galaxy-commits January 2014

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commit/galaxy-central: greg: A bit of code cleanup and enhanced logging for the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5378f0517318/ Changeset: 5378f0517318 User: greg Date: 2014-01-02 22:39:46 Summary: A bit of code cleanup and enhanced logging for the tool shed's install and test framework. Affected #: 3 files diff -r 1b0c9587a1da4adc4b75f843f10191e7136cf719 -r 5378f0517318861997ae7be112bbbf4098bdf7ce lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -209,6 +209,11 @@ repository_metadata.time_last_tested = datetime.datetime.utcnow() flush_needed = True elif hasattr( repository_metadata, key ): + # log information when setting attributes associated with the Tool Shed's install and test framework. + if key in [ 'do_not_test', 'includes_tools', 'missing_test_components', 'test_install_error', + 'tools_functionally_correct' ]: + log.debug( 'Setting repository_metadata table column %s to value %s for changeset_revision %s via the Tool Shed API.' % \ + ( str( key ), str( new_value ), str( repository_metadata.changeset_revision ) ) ) setattr( repository_metadata, key, new_value ) flush_needed = True if flush_needed: diff -r 1b0c9587a1da4adc4b75f843f10191e7136cf719 -r 5378f0517318861997ae7be112bbbf4098bdf7ce test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -811,7 +811,7 @@ def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): """ - Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method + Update the repository metadata tool_test_results and appropriate flags using the Tool Shed API. This method updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags to the appropriate values and updates the time_last_tested field to the value of the received time_tested. """ diff -r 1b0c9587a1da4adc4b75f843f10191e7136cf719 -r 5378f0517318861997ae7be112bbbf4098bdf7ce test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -52,14 +52,13 @@ from paste import httpserver from functional import database_contexts +import functional.test_toolbox as imported_test_toolbox log = logging.getLogger( 'install_and_test_repositories_with_tools' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' ) -test_toolbox = None - # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) @@ -137,6 +136,8 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + global test_toolbox + test_toolbox = imported_test_toolbox # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' @@ -441,9 +442,6 @@ app = UniverseApplication( **kwargs ) database_contexts.galaxy_context = app.model.context database_contexts.install_context = app.install_model.context - global test_toolbox - import functional.test_toolbox as imported_test_toolbox - test_toolbox = imported_test_toolbox log.debug( "Embedded Galaxy application started..." ) # ---- Run galaxy webserver ------------------------------------------------------ @@ -577,15 +575,12 @@ """ tests_to_delete = [] tools_to_delete_by_id = [] - # Push all the toolbox tests to module level G = globals() - # Eliminate all previous tests from G. for key, val in G.items(): if key.startswith( 'TestForTool_' ): del G[ key ] - global test_toolbox # Find all tests previously generated by twill. for key in test_toolbox.__dict__: if key.startswith( 'TestForTool_' ): @@ -609,17 +604,19 @@ def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): """Test tools contained in the received repository.""" + # Set the global variable 'test_toolbox', so that test.functional.test_toolbox will generate the + # appropriate test methods. + test_toolbox.toolbox = app.toolbox + # Get the attributes that identify the repository whose contained tools are being tested. name = str( repository.name ) owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the - # appropriate test methods. At this point, app.toolbox contains the upload tool and all tools contained - # in the repository. - test_toolbox.toolbox = app.toolbox - # Generate the test methods for this installed repository. We need to pass in True here, or it will look - # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. - test_toolbox.build_tests( testing_shed_tools=True, master_api_key=install_and_test_base_util.default_galaxy_master_api_key ) + # Generate the test methods for this installed repository. We need to pass testing_shed_tools=True here + # or twill will look in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test + # files. + test_toolbox.build_tests( testing_shed_tools=True, + master_api_key=install_and_test_base_util.default_galaxy_master_api_key ) # Set up nose to run the generated functional tests. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) @@ -678,7 +675,8 @@ can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) - # Remove twills' old generated test before building the new tests for the current tools. + # Remove the just-executed tests so twill will not find and re-test them along with the tools + # contained in the next repository. remove_tests( app ) return install_and_test_statistics_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Clean up and fix tool shed functional test script 1300.
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1b0c9587a1da/ Changeset: 1b0c9587a1da User: inithello Date: 2014-01-02 21:29:13 Summary: Clean up and fix tool shed functional test script 1300. Affected #: 1 file diff -r 809b87af4983e40382d16f4f1a72896328d84f5e -r 1b0c9587a1da4adc4b75f843f10191e7136cf719 test/tool_shed/functional/test_1300_reset_all_metadata.py --- a/test/tool_shed/functional/test_1300_reset_all_metadata.py +++ b/test/tool_shed/functional/test_1300_reset_all_metadata.py @@ -1,4 +1,5 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os + datatypes_repository_name = 'emboss_datatypes_0020' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." @@ -6,6 +7,29 @@ emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga' workflow_name = 'Workflow for 0060_filter_workflow_repository' +filtering_repository_description = "Galaxy's filtering tool for test 0040" +filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040" + +category_0000_name='Test 0000 Basic Repository Features 1' +category_0001_name='Test 0000 Basic Repository Features 2' +category_0010_name='Test 0010 Repository With Tool Dependencies' +category_0020_name='Test 0020 Basic Repository Dependencies' +category_0030_name='Test 0030 Repository Dependency Revisions' +category_0040_name='test_0040_repository_circular_dependencies' +category_0050_name='test_0050_repository_n_level_circular_dependencies' +category_0060_name='Test 0060 Workflow Features' + +''' +This script will run in one of two possible ways: + +1. Directly, by calling sh run_functional_tests.sh -toolshed test/tool_shed/functional/test_1300_reset_all_metadata.py. + -OR- +2. After the previous test scripts have completed. + +In the first case, it is desirable to have the Galaxy database in a state that is as close as possible to the state it would +be in following the second case. This means explicitly installing whatever repositories would be in an installed state following +the previous test scripts. +''' base_datatypes_count = 0 repository_datatypes_count = 0 @@ -14,6 +38,7 @@ class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ): '''Verify that the "Reset selected metadata" feature works.''' + def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() @@ -26,92 +51,108 @@ admin_user = self.test_db_util.get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) - def test_0005_create_repositories_and_categories( self ): - '''Ensure that the necessary categories and repositories exist for these tests.''' + + def test_0005_create_categories( self ): + '''Create the categories for the repositories in this test script.''' + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + category_0000 = self.create_category( name=category_0000_name, description='Test 0000 Basic Repository Features 1' ) + category_0001 = self.create_category( name=category_0001_name, description='Test 0000 Basic Repository Features 2' ) + category_0010 = self.create_category( name=category_0010_name, description='Tests for a repository with tool dependencies.' ) + category_0020 = self.create_category( name=category_0020_name, description='Testing basic repository dependency features.' ) + category_0030 = self.create_category( name=category_0030_name, description='Testing repository dependencies by revision.' ) + category_0040 = self.create_category( name=category_0040_name, description='Testing handling of circular repository dependencies.' ) + category_0050 = self.create_category( name=category_0050_name, description='Testing handling of circular repository dependencies to n levels.' ) + category_0060 = self.create_category( name=category_0060_name, description='Test 0060 - Workflow Features' ) + + def test_0010_create_repositories_from_0000_series( self ): + '''Create repository filtering_0000 if necessary.''' global repository_datatypes_count global running_standalone - category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' ) - category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' ) - category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' ) - category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' ) - category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' ) - category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' ) - category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' ) - category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + category = self.create_category( name=category_0000_name, description='' ) repository = self.get_or_create_repository( name='filtering_0000', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0000.id ) ) + category_id=self.security.encode_id( category.id ) ) if self.repository_is_new( repository ): - self.upload_file( repository, - filename='filtering/filtering_1.1.0.tar', - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded filtering 1.1.0 tarball.', - strings_displayed=[], - strings_not_displayed=[] ) - self.upload_file( repository, - filename='filtering/filtering_2.2.0.tar', - filepath=None, - valid_tools_only=True, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded filtering 2.2.0 tarball.', - strings_displayed=[], - strings_not_displayed=[] ) + running_standalone = True + self.upload_file( repository, + filename='filtering/filtering_1.1.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 1.1.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='filtering/filtering_2.2.0.tar', + filepath=None, + valid_tools_only=True, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded filtering 2.2.0 tarball.', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0015_create_repositories_from_0010_series( self ): + '''Create repository freebayes_0010.''' + category = self.create_category( name=category_0010_name, description='' ) repository = self.get_or_create_repository( name='freebayes_0010', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0010.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): - self.upload_file( repository, - filename='freebayes/freebayes.xml', - filepath=None, - valid_tools_only=False, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded freebayes.xml.', - strings_displayed=[], - strings_not_displayed=[] ) - self.upload_file( repository, - filename='freebayes/tool_data_table_conf.xml.sample', - filepath=None, - valid_tools_only=False, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded tool_data_table_conf.xml.sample', - strings_displayed=[], - strings_not_displayed=[] ) - self.upload_file( repository, - filename='freebayes/sam_fa_indices.loc.sample', - filepath=None, - valid_tools_only=False, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded sam_fa_indices.loc.sample', - strings_displayed=[], - strings_not_displayed=[] ) - self.upload_file( repository, - filename='freebayes/tool_dependencies.xml', - filepath=None, - valid_tools_only=False, - uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded tool_dependencies.xml', - strings_displayed=[], - strings_not_displayed=[] ) + self.upload_file( repository, + filename='freebayes/freebayes.xml', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded freebayes.xml.', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='freebayes/tool_data_table_conf.xml.sample', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded tool_data_table_conf.xml.sample', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='freebayes/sam_fa_indices.loc.sample', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded sam_fa_indices.loc.sample', + strings_displayed=[], + strings_not_displayed=[] ) + self.upload_file( repository, + filename='freebayes/tool_dependencies.xml', + filepath=None, + valid_tools_only=False, + uncompress_file=True, + remove_repo_files_not_in_tar=False, + commit_message='Uploaded tool_dependencies.xml', + strings_displayed=[], + strings_not_displayed=[] ) + + def test_0020_create_repositories_from_0020_series( self ): + '''Create repositories emboss_0020 and emboss_datatypes_0020 if necessary.''' + category = self.create_category( name=category_0020_name, description='' ) repository = self.get_or_create_repository( name='emboss_datatypes_0020', description="Galaxy applicable data formats used by Emboss tools.", long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0010.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, @@ -127,7 +168,7 @@ description='Galaxy wrappers for Emboss version 5.0.0 tools', long_description='Galaxy wrappers for Emboss version 5.0.0 tools', owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0020.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='emboss/emboss.tar', @@ -138,14 +179,17 @@ commit_message='Uploaded emboss.tar', strings_displayed=[], strings_not_displayed=[] ) + + def test_0025_create_repositories_from_0030_series( self ): + '''Create repositories emboss_0030, emboss_5_0030, emboss_6_0030, and emboss_datatypes_0030.''' + category = self.create_category( name=category_0030_name, description='' ) datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030', description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0030.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( datatypes_repository ): - running_standalone = True self.upload_file( datatypes_repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, @@ -160,7 +204,7 @@ description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0030.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( emboss_5_repository, filename='emboss/emboss.tar', @@ -178,7 +222,7 @@ description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0030.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( emboss_6_repository, filename='emboss/emboss.tar', @@ -196,7 +240,7 @@ description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0030.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( emboss_repository, filename='emboss/emboss.tar', @@ -212,68 +256,82 @@ self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path ) dependency_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip( emboss_6_repository ) ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path ) + + def test_0030_create_repositories_from_0040_series( self ): + '''Create repositories freebayes_0040 and filtering_0040.''' + category = self.create_category( name=category_0040_name, description='' ) repository = self.get_or_create_repository( name='freebayes_0040', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0040.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) + + if self.repository_is_new( repository ): self.upload_file( repository, - filename='freebayes/freebayes.tar', + filename='freebayes/freebayes.tar', filepath=None, valid_tools_only=True, uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded freebayes tarball.', + remove_repo_files_not_in_tar=False, + commit_message='Uploaded the tool tarball.', strings_displayed=[], strings_not_displayed=[] ) + repository = self.get_or_create_repository( name='filtering_0040', - description="Galaxy's filtering tool", - long_description="Long description of Galaxy's filtering tool", + description=filtering_repository_description, + long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0040.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, - filename='filtering/filtering_1.1.0.tar', + filename='filtering/filtering_1.1.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, - remove_repo_files_not_in_tar=False, - commit_message='Uploaded filtering 1.1.0 tarball.', + remove_repo_files_not_in_tar=False, + commit_message='Uploaded the tool tarball for filtering 1.1.0.', strings_displayed=[], strings_not_displayed=[] ) + repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name ) + filtering_repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_1340', additional_paths=[ 'filtering' ] ) + repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) ) + self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name ) - filtering_repository = self.test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name ) - repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] ) - dependency_tuple = ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) - self.create_repository_dependency( repository=filtering_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path ) - dependency_tuple = ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ) - self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ dependency_tuple ], filepath=repository_dependencies_path ) + repository_dependencies_path = self.generate_temp_path( 'test_1340', additional_paths=[ 'freebayes' ] ) + repository_tuple = ( self.url, repository.name, repository.user.username, self.get_repository_tip( repository ) ) + self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) + + def test_0035_create_repositories_from_0050_series( self ): + '''Create repositories emboss_0050, emboss_datatypes_0050, filtering_0050, freebayes_0050.''' + category = self.create_category( name=category_0050_name, description='' ) datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050', description="Datatypes for emboss", long_description="Long description of Emboss' datatypes", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0050.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( datatypes_repository ): emboss_repository = self.get_or_create_repository( name='emboss_0050', description="Galaxy's emboss tool", long_description="Long description of Galaxy's emboss tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0050.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) filtering_repository = self.get_or_create_repository( name='filtering_0050', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0050.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) freebayes_repository = self.get_or_create_repository( name='freebayes_0050', description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0050.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( datatypes_repository, filename='emboss/datatypes/datatypes_conf.xml', @@ -325,11 +383,14 @@ ( self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip( filtering_repository ) ), ( self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip( freebayes_repository ) ) ] self.create_repository_dependency( repository=freebayes_repository, repository_tuples=dependency_tuples, filepath=repository_dependencies_path ) + + def test_0035_create_repositories_from_0060_series( self ): + category = self.create_category( name=category_0060_name, description='' ) workflow_repository = self.get_or_create_repository( name='filtering_0060', description="Galaxy's filtering tool", long_description="Long description of Galaxy's filtering tool", owner=common.test_user_1_name, - category_id=self.security.encode_id( category_0060.id ), + category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( workflow_repository ): workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read() @@ -356,8 +417,8 @@ commit_message='Uploaded filtering 2.2.0 tarball.', strings_displayed=[], strings_not_displayed=[] ) - - def test_0010_install_all_missing_repositories( self ): + + def test_9900_install_all_missing_repositories( self ): '''Call the install_repository method to ensure that all required repositories are installed.''' global repository_datatypes_count global base_datatypes_count @@ -365,31 +426,24 @@ self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) base_datatypes_count = int( self.get_datatypes_count() ) - category_0000 = 'Test 0000 Basic Repository Features 1' - category_0001 = 'Test 0000 Basic Repository Features 2' - category_0010 = 'Test 0010 Repository With Tool Dependencies' - category_0020 = 'Test 0020 Basic Repository Dependencies' - category_0030 = 'Test 0030 Repository Dependency Revisions' - category_0040 = 'test_0040_repository_circular_dependencies' - category_0050 = 'test_0050_repository_n_level_circular_dependencies' - category_0060 = 'Test 0060 Workflow Features' - self.install_repository( 'filtering_0000', common.test_user_1_name, category_0000, strings_displayed=[] ) - self.install_repository( 'freebayes_0010', common.test_user_1_name, category_0010, strings_displayed=[] ) - self.install_repository( 'emboss_0020', common.test_user_1_name, category_0020, strings_displayed=[] ) - self.install_repository( 'emboss_5_0030', common.test_user_1_name, category_0030, strings_displayed=[] ) - self.install_repository( 'filtering_0040', common.test_user_1_name, category_0040, strings_displayed=[] ) - self.install_repository( 'freebayes_0050', common.test_user_1_name, category_0050, strings_displayed=[] ) - self.install_repository( 'filtering_0060', common.test_user_1_name, category_0060, strings_displayed=[] ) + self.install_repository( 'filtering_0000', common.test_user_1_name, category_0000_name, strings_displayed=[] ) + self.install_repository( 'freebayes_0010', common.test_user_1_name, category_0010_name, strings_displayed=[] ) + self.install_repository( 'emboss_0020', common.test_user_1_name, category_0020_name, strings_displayed=[] ) + self.install_repository( 'emboss_5_0030', common.test_user_1_name, category_0030_name, strings_displayed=[] ) + self.install_repository( 'freebayes_0050', common.test_user_1_name, category_0050_name, strings_displayed=[] ) + self.install_repository( 'filtering_0060', common.test_user_1_name, category_0060_name, strings_displayed=[] ) current_datatypes = int( self.get_datatypes_count() ) # If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes # have been added, otherwise verify that the count is unchanged. if running_standalone: - assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.' + message = 'Installing emboss did not add new datatypes.\nFound: %d\nExpected: %d' % \ + ( current_datatypes, base_datatypes_count + repository_datatypes_count ) + assert current_datatypes > base_datatypes_count, message else: assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.' - - def test_0015_reset_metadata_on_all_repositories( self ): + + def test_9905_reset_metadata_on_all_repositories( self ): '''Reset metadata on all repositories, then verify that it has not changed.''' repository_metadata = dict() repositories = self.test_db_util.get_all_installed_repositories( actually_installed=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: fix for progress-bar affecting the quota progress bar
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/809b87af4983/ Changeset: 809b87af4983 User: martenson Date: 2014-01-02 21:26:47 Summary: fix for progress-bar affecting the quota progress bar Affected #: 2 files diff -r dd922b9ef485ca3140bfd5b4dbc7625be6b6a6c4 -r 809b87af4983e40382d16f4f1a72896328d84f5e static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -635,7 +635,7 @@ }, updateProgress: function(){ this.progress += this.progressStep; - $('.progress-bar').width(Math.round(this.progress) + '%'); + $('.progress-bar-import').width(Math.round(this.progress) + '%'); txt_representation = Math.round(this.progress) + '% Complete'; $('.completion_span').text(txt_representation); }, @@ -648,7 +648,7 @@ 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" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + 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>'); diff -r dd922b9ef485ca3140bfd5b4dbc7625be6b6a6c4 -r 809b87af4983e40382d16f4f1a72896328d84f5e 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.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),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 i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});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 id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</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(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');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(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');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</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("")},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},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({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.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});this.modal.bindEvents(event);$(".peek").html(v.get("peek"));var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#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===""){r.stopPropagation();return}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")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},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();q.modal.enableButton("Import");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").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},download:function(q,u){var s=[];$("#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]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(t){q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("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:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#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();return this}});return{GalaxyApp:f}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),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 i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});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 id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</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(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');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(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');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</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("")},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},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});this.modal.bindEvents(event);$(".peek").html(v.get("peek"));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)}this.modal.show()},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=$(r.target.parentElement);s="td"}}if(t===""){r.stopPropagation();return}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#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=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("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});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();q.modal.enableButton("Import");return}var t=$.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)},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("")},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")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(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!==""},template_new_library: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("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){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();return this}});return{GalaxyApp:f}}); \ 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: martenson: generated CSS files for libraries
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd922b9ef485/ Changeset: dd922b9ef485 User: martenson Date: 2014-01-02 19:51:51 Summary: generated CSS files for libraries Affected #: 2 files diff -r b6bfb1ba68466a7726e5a2f03701d03c7da9de8f -r dd922b9ef485ca3140bfd5b4dbc7625be6b6a6c4 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -183,7 +183,7 @@ .btn{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}.btn:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .btn:hover,.btn:focus{color:#333;text-decoration:none} .btn:active,.btn.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)} -.btn.disabled,.btn[disabled],fieldset[disabled] .btn{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +.btn.disabled,.btn[disabled],fieldset[disabled] .btn{cursor:not-allowed;pointer-events:none;opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} .btn-default{color:#333;background-color:#f2f2f2;border-color:#bfbfbf}.btn-default:hover,.btn-default:focus,.btn-default:active,.btn-default.active,.open .dropdown-toggle.btn-default{color:#333;background-color:#dedede;border-color:#a1a1a1} .btn-default:active,.btn-default.active,.open .dropdown-toggle.btn-default{background-image:none} .btn-default.disabled,.btn-default[disabled],fieldset[disabled] .btn-default,.btn-default.disabled:hover,.btn-default[disabled]:hover,fieldset[disabled] .btn-default:hover,.btn-default.disabled:focus,.btn-default[disabled]:focus,fieldset[disabled] .btn-default:focus,.btn-default.disabled:active,.btn-default[disabled]:active,fieldset[disabled] .btn-default:active,.btn-default.disabled.active,.btn-default[disabled].active,fieldset[disabled] .btn-default.active{background-color:#f2f2f2;border-color:#bfbfbf} @@ -694,15 +694,15 @@ .well{min-height:20px;padding:19px;margin-bottom:20px;background-color:#eee;border:1px solid #ddd;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.05);box-shadow:inset 0 1px 1px rgba(0,0,0,0.05)}.well blockquote{border-color:#ddd;border-color:rgba(0,0,0,0.15)} .well-lg{padding:24px;border-radius:5px} .well-sm{padding:9px;border-radius:2px} -.close{float:right;font-size:18px;font-weight:bold;line-height:1;color:#000;text-shadow:0 1px 0 #fff;opacity:.2;filter:alpha(opacity=20)}.close:hover,.close:focus{color:#000;text-decoration:none;cursor:pointer;opacity:.5;filter:alpha(opacity=50)} +.close{float:right;font-size:18px;font-weight:bold;line-height:1;color:#000;text-shadow:0 1px 0 #fff;filter:alpha(opacity=20);opacity:.2;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=20);filter:alpha(opacity=20)}.close:hover,.close:focus{color:#000;text-decoration:none;cursor:pointer;filter:alpha(opacity=50);opacity:.5;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=50);filter:alpha(opacity=50)} button.close{padding:0;cursor:pointer;background:transparent;border:0;-webkit-appearance:none} .modal-open{overflow:hidden}body.modal-open,.modal-open .navbar-fixed-top,.modal-open .navbar-fixed-bottom{margin-right:15px} .modal{display:none;overflow:auto;overflow-y:scroll;position:fixed;top:0;right:0;bottom:0;left:0;z-index:1040}.modal.fade .modal-dialog{-webkit-transform:translate(0, -25%);-ms-transform:translate(0, -25%);transform:translate(0, -25%);-webkit-transition:-webkit-transform 0.3s ease-out;-moz-transition:-moz-transform 0.3s ease-out;-o-transition:-o-transform 0.3s ease-out;transition:transform 0.3s ease-out} .modal.in .modal-dialog{-webkit-transform:translate(0, 0);-ms-transform:translate(0, 0);transform:translate(0, 0)} .modal-dialog{margin-left:auto;margin-right:auto;width:auto;padding:10px;z-index:1050} .modal-content{position:relative;background-color:#fff;border:1px solid #999;border:1px solid rgba(0,0,0,0.2);border-radius:5px;-webkit-box-shadow:0 3px 9px rgba(0,0,0,0.5);box-shadow:0 3px 9px rgba(0,0,0,0.5);background-clip:padding-box;outline:none} -.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1030;background-color:#000}.modal-backdrop.fade{opacity:0;filter:alpha(opacity=0)} -.modal-backdrop.in{opacity:.5;filter:alpha(opacity=50)} +.modal-backdrop{position:fixed;top:0;right:0;bottom:0;left:0;z-index:1030;background-color:#000}.modal-backdrop.fade{filter:alpha(opacity=0);opacity:0;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=0);filter:alpha(opacity=0)} +.modal-backdrop.in{filter:alpha(opacity=50);opacity:.5;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=50);filter:alpha(opacity=50)} .modal-header{padding:15px;border-bottom:1px solid #bfbfbf;min-height:16.428571429px} .modal-header .close{margin-top:-2px} .modal-title{margin:0;line-height:1.428571429} @@ -714,7 +714,7 @@ .modal-footer .btn+.btn{margin-left:5px;margin-bottom:0} .modal-footer .btn-group .btn+.btn{margin-left:-1px} .modal-footer .btn-block+.btn-block{margin-left:0} -@media screen and (min-width:768px){.modal-dialog{left:50%;right:auto;width:600px;padding-top:30px;padding-bottom:30px} .modal-content{-webkit-box-shadow:0 5px 15px rgba(0,0,0,0.5);box-shadow:0 5px 15px rgba(0,0,0,0.5)}}.tooltip{position:absolute;z-index:1030;display:block;visibility:visible;font-size:11px;line-height:1.4;opacity:0;filter:alpha(opacity=0)}.tooltip.in{opacity:.9;filter:alpha(opacity=90)} +@media screen and (min-width:768px){.modal-dialog{left:50%;right:auto;width:600px;padding-top:30px;padding-bottom:30px} .modal-content{-webkit-box-shadow:0 5px 15px rgba(0,0,0,0.5);box-shadow:0 5px 15px rgba(0,0,0,0.5)}}.tooltip{position:absolute;z-index:1030;display:block;visibility:visible;font-size:11px;line-height:1.4;filter:alpha(opacity=0);opacity:0;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=0);filter:alpha(opacity=0)}.tooltip.in{filter:alpha(opacity=90);opacity:.9;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=90);filter:alpha(opacity=90)} .tooltip.top{margin-top:-3px;padding:5px 0} .tooltip.right{margin-left:3px;padding:0 5px} .tooltip.bottom{margin-top:3px;padding:5px 0} @@ -1263,7 +1263,60 @@ .upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit} .upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff} .upload-box .symbol{cursor:pointer} -.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} +.libraryRow{background-color:#ebd9b2} +.datasetHighlighted{background-color:#f9f9f9} +.libraryItemDeleted-True{font-style:italic} +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} +tr.light td{background-color:white;color:black} +tr.light:hover td{background-color:#f5f5f5;color:#8389a1} +tr.dark td{background-color:#8389a1;color:white} +tr.dark:hover td{background-color:#bbbfd0;color:white} +a.dark:hover{color:yellow} +a.dark{color:white} +th.button_heading{width:7em} +div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} +div.library_breadcrumb a:hover{color:green} +img.expanderIcon{padding-right:4px} +input.datasetCheckbox,li,ul{padding:0;margin:0} +.rowTitle{padding:2px} +ul{list-style:none} +.libraryTitle th{text-align:left} +pre.peek{background:white;color:black;width:100%;overflow:auto} +pre.peek th{color:white;background:#ebd9b2} +span.expandLink{padding-left:12px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat} +.folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat} +.folderRow span.rowIcon{float:left;margin-right:5px;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png)} +.libraryItem-error{margin-right:2px;padding:0 2px 0 2px;border:1px solid #dd1c15;background:#f9c7c5} +.libraryItem-queued{margin-right:2px;padding:0 2px 0 2px;border:1px solid #bfbfbf;background:#eee} +.libraryItem-running{margin-right:2px;padding:0 2px 0 2px;border:1px solid #aa6;background:#ffc} +.libraryItem-upload{margin-right:2px;padding:0 2px 0 2px;border:1px solid #1197c0;background:#a6e4f7} +.toast-title{font-weight:bold} +.toast-message{-ms-word-wrap:break-word;word-wrap:break-word}.toast-message a,.toast-message label{color:#fff} +.toast-message a:hover{color:#ccc;text-decoration:none} +.toast-close-button{position:relative;right:-0.3em;top:-0.3em;float:right;font-size:20px;font-weight:bold;color:#fff;-webkit-text-shadow:0 1px 0 #fff;text-shadow:0 1px 0 #fff;filter:alpha(opacity=80);opacity:.8;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=80);filter:alpha(opacity=80)}.toast-close-button:hover,.toast-close-button:focus{color:#000;text-decoration:none;cursor:pointer;filter:alpha(opacity=40);opacity:.4;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=40);filter:alpha(opacity=40)} +button.toast-close-button{padding:0;cursor:pointer;background:transparent;border:0;-webkit-appearance:none} +.toast-top-full-width{top:0;right:0;width:100%} +.toast-bottom-full-width{bottom:0;right:0;width:100%} +.toast-top-left{top:12px;left:12px} +.toast-top-right{top:12px;right:12px} +.toast-bottom-right{right:12px;bottom:12px} +.toast-bottom-left{bottom:12px;left:12px} +#toast-container{position:fixed;z-index:999999;}#toast-container *{-moz-box-sizing:border-box;-webkit-box-sizing:border-box;box-sizing:border-box} +#toast-container>div{margin:4em 0 6px;padding:15px 15px 15px 50px;width:300px;-moz-border-radius:3px 3px 3px 3px;-webkit-border-radius:3px 3px 3px 3px;border-radius:3px 3px 3px 3px;background-position:15px center;background-repeat:no-repeat;-moz-box-shadow:0 0 12px #999;-webkit-box-shadow:0 0 12px #999;box-shadow:0 0 12px #999;color:#fff;filter:alpha(opacity=80);opacity:.8;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=80);filter:alpha(opacity=80)} +#toast-container>:hover{-moz-box-shadow:0 0 12px #000;-webkit-box-shadow:0 0 12px #000;box-shadow:0 0 12px #000;opacity:1;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=100);filter:alpha(opacity=100);cursor:pointer} +#toast-container>.toast-info{background-image:url("data:image/png;base64,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") !important} +#toast-container>.toast-error{background-image:url("data:image/png;base64,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") !important} +#toast-container>.toast-success{background-image:url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAAYCAYAAADgdz34AAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAAADsSURBVEhLY2AYBfQMgf///3P8+/evAIgvA/FsIF+BavYDDWMBGroaSMMBiE8VC7AZDrIFaMFnii3AZTjUgsUUWUDA8OdAH6iQbQEhw4HyGsPEcKBXBIC4ARhex4G4BsjmweU1soIFaGg/WtoFZRIZdEvIMhxkCCjXIVsATV6gFGACs4Rsw0EGgIIH3QJYJgHSARQZDrWAB+jawzgs+Q2UO49D7jnRSRGoEFRILcdmEMWGI0cm0JJ2QpYA1RDvcmzJEWhABhD/pqrL0S0CWuABKgnRki9lLseS7g2AlqwHWQSKH4oKLrILpRGhEQCw2LiRUIa4lwAAAABJRU5ErkJggg==") !important} +#toast-container>.toast-warning{background-image:url("data:image/png;base64,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") !important} +#toast-container.toast-top-full-width>div,#toast-container.toast-bottom-full-width>div{width:96%;margin:auto} +.toast{background-color:#030303} +.toast-success{background-color:#51a351} +.toast-error{background-color:#bd362f} +.toast-info{background-color:#2f96b4} +.toast-warning{background-color:#f89406} +@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} .clear:after{clear:both} @@ -1356,7 +1409,7 @@ 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)} -input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus,input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{color:#333;background-color:#dedede;border-color:#a1a1a1} input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{background-image:none} input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button,input[type="submit"].disabled:hover,button.disabled:hover,input[type="submit"][disabled]:hover,button[disabled]:hover,fieldset[disabled] input[type="submit"]:hover,fieldset[disabled] button:hover,input[type="submit"].disabled:focus,button.disabled:focus,input[type="submit"][disabled]:focus,button[disabled]:focus,fieldset[disabled] input[type="submit"]:focus,fieldset[disabled] button:focus,input[type="submit"].disabled:active,button.disabled:active,input[type="submit"][disabled]:active,button[disabled]:active,fieldset[disabled] input[type="submit"]:active,fieldset[disabled] button:active,input[type="submit"].disabled.active,button.disabled.active,input[type="submit"][disabled].active,button[disabled].active,fieldset[disabled] input[type="submit"].active,fieldset[disabled] button.active{background-color:#f2f2f2;border-color:#bfbfbf} @@ -1457,14 +1510,14 @@ 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}button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} button:hover,button:focus{color:#333;text-decoration:none} button: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)} -button.disabled,button[disabled],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +button.disabled,button[disabled],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} button:hover,button:focus,button:active,button.active,.open .dropdown-togglebutton{color:#333;background-color:#dedede;border-color:#a1a1a1} button:active,button.active,.open .dropdown-togglebutton{background-image:none} button.disabled,button[disabled],fieldset[disabled] button,button.disabled:hover,button[disabled]:hover,fieldset[disabled] button:hover,button.disabled:focus,button[disabled]:focus,fieldset[disabled] button:focus,button.disabled:active,button[disabled]:active,fieldset[disabled] button:active,button.disabled.active,button[disabled].active,fieldset[disabled] button.active{background-color:#f2f2f2;border-color:#bfbfbf} .action-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}.action-button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .action-button:hover,.action-button:focus{color:#333;text-decoration:none} .action-button:active,.action-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)} -.action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +.action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button{cursor:not-allowed;pointer-events:none;opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} .action-button:hover,.action-button:focus,.action-button:active,.action-button.active,.open .dropdown-toggle.action-button{color:#333;background-color:#dedede;border-color:#a1a1a1} .action-button:active,.action-button.active,.open .dropdown-toggle.action-button{background-image:none} .action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button,.action-button.disabled:hover,.action-button[disabled]:hover,fieldset[disabled] .action-button:hover,.action-button.disabled:focus,.action-button[disabled]:focus,fieldset[disabled] .action-button:focus,.action-button.disabled:active,.action-button[disabled]:active,fieldset[disabled] .action-button:active,.action-button.disabled.active,.action-button[disabled].active,fieldset[disabled] .action-button.active{background-color:#f2f2f2;border-color:#bfbfbf} @@ -1474,7 +1527,7 @@ .menubutton{padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;border:1px solid transparent;border-radius:3px;white-space:nowrap;user-select:none;white-space:normal;color:#333;background-color:#f2f2f2;border-color:#bfbfbf;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .menubutton:hover,.menubutton:focus{color:#333;text-decoration:none} .menubutton:active,.menubutton.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)} -.menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +.menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton{cursor:not-allowed;pointer-events:none;opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} .menubutton:hover,.menubutton:focus,.menubutton:active,.menubutton.active,.open .dropdown-toggle.menubutton{color:#333;background-color:#dedede;border-color:#a1a1a1} .menubutton:active,.menubutton.active,.open .dropdown-toggle.menubutton{background-image:none} .menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton,.menubutton.disabled:hover,.menubutton[disabled]:hover,fieldset[disabled] .menubutton:hover,.menubutton.disabled:focus,.menubutton[disabled]:focus,fieldset[disabled] .menubutton:focus,.menubutton.disabled:active,.menubutton[disabled]:active,fieldset[disabled] .menubutton:active,.menubutton.disabled.active,.menubutton[disabled].active,fieldset[disabled] .menubutton.active{background-color:#f2f2f2;border-color:#bfbfbf} @@ -1636,7 +1689,7 @@ #content_table td{text-align:right;white-space:nowrap;padding:2px 10px} #content_table td.stringalign{text-align:left} .toolMenuAndView .toolForm{float:left;background-color:white;margin:10px} -.text-and-autocomplete-select{background:none;position:relative;padding-right:18px}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;margin-left:2px;vertical-align:middle;border-top:4px solid #000;border-right:4px solid transparent;border-left:4px solid transparent;border-bottom:0 dotted;content:"";opacity:80;filter:alpha(opacity=8000)}.btn-default .text-and-autocomplete-select:after{border-top-color:#333} +.text-and-autocomplete-select{background:none;position:relative;padding-right:18px}.text-and-autocomplete-select:after{margin-top:6px;position:absolute;top:2px;right:6px;width:10px;height:10px;display:inline-block;width:0;height:0;margin-left:2px;vertical-align:middle;border-top:4px solid #000;border-right:4px solid transparent;border-left:4px solid transparent;border-bottom:0 dotted;content:"";filter:alpha(opacity=8000);opacity:80;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=8000);filter:alpha(opacity=8000)}.btn-default .text-and-autocomplete-select:after{border-top-color:#333} .btn-primary .text-and-autocomplete-select:after,.btn-success .text-and-autocomplete-select:after,.btn-warning .text-and-autocomplete-select:after,.btn-danger .text-and-autocomplete-select:after,.btn-info .text-and-autocomplete-select:after{border-top-color:#fff} .icon-button.general-question{background:url(question-octagon-frame.png) no-repeat;float:right;margin-top:3px;margin-right:4px} .icon-button.tag-question{background:url(question-balloon.png) no-repeat;float:right;margin-top:3px;margin-right:4px} diff -r b6bfb1ba68466a7726e5a2f03701d03c7da9de8f -r dd922b9ef485ca3140bfd5b4dbc7625be6b6a6c4 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -6,6 +6,15 @@ 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} +tr.light td{background-color:white;color:black} +tr.light:hover td{background-color:#f5f5f5;color:#8389a1} +tr.dark td{background-color:#8389a1;color:white} +tr.dark:hover td{background-color:#bbbfd0;color:white} +a.dark:hover{color:yellow} +a.dark{color:white} +th.button_heading{width:7em} +div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} +div.library_breadcrumb a:hover{color:green} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: forgot the packed versions of JS
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b6bfb1ba6846/ Changeset: b6bfb1ba6846 User: martenson Date: 2014-01-02 19:38:04 Summary: forgot the packed versions of JS Affected #: 2 files diff -r c98b209d93d15551ba1ae26c7aa95babf7b8be33 -r b6bfb1ba68466a7726e5a2f03701d03c7da9de8f 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.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),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 i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});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 id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</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(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');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(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');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</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("")},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},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});this.modal.bindEvents(event,this);$(".peek").html(v.get("peek"));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)}this.modal.show()},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=$(r.target.parentElement);s="td"}}if(t===""){r.stopPropagation();return}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#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=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("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});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();q.modal.enableButton("Import");return}var t=$.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;$(".progress-bar").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},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" 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("")},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")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(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!==""},template_new_library: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("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){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();return this}});return{GalaxyApp:f}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),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 i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});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 id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</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(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');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(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');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</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("")},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},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({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.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});this.modal.bindEvents(event);$(".peek").html(v.get("peek"));var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#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===""){r.stopPropagation();return}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")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},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();q.modal.enableButton("Import");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").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},download:function(q,u){var s=[];$("#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]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(t){q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("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:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#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();return this}});return{GalaxyApp:f}}); \ No newline at end of file diff -r c98b209d93d15551ba1ae26c7aa95babf7b8be33 -r b6bfb1ba68466a7726e5a2f03701d03c7da9de8f static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){b.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(c,b){$(document).off("keyup",function(d){if(d.keyCode==27){b.hide()}});$("html").off("click",function(d){b.hide()});$(".modal-content").off("click",function(d){d.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);if(this.options.height){this.$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.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}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){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){self.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(b){$(document).off("keyup",function(c){if(c.keyCode==27){self.hide()}});$("html").off("click",function(c){self.hide()});$(".modal-content").off("click",function(c){c.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);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.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,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.$el.remove()}this.setElement(this.template(this.options.title));this.$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.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){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">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: better context handling in library javascript
by commits-noreply＠bitbucket.org 03 Jan '14

03 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c98b209d93d1/ Changeset: c98b209d93d1 User: martenson Date: 2014-01-02 19:31:24 Summary: better context handling in library javascript Affected #: 2 files diff -r 72027582a03ddee4ba050d1ffc1bdf8991b1eda4 -r c98b209d93d15551ba1ae26c7aa95babf7b8be33 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -415,7 +415,7 @@ 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data } }); - this.modal.bindEvents(event, this); + this.modal.bindEvents(event); $(".peek").html(item.get("peek")); var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); diff -r 72027582a03ddee4ba050d1ffc1bdf8991b1eda4 -r c98b209d93d15551ba1ae26c7aa95babf7b8be33 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -38,7 +38,7 @@ }) // bind the 'click anywhere' to hide() function... $('html').on('click', function(event){ - that.hide(); + self.hide(); }) // ...but don't hide if the click is on modal content $('.modal-content').on('click', function(event){ @@ -47,14 +47,14 @@ }, // unbind the click-to-hide function - unbindEvents: function(event, that){ + unbindEvents: function(event){ // bind the ESC key to hide() function $(document).off('keyup', function(event){ - if (event.keyCode == 27) { that.hide(); } + if (event.keyCode == 27) { self.hide(); } }) // unbind the 'click anywhere' to hide() function... $('html').off('click', function(event){ - that.hide(); + self.hide(); }) $('.modal-content').off('click', function(event){ event.stopPropagation(); 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 02 Jan '14

02 Jan '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72027582a03d/ Changeset: 72027582a03d User: inithello Date: 2014-01-02 18:00:02 Summary: Account for the behavior of mutable types used as default method parameters. Affected #: 1 file diff -r 5563247528c8b1ac5f3c837bdd492c3b49c4b5e7 -r 72027582a03ddee4ba050d1ffc1bdf8991b1eda4 test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- a/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -175,5 +175,7 @@ preview_strings_displayed=preview_strings_displayed, post_submit_strings_displayed=[ repository.name, repository.name, 'New' ], includes_tools_for_display_in_tool_panel=True ) - repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) - self.display_installed_repository_manage_page( repository, strings_not_displayed=[ 'Repository dependencies' ] ) + installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) + self.display_installed_repository_manage_page( installed_repository=installed_repository, + strings_displayed=[], + strings_not_displayed=[ 'Repository dependencies' ] ) https://bitbucket.org/galaxy/galaxy-central/commits/dbf3724c953b/ Changeset: dbf3724c953b Branch: extended_metadata User: inithello Date: 2014-01-02 18:11:11 Summary: Close branch extended_metadata. Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/0fd0bfad4765/ Changeset: 0fd0bfad4765 Branch: page-api User: inithello Date: 2014-01-02 18:11:49 Summary: Close branch page-api. Affected #: 0 files 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: removed manual setting of ‘200’ response code because it causes httpexception module errors
by commits-noreply＠bitbucket.org 02 Jan '14

02 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5563247528c8/ Changeset: 5563247528c8 User: martenson Date: 2014-01-02 17:25:02 Summary: removed manual setting of ‘200’ response code because it causes httpexception module errors Affected #: 1 file diff -r 2e54fd51118797935c299c5f34b37ac48f780900 -r 5563247528c8b1ac5f3c837bdd492c3b49c4b5e7 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -57,7 +57,6 @@ rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) - trans.response.status = 200 return rval @web.expose @@ -225,14 +224,12 @@ archive = util.streamball.ZipBall(tmpf, tmpd) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() - trans.response.status = 200 return archive.stream else: trans.response.set_content_type( "application/x-tar" ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() - trans.response.status = 200 return archive.stream elif format == 'uncompressed': if len(lddas) != 1: @@ -248,7 +245,6 @@ fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: - trans.response.status = 200 return open( single_dataset.file_name ) except: trans.response.status = 500 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Update functional test's string checks to account for changes in the way grids are rendered.
by commits-noreply＠bitbucket.org 02 Jan '14

02 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2e54fd511187/ Changeset: 2e54fd511187 User: inithello Date: 2014-01-02 15:12:43 Summary: Update functional test's string checks to account for changes in the way grids are rendered. Affected #: 1 file diff -r 593fce2b6335865d1225cdd23cfaf3e388ab1140 -r 2e54fd51118797935c299c5f34b37ac48f780900 test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -108,12 +108,12 @@ '''Attempt to install the already installed filtering repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) # The page displayed after installation is the ajaxian "Montior installing tool shed repositories" page. Since the filter - # repository was already installed, nothing will be in the process of being installed, so the grid will display 'No Items'. - post_submit_strings_displayed = [ 'No Items' ] + # repository was already installed, nothing will be in the process of being installed, so the grid will not display 'filtering_0000'. + post_submit_strings_not_displayed = [ 'filtering_0000' ] self.install_repository( 'filtering_0000', common.test_user_1_name, 'Test 0000 Basic Repository Features 1', - post_submit_strings_displayed=post_submit_strings_displayed ) + post_submit_strings_not_displayed=post_submit_strings_not_displayed ) strings_displayed = [ 'filtering_0000', "Galaxy's filtering tool", 'user1', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix update manager functional test.
by commits-noreply＠bitbucket.org 02 Jan '14

02 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/593fce2b6335/ Changeset: 593fce2b6335 User: inithello Date: 2014-01-02 15:01:46 Summary: Fix update manager functional test. Affected #: 1 file diff -r 8e1a2e81499c780acf08c3f195717a3523f4e55d -r 593fce2b6335865d1225cdd23cfaf3e388ab1140 test/tool_shed/functional/test_1410_update_manager.py --- a/test/tool_shed/functional/test_1410_update_manager.py +++ b/test/tool_shed/functional/test_1410_update_manager.py @@ -123,9 +123,8 @@ self.galaxy_login( email=common.admin_email, username=common.admin_username ) repository = self.test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.update_tool_shed_status() - ok_icon = '/static/june_2007_style/blue/ok_small.png' - ok_title = 'This is the latest installable revision of this repository' + ok_title = r'title=\"Updates are available in the Tool Shed for this revision\"' updates_icon = '/static/images/icon_warning_sml.gif' - strings_displayed = [ '<img src="%s" class="icon-button" title="%s"/><img src="%s' % ( ok_icon, ok_title, updates_icon ) ] + strings_displayed = [ ok_title, updates_icon ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits January 2014