3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/20ed0e6f5700/ Changeset: 20ed0e6f5700 User: jmchilton Date: 2014-09-28 00:50:09+00:00 Summary: Merge next-stable. Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/fe0cdf1166a8/ Changeset: fe0cdf1166a8 Branch: next-stable User: jmchilton Date: 2014-09-28 00:37:21+00:00 Summary: Fix tool migrations to respect GALAXY_CONFIG_* environment variables. Thanks to Bjoern for the bug report. Affected #: 1 file diff -r 1af9145657c0fc74175ee57fd2d696b9fc454a8d -r fe0cdf1166a841eb4b06dae4b40f552d12d947c7 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -19,6 +19,7 @@ from galaxy.model.orm.scripts import require_dialect_egg from galaxy.model.orm.scripts import read_config_file_arg +from galaxy.util.properties import load_app_properties log = logging.getLogger( __name__ ) @@ -28,18 +29,19 @@ sys.exit( 1 ) repo = 'lib/tool_shed/galaxy_install/migrate' +properties = load_app_properties( ini_file=config_file ) cp = SafeConfigParser() cp.read( config_file ) if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] -elif cp.has_option( "app:main", "install_database_connection" ): - db_url = cp.get( "app:main", "install_database_connection" ) -elif cp.has_option( "app:main", "database_connection" ): - db_url = cp.get( "app:main", "database_connection" ) -elif cp.has_option( "app:main", "database_file" ): - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" ) +elif "install_database_connection" in properties: + db_url = properties[ "install_database_connection" ] +elif "database_connection" in properties: + db_url = properties[ "database_connection" ] +elif "database_file" in properties: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties[ "database_file" ] else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" https://bitbucket.org/galaxy/galaxy-central/commits/0ef7a9e69737/ Changeset: 0ef7a9e69737 User: jmchilton Date: 2014-09-28 00:51:04+00:00 Summary: Merge next-stable. Affected #: 1 file diff -r 20ed0e6f5700dfee42cd0d82a2d5e4275fbe1829 -r 0ef7a9e6973794876c3aee484512fb6c23de517d scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -19,6 +19,7 @@ from galaxy.model.orm.scripts import require_dialect_egg from galaxy.model.orm.scripts import read_config_file_arg +from galaxy.util.properties import load_app_properties log = logging.getLogger( __name__ ) @@ -28,18 +29,19 @@ sys.exit( 1 ) repo = 'lib/tool_shed/galaxy_install/migrate' +properties = load_app_properties( ini_file=config_file ) cp = SafeConfigParser() cp.read( config_file ) if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] -elif cp.has_option( "app:main", "install_database_connection" ): - db_url = cp.get( "app:main", "install_database_connection" ) -elif cp.has_option( "app:main", "database_connection" ): - db_url = cp.get( "app:main", "database_connection" ) -elif cp.has_option( "app:main", "database_file" ): - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" ) +elif "install_database_connection" in properties: + db_url = properties[ "install_database_connection" ] +elif "database_connection" in properties: + db_url = properties[ "database_connection" ] +elif "database_file" in properties: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % properties[ "database_file" ] else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" 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.