1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/365e1cef25a5/ Changeset: 365e1cef25a5 User: jmchilton Date: 2014-06-13 07:58:23 Summary: Fix failing unit tests for 60d8de4. Affected #: 4 files diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -153,7 +153,7 @@ <!-- <param id="docker_sudo">false</param> --><!-- Following option can be used to tweak sudo command used by default. --> - <!-- <param id="docker_sudo_cmd">/usr/bin/sudo --extra_param</param> --> + <!-- <param id="docker_sudo_cmd">/usr/bin/sudo -extra_param</param> --><!-- By default, docker container will not have any networking enabled. host networking can be bridged by uncommenting next option http://docs.docker.io/reference/run/#network-settings diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 lib/galaxy/tools/deps/containers.py --- a/lib/galaxy/tools/deps/containers.py +++ b/lib/galaxy/tools/deps/containers.py @@ -99,6 +99,12 @@ return asbool(destination_info.get("%s_enabled" % container_type, False)) +class NullContainerFinder(object): + + def find_container(self, tool_info, destination_info, job_info): + return [] + + class ContainerRegistry(): def __init__(self): diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 lib/galaxy/tools/deps/requirements.py --- a/lib/galaxy/tools/deps/requirements.py +++ b/lib/galaxy/tools/deps/requirements.py @@ -53,14 +53,14 @@ ... contents_document = '''<tool><requirements>%s</requirements></tool>''' ... root = ElementTree.fromstring( contents_document % contents ) ... return parse_requirements_from_xml( root ) - >>> reqs = load_requirements('''<requirement>bwa</requirement>''') + >>> reqs, containers = load_requirements('''<requirement>bwa</requirement>''') >>> reqs[0].name 'bwa' >>> reqs[0].version is None True >>> reqs[0].type 'package' - >>> reqs = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''') + >>> reqs, containers = load_requirements('''<requirement type="binary" version="1.3.3">cufflinks</requirement>''') >>> reqs[0].name 'cufflinks' >>> reqs[0].version diff -r 972bd6fbd63f372cc80096e0c099c5e17d33dfe7 -r 365e1cef25a5ef79ed64934e0b1c483ae73a7445 test/unit/tools_support.py --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -16,6 +16,7 @@ from galaxy.util import parse_xml from galaxy.util.dbkeys import GenomeBuilds from galaxy.jobs import NoopQueue +from galaxy.tools.deps.containers import NullContainerFinder class UsesApp( object ): @@ -126,6 +127,7 @@ self.security_agent = GalaxyRBACAgent( self.model ) self.tool_data_tables = {} self.dataset_collections_service = None + self.container_finder = NullContainerFinder() class MockContext(object): 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.