December 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: inithello: Functional tests for n levels of circular repository dependencies.
by Bitbucket 11 Dec '12

11 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/376a3714dc15/ changeset: 376a3714dc15 user: inithello date: 2012-12-11 20:29:28 summary: Functional tests for n levels of circular repository dependencies. affected #: 7 files diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -10,6 +10,8 @@ new_repository_dependencies_xml = '''<?xml version="1.0"?><repositories${description}> - <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" /> +${dependency_lines} </repositories> ''' + +new_repository_dependencies_line = ''' <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" />''' \ No newline at end of file diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -22,12 +22,6 @@ self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None ) self.tool_shed_test_file = None self.shed_tools_dict = {} - self.keepOutdir = os.environ.get( 'TOOL_SHED_TEST_SAVE', '' ) - if self.keepOutdir > '': - try: - os.makedirs( self.keepOutdir ) - except: - pass self.home() def browse_repository( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) @@ -50,9 +44,11 @@ url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def check_repository_dependency( self, repository, depends_on_repository, depends_on_changeset_revision ): + def check_repository_dependency( self, repository, depends_on_repository, depends_on_changeset_revision, changeset_revision=None ): + if changeset_revision is None: + changeset_revision = self.get_repository_tip( repository ) strings_displayed = [ depends_on_repository.name, depends_on_repository.user.username, depends_on_changeset_revision ] - self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed ) def check_repository_metadata( self, repository, tip_only=True ): if tip_only: assert self.tip_has_metadata( repository ) and len( self.get_repository_metadata_revisions( repository ) ) == 1, \ @@ -216,21 +212,24 @@ else: string = string.replace( character, replacement ) return string - def generate_repository_dependency_xml( self, repository, xml_filename, dependency_description='' ): + def generate_repository_dependency_xml( self, repositories, xml_filename, dependency_description='' ): file_path = os.path.split( xml_filename )[0] if not os.path.exists( file_path ): os.makedirs( file_path ) - changeset_revision = self.get_repository_tip( repository ) + dependency_entries = [] + for repository in repositories: + changeset_revision = self.get_repository_tip( repository ) + template = string.Template( common.new_repository_dependencies_line ) + dependency_entries.append( template.safe_substitute( toolshed_url=self.url, + owner=repository.user.username, + repository_name=repository.name, + changeset_revision=changeset_revision ) ) if dependency_description: description = ' description="%s"' % dependency_description else: description = dependency_description template_parser = string.Template( common.new_repository_dependencies_xml ) - repository_dependency_xml = template_parser.safe_substitute( toolshed_url=self.url, - owner=repository.user.username, - repository_name=repository.name, - changeset_revision=changeset_revision, - description=description ) + repository_dependency_xml = template_parser.safe_substitute( description=description, dependency_lines='\n'.join( dependency_entries ) ) # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def generate_temp_path( self, test_script_path, additional_paths=[] ): diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -55,7 +55,7 @@ repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] ) - self.generate_repository_dependency_xml( datatypes_repository, + self.generate_repository_dependency_xml( [ datatypes_repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) self.upload_file( repository, 'repository_dependencies.xml', diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -73,7 +73,7 @@ '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) - self.generate_repository_dependency_xml( datatypes_repository, + self.generate_repository_dependency_xml( [ datatypes_repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) self.upload_file( emboss_5_repository, @@ -93,7 +93,7 @@ emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) - self.generate_repository_dependency_xml( emboss_5_repository, + self.generate_repository_dependency_xml( [ emboss_5_repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Emboss requires the Emboss 5 repository.' ) self.upload_file( emboss_repository, @@ -105,7 +105,7 @@ emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '6' ] ) - self.generate_repository_dependency_xml( emboss_6_repository, + self.generate_repository_dependency_xml( [ emboss_6_repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Emboss requires the Emboss 6 repository.' ) self.upload_file( emboss_repository, diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -63,7 +63,7 @@ repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'filtering' ] ) - self.generate_repository_dependency_xml( repository, + self.generate_repository_dependency_xml( [ repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Filtering 1.1.0 depends on the freebayes repository.' ) self.upload_file( filtering_repository, @@ -79,7 +79,7 @@ repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] ) - self.generate_repository_dependency_xml( repository, + self.generate_repository_dependency_xml( [ repository ], self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Freebayes depends on the filtering repository.' ) self.upload_file( freebayes_repository, @@ -95,8 +95,5 @@ # Freebayes revision 0 -> filtering revision 1. # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. # In this case, the displayed dependency will specify the tip revision, but this will not always be the case. - filtering_strings_displayed = [ freebayes_repository_name, common.test_user_1_name, self.get_repository_tip( freebayes_repository ) ] - freebayes_strings_displayed = [ filtering_repository_name, common.test_user_1_name, self.get_repository_tip( filtering_repository ) ] - self.display_manage_repository_page( filtering_repository, strings_displayed=filtering_strings_displayed ) - self.display_manage_repository_page( freebayes_repository, strings_displayed=freebayes_strings_displayed ) - + self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip( freebayes_repository ) ) + self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip( filtering_repository ) ) diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/functional/test_0050_circular_n_levels.py --- /dev/null +++ b/test/tool_shed/functional/test_0050_circular_n_levels.py @@ -0,0 +1,129 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role + +emboss_datatypes_repository_name = 'emboss_datatypes_0050' +emboss_datatypes_repository_description = "Datatypes for emboss" +emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes" + +emboss_repository_name = 'emboss_0050' +emboss_repository_description = "Galaxy's emboss tool" +emboss_repository_long_description = "Long description of Galaxy's emboss tool" + +freebayes_repository_name = 'freebayes_0050' +freebayes_repository_description = "Galaxy's freebayes tool" +freebayes_repository_long_description = "Long description of Galaxy's freebayes tool" + +filtering_repository_name = 'filtering_0050' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +default_category = 'test_0050_repository_n_level_circular_dependencies' +default_category_description = 'Testing handling of circular repository dependencies to n levels.' + +class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ): + '''Verify that the code correctly handles circular dependencies down to n levels.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = 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 = get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( default_category, default_category_description ) + def test_0010_create_emboss_datatypes_repository( self ): + '''Create and populate emboss_datatypes_0050.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.create_repository( emboss_datatypes_repository_name, + emboss_datatypes_repository_description, + repository_long_description=emboss_datatypes_repository_long_description, + categories=[ default_category ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'emboss/datatypes/datatypes_conf.xml', + strings_displayed=[], + commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_create_emboss_repository( self ): + '''Create and populate emboss_0050.''' + self.create_repository( emboss_repository_name, + emboss_repository_description, + repository_long_description=emboss_repository_long_description, + categories=[ default_category ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'emboss/emboss.tar', + strings_displayed=[], + commit_message='Uploaded tool tarball.' ) + datatypes_repository = get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'emboss' ] ) + self.generate_repository_dependency_xml( [ datatypes_repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Emboss depends on the emboss_datatypes repository.' ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on emboss_datatypes.' ) + def test_0020_create_filtering_repository( self ): + '''Create and populate filtering_0050.''' + self.create_repository( filtering_repository_name, + filtering_repository_description, + repository_long_description=filtering_repository_long_description, + categories=[ default_category ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'filtering' ] ) + self.generate_repository_dependency_xml( [ emboss_repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Filtering depends on the emboss repository.' ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on emboss.' ) + def test_0025_create_freebayes_repository( self ): + '''Create and populate freebayes_0050.''' + self.create_repository( freebayes_repository_name, + freebayes_repository_description, + repository_long_description=freebayes_repository_long_description, + categories=[ default_category ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + emboss_datatypes_repository = get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] ) + previous_tip = self.get_repository_tip( repository ) + self.generate_repository_dependency_xml( [ emboss_datatypes_repository, emboss_repository, filtering_repository, repository ], + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Freebayes depends on the filtering repository.' ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on filtering.' ) + self.display_manage_repository_page( repository, strings_not_displayed=[ previous_tip ] ) + def test_0030_verify_repository_dependencies( self ): + '''Verify that the generated dependency circle does not cause an infinite loop.''' + emboss_datatypes_repository = get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name ) + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + filtering_repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + for repository in [ emboss_datatypes_repository, emboss_repository, filtering_repository ]: + self.check_repository_dependency( freebayes_repository, repository, self.get_repository_tip( repository ) ) + self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'Freebayes depends on the filtering repository.' ] ) diff -r a7ea7728829dcc5395606bd402805d2ac972d6c6 -r 376a3714dc1510d3a1405575fc2667b68a28a695 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -67,9 +67,7 @@ # ---- Configuration ------------------------------------------------------ tool_shed_test_host = os.environ.get( 'TOOL_SHED_TEST_HOST', default_tool_shed_test_host ) tool_shed_test_port = os.environ.get( 'TOOL_SHED_TEST_PORT', None ) - tool_shed_test_save = os.environ.get( 'TOOL_SHED_TEST_SAVE', None ) tool_path = os.environ.get( 'TOOL_SHED_TEST_TOOL_PATH', 'tools' ) - start_server = 'TOOL_SHED_TEST_EXTERNAL' not in os.environ if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_tool_shed_locales tool_shed_test_file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', default_tool_shed_test_file_dir ) @@ -84,57 +82,27 @@ tool_dependency_dir = os.environ.get( 'TOOL_SHED_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'TOOL_SHED_USE_DISTRIBUTED_OBJECT_STORE', False ) - if start_server: - if not os.path.isdir( tool_shed_test_tmp_dir ): - os.mkdir( tool_shed_test_tmp_dir ) - psu_production = False - tool_shed_test_proxy_port = None - if 'TOOL_SHED_TEST_PSU_PRODUCTION' in os.environ: - if not tool_shed_test_port: - raise Exception( 'Set TOOL_SHED_TEST_PORT to the port to which the proxy server will proxy' ) - tool_shed_test_proxy_port = os.environ.get( 'TOOL_SHED_TEST_PROXY_PORT', None ) - if not tool_shed_test_proxy_port: - raise Exception( 'Set TOOL_SHED_TEST_PROXY_PORT to the port on which the proxy server is listening' ) - base_file_path = os.environ.get( 'TOOL_SHED_TEST_BASE_FILE_PATH', None ) - if not base_file_path: - raise Exception( 'Set TOOL_SHED_TEST_BASE_FILE_PATH to the directory which will contain the dataset files directory' ) - base_new_file_path = os.environ.get( 'TOOL_SHED_TEST_BASE_NEW_FILE_PATH', None ) - if not base_new_file_path: - raise Exception( 'Set TOOL_SHED_TEST_BASE_NEW_FILE_PATH to the directory which will contain the temporary directory' ) - database_connection = os.environ.get( 'TOOL_SHED_TEST_DBURI', None ) - if not database_connection: - raise Exception( 'Set TOOL_SHED_TEST_DBURI to the URI of the database to be used for tests' ) - nginx_upload_store = os.environ.get( 'TOOL_SHED_TEST_NGINX_UPLOAD_STORE', None ) - if not nginx_upload_store: - raise Exception( 'Set TOOL_SHED_TEST_NGINX_UPLOAD_STORE to the path where the nginx upload module places uploaded files' ) - file_path = tempfile.mkdtemp( dir=base_file_path ) - new_repos_path = tempfile.mkdtemp( dir=base_new_file_path ) - hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - kwargs = dict( database_engine_option_pool_size = '10', - database_engine_option_max_overflow = '20', - database_engine_option_strategy = 'threadlocal', - static_enabled = 'False', - debug = 'False' ) - psu_production = True - else: - if 'TOOL_SHED_TEST_DBPATH' in os.environ: - db_path = os.environ[ 'TOOL_SHED_TEST_DBPATH' ] - else: - tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - db_path = os.path.join( tempdir, 'database' ) - file_path = os.path.join( db_path, 'files' ) - hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) - if 'TOOL_SHED_TEST_DBURI' in os.environ: - database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] - else: - database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) - kwargs = {} - for dir in [ tool_shed_test_tmp_dir ]: - try: - os.makedirs( dir ) - except OSError: - pass + if not os.path.isdir( tool_shed_test_tmp_dir ): + os.mkdir( tool_shed_test_tmp_dir ) + tool_shed_test_proxy_port = None + if 'TOOL_SHED_TEST_DBPATH' in os.environ: + db_path = os.environ[ 'TOOL_SHED_TEST_DBPATH' ] + else: + tempdir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + db_path = os.path.join( tempdir, 'database' ) + file_path = os.path.join( db_path, 'files' ) + hgweb_config_file_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir ) + if 'TOOL_SHED_TEST_DBURI' in os.environ: + database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] + else: + database_connection = 'sqlite:///' + os.path.join( db_path, 'universe.sqlite' ) + kwargs = {} + for dir in [ tool_shed_test_tmp_dir ]: + try: + os.makedirs( dir ) + except OSError: + pass print "Database connection:", database_connection @@ -145,89 +113,78 @@ # ---- Build Application -------------------------------------------------- app = None - if start_server: - global_conf = { '__file__' : 'community_wsgi.ini.sample' } - if psu_production: - global_conf = None - if not database_connection.startswith( 'sqlite://' ): - kwargs[ 'database_engine_option_max_overflow' ] = '20' - if tool_dependency_dir is not None: - kwargs[ 'tool_dependency_dir' ] = tool_dependency_dir - if use_distributed_object_store: - kwargs[ 'object_store' ] = 'distributed' - kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' + global_conf = { '__file__' : 'community_wsgi.ini.sample' } + if not database_connection.startswith( 'sqlite://' ): + kwargs[ 'database_engine_option_max_overflow' ] = '20' + if tool_dependency_dir is not None: + kwargs[ 'tool_dependency_dir' ] = tool_dependency_dir + if use_distributed_object_store: + kwargs[ 'object_store' ] = 'distributed' + kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' - app = UniverseApplication( job_queue_workers = 5, - id_secret = 'changethisinproductiontoo', - template_path = 'templates', - database_connection = database_connection, - database_engine_option_pool_size = '10', - file_path = file_path, - new_file_path = new_repos_path, - tool_path=tool_path, - datatype_converters_config_file = 'datatype_converters_conf.xml.sample', - tool_parse_help = False, - tool_data_table_config_path = tool_data_table_config_path, - shed_tool_data_table_config = shed_tool_data_table_config, - log_destination = "stdout", - use_heartbeat = False, - allow_user_creation = True, - allow_user_deletion = True, - admin_users = 'test(a)bx.psu.edu', - global_conf = global_conf, - running_functional_tests = True, - hgweb_config_dir = hgweb_config_dir, - **kwargs ) + app = UniverseApplication( job_queue_workers = 5, + id_secret = 'changethisinproductiontoo', + template_path = 'templates', + database_connection = database_connection, + database_engine_option_pool_size = '10', + file_path = file_path, + new_file_path = new_repos_path, + tool_path=tool_path, + datatype_converters_config_file = 'datatype_converters_conf.xml.sample', + tool_parse_help = False, + tool_data_table_config_path = tool_data_table_config_path, + shed_tool_data_table_config = shed_tool_data_table_config, + log_destination = "stdout", + use_heartbeat = False, + allow_user_creation = True, + allow_user_deletion = True, + admin_users = 'test(a)bx.psu.edu', + global_conf = global_conf, + running_functional_tests = True, + hgweb_config_dir = hgweb_config_dir, + **kwargs ) - log.info( "Embedded Universe application started" ) + log.info( "Embedded Universe application started" ) # ---- Run webserver ------------------------------------------------------ server = None - if start_server: - webapp = buildapp.app_factory( dict( database_file=database_connection ), - use_translogger=False, - static_enabled=False, - app=app ) - if tool_shed_test_port is not None: - server = httpserver.serve( webapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False ) + webapp = buildapp.app_factory( dict( database_file=database_connection ), + use_translogger=False, + static_enabled=False, + app=app ) + if tool_shed_test_port is not None: + server = httpserver.serve( webapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False ) + else: + random.seed() + for i in range( 0, 9 ): + try: + tool_shed_test_port = str( random.randint( default_tool_shed_test_port_min, default_tool_shed_test_port_max ) ) + log.debug( "Attempting to serve app on randomly chosen port: %s" % tool_shed_test_port ) + server = httpserver.serve( webapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False ) + break + except socket.error, e: + if e[0] == 98: + continue + raise else: - random.seed() - for i in range( 0, 9 ): - try: - tool_shed_test_port = str( random.randint( default_tool_shed_test_port_min, default_tool_shed_test_port_max ) ) - log.debug( "Attempting to serve app on randomly chosen port: %s" % tool_shed_test_port ) - server = httpserver.serve( webapp, host=tool_shed_test_host, port=tool_shed_test_port, start_loop=False ) - break - except socket.error, e: - if e[0] == 98: - continue - raise - else: - raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % ( default_tool_shed_test_port_min, default_tool_shed_test_port_max ) ) - if tool_shed_test_proxy_port: - os.environ[ 'TOOL_SHED_TEST_PORT' ] = tool_shed_test_proxy_port - else: - os.environ[ 'TOOL_SHED_TEST_PORT' ] = tool_shed_test_port - t = threading.Thread( target=server.serve_forever ) - t.start() - # Test if the server is up - for i in range( 10 ): - # Directly test the app, not the proxy. - conn = httplib.HTTPConnection( tool_shed_test_host, tool_shed_test_port ) - conn.request( "GET", "/" ) - if conn.getresponse().status == 200: - break - time.sleep( 0.1 ) - else: - raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) - # Test if the proxy server is up. - if psu_production: - # Directly test the app, not the proxy. - conn = httplib.HTTPConnection( tool_shed_test_host, tool_shed_test_proxy_port ) - conn.request( "GET", "/" ) - if not conn.getresponse().status == 200: - raise Exception( "Test HTTP proxy server did not return '200 OK'" ) - log.info( "Embedded web server started" ) + raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % ( default_tool_shed_test_port_min, default_tool_shed_test_port_max ) ) + if tool_shed_test_proxy_port: + os.environ[ 'TOOL_SHED_TEST_PORT' ] = tool_shed_test_proxy_port + else: + os.environ[ 'TOOL_SHED_TEST_PORT' ] = tool_shed_test_port + t = threading.Thread( target=server.serve_forever ) + t.start() + # Test if the server is up + for i in range( 10 ): + # Directly test the app, not the proxy. + conn = httplib.HTTPConnection( tool_shed_test_host, tool_shed_test_port ) + conn.request( "GET", "/" ) + if conn.getresponse().status == 200: + break + time.sleep( 0.1 ) + else: + raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) + log.info( "Embedded web server started" ) # We don't add the tests to the path until everything is up and running new_path = [ os.path.join( cwd, 'test' ) ] new_path.extend( sys.path[1:] ) @@ -239,9 +196,6 @@ log.info( "Functional tests will be run against %s:%s" % ( tool_shed_test_host, tool_shed_test_port ) ) success = False try: - # What requires these? Handy for (eg) functional tests to save outputs? - if tool_shed_test_save: - os.environ[ 'TOOL_SHED_TEST_SAVE' ] = tool_shed_test_save # Pass in through script set env, will leave a copy of ALL test validate files. os.environ[ 'TOOL_SHED_TEST_HOST' ] = tool_shed_test_host if tool_shed_test_file_dir: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dan: Add 'checkers' namespace before calls to .check_*.
by Bitbucket 11 Dec '12

11 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a7ea7728829d/ changeset: a7ea7728829d user: dan date: 2012-12-11 20:14:14 summary: Add 'checkers' namespace before calls to .check_*. affected #: 1 file diff -r eed6dd67514b5e5ab0174f181af9514dea7a8d33 -r a7ea7728829dcc5395606bd402805d2ac972d6c6 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -846,17 +846,17 @@ if is_column_based( file_path ): return True # If the file is any of the following, don't copy it. - if check_html( file_path ): + if checkers.check_html( file_path ): return False - if check_image( file_path ): + if checkers.check_image( file_path ): return False - if check_binary( name=file_path ): + if checkers.check_binary( name=file_path ): return False - if is_bz2( file_path ): + if checkers.is_bz2( file_path ): return False - if is_gzip( file_path ): + if checkers.is_gzip( file_path ): return False - if check_zip( file_path ): + if checkers.check_zip( file_path ): return False # Default to copying the file if none of the above are true. return 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.

1 0

commit/galaxy-central: greg: Fix for building tool dependencies container.
by Bitbucket 11 Dec '12

11 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/eed6dd67514b/ changeset: eed6dd67514b user: greg date: 2012-12-11 17:54:09 summary: Fix for building tool dependencies container. affected #: 1 file diff -r 71c3b867efd1d8074a59659ed7320c1e6a3d9ed3 -r eed6dd67514b5e5ab0174f181af9514dea7a8d33 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -99,7 +99,7 @@ repository_dependencies=repository_dependencies ) containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder if tool_dependencies: - folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=True ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder except Exception, e: log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) 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: greg: Fix for resetting all metadata on a tool shed repository.
by Bitbucket 11 Dec '12

11 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/71c3b867efd1/ changeset: 71c3b867efd1 user: greg date: 2012-12-11 17:37:53 summary: Fix for resetting all metadata on a tool shed repository. affected #: 1 file diff -r 1cdb5f5eb6d061b3232c4f7725839a9fe287355a -r 71c3b867efd1d8074a59659ed7320c1e6a3d9ed3 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -726,7 +726,7 @@ relative_path, filename = os.path.split( sample_file ) if filename == 'tool_data_table_conf.xml.sample': new_table_elems, error_message = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, - tool_data_path=original_tool_data_path, + tool_data_path=app.config.tool_data_path, shed_tool_data_table_config=app.config.shed_tool_data_table_config, persist=persist ) if error_message: @@ -771,7 +771,7 @@ if not valid: invalid_file_tups.append( ( name, error_message ) ) else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_copy_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: @@ -1329,32 +1329,32 @@ relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file -def get_sample_files_from_disk( repository_files_dir, tool_path = None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): +def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. work_dir = repository_files_dir sample_file_metadata_paths = [] sample_file_copy_paths = [] for root, dirs, files in os.walk( repository_files_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: - full_path_to_sample_file = os.path.join( root, name ) - stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) - if stripped_path_to_sample_file.startswith( '/' ): - stripped_path_to_sample_file = stripped_path_to_sample_file[ 1: ] - relative_path_to_sample_file = os.path.join( relative_install_dir, stripped_path_to_sample_file ) - if os.path.exists( relative_path_to_sample_file ): - sample_file_copy_paths.append( relative_path_to_sample_file ) - else: - sample_file_copy_paths.append( full_path_to_sample_file ) + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + if resetting_all_metadata_on_repository: + full_path_to_sample_file = os.path.join( root, name ) + stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) + if stripped_path_to_sample_file.startswith( '/' ): + stripped_path_to_sample_file = stripped_path_to_sample_file[ 1: ] + relative_path_to_sample_file = os.path.join( relative_install_dir, stripped_path_to_sample_file ) + if os.path.exists( relative_path_to_sample_file ): + sample_file_copy_paths.append( relative_path_to_sample_file ) else: - relative_path_to_sample_file = os.path.join( root, name ) - sample_file_copy_paths.append( relative_path_to_sample_file ) - if tool_path and relative_install_dir: - if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ): - relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] + sample_file_copy_paths.append( full_path_to_sample_file ) + else: + relative_path_to_sample_file = os.path.join( root, name ) + sample_file_copy_paths.append( relative_path_to_sample_file ) + if tool_path and relative_install_dir: + if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ): + relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): 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: inithello: Functional tests for repositories with circular repository dependencies.
by Bitbucket 11 Dec '12

11 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1cdb5f5eb6d0/ changeset: 1cdb5f5eb6d0 user: inithello date: 2012-12-11 16:47:31 summary: Functional tests for repositories with circular repository dependencies. affected #: 4 files diff -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 -r 1cdb5f5eb6d061b3232c4f7725839a9fe287355a test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -50,6 +50,9 @@ url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def check_repository_dependency( self, repository, depends_on_repository, depends_on_changeset_revision ): + strings_displayed = [ depends_on_repository.name, depends_on_repository.user.username, depends_on_changeset_revision ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) def check_repository_metadata( self, repository, tip_only=True ): if tip_only: assert self.tip_has_metadata( repository ) and len( self.get_repository_metadata_revisions( repository ) ) == 1, \ @@ -353,7 +356,7 @@ **kwd ): self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) if valid_tools_only: - strings_displayed.append( "has been successfully uploaded to the repository." ) + strings_displayed.extend( [ 'has been successfully', 'uploaded to the repository.' ] ) for key in kwd: tc.fv( "1", key, kwd[ key ] ) tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) ) diff -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 -r 1cdb5f5eb6d061b3232c4f7725839a9fe287355a test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -18,7 +18,7 @@ self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) test_user_1 = get_user( common.test_user_1_email ) - assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email test_user_1_private_role = get_private_role( test_user_1 ) self.logout() self.login( email=common.admin_email, username=common.admin_username ) @@ -28,7 +28,7 @@ def test_0005_create_category( self ): """Create a category for this test suite""" self.create_category( 'Test 0030 Repository Dependency Revisions', 'Testing repository dependencies by revision.' ) - def test_0005_create_repositories( self ): + def test_0010_create_repositories( self ): '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes, and emboss repositories and populate the emboss_datatypes repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) @@ -69,7 +69,7 @@ strings_displayed=[] ) emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' ) - def test_0010_generate_repository_dependencies_for_emboss_5( self ): + def test_0015_generate_repository_dependencies_for_emboss_5( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) @@ -80,7 +80,7 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded repository_depepndencies.xml.' ) - def test_0015_generate_repository_dependencies_for_emboss_6( self ): + def test_0020_generate_repository_dependencies_for_emboss_6( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.''' emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) @@ -88,7 +88,7 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded repository_depepndencies.xml.' ) - def test_0020_generate_repository_dependency_on_emboss_5( self ): + def test_0025_generate_repository_dependency_on_emboss_5( self ): '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.''' emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) @@ -100,7 +100,7 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded dependency configuration specifying emboss_5' ) - def test_0025_generate_repository_dependency_on_emboss_6( self ): + def test_0030_generate_repository_dependency_on_emboss_6( self ): '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.''' emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) @@ -112,7 +112,7 @@ 'repository_dependencies.xml', filepath=repository_dependencies_path, commit_message='Uploaded dependency configuration specifying emboss_6' ) - def test_0030_verify_repository_dependency_revisions( self ): + def test_0035_verify_repository_dependency_revisions( self ): '''Verify that different metadata revisions of the emboss repository have different repository dependencies.''' repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ] diff -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 -r 1cdb5f5eb6d061b3232c4f7725839a9fe287355a test/tool_shed/functional/test_0040_repository_circular_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py @@ -0,0 +1,102 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role + +freebayes_repository_name = 'freebayes_0040' +freebayes_repository_name_description = "Galaxy's freebayes tool" +freebayes_repository_name_long_description = "Long description of Galaxy's freebayes tool" + +filtering_repository_name = 'filtering_0040' +filtering_repository_description = "Galaxy's filtering tool" +filtering_repository_long_description = "Long description of Galaxy's filtering tool" + +class TestRepositoryCircularDependencies( ShedTwillTestCase ): + '''Verify that the code correctly handles circular dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = get_private_role( test_user_1 ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = 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 = get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( 'test_0040_repository_circular_dependencies', 'Testing handling of circular repository dependencies.' ) + def test_0010_create_freebayes_repository_name( self ): + '''Create and populate freebayes_0040.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.create_repository( freebayes_repository_name, + freebayes_repository_name_description, + repository_long_description=freebayes_repository_name_long_description, + categories=[ 'test_0040_repository_circular_dependencies' ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'freebayes/freebayes.tar', + strings_displayed=[], + commit_message='Uploaded freebayes.tar.' ) + def test_0015_create_filtering_repository( self ): + '''Create and populate filtering_0040.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + self.create_repository( filtering_repository_name, + filtering_repository_description, + repository_long_description=filtering_repository_long_description, + categories=[ 'test_0040_repository_circular_dependencies' ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + self.upload_file( repository, + 'filtering/filtering_1.1.0.tar', + strings_displayed=[], + commit_message='Uploaded filtering.tar.' ) + def test_0020_create_dependency_on_freebayes( self ): + '''Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.''' + # The dependency structure should look like: + # Filtering revision 0 -> freebayes revision 0. + # Freebayes revision 0 -> filtering revision 1. + # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. + repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + filtering_repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'filtering' ] ) + self.generate_repository_dependency_xml( repository, + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Filtering 1.1.0 depends on the freebayes repository.' ) + self.upload_file( filtering_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on freebayes' ) + def test_0025_create_dependency_on_filtering( self ): + '''Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.''' + # The dependency structure should look like: + # Filtering revision 0 -> freebayes revision 0. + # Freebayes revision 0 -> filtering revision 1. + # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. + repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0040', additional_paths=[ 'freebayes' ] ) + self.generate_repository_dependency_xml( repository, + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), + dependency_description='Freebayes depends on the filtering repository.' ) + self.upload_file( freebayes_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded dependency on filtering' ) + def test_0030_verify_repository_dependencies( self ): + '''Verify that each repository can depend on the other without causing an infinite loop.''' + filtering_repository = get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) + freebayes_repository = get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) + # The dependency structure should look like: + # Filtering revision 0 -> freebayes revision 0. + # Freebayes revision 0 -> filtering revision 1. + # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. + # In this case, the displayed dependency will specify the tip revision, but this will not always be the case. + filtering_strings_displayed = [ freebayes_repository_name, common.test_user_1_name, self.get_repository_tip( freebayes_repository ) ] + freebayes_strings_displayed = [ filtering_repository_name, common.test_user_1_name, self.get_repository_tip( filtering_repository ) ] + self.display_manage_repository_page( filtering_repository, strings_displayed=filtering_strings_displayed ) + self.display_manage_repository_page( freebayes_repository, strings_displayed=freebayes_strings_displayed ) + diff -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 -r 1cdb5f5eb6d061b3232c4f7725839a9fe287355a test/tool_shed/test_data/freebayes/freebayes.tar Binary file test/tool_shed/test_data/freebayes/freebayes.tar has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/795a1799e7dc/ changeset: 795a1799e7dc user: carlfeberhard date: 2012-12-10 23:44:11 summary: Fixes to history functional tests; Twilltestcase: added function to parse and check json, exact string matcher affected #: 5 files diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -130,6 +130,7 @@ history_panel_template = "root/history.mako" else: + # get all datasets server-side, client-side will get flags and render appropriately datasets = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -241,8 +241,9 @@ try: os.makedirs( dir ) except OSError: - pass - print "Database connection:", database_connection + pass + log.info( "Database connection:", database_connection ) + # ---- Build Application -------------------------------------------------- app = None if start_server: @@ -412,6 +413,8 @@ if os.path.exists( tempdir ) and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: log.info( "Cleaning up temporary files in %s" % tempdir ) shutil.rmtree( tempdir ) + else: + log.info( "GALAXY_TEST_NO_CLEANUP is on. Temporary files in %s" % tempdir ) except: pass if psu_production and 'GALAXY_TEST_NO_CLEANUP' not in os.environ: diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -310,11 +310,12 @@ // ostensibly, this is the App // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... // ...use mako to 'bootstrap' the models - var user = ${ get_current_user() }, + var page_show_deleted = ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, + page_show_hidden = ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, + + user = ${ get_current_user() }, history = ${ get_history( history.id ) }, hdas = ${ get_hdas( history.id, datasets ) }; - var currUser = new User( user ); - if( !Galaxy.currUser ){ Galaxy.currUser = currUser; } // add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour @@ -326,8 +327,8 @@ urlTemplates : galaxy_paths.attributes, logger : ( debugging )?( console ):( null ), // is page sending in show settings? if so override history's - show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, - show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } + show_deleted : page_show_deleted, + show_hidden : page_show_hidden }); historyPanel.render(); @@ -337,15 +338,16 @@ // urlTemplates : galaxy_paths.attributes, // logger : ( debugging )?( console ):( null ), // // is page sending in show settings? if so override history's - // show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, - // show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } + // show_deleted : page_show_deleted, + // show_hidden : page_show_hidden //}); //historyPanel.model.loadFromApi( history.id ); // set it up to be accessible across iframes //TODO:?? mem leak top.Galaxy.currHistoryPanel = historyPanel; - + var currUser = new User( user ); + if( !Galaxy.currUser ){ Galaxy.currUser = currUser; } // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -249,8 +249,9 @@ page = self.last_page() if page.find( 'error' ) > -1: raise AssertionError('Errors in the history for user %s' % self.user ) + def check_history_for_string( self, patt, show_deleted=False ): - """Looks for 'string' in history page""" + """Breaks patt on whitespace and searches for each element seperately in the history""" self.home() if show_deleted: self.visit_page( "history?show_deleted=True" ) @@ -264,11 +265,57 @@ errmsg = "no match to '%s'\npage content written to '%s'" % ( subpatt, fname ) raise AssertionError( errmsg ) self.home() + + def check_history_for_exact_string( self, string, show_deleted=False ): + """Looks for exact match to 'string' in history page""" + self.home() + if show_deleted: + self.visit_page( "history?show_deleted=True" ) + else: + self.visit_page( "history" ) + try: + tc.find( string ) + except: + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = "no match to '%s'\npage content written to '%s'" % ( string, fname ) + raise AssertionError( errmsg ) + self.home() + + def check_history_json( self, pattern, check_fn, show_deleted=None, multiline=True ): + """ + Tries to find a JSON string in the history page using the regex pattern, + parse it, and assert check_fn returns True when called on that parsed + data. + """ + self.home() + if show_deleted: + self.visit_page( "history?show_deleted=True" ) + elif show_deleted == False: + self.visit_page( "history?show_deleted=False" ) + else: + self.visit_page( "history" ) + try: + tc.find( pattern, flags=( 'm' if multiline else '' ) ) + # twill stores the regex match in a special stack variable + match = twill.namespaces.get_twill_glocals()[1][ '__match__' ] + json_data = from_json_string( match ) + assert check_fn( json_data ), 'failed check_fn' + + except Exception, exc: + log.error( exc, exc_info=True ) + fname = self.write_temp_file( tc.browser.get_html() ) + errmsg = ( "json '%s' could not be found or failed check_fn" % ( pattern ) + + "\npage content written to '%s'" % ( fname ) ) + raise AssertionError( errmsg ) + + self.home() + def clear_history( self ): """Empties a history of all datasets""" self.visit_page( "clear_history" ) self.check_history_for_string( 'Your history is empty' ) self.home() + def delete_history( self, id ): """Deletes one or more histories""" history_list = self.get_histories_as_data_list() @@ -279,6 +326,7 @@ check_str = 'Deleted %d %s' % ( num_deleted, iff( num_deleted != 1, "histories", "history" ) ) self.check_page_for_string( check_str ) self.home() + def delete_current_history( self, strings_displayed=[] ): """Deletes the current history""" self.home() @@ -286,16 +334,19 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) self.home() + def get_histories_as_data_list( self ): """Returns the data elements of all histories""" tree = self.histories_as_xml_tree() data_list = [ elem for elem in tree.findall("data") ] return data_list + def get_history_as_data_list( self, show_deleted=False ): """Returns the data elements of a history""" tree = self.history_as_xml_tree( show_deleted=show_deleted ) data_list = [ elem for elem in tree.findall("data") ] return data_list + def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" self.home() @@ -303,6 +354,7 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree + def histories_as_xml_tree( self ): """Returns a parsed xml object of all histories""" self.home() @@ -310,6 +362,7 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree + def history_options( self, user=False, active_datasets=False, activatable_datasets=False, histories_shared_by_others=False ): """Mimics user clicking on history options link""" self.home() @@ -329,6 +382,7 @@ self.check_page_for_string( 'Rename</a> current history' ) self.check_page_for_string( 'Delete</a> current history' ) self.home() + def new_history( self, name=None ): """Creates a new, empty history""" self.home() @@ -338,6 +392,7 @@ self.visit_url( "%s/history_new" % self.url ) self.check_history_for_string('Your history is empty') self.home() + def rename_history( self, id, old_name, new_name ): """Rename an existing history""" self.home() @@ -345,6 +400,7 @@ check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) ) self.check_page_for_string( check_str ) self.home() + def set_history( self ): """Sets the history (stores the cookies for this run)""" if self.history_id: @@ -353,6 +409,7 @@ else: self.new_history() self.home() + def share_current_history( self, email, strings_displayed=[], strings_displayed_after_submit=[], action='', action_strings_displayed=[], action_strings_displayed_after_submit=[] ): """Share the current history with different users""" @@ -372,6 +429,7 @@ for check_str in action_strings_displayed_after_submit: self.check_page_for_string( check_str ) self.home() + def share_histories_with_users( self, ids, emails, strings_displayed=[], strings_displayed_after_submit=[], action=None, action_strings_displayed=[] ): """Share one or more histories with one or more different users""" @@ -389,6 +447,7 @@ for check_str in action_strings_displayed: self.check_page_for_string( check_str ) self.home() + def unshare_history( self, history_id, user_id, strings_displayed=[] ): """Unshare a history that has been shared with another user""" self.visit_url( "%s/history/list?id=%s&operation=share+or+publish" % ( self.url, history_id ) ) @@ -396,12 +455,14 @@ self.check_page_for_string( check_str ) self.visit_url( "%s/history/sharing?unshare_user=%s&id=%s" % ( self.url, user_id, history_id ) ) self.home() + def switch_history( self, id='', name='' ): """Switches to a history in the current list of histories""" self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) if name: - self.check_history_for_string( escape( name ) ) + self.check_history_for_exact_string( name ) self.home() + def view_stored_active_histories( self, strings_displayed=[] ): self.home() self.visit_page( "history/list" ) @@ -698,11 +759,13 @@ # if the server's env has GALAXY_TEST_SAVE, save the output file to that dir if self.keepOutdir: ofn = os.path.join( self.keepOutdir, os.path.basename( local_name ) ) + log.debug( 'keepoutdir: %s, ofn: %s', self.keepOutdir, ofn ) try: shutil.copy( temp_name, ofn ) except Exception, exc: error_log_msg = ( 'TwillTestCase could not save output file %s to %s: ' % ( temp_name, ofn ) ) error_log_msg += str( exc ) + log.error( error_log_msg, exc_info=True ) else: log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % ( self.keepOutdir, ofn ) ) diff -r e19bf2b117638221414239698f840730a2cd0569 -r 795a1799e7dcf092b14f7e2a2dba3fb389403531 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -250,8 +250,7 @@ sa_session.query( galaxy.model.HistoryDatasetAssociation ) .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) - .first() - ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" self.delete_history_item( str( hda_2_bed.id ) ) @@ -260,8 +259,7 @@ sa_session.query( galaxy.model.HistoryDatasetAssociation ) .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) - .first() - ) + .first() ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" self.delete_history_item( str( hda_3_bed.id ) ) @@ -281,39 +279,52 @@ self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history3.name ] ) # Switch to the cloned history to make sure activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone2.id ), name=history3_clone2.name ) - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" - hda_3_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \ - .first() + hda_3_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3_clone2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) + .first() ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" + # Make sure the deleted datasets are included in the cloned history - check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_2_bed.id - self.check_history_for_string( check_str, show_deleted=True ) - check_str = 'This dataset has been deleted. Click undelete id=%d' % hda_3_bed.id - self.check_history_for_string( check_str, show_deleted=True ) + # check for encoded ids + # - these will be available bc the refreshed page will have bootstrapped json for the hdas + #NOTE: that these WON'T be available when refreshes become less common + # (when the backbone.js is fully integrated and refreshes aren't used after every history function) + self.check_history_for_exact_string( self.security.encode_id( hda_2_bed.id ), show_deleted=True ) + self.check_history_for_exact_string( self.security.encode_id( hda_3_bed.id ), show_deleted=True ) + # Test cloning only active datasets - self.clone_history( self.security.encode_id( history3.id ), - 'active', - strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) + self.clone_history( + self.security.encode_id( history3.id ), + 'active', + strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history3_clone3 - history3_clone3 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + history3_clone3 = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() + ) assert history3_clone3 is not None, "Problem retrieving history3_clone3 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed = ["Clone of '%s'" % history3.name ] ) - # Switch to the cloned history to make sure activatable datasets were cloned + + # Switch to the cloned history to make sure ONLY activatable datasets were cloned self.switch_history( id=self.security.encode_id( history3_clone3.id ) ) # Make sure the deleted datasets are NOT included in the cloned history + # - again using the bootstrapped json for the hdas try: - self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True ) + self.check_history_for_exact_string( '"deleted": true', show_deleted=True ) + #self.check_history_for_string( 'This dataset has been deleted.', show_deleted=True ) raise AssertionError, "Deleted datasets incorrectly included in cloned history history3_clone3" except: pass @@ -349,6 +360,7 @@ # Shared history3 should be in regular_user3's list of shared histories self.view_shared_histories( cstrings_displayed=[ history3.name, admin_user.email ] ) """ + def test_045_change_permissions_on_current_history( self ): """Testing changing permissions on the current history""" # Logged in as regular_user3 @@ -402,6 +414,7 @@ current_history_permissions.sort() if current_history_permissions != history5_default_permissions: raise AssertionError, "With logout and login, the history default permissions are not preserved" + def test_050_sharing_restricted_history_by_making_datasets_public( self ): """Testing sharing a restricted history by making the datasets public""" # Logged in as admin_user @@ -432,6 +445,7 @@ self.check_history_for_string( 'chr1' ) self.logout() self.login( email=admin_user.email ) + def test_055_sharing_restricted_history_by_making_new_sharing_role( self ): """Testing sharing a restricted history by associating a new sharing role with protected datasets""" # At this point, history5 should have 1 item, 1.bed, which is public. We'll add another @@ -506,6 +520,7 @@ self.display_history_item( str( hda_2_bed.id ), strings_displayed=[ 'chr1' ] ) # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone2.id ) ) + def test_060_sharing_restricted_history_with_multiple_users_by_changing_no_permissions( self ): """Testing sharing a restricted history with multiple users, making no permission changes""" # Logged in as regular_user2 @@ -515,10 +530,12 @@ # regular_user2 should be able to access history5's 2.bed dataset since it is associated with a # sharing role, and regular_user3 should be able to access history5's 1.bed, but not 2.bed even # though they can see it in their shared history. + # We first need to unshare history5 from regular_user2 so that we can re-share it. self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user2.id ), strings_displayed=[ regular_user1.email, regular_user2.email ] ) + # Make sure the history was unshared correctly self.logout() self.login( email=regular_user2.email ) @@ -528,11 +545,14 @@ raise AssertionError, "history5 still shared with regular_user2 after unsharing it with that user." except: pass + self.logout() self.login( admin_user.email ) email = '%s,%s' % ( regular_user2.email, regular_user3.email ) - strings_displayed_after_submit = [ 'The following datasets can be shared with %s with no changes' % email, - 'The following datasets can be shared with %s by updating their permissions' % email ] + strings_displayed_after_submit = [ + 'The following datasets can be shared with %s with no changes' % email, + 'The following datasets can be shared with %s by updating their permissions' % email ] + # history5 will be shared with regular_user1, regular_user2 and regular_user3 self.share_current_history( email, strings_displayed_after_submit=strings_displayed_after_submit, @@ -547,30 +567,35 @@ 'activatable', strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history5_clone3 - history5_clone3 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user2.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + history5_clone3 = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==regular_user2.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert history5_clone3 is not None, "Problem retrieving history5_clone3 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone3.id ), name=history5_clone3.name ) - # Make sure both datasets are in the history + # Make sure both datasets are in the history self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history - hda_1_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ - .first() + hda_1_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public self.display_history_item( str( hda_1_bed.id ), strings_displayed=[ 'chr1' ] ) # Make sure 2.bed is accessible since it is associated with a sharing role @@ -582,34 +607,39 @@ self.login( email=regular_user3.email ) # Shared history5 should be in regular_user2's list of shared histories self.view_shared_histories( strings_displayed=[ history5.name, admin_user.email ] ) + # Clone restricted history5 self.clone_history( self.security.encode_id( history5.id ), 'activatable', strings_displayed_after_submit=[ 'is now included in your previously stored histories.' ] ) global history5_clone4 - history5_clone4 = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==regular_user3.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + history5_clone4 = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==regular_user3.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert history5_clone4 is not None, "Problem retrieving history5_clone4 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history5.name ] ) # Make sure the dataset is accessible self.switch_history( id=self.security.encode_id( history5_clone4.id ), name=history5_clone4.name ) - # Make sure both datasets are in the history + # Make sure both datasets are in the history self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history - hda_1_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ - .first() + hda_1_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) + .first() ) assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_clone4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" # Make sure 1.bed is accessible since it is public self.display_history_item( str( hda_1_bed.id ), strings_displayed=[ 'chr1' ] ) @@ -619,20 +649,31 @@ raise AssertionError, "History item 2.bed is accessible by user %s when is should not be" % regular_user3.email except: pass - self.check_history_for_string( 'You do not have permission to view this dataset' ) + + # check the history page json for hda_2_bed and if it's accessible + def hda_2_bed_is_inaccessible( hda_list ): + for hda in hda_list: + if hda[ 'id' ] == self.security.encode_id( hda_2_bed.id ): + return ( not hda[ 'accessible' ] ) + return False + self.check_history_json( r'\bhdas\s*=\s*(.*);', hda_2_bed_is_inaccessible ) + # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin self.logout() self.login( email=admin_user.email ) self.view_history( str( hda_2_bed.history_id ), strings_displayed=[ '<td>NM_005997_cds_0_0_chr1_147962193_r</td>' ] ) self.logout() self.login( email=regular_user3.email ) + # Delete the clone so the next test will be valid self.delete_history( id=self.security.encode_id( history5_clone4.id ) ) + def test_065_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" - # Logged in as regular_user3 + # Logged in as regular_user3 - login as admin self.logout() self.login( email=admin_user.email ) + # Unshare history5 from regular_user2 self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user2.id ), @@ -641,7 +682,8 @@ self.unshare_history( self.security.encode_id( history5.id ), self.security.encode_id( regular_user3.id ), strings_displayed=[ regular_user1.email, regular_user3.email ] ) - # Make sure the history was unshared correctly + + # Make sure the histories were unshared correctly self.logout() self.login( email=regular_user2.email ) self.visit_page( "root/history_options" ) @@ -650,6 +692,7 @@ raise AssertionError, "history5 still shared with regular_user2 after unshaing it with that user." except: pass + self.logout() self.login( email=regular_user3.email ) self.visit_page( "root/history_options" ) @@ -660,42 +703,73 @@ pass self.logout() self.login( email=admin_user.email ) + def test_070_history_show_and_hide_deleted_datasets( self ): """Testing displaying deleted history items""" + #NOTE: due to the new client-side rendering of the history, this test isn't very apt + # (a) searching for strings in the dom doesn't work (they won't be twill's html) and + # (b) all datasets are included in the bootstrapped hda json regardless of the show_deleted setting + #CE: for now, I'm changing this to simply check whether the show_deleted flag + # is being properly passed to the history control + #TODO: this test needs to be moved to client-side testing framework (selenium or other) + # Logged in as admin_user + # create a new history and upload a new hda (1.bed) into it self.new_history( name=urllib.quote( 'show hide deleted datasets' ) ) - latest_history = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + latest_history = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert latest_history is not None, "Problem retrieving latest_history from database" self.upload_file('1.bed', dbkey='hg18') - latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ - .first() + latest_hda = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) + .first() ) + + # delete that item and make sure the 'history empty' message shows self.home() + log.info( 'deleting last hda' ) self.delete_history_item( str( latest_hda.id ) ) - self.check_history_for_string( 'Your history is empty' ) + # check the historyPanel settings.show_deleted for a null json value (no show_deleted in query string) + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == None ) + + # reload this history with the show_deleted flag set in the query string + # the deleted dataset should be there with the proper 'deleted' text self.home() - self.visit_url( "%s/history/?show_deleted=True" % self.url ) - self.check_page_for_string( 'This dataset has been deleted.' ) - self.check_page_for_string( '1.bed' ) + log.info( 'turning show_deleted on' ) + #self.visit_url( "%s/history/?show_deleted=True" % self.url ) + # check the historyPanel settings.show_deleted for a true json value + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == True, show_deleted=True ) + + # reload this history again with the show_deleted flag set TO FALSE in the query string + # make sure the 'history empty' message shows self.home() - self.visit_url( "%s/history/?show_deleted=False" % self.url ) - self.check_page_for_string( 'Your history is empty' ) + log.info( 'turning show_deleted off' ) + #self.visit_url( "%s/history/?show_deleted=False" % self.url ) + # check the historyPanel settings.show_deleted for a false json value + self.check_history_json( r'\bpage_show_deleted\s*=\s*(.*),', lambda x: x == False, show_deleted=False ) + + # delete this history self.delete_history( self.security.encode_id( latest_history.id ) ) + def test_075_deleting_and_undeleting_history_items( self ): """Testing deleting and un-deleting history items""" # logged in as admin_user + # Deleting the current history in the last method created a new history - latest_history = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.user_id==admin_user.id ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + latest_history = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() ) assert latest_history is not None, "Problem retrieving latest_history from database" - self.rename_history( self.security.encode_id( latest_history.id ), latest_history.name, new_name=urllib.quote( 'delete undelete history items' ) ) + + self.rename_history( self.security.encode_id( latest_history.id ), + latest_history.name, new_name=urllib.quote( 'delete undelete history items' ) ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ @@ -722,6 +796,7 @@ self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) self.delete_history( self.security.encode_id( latest_history.id ) ) + def test_080_copying_history_items_between_histories( self ): """Testing copying history items between histories""" # logged in as admin_user @@ -776,6 +851,7 @@ self.check_history_for_string( hda1.name ) self.delete_history( self.security.encode_id( history6.id ) ) self.delete_history( self.security.encode_id( history7.id ) ) + def test_085_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to to be valid""" # logged in as admin_user Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle circular repository dependencies to "n" levels of depth.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e19bf2b11763/ changeset: e19bf2b11763 user: greg date: 2012-12-10 22:27:29 summary: Handle circular repository dependencies to "n" levels of depth. affected #: 3 files diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,8 +1,6 @@ import os, tempfile, shutil, logging, urllib2 from galaxy import util -from galaxy.datatypes.checkers import * -from galaxy.util.json import * -from galaxy.util.shed_util_common import * +from shed_util_common import * from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed.encoding_util import * diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -194,28 +194,18 @@ option_value = trans.security.encode_id( repository.id ) repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): - """ - Handle circular repository dependencies that could result in an infinite loop by determining if it is safe to add an entry to the - repository dependencies container. - """ - # First check for an exact match - if this is true, the changeset revision was not updated. - repository_dependency_as_key = container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], - repository_dependency[ 1 ], - repository_dependency[ 2 ], - repository_dependency[ 3] ) - current_repository_key_as_repository_dependency = current_repository_key.split( container_util.STRSEP ) - if repository_dependency_as_key in all_repository_dependencies: - val = all_repository_dependencies[ repository_dependency_as_key ] - if current_repository_key_as_repository_dependency in val: - return False - # Now handle the case where an update to the changeset revision was done, so everything will match except the changeset_revision. - repository_dependency_as_partial_key = container_util.STRSEP.join( [ repository_dependency[ 0 ], repository_dependency[ 1 ], repository_dependency[ 2 ] ] ) - for key in all_repository_dependencies: - if key.startswith( repository_dependency_as_partial_key ): - val = all_repository_dependencies[ key ] - if current_repository_key_as_repository_dependency in val: - return False +def can_add_to_key_rd_dicts( key_rd_dict, key_rd_dicts ): + """Handle the case where an update to the changeset revision was done.""" + k = key_rd_dict.keys()[ 0 ] + rd = key_rd_dict[ k ] + partial_rd = rd[ 0:3 ] + for kr_dict in key_rd_dicts: + key = kr_dict.keys()[ 0 ] + if key == k: + val = kr_dict[ key ] + for repository_dependency in val: + if repository_dependency[ 0:3 ] == partial_rd: + return False return True def can_generate_tool_dependency_metadata( root, metadata_dict ): """ @@ -555,13 +545,15 @@ metadata = repository_metadata.metadata if metadata: # Get a dictionary of all repositories upon which the contents of the received repository depends. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, - all_repository_dependencies=None ) + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), str( repository_clone_url ), @@ -1037,6 +1029,11 @@ if ctx_file_name == stripped_filename: return manifest_ctx, ctx_file return None, None +def get_key_for_repository_changeset_revision( toolshed_base_url, repository, repository_metadata ): + return container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, + repository_name=repository.name, + repository_owner=repository.user.username, + changeset_revision=repository_metadata.changeset_revision ) def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to @@ -1197,123 +1194,68 @@ .filter( and_( trans.model.Repository.table.c.name == name, trans.model.Repository.table.c.user_id == user.id ) ) \ .first() -def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, repository_dependencies=None, - all_repository_dependencies=None, handled=None ): +def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, + handled_key_rd_dicts=None, circular_repository_dependencies=None ): """ Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). This method ensures that all required repositories to the nth degree are returned. """ - if handled is None: - handled = [] + if handled_key_rd_dicts is None: + handled_key_rd_dicts = [] if all_repository_dependencies is None: all_repository_dependencies = {} - if repository_dependencies is None: - repository_dependencies = [] + if key_rd_dicts_to_be_processed is None: + key_rd_dicts_to_be_processed = [] + if circular_repository_dependencies is None: + circular_repository_dependencies = [] + # Assume the current repository does not have repository dependencies defined for it. + current_repository_key = None metadata = repository_metadata.metadata if metadata and 'repository_dependencies' in metadata: + current_repository_key = get_key_for_repository_changeset_revision( toolshed_base_url, repository, repository_metadata ) repository_dependencies_dict = metadata[ 'repository_dependencies' ] - # The repository_dependencies entry in the metadata is a dictionary that may have a value for a 'description' key. We want to - # store the value of this key only once, the first time through this recursive method. - current_repository_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, - repository_name=repository.name, - repository_owner=repository.user.username, - changeset_revision=repository_metadata.changeset_revision ) if not all_repository_dependencies: - # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. - all_repository_dependencies[ 'root_key' ] = current_repository_key - all_repository_dependencies[ current_repository_key ] = [] - if 'description' not in all_repository_dependencies: - description = repository_dependencies_dict.get( 'description', None ) - all_repository_dependencies[ 'description' ] = description - # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. - repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] - if repository_dependencies_tups and current_repository_key: - # Remove all repository dependencies that point to a revision within its own repository. - repository_dependencies_tups = remove_ropository_dependency_reference_to_self( repository_dependencies_tups, current_repository_key ) - for repository_dependency in repository_dependencies_tups: - if repository_dependency not in handled and repository_dependency not in repository_dependencies: - # The following if statement handles repositories dependencies that are circular in nature. - if current_repository_key: - if current_repository_key in all_repository_dependencies: - # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. - all_repository_dependencies_val = all_repository_dependencies[ current_repository_key ] - if repository_dependency not in all_repository_dependencies_val: - all_repository_dependencies_val.append( repository_dependency ) - all_repository_dependencies[ current_repository_key ] = all_repository_dependencies_val - elif can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): - # We don't have a circular dependency that could result in an infinite loop. - all_repository_dependencies[ current_repository_key ] = [ repository_dependency ] - repository_dependencies.append( repository_dependency ) - else: - # The current repository does not have repository dependencies defined for it. - current_repository_key = None - # The following if statement handles repositories dependencies that are circular in nature. - if current_repository_key and current_repository_key in all_repository_dependencies: - repository_dependencies_tups = [ rd for rd in all_repository_dependencies[ current_repository_key ] ] - if repository_dependencies_tups: - repository_dependency = repository_dependencies_tups.pop( 0 ) - if repository_dependency not in handled: - handled.append( repository_dependency ) - if repository_dependency in repository_dependencies: - repository_dependencies.remove( repository_dependency ) - toolshed, name, owner, changeset_revision = repository_dependency - if tool_shed_is_this_tool_shed( toolshed ): - required_repository = get_repository_by_name_and_owner( trans, name, owner ) - required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( required_repository.id ), - changeset_revision ) - if required_repository_metadata: - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - else: - # The repository changeset_revision is no longer installable, so see if there's been an update. - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - required_changeset_revision = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision ) - required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( required_repository.id ), - required_changeset_revision ) - if required_repository_metadata: - # The changeset_revision defined in a repository_dependencies.xml file is outdated, so we need to fix appropriate - # entries in our all_repository_dependencies dictionary. - updated_repository_dependency = [ toolshed, name, owner, required_changeset_revision ] - for k, v in all_repository_dependencies.items(): - if k in [ 'root_key', 'description' ]: - continue - for i, current_repository_dependency in enumerate( v ): - cts, cn, co, ccr = current_repository_dependency - if toolshed == cts and name == cn and owner == co and changeset_revision == ccr: - if updated_repository_dependency in v: - # We've already stored the updated repository_dependency, so remove the outdated one. - v = v.remove( repository_dependency ) - all_repository_dependencies[ k ] = v - else: - # Store the updated repository_dependency. - v[ i ] = updated_repository_dependency - all_repository_dependencies[ k ] = v - if required_repository_metadata: - # The required_repository_metadata changeset_revision is installable. - required_metadata = required_repository_metadata.metadata - if required_metadata: - for repository_dependency in repository_dependencies_tups: - if repository_dependency not in repository_dependencies: - repository_dependencies.append( repository_dependency ) - return get_repository_dependencies_for_changeset_revision( trans=trans, - repo=required_repo, - repository=required_repository, - repository_metadata=required_repository_metadata, - toolshed_base_url=toolshed, - repository_dependencies=repository_dependencies, - all_repository_dependencies=all_repository_dependencies, - handled=handled ) - else: - # The repository is in a different tool shed, so build an url and send a request. - error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " - error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) - log.debug( error_message ) + all_repository_dependencies = initialize_all_repository_dependencies( current_repository_key, + repository_dependencies_dict, + all_repository_dependencies ) + # Handle the repository dependencies defined in the current repository, if any, and populate the various repository dependency objects for + # this round of processing. + current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies = \ + populate_repository_dependency_objects_for_processing( trans, + current_repository_key, + repository_dependencies_dict, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies, + all_repository_dependencies ) + if current_repository_key: + if current_repository_key_rd_dicts: + # There should be only a single current_repository_key_rd_dict in this list. + current_repository_key_rd_dict = current_repository_key_rd_dicts[ 0 ] + # Handle circular repository dependencies. + if not in_circular_repository_dependencies( current_repository_key_rd_dict, circular_repository_dependencies ): + if current_repository_key in all_repository_dependencies: + handle_current_repository_dependency( trans, + current_repository_key, + key_rd_dicts_to_be_processed, + all_repository_dependencies, + handled_key_rd_dicts, + circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) return all_repository_dependencies +def get_repository_dependency_as_key( repository_dependency ): + return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], + repository_dependency[ 1 ], + repository_dependency[ 2 ], + repository_dependency[ 3] ) def get_repository_file_contents( file_path ): if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) @@ -1415,11 +1357,77 @@ relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths +def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): + updated_key_rd_dicts = [] + for key_rd_dict in key_rd_dicts: + key = key_rd_dict.keys()[ 0 ] + repository_dependency = key_rd_dict[ key ] + toolshed, name, owner, changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( toolshed ): + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + # The repository changeset_revision is installable, so no updates are available. + new_key_rd_dict = {} + new_key_rd_dict[ key ] = repository_dependency + updated_key_rd_dicts.append( key_rd_dict ) + else: + # The repository changeset_revision is no longer installable, so see if there's been an update. + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + new_key_rd_dict = {} + new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ] + # We have the updated changset revision. + updated_key_rd_dicts.append( new_key_rd_dict ) + return updated_key_rd_dicts def get_user_by_username( trans, username ): """Get a user from the database by username""" return trans.sa_session.query( trans.model.User ) \ .filter( trans.model.User.table.c.username == username ) \ .one() +def handle_circular_repository_dependency( repository_key, repository_dependency, circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies ): + all_repository_dependencies_root_key = all_repository_dependencies[ 'root_key' ] + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + update_circular_repository_dependencies( repository_key, + repository_dependency, + all_repository_dependencies[ repository_dependency_as_key ], + circular_repository_dependencies ) + if all_repository_dependencies_root_key != repository_dependency_as_key: + all_repository_dependencies[ repository_key ] = [ repository_dependency ] + return circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies +def handle_current_repository_dependency( trans, current_repository_key, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, + circular_repository_dependencies ): + current_repository_key_rd_dicts = [] + for rd in all_repository_dependencies[ current_repository_key ]: + rd_copy = [ str( item ) for item in rd ] + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = rd_copy + current_repository_key_rd_dicts.append( new_key_rd_dict ) + if current_repository_key_rd_dicts: + toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + handle_key_rd_dicts_for_repository( trans, + current_repository_key, + current_repository_key_rd_dicts, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies ) + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=toolshed, + key_rd_dicts_to_be_processed=key_rd_dicts_to_be_processed, + all_repository_dependencies=all_repository_dependencies, + handled_key_rd_dicts=handled_key_rd_dicts, + circular_repository_dependencies=circular_repository_dependencies ) def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ): """ This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an @@ -1438,6 +1446,56 @@ else: deleted_tool_dependency_names.append( original_dependency_val_dict[ 'name' ] ) return updated_tool_dependency_names, deleted_tool_dependency_names +def handle_key_rd_dicts_for_repository( trans, current_repository_key, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies ): + key_rd_dict = repository_key_rd_dicts.pop( 0 ) + repository_dependency = key_rd_dict[ current_repository_key ] + toolshed, name, owner, changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( toolshed ): + required_repository = get_repository_by_name_and_owner( trans, name, owner ) + required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( required_repository.id ), + changeset_revision ) + if required_repository_metadata: + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + # The required_repository_metadata changeset_revision is installable. + required_metadata = required_repository_metadata.metadata + if required_metadata: + for current_repository_key_rd_dict in repository_key_rd_dicts: + if not in_key_rd_dicts( current_repository_key_rd_dict, key_rd_dicts_to_be_processed ): + key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict ) + # Mark the current repository_dependency as handled_key_rd_dicts. + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ): + handled_key_rd_dicts.append( key_rd_dict ) + # Remove the current repository from the list of repository_dependencies to be processed. + if in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + key_rd_dicts_to_be_processed = remove_from_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ) + else: + # The repository is in a different tool shed, so build an url and send a request. + error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " + error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) + log.debug( error_message ) + return toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts +def handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ): + next_repository_key_rd_dict = key_rd_dicts_to_be_processed.pop( 0 ) + next_repository_key_rd_dicts = [ next_repository_key_rd_dict ] + next_repository_key = next_repository_key_rd_dict.keys()[ 0 ] + toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + handle_key_rd_dicts_for_repository( trans, + next_repository_key, + next_repository_key_rd_dicts, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies ) + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=toolshed, + key_rd_dicts_to_be_processed=key_rd_dicts_to_be_processed, + all_repository_dependencies=all_repository_dependencies, + handled_key_rd_dicts=handled_key_rd_dicts, + circular_repository_dependencies=circular_repository_dependencies ) def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ): # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. message = '' @@ -1489,8 +1547,59 @@ message = str( e ) error = True return error, message +def in_all_repository_dependencies( repository_key, repository_dependency, all_repository_dependencies ): + """Return True if { repository_key :repository_dependency } is in all_repository_dependencies.""" + for key, val in all_repository_dependencies.items(): + if key != repository_key: + continue + if repository_dependency in val: + return True + return False +def in_circular_repository_dependencies( repository_key_rd_dict, circular_repository_dependencies ): + """ + Return True if any combination of a circular dependency tuple is the key : value pair defined in the received repository_key_rd_dict. This + means that each circular dependency tuple is converted into the key : value pair for vomparision. + """ + for tup in circular_repository_dependencies: + rd_0, rd_1 = tup + rd_0_as_key = get_repository_dependency_as_key( rd_0 ) + rd_1_as_key = get_repository_dependency_as_key( rd_1 ) + if rd_0_as_key in repository_key_rd_dict and repository_key_rd_dict[ rd_0_as_key ] == rd_1: + return True + if rd_1_as_key in repository_key_rd_dict and repository_key_rd_dict[ rd_1_as_key ] == rd_0: + return True + return False +def in_key_rd_dicts( key_rd_dict, key_rd_dicts ): + k = key_rd_dict.keys()[ 0 ] + v = key_rd_dict[ k ] + for key_rd_dict in key_rd_dicts: + for key, val in key_rd_dict.items(): + if key == k and val == v: + return True + return False +def is_circular_repository_dependency( repository_key, repository_dependency, all_repository_dependencies ): + """ + Return True if the received repository_dependency is a key in all_repository_dependencies whose list of repository dependencies + includes the received repository_key. + """ + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + for key, val in all_repository_dependencies.items(): + if key != repository_dependency_as_key: + continue + if repository_key_as_repository_dependency in val: + return True + return False def is_downloadable( metadata_dict ): return 'datatypes' in metadata_dict or 'repository_dependencies' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict +def initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ): + # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. + all_repository_dependencies[ 'root_key' ] = current_repository_key + all_repository_dependencies[ current_repository_key ] = [] + # Store the value of the 'description' key only once, the first time through this recursive method. + description = repository_dependencies_dict.get( 'description', None ) + all_repository_dependencies[ 'description' ] = description + return all_repository_dependencies def load_tool_from_config( app, full_path ): try: tool = app.toolbox.load_tool( full_path ) @@ -1553,24 +1662,78 @@ "key": full_path } folder_contents.append( node ) return folder_contents +def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, + handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): + current_repository_key_rd_dicts = [] + for rd in repository_dependencies_dict[ 'repository_dependencies' ]: + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = rd + current_repository_key_rd_dicts.append( new_key_rd_dict ) + if current_repository_key_rd_dicts and current_repository_key: + # Remove all repository dependencies that point to a revision within its own repository. + current_repository_key_rd_dicts = remove_ropository_dependency_reference_to_self( current_repository_key_rd_dicts ) + current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, current_repository_key_rd_dicts ) + for key_rd_dict in current_repository_key_rd_dicts: + is_circular = False + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + repository_dependency = key_rd_dict[ current_repository_key ] + if current_repository_key in all_repository_dependencies: + # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. + all_repository_dependencies_val = all_repository_dependencies[ current_repository_key ] + if repository_dependency not in all_repository_dependencies_val: + all_repository_dependencies_val.append( repository_dependency ) + all_repository_dependencies[ current_repository_key ] = all_repository_dependencies_val + elif not in_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): + # Handle circular repository dependencies. + if is_circular_repository_dependency( current_repository_key, repository_dependency, all_repository_dependencies ): + is_circular = True + circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies = \ + handle_circular_repository_dependency( current_repository_key, + repository_dependency, + circular_repository_dependencies, + handled_key_rd_dicts, + all_repository_dependencies ) + else: + all_repository_dependencies[ current_repository_key ] = [ repository_dependency ] + if not is_circular and can_add_to_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = repository_dependency + key_rd_dicts_to_be_processed.append( new_key_rd_dict ) + return current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: shutil.rmtree( dir ) except: pass -def remove_ropository_dependency_reference_to_self( repository_dependencies, repository_key ): +def remove_from_key_rd_dicts( key_rd_dict, key_rd_dicts ): + k = key_rd_dict.keys()[ 0 ] + v = key_rd_dict[ k ] + clean_key_rd_dicts = [] + for krd_dict in key_rd_dicts: + key = krd_dict.keys()[ 0 ] + val = krd_dict[ key ] + if key == k and val == v: + continue + clean_key_rd_dicts.append( krd_dict ) + return clean_key_rd_dicts +def remove_ropository_dependency_reference_to_self( key_rd_dicts ): """Remove all repository dependencies that point to a revision within its own repository.""" - clean_repository_dependencies = [] - repository_tup = repository_key.split( container_util.STRSEP ) + clean_key_rd_dicts = [] + key = key_rd_dicts[ 0 ].keys()[ 0 ] + repository_tup = key.split( container_util.STRSEP ) rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_tup - for repository_dependency in repository_dependencies: + for key_rd_dict in key_rd_dicts: + k = key_rd_dict.keys()[ 0 ] + repository_dependency = key_rd_dict[ k ] toolshed, name, owner, changeset_revision = repository_dependency if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) else: - clean_repository_dependencies.append( repository_dependency ) - return clean_repository_dependencies + new_key_rd_dict = {} + new_key_rd_dict[ key ] = repository_dependency + clean_key_rd_dicts.append( new_key_rd_dict ) + return clean_key_rd_dicts def remove_tool_dependency_installation_directory( dependency_install_dir ): if os.path.exists( dependency_install_dir ): try: @@ -1841,6 +2004,19 @@ else: translated_string = '' return translated_string +def update_circular_repository_dependencies( repository_key, repository_dependency, repository_dependencies, circular_repository_dependencies ): + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + if repository_key_as_repository_dependency in repository_dependencies: + found = False + for tup in circular_repository_dependencies: + if repository_dependency in tup and repository_key_as_repository_dependency in tup: + # The circular dependency has already been included. + found = True + if not found: + new_circular_tup = [ repository_dependency, repository_key_as_repository_dependency ] + circular_repository_dependencies.append( new_circular_tup ) + return circular_repository_dependencies def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates @@ -1889,8 +2065,7 @@ sa_session.flush() new_tool_dependency = tool_dependency else: - # We have no new tool dependency definition based on a matching dependency name, so remove the existing tool dependency record - # from the database. + # We have no new tool dependency definition based on a matching dependency name, so remove the existing tool dependency record from the database. log.debug( "Deleting tool dependency with name '%s', type '%s' and version '%s' from the database since it is no longer defined." % \ ( str( tool_dependency.name ), str( tool_dependency.type ), str( tool_dependency.version ) ) ) sa_session.delete( tool_dependency ) diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1782,14 +1782,14 @@ is_malicious = repository_metadata.malicious if repository_metadata: # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -1895,14 +1895,14 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) else: repository_metadata_id = None metadata = None @@ -2417,14 +2417,14 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) else: repository_metadata_id = None metadata = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for value_to_display_text in DatasetToolparameter when encountering a non-set optional multiple dataset; inspired by a patch from Kyle Ellrott.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c460f284077f/ changeset: c460f284077f user: dan date: 2012-12-10 22:14:05 summary: Fix for value_to_display_text in DatasetToolparameter when encountering a non-set optional multiple dataset; inspired by a patch from Kyle Ellrott. affected #: 1 file diff -r fc84a8b469c3181be64083a91d0fc2faae5e73ef -r c460f284077f0b400901e4cd791d94a311425751 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1605,7 +1605,7 @@ return value.file_name def value_to_display_text( self, value, app ): - if not isinstance(value, list): + if value and not isinstance( value, list ): value = [ value ] if value: return ", ".join( [ "%s: %s" % ( item.hid, item.name ) for item in value ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use tile region in place of tile index for simplicity.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fc84a8b469c3/ changeset: fc84a8b469c3 user: jgoecks date: 2012-12-10 22:08:44 summary: Trackster: use tile region in place of tile index for simplicity. affected #: 1 file diff -r c3acc86490780d1949c4a3abf1263ace7c5ece6c -r fc84a8b469c3181be64083a91d0fc2faae5e73ef static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2762,23 +2762,27 @@ } */ }, + /** * Generate a key for the tile cache. * TODO: create a TileCache object (like DataCache) and generate key internally. */ - _gen_tile_cache_key: function(w_scale, tile_index) { - return w_scale + '_' + tile_index; + _gen_tile_cache_key: function(w_scale, tile_region) { + return w_scale + '_' + tile_region; }, + /** * Request that track be drawn. */ request_draw: function(force, clear_after) { this.view.request_redraw(false, force, clear_after, this); }, + /** * Actions to be taken before drawing. */ before_draw: function() {}, + /** * Draw track. It is possible to force a redraw rather than use cached tiles and/or clear old * tiles after drawing new tiles. @@ -2826,7 +2830,8 @@ is_tile = function(o) { return (o && 'track' in o); }; // Draw tiles. while ( ( tile_index * TILE_SIZE * resolution ) < high ) { - var draw_result = this.draw_helper( force, tile_index, resolution, this.tiles_div, w_scale ); + var tile_region = this._get_tile_bounds(tile_index, resolution), + draw_result = this.draw_helper( force, tile_region, resolution, this.tiles_div, w_scale ); if ( is_tile(draw_result) ) { drawn_tiles.push( draw_result ); } else { @@ -2871,10 +2876,9 @@ * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a * jQuery.Deferred object that is fulfilled when tile can be drawn again. */ - draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { var track = this, - key = this._gen_tile_cache_key(w_scale, tile_index), - region = this._get_tile_bounds(tile_index, resolution); + key = this._gen_tile_cache_key(w_scale, region); // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -3022,7 +3026,7 @@ /** * Returns a genome region that corresponds to a tile at a particular resolution - */ + */ _get_tile_bounds: function(tile_index, resolution) { var tile_low = Math.floor( tile_index * TILE_SIZE * resolution ), tile_length = Math.ceil( TILE_SIZE * resolution ), @@ -3223,11 +3227,10 @@ this.action_icons.param_space_viz_icon.hide(); }, can_draw: Drawable.prototype.can_draw, - draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, - key = this._gen_tile_cache_key(w_scale, tile_index), - region = this._get_tile_bounds(tile_index, resolution); + key = this._gen_tile_cache_key(w_scale, region); // Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -3446,9 +3449,9 @@ /** * Only retrieves data and draws tile if reference data can be displayed. */ - draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, region, resolution, parent_element, w_scale, kwargs) { if (w_scale > this.view.canvas_manager.char_width_px) { - return TiledTrack.prototype.draw_helper.call(this, force, tile_index, resolution, parent_element, w_scale, kwargs); + return TiledTrack.prototype.draw_helper.call(this, force, region, resolution, parent_element, w_scale, kwargs); } else { this.hide_contents(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use underscore methods to simplify tile search/iteration and remove old debugging statement.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c3acc8649078/ changeset: c3acc8649078 user: jgoecks date: 2012-12-10 21:47:05 summary: Trackster: use underscore methods to simplify tile search/iteration and remove old debugging statement. affected #: 1 file diff -r 3ee0e5ee1b375c0fd580c26a93850f2fa44f93f0 -r c3acc86490780d1949c4a3abf1263ace7c5ece6c static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2854,21 +2854,17 @@ // // If some tiles have icons, set padding of tiles without icons so features and rows align. // - var icons_present = false; - for (var tile_index = 0; tile_index < tiles.length; tile_index++) { - if (tiles[tile_index].has_icons) { - icons_present = true; - break; - } - } + var icons_present = _.find(tiles, function(tile) { + return tile.has_icons; + }); + if (icons_present) { - for (var tile_index = 0; tile_index < tiles.length; tile_index++) { - tile = tiles[tile_index]; + _.each(tiles, function(tile) { if (!tile.has_icons) { // Need to align with other tile(s) that have icons. tile.html_elt.css("padding-top", ERROR_PADDING); } - } + }); } }, /** @@ -4045,7 +4041,6 @@ var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq); var feature_mapper = null; - // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); ctx.fillStyle = this.prefs.block_color; ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "right"; 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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