1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41c6ee05c8ac/ Changeset: 41c6ee05c8ac User: inithello Date: 2013-12-17 21:54:55 Summary: Fixes for test scripts 1010, 1080, 1400, and 1460. Affected #: 5 files diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1338,7 +1338,7 @@ def verify_installed_repository_data_table_entries( self, required_data_table_entries ): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] - data_tables = xml_util.parse_xml( self.shed_tool_data_table_conf ) + data_tables, error_message = xml_util.parse_xml( self.shed_tool_data_table_conf ) found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -285,6 +285,7 @@ 'Uninstalled' ] self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' ) def test_0065_reinstall_column_repository( self ): @@ -330,6 +331,7 @@ 'Deactivated' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) def test_0075_uninstall_column_repository( self ): @@ -387,8 +389,8 @@ common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=False ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) - self.test_db_util.ga_refresh( installed_column_repository ) - self.test_db_util.ga_refresh( installed_convert_repository ) + self.test_db_util.install_session.refresh( installed_column_repository ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, '' ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1160_circular_prior_installation_required.py --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -247,7 +247,7 @@ convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) # Filtering was selected for reinstallation, so convert chars and column maker should have been installed first. for repo in [ convert_repository, column_repository, filter_repository ]: - self.test_db_util.ga_session.refresh( repo ) + self.test_db_util.install_session.refresh( repo ) assert filter_repository.update_time > convert_repository.update_time, 'Prior installed convert_chars_0160 shows a later update time than filtering_0160' assert filter_repository.update_time > column_repository.update_time, 'Prior installed column_maker_0160 shows a later update time than filtering_0160' diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -34,8 +34,8 @@ migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0', 'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib', - 'zlib and libpthread', 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', - 'samtools', '0.1.16', 'cufflinks', '2.1.1', 'R', '2.11.0' ] + 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', 'samtools', '0.1.16', 'cufflinks', + '2.1.1', 'R', '2.11.0' ] migration_scripts = [ '0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh', '0007_tools.sh', '0008_tools.sh' ] stages.extend( migration_scripts + migrated_tool_dependencies + migrated_repository_names ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -391,7 +391,7 @@ use_heartbeat = False ) # ---- Build Galaxy Application -------------------------------------------------- - if not galaxy_database_connection.startswith( 'sqlite://' ): + if not galaxy_database_connection.startswith( 'sqlite://' ) and not install_galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' kwargs[ 'database_engine_option_max_overflow' ] = '20' galaxyapp = GalaxyUniverseApplication( **kwargs ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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