1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/14ab08c0fbfe/ Changeset: 14ab08c0fbfe User: inithello Date: 2013-03-22 00:23:43 Summary: Update install and test script to correctly load tool data tables. Affected #: 1 file
diff -r b79e2393c8ad8c88bda682e0767f572c0c09e26a -r 14ab08c0fbfe3e9735e94f4e399aeabc870fe4b2 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -107,12 +107,21 @@ else: additional_tool_data_tables = None additional_tool_data_path = None -# And set up a blank tool_data_table_conf.xml and shed_tool_data_table_conf.xml. + +# Also set up default tool data tables. +if os.path.exists( 'tool_data_table_conf.xml' ): + tool_data_table_conf = 'tool_data_table_conf.xml' +elif os.path.exists( 'tool_data_table_conf.xml.sample' ): + tool_data_table_conf = 'tool_data_table_conf.xml.sample' +else: + tool_data_table_conf = None + +# And set up a blank shed_tool_data_table_conf.xml. tool_data_table_conf_xml_template = '''<?xml version="1.0"?><tables></tables> ''' - + # The tool shed url and api key must be set for this script to work correctly. Additionally, if the tool shed url does not # point to one of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF needs to point to a tool sheds configuration file # that contains a definition for that tool shed. @@ -328,7 +337,7 @@ galaxy_test_proxy_port = None # Set up the configuration files for the Galaxy instance. shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) - galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_data_table_conf.xml' ) ) + galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', tool_data_table_conf ) galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) @@ -350,7 +359,7 @@ galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir, prefix='shed_tools' ) galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir @@ -367,9 +376,6 @@
print "Database connection: ", database_connection
- # Generate the tool_data_table_conf.xml file. - file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) - os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF' ] = galaxy_tool_data_table_conf_file # Generate the shed_tool_data_table_conf.xml file. file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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