - // library synopsis - var current_library_synopsis = library.get('synopsis'); - var new_html = '<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">'; - $library_row.children('td').eq(2).html(new_html); - if (typeof current_library_synopsis !== undefined){ - $library_row.find('.input_library_synopsis').val(current_library_synopsis); - } - } else { - $library_row.children('td').eq(0).html(library.get('name')); - $library_row.children('td').eq(1).html(library.get('description')); - $library_row.children('td').eq(2).html(library.get('synopsis')); - } - - }, - - cancel_library_modification: function(event){ - var $library_row = $(event.target).closest('tr'); - var library = this.collection.get($library_row.data('id')); - this.toggle_library_modification($library_row); - - $library_row.children('td').eq(0).html(library.get('name')); - $library_row.children('td').eq(1).html(library.get('description')); - $library_row.children('td').eq(2).html(library.get('synopsis')); - }, - - undelete_library: function(event){ - var $library_row = $(event.target).closest('tr'); - var library = this.collection.get($library_row.data('id')); - this.toggle_library_modification($library_row); - - // mark the library undeleted - library.url = library.urlRoot + library.id + '?undelete=true'; - library.destroy({ - success: function (library) { - // add the newly undeleted library back to the collection - // backbone does not accept changes through destroy, so update it too - library.set('deleted', false); - galaxyLibraryview.collection.add(library); - $library_row.removeClass('active'); - mod_toastr.success('Library has been undeleted'); - }, - error: function(){ - mod_toastr.error('An error occured while undeleting the library :('); - } - }); - }, - - delete_library: function(event){ - var $library_row = $(event.target).closest('tr'); - var library = this.collection.get($library_row.data('id')); - this.toggle_library_modification($library_row); - - // mark the library deleted - library.destroy({ - success: function (library) { - // add the new deleted library back to the collection - $library_row.remove(); - library.set('deleted', true); - galaxyLibraryview.collection.add(library); - mod_toastr.success('Library has been marked deleted'); - }, - error: function(){ - mod_toastr.error('An error occured during deleting the library :('); - } - }); - - }, - - redirectToHome: function(){ - window.location = '../'; - }, - redirectToLogin: function(){ - window.location = '/user/login'; - }, - - // show/hide create library modal - show_library_modal : function (event){ - event.preventDefault(); - event.stopPropagation(); - - // create modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Create New Library', - body : this.templateNewLibraryInModal(), - buttons : { - 'Create' : function() {self.create_new_library_event()}, - 'Close' : function() {self.modal.hide();} - } - }); - }, - - // create the new library from modal - create_new_library_event: function(){ - var libraryDetails = this.serialize_new_library(); - if (this.validate_new_library(libraryDetails)){ - var library = new Library(); - var self = this; - library.save(libraryDetails, { - success: function (library) { - self.collection.add(library); - self.modal.hide(); - self.clear_library_modal(); - self.render(); - mod_toastr.success('Library created'); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - } else { - mod_toastr.error('Library\'s name is missing'); - } - return false; - }, - - // clear the library modal once saved - clear_library_modal : function(){ - $("input[name='Name']").val(''); - $("input[name='Description']").val(''); - $("input[name='Synopsis']").val(''); - }, - - // serialize data from the form - serialize_new_library : function(){ - return { - name: $("input[name='Name']").val(), - description: $("input[name='Description']").val(), - synopsis: $("input[name='Synopsis']").val() - }; - }, - - // validate new library info - validate_new_library: function(libraryDetails){ - return libraryDetails.name !== ''; - } -}); - -var ToolbarView = Backbone.View.extend({ - el: '#center', - - events: { - 'click #create_new_library_btn' : 'delegate_modal', - 'click #include_deleted_chk' : 'check_include_deleted' - }, - - initialize: function(){ - this.render(); - }, - - delegate_modal: function(event){ - // probably should refactor to have this functionality in this view, not in the library view - galaxyLibraryview.show_library_modal(event); - }, - - // include or exclude deleted libraries from the view - check_include_deleted: function(event){ - if (event.target.checked){ - galaxyLibraryview.render( {'with_deleted': true} ); - } else{ - galaxyLibraryview.render({'with_deleted': false}); - } - }, - - render: function(){ - var toolbar_template = this.templateToolBar() - this.$el.html(toolbar_template()) - }, - - templateToolBar: function(){ - tmpl_array = []; - - tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">'); - // TOOLBAR - tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">'); - tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>'); - tmpl_array.push(' </div>'); - tmpl_array.push(' </div>'); - tmpl_array.push(' <div id="libraries_element">'); - tmpl_array.push(' </div>'); - tmpl_array.push('</div>'); - - return _.template(tmpl_array.join('')); - } -}) + "libs/toastr", + "mvc/library/library-model", + "mvc/library/library-folderlist-view", + "mvc/library/library-librarylist-view", + "mvc/library/library-librarytoolbar-view"], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_library_model, + mod_folderlist_view, + mod_librarylist_view, + mod_librarytoolbar_view) { //ROUTER var LibraryRouter = Backbone.Router.extend({ @@ -1202,16 +36,17 @@ var GalaxyLibrary = Backbone.View.extend({ initialize : function(){ - toolbarView = new ToolbarView(); - galaxyLibraryview = new GalaxyLibraryview(); + toolbarView = new mod_librarytoolbar_view.ToolbarView(); + galaxyLibraryview = new mod_librarylist_view.GalaxyLibraryview(); library_router = new LibraryRouter(); - folderContentView = new FolderContentView(); + + folderContentView = null; library_router.on('route:libraries', function() { // initialize and render the toolbar first - toolbarView = new ToolbarView(); + toolbarView = new mod_librarytoolbar_view.ToolbarView(); // initialize and render libraries second - galaxyLibraryview = new GalaxyLibraryview(); + galaxyLibraryview = new mod_librarylist_view.GalaxyLibraryview(); }); library_router.on('route:sort_libraries', function(sort_by, order) { @@ -1222,6 +57,7 @@ library_router.on('route:folder_content', function(id) { // render folder contents + if (!folderContentView) {folderContentView = new mod_folderlist_view.FolderContentView();} folderContentView.render({id: id}); }); diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 static/scripts/mvc/library/library-folderlist-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -0,0 +1,713 @@ +// dependencies +define([ + "galaxy.masthead", + "utils/utils", + "libs/toastr", + "mvc/library/library-model"], +function(mod_masthead, + mod_utils, + mod_toastr, + mod_library_model) { + + //main view for folder browsing +var FolderContentView = Backbone.View.extend({ + // main element definition + el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + + // initialize + initialize : function(){ + this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); + }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + // main template for folder browsing + templateFolder : function (){ + var tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>'); + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(path, function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); + + + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date (UTC)</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div class="modal_table">'); + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + templateNewFolderInModal: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="new_folder_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', + 'click #toolbtn_create_folder' : 'createFolderFromModal', + 'click .library-dataset' : 'showDatasetDetails', + 'click .dataset_row' : 'selectClickedRow' + }, + +// MMMMMMMMMMMMMMMMMM +// === FUNCTIONS ==== +// MMMMMMMMMMMMMMMMMM + + //render the folder view + render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; + var that = this; + + var folderContainer = new mod_library_model.FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); + that.$el.html(template); + + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }) + }, + + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + + //TODO check whether we already have the data + + //load the ID of the row + var id = $(event.target).parent().parent().parent().attr('id'); + if (typeof id === 'undefined'){ + id = $(event.target).parent().attr('id'); + } + if (typeof id === 'undefined'){ + id = $(event.target).parent().parent().attr('id') + } + + //create new item + var item = new mod_library_model.Item(); + var histories = new mod_library_model.GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { + // TODO can render here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){ + self.renderModalAfterFetch(item, histories) + }, + error: function(){ + mod_toastr.error('An error occured during fetching histories:('); + self.renderModalAfterFetch(item) + } + }); + }, + error: function(){ + mod_toastr.error('An error occured during loading dataset details :('); + } + }); + }, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + // make modal + var self = this; + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide() } + } + }); + + $(".peek").html('Peek:' + item.get("peek")); + + // show the import-into-history footer only if the request for histories succeeded + if (typeof history.models !== undefined){ + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + } + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new mod_library_model.HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + mod_toastr.success('Dataset imported'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + mod_toastr.error('An error occured! Dataset not imported. Please try again.') + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox').each(function () { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); + }); + // Show the tools in menu + this.checkTools(); + }, + + // Check checkbox on row itself or row checkbox click + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } + } else { + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } + } + this.checkTools(); + }, + + makeDarkRow: function($row){ + $row.removeClass('light'); + $row.find('a').removeClass('light'); + $row.addClass('dark'); + $row.find('a').addClass('dark'); + $row.find('span').removeClass('fa-file-o'); + $row.find('span').addClass('fa-file'); + + }, + + makeWhiteRow: function($row){ + $row.removeClass('dark'); + $row.find('a').removeClass('dark'); + $row.addClass('light'); + $row.find('a').addClass('light'); + $row.find('span').addClass('fa-file-o'); + $row.find('span').removeClass('fa-file'); + }, + + // show toolbar in case something is selected + checkTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new mod_library_model.GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = Galaxy.modal; + self.modal.show({ + closing_events : true, + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide();} + } + }); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button to prevent multiple submission + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new mod_library_model.HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other (request FIFO queue) + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + mod_toastr.success('All datasets imported'); + this.modal.hide(); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + // responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar-import').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data, 'get'); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + + mod_toastr.info('Your download will begin soon'); + }; + }, + + // shows modal for creating folder + createFolderFromModal: function(){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Create New Folder', + body : this.templateNewFolderInModal(), + buttons : { + 'Create' : function() {self.create_new_folder_event()}, + 'Close' : function() {self.modal.hide(); self.modal = null;} + } + }); + }, + + // create the new folder from modal + create_new_folder_event: function(){ + var folderDetails = this.serialize_new_folder(); + if (this.validate_new_folder(folderDetails)){ + var folder = new mod_library_model.FolderAsModel(); + + url_items = Backbone.history.fragment.split('/'); + current_folder_id = url_items[url_items.length-1]; + folder.url = folder.urlRoot + '/' + current_folder_id ; + + var self = this; + folder.save(folderDetails, { + success: function (folder) { + self.modal.hide(); + mod_toastr.success('Folder created'); + self.render({id: current_folder_id}); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } else { + mod_toastr.error('Folder\'s name is missing'); + } + return false; + }, + + // serialize data from the form + serialize_new_folder : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val() + }; + }, + + // validate new library info + validate_new_folder: function(folderDetails){ + return folderDetails.name !== ''; + } + + }); + +// return +return { + FolderContentView: FolderContentView +}; + +}); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: libraries - exposed to anonymous users, allowed editing, deleting, undeleting, improved 'include deleted' filter, refactoring toolbar to have its own view
by commits-noreply＠bitbucket.org 24 Mar '14

24 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/33cc6056d837/ Changeset: 33cc6056d837 User: martenson Date: 2014-03-24 16:16:36 Summary: libraries - exposed to anonymous users, allowed editing, deleting, undeleting, improved 'include deleted' filter, refactoring toolbar to have its own view Affected #: 6 files diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -209,7 +209,7 @@ '/api/libraries/:id', controller='libraries', action='update', - conditions=dict( method=[ "PATCH" ] ) ) + conditions=dict( method=[ "PATCH", 'PUT' ] ) ) webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -19,7 +19,7 @@ // LIBRARY var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries' + urlRoot: '/api/libraries/' }); // FOLDER AS MODEL @@ -122,7 +122,7 @@ // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); - tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); + tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); @@ -208,7 +208,7 @@ var tmpl_array = []; tmpl_array.push('<div class="modal_table">'); - tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); @@ -266,9 +266,9 @@ templateHistorySelectInModal : function(){ var tmpl_array = []; - tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); tmpl_array.push(' <% }); %>'); @@ -457,7 +457,7 @@ } }); - $(".peek").html(item.get("peek")); + $(".peek").html('Peek:' + item.get("peek")); // show the import-into-history footer only if the request for histories succeeded if (typeof history.models !== undefined){ @@ -783,10 +783,14 @@ // galaxy library view var GalaxyLibraryview = Backbone.View.extend({ - el: '#center', + el: '#libraries_element', events: { - 'click #create_new_library_btn' : 'show_library_modal' + 'click .edit_library_btn' : 'edit_button_event', + 'click .save_library_btn' : 'save_library_modification', + 'click .cancel_library_btn' : 'cancel_library_modification', + 'click .delete_library_btn' : 'delete_library', + 'click .undelete_library_btn' : 'undelete_library' }, modal: null, @@ -801,19 +805,15 @@ this.collection.fetch({ success: function(libraries){ viewContext.render(); + // initialize the library tooltips + $("#center [data-toggle]").tooltip(); + // modification of upper DOM element to show scrollbars due to the #center element inheritance + $("#center").css('overflow','auto'); }, error: function(model, response){ - - if (response.statusCode().status === 403){ //TODO open to public - mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); - setTimeout(that.redirectToLogin, 3000); - } else { - mod_toastr.error('An error occured. Please try again.'); - } + mod_toastr.error('An error occured. Please try again.'); } }) - // modification of upper DOM element to show scrollbars due to the #center element inheritance - $("#center").css('overflow','auto'); }, /** Renders the libraries table either from the object's own collection, @@ -875,39 +875,40 @@ templateLibraryList: function(){ tmpl_array = []; - tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); - - tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); - tmpl_array.push('<div id="library_toolbar">'); - tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>'); - tmpl_array.push('</div>'); - + tmpl_array.push('<div class="library_container table-responsive">'); tmpl_array.push('<% if(libraries.length === 0) { %>'); tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>"); tmpl_array.push('<% } else{ %>'); tmpl_array.push('<table class="grid table table-condensed">'); tmpl_array.push(' <thead>'); - tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); - tmpl_array.push(' <th>description</th>'); - tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); + tmpl_array.push(' <th style="width:22%;">description</th>'); + tmpl_array.push(' <th style="width:22%;">synopsis</th> '); + tmpl_array.push(' <th style="width:26%;"></th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); - tmpl_array.push(' <tr>'); + tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">'); tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td class="right-center">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>'); + tmpl_array.push(' </td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); tmpl_array.push('<% }%>'); - tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); }, - + templateNewLibraryInModal: function(){ tmpl_array = []; @@ -922,6 +923,148 @@ return tmpl_array.join(''); }, + save_library_modification: function(event){ + var $library_row = $(event.target).closest('tr'); + var library = this.collection.get($library_row.data('id')); + + var is_changed = false; + + var new_name = $library_row.find('.input_library_name').val(); + if (typeof new_name !== 'undefined' && new_name !== library.get('name') ){ + if (new_name.length > 2){ + library.set("name", new_name); + is_changed = true; + } else{ + mod_toastr.warning('Library name has to be at least 3 characters long'); + return + } + } + + var new_description = $library_row.find('.input_library_description').val(); + if (typeof new_description !== 'undefined' && new_description !== library.get('description') ){ + library.set("description", new_description); + is_changed = true; + } + + var new_synopsis = $library_row.find('.input_library_synopsis').val(); + if (typeof new_synopsis !== 'undefined' && new_synopsis !== library.get('synopsis') ){ + library.set("synopsis", new_synopsis); + is_changed = true; + } + + if (is_changed){ + library.save(null, { + patch: true, + success: function(library) { + mod_toastr.success('Changes to library saved'); + galaxyLibraryview.toggle_library_modification($library_row); + }, + error: function(model, response){ + mod_toastr.error('An error occured during updating the library :('); + } + }); + } + }, + + edit_button_event: function(event){ + this.toggle_library_modification($(event.target).closest('tr')); + }, + + toggle_library_modification: function($library_row){ + var library = this.collection.get($library_row.data('id')); + + $library_row.find('.edit_library_btn').toggle(); + $library_row.find('.save_library_btn').toggle(); + $library_row.find('.cancel_library_btn').toggle(); + if (library.get('deleted')){ + $library_row.find('.undelete_library_btn').toggle(); + } else { + $library_row.find('.delete_library_btn').toggle(); + } + + if ($library_row.find('.edit_library_btn').is(':hidden')){ + // library name + var current_library_name = library.get('name'); + var new_html = '<input type="text" class="form-control input_library_name" placeholder="name">'; + $library_row.children('td').eq(0).html(new_html); + if (typeof current_library_name !== undefined){ + $library_row.find('.input_library_name').val(current_library_name); + } + // library description + var current_library_description = library.get('description'); + var new_html = '<input type="text" class="form-control input_library_description" placeholder="description">'; + $library_row.children('td').eq(1).html(new_html); + if (typeof current_library_description !== undefined){ + $library_row.find('.input_library_description').val(current_library_description); + } + // library synopsis + var current_library_synopsis = library.get('synopsis'); + var new_html = '<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">'; + $library_row.children('td').eq(2).html(new_html); + if (typeof current_library_synopsis !== undefined){ + $library_row.find('.input_library_synopsis').val(current_library_synopsis); + } + } else { + $library_row.children('td').eq(0).html(library.get('name')); + $library_row.children('td').eq(1).html(library.get('description')); + $library_row.children('td').eq(2).html(library.get('synopsis')); + } + + }, + + cancel_library_modification: function(event){ + var $library_row = $(event.target).closest('tr'); + var library = this.collection.get($library_row.data('id')); + this.toggle_library_modification($library_row); + + $library_row.children('td').eq(0).html(library.get('name')); + $library_row.children('td').eq(1).html(library.get('description')); + $library_row.children('td').eq(2).html(library.get('synopsis')); + }, + + undelete_library: function(event){ + var $library_row = $(event.target).closest('tr'); + var library = this.collection.get($library_row.data('id')); + this.toggle_library_modification($library_row); + + // mark the library undeleted + library.url = library.urlRoot + library.id + '?undelete=true'; + library.destroy({ + success: function (library) { + // add the newly undeleted library back to the collection + // backbone does not accept changes through destroy, so update it too + library.set('deleted', false); + galaxyLibraryview.collection.add(library); + $library_row.removeClass('active'); + mod_toastr.success('Library has been undeleted'); + }, + error: function(){ + mod_toastr.error('An error occured while undeleting the library :('); + } + }); + }, + + delete_library: function(event){ + var $library_row = $(event.target).closest('tr'); + var library = this.collection.get($library_row.data('id')); + this.toggle_library_modification($library_row); + + // mark the library deleted + library.destroy({ + success: function (library) { + // add the new deleted library back to the collection + $library_row.remove(); + library.set('deleted', true); + galaxyLibraryview.collection.add(library); + mod_toastr.success('Library has been marked deleted'); + }, + error: function(){ + mod_toastr.error('An error occured during deleting the library :('); + } + }); + + }, + redirectToHome: function(){ window.location = '../'; }, @@ -994,6 +1137,56 @@ } }); +var ToolbarView = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'delegate_modal', + 'click #include_deleted_chk' : 'check_include_deleted' + }, + + initialize: function(){ + this.render(); + }, + + delegate_modal: function(event){ + // probably should refactor to have this functionality in this view, not in the library view + galaxyLibraryview.show_library_modal(event); + }, + + // include or exclude deleted libraries from the view + check_include_deleted: function(event){ + if (event.target.checked){ + galaxyLibraryview.render( {'with_deleted': true} ); + } else{ + galaxyLibraryview.render({'with_deleted': false}); + } + }, + + render: function(){ + var toolbar_template = this.templateToolBar() + this.$el.html(toolbar_template()) + }, + + templateToolBar: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">'); + // TOOLBAR + tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">'); + tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' <div id="libraries_element">'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + } +}) //ROUTER var LibraryRouter = Backbone.Router.extend({ @@ -1007,18 +1200,18 @@ // galaxy library wrapper View var GalaxyLibrary = Backbone.View.extend({ - // folderContentView : null, - // galaxyLibraryview : null, initialize : function(){ - + toolbarView = new ToolbarView(); galaxyLibraryview = new GalaxyLibraryview(); library_router = new LibraryRouter(); folderContentView = new FolderContentView(); library_router.on('route:libraries', function() { - // render libraries list - galaxyLibraryview.render(); + // initialize and render the toolbar first + toolbarView = new ToolbarView(); + // initialize and render libraries second + galaxyLibraryview = new GalaxyLibraryview(); }); library_router.on('route:sort_libraries', function(sort_by, order) { @@ -1028,9 +1221,7 @@ }); library_router.on('route:folder_content', function(id) { - // if (this.folderContentView === null){ - // } - // render folder's contents + // render folder contents folderContentView.render({id: id}); }); diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(k,h,m){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var n=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:j});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<ol class="breadcrumb">');q.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');q.push(" <% _.each(path, function(path_item) { %>");q.push(" <% if (path_item[0] != id) { %>");q.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');q.push("<% } else { %>");q.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');q.push(" <% } %>");q.push(" <% }); %>");q.push("</ol>");q.push('<table id="folder_table" class="grid table table-condensed">');q.push(" <thead>");q.push(' <th class="button_heading"></th>');q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date (UTC)</th>");q.push(" </thead>");q.push(" <tbody>");q.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Folder" class="fa fa-folder-o"></span>');q.push(" </td>");q.push(" <td></td>");q.push(" <td>");q.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } else { %>");q.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Dataset" class="fa fa-file-o"></span>');q.push(" </td>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } %> ");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div class="modal_table">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded (UTC)</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new e({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)},error:function(){m.error("An error occured :(")}})},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().parent().attr("id");if(typeof u==="undefined"){u=$(t.target).parent().attr("id")}if(typeof u==="undefined"){u=$(t.target).parent().parent().attr("id")}var s=new i();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)},error:function(){m.error("An error occured during fetching histories:(");q.renderModalAfterFetch(v)}})},error:function(){m.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide()}}});$(".peek").html(v.get("peek"));if(typeof history.models!==undefined){var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark");q.find("span").removeClass("fa-file-o");q.find("span").addClass("fa-file")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light");q.find("span").addClass("fa-file-o");q.find("span").removeClass("fa-file")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=Galaxy.modal;r.modal.show({closing_events:true,title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide()}}})},error:function(){m.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){q.create_new_folder_event()},Close:function(){q.modal.hide();q.modal=null}}})},create_new_folder_event:function(){var q=this.serialize_new_folder();if(this.validate_new_folder(q)){var s=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];s.url=s.urlRoot+"/"+current_folder_id;var r=this;s.save(q,{success:function(t){r.modal.hide();m.success("Folder created");r.render({id:current_folder_id})},error:function(){m.error("An error occured :(")}})}else{m.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(q){return q.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},modal:null,collection:null,initialize:function(){var q=this;this.collection=new n();this.collection.fetch({success:function(r){q.render()},error:function(s,r){if(r.statusCode().status===403){m.info("Please log in first. Redirecting to login page in 3s.");setTimeout(that.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}});$("#center").css("overflow","auto")},render:function(r){var s=this.templateLibraryList();var t=null;var q=false;var u=null;if(typeof r!=="undefined"){q=typeof r.with_deleted!=="undefined"?r.with_deleted:false;u=typeof r.models!=="undefined"?r.models:null}if(this.collection!==null&&u===null){if(q){t=this.collection.models}else{t=this.collection.where({deleted:false})}}else{if(u!==null){t=u}else{t=[]}}this.$el.html(s({libraries:t,order:this.collection.sort_order}))},sortLibraries:function(r,q){if(r==="name"){if(q==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return 1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}return 0}}else{if(q==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return -1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push("</div>");tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}})},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new f();var q=this;r.save(s,{success:function(t){q.collection.add(t);q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""}});var p=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){galaxyLibraryview=new a();library_router=new p();folderContentView=new l();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:sort_libraries",function(r,q){galaxyLibraryview.sortLibraries(r,q);galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(l,i,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries/"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var j=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:j});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var k=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:k});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<ol class="breadcrumb">');r.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');r.push(" <% _.each(path, function(path_item) { %>");r.push(" <% if (path_item[0] != id) { %>");r.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');r.push("<% } else { %>");r.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');r.push(" <% } %>");r.push(" <% }); %>");r.push("</ol>");r.push('<table id="folder_table" class="grid table table-condensed">');r.push(" <thead>");r.push(' <th class="button_heading"></th>');r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Folder" class="fa fa-folder-o"></span>');r.push(" </td>");r.push(" <td></td>");r.push(" <td>");r.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } else { %>");r.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Dataset" class="fa fa-file-o"></span>');r.push(" </td>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } %> ");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div class="modal_table">');r.push(' <table class="grid table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().parent().attr("id");if(typeof v==="undefined"){v=$(u.target).parent().attr("id")}if(typeof v==="undefined"){v=$(u.target).parent().parent().attr("id")}var t=new j();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html("Peek:"+w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark");r.find("span").removeClass("fa-file-o");r.find("span").addClass("fa-file")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light");r.find("span").addClass("fa-file-o");r.find("span").removeClass("fa-file")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#libraries_element",events:{"click .edit_library_btn":"edit_button_event","click .save_library_btn":"save_library_modification","click .cancel_library_btn":"cancel_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},modal:null,collection:null,initialize:function(){var r=this;this.collection=new o();this.collection.fetch({success:function(s){r.render();$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},error:function(t,s){n.error("An error occured. Please try again.")}})},render:function(s){var t=this.templateLibraryList();var u=null;var r=false;var v=null;if(typeof s!=="undefined"){r=typeof s.with_deleted!=="undefined"?s.with_deleted:false;v=typeof s.models!=="undefined"?s.models:null}if(this.collection!==null&&v===null){if(r){u=this.collection.models}else{u=this.collection.where({deleted:false})}}else{if(v!==null){u=v}else{u=[]}}this.$el.html(t({libraries:u,order:this.collection.sort_order}))},sortLibraries:function(s,r){if(s==="name"){if(r==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return -1}return 0}}else{if(r==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">');tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},save_library_modification:function(u){var t=$(u.target).closest("tr");var r=this.collection.get(t.data("id"));var s=false;var w=t.find(".input_library_name").val();if(typeof w!=="undefined"&&w!==r.get("name")){if(w.length>2){r.set("name",w);s=true}else{n.warning("Library name has to be at least 3 characters long");return}}var v=t.find(".input_library_description").val();if(typeof v!=="undefined"&&v!==r.get("description")){r.set("description",v);s=true}var x=t.find(".input_library_synopsis").val();if(typeof x!=="undefined"&&x!==r.get("synopsis")){r.set("synopsis",x);s=true}if(s){r.save(null,{patch:true,success:function(y){n.success("Changes to library saved");galaxyLibraryview.toggle_library_modification(t)},error:function(z,y){n.error("An error occured during updating the library :(")}})}},edit_button_event:function(r){this.toggle_library_modification($(r.target).closest("tr"))},toggle_library_modification:function(u){var r=this.collection.get(u.data("id"));u.find(".edit_library_btn").toggle();u.find(".save_library_btn").toggle();u.find(".cancel_library_btn").toggle();if(r.get("deleted")){u.find(".undelete_library_btn").toggle()}else{u.find(".delete_library_btn").toggle()}if(u.find(".edit_library_btn").is(":hidden")){var s=r.get("name");var w='<input type="text" class="form-control input_library_name" placeholder="name">';u.children("td").eq(0).html(w);if(typeof s!==undefined){u.find(".input_library_name").val(s)}var t=r.get("description");var w='<input type="text" class="form-control input_library_description" placeholder="description">';u.children("td").eq(1).html(w);if(typeof t!==undefined){u.find(".input_library_description").val(t)}var v=r.get("synopsis");var w='<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">';u.children("td").eq(2).html(w);if(typeof v!==undefined){u.find(".input_library_synopsis").val(v)}}else{u.children("td").eq(0).html(r.get("name"));u.children("td").eq(1).html(r.get("description"));u.children("td").eq(2).html(r.get("synopsis"))}},cancel_library_modification:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);s.children("td").eq(0).html(r.get("name"));s.children("td").eq(1).html(r.get("description"));s.children("td").eq(2).html(r.get("synopsis"))},undelete_library:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);r.url=r.urlRoot+r.id+"?undelete=true";r.destroy({success:function(u){u.set("deleted",false);galaxyLibraryview.collection.add(u);s.removeClass("active");n.success("Library has been undeleted")},error:function(){n.error("An error occured while undeleting the library :(")}})},delete_library:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);r.destroy({success:function(u){s.remove();u.set("deleted",true);galaxyLibraryview.collection.add(u);n.success("Library has been marked deleted")},error:function(){n.error("An error occured during deleting the library :(")}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.collection.add(u);r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var h=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},delegate_modal:function(r){galaxyLibraryview.show_library_modal(r)},check_include_deleted:function(r){if(r.target.checked){galaxyLibraryview.render({with_deleted:true})}else{galaxyLibraryview.render({with_deleted:false})}},render:function(){var r=this.templateToolBar();this.$el.html(r())},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});var q=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){toolbarView=new h();galaxyLibraryview=new a();library_router=new q();folderContentView=new m();library_router.on("route:libraries",function(){toolbarView=new h();galaxyLibraryview=new a()});library_router.on("route:sort_libraries",function(s,r){galaxyLibraryview.sortLibraries(s,r);galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1295,6 +1295,7 @@ div.libraryItemBody{padding:4px 4px 2px 4px} li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} +td.right-center{vertical-align:middle !important;text-align:right} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -6,6 +6,7 @@ div.libraryItemBody{padding:4px 4px 2px 4px} li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8} li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9} +td.right-center{vertical-align:middle !important;text-align:right} .library_table td{border-top:1px solid #5f6990 !important} .library_table th{border-bottom:2px solid #5f6990 !important} .library_table a{color:#0A143D}.library_table a:hover{color:maroon} diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,6 +29,11 @@ background-color: @table-bg-accent; } +td.right-center{ + vertical-align: middle !important; + text-align: right; + +} .library_table{ td { 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