2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ff39b398d5f/ Changeset: 8ff39b398d5f User: inithello Date: 2013-12-13 20:30:19 Summary: Fix for the install and test framework failing to retrieve a list of repositories to test from a tool shed tracking stable. Affected #: 1 file diff -r 5fb649265c513d6efd1e9d6c93ab06e6996e2008 -r 8ff39b398d5f3f275e55c42f69f6b5038e9d621d 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 @@ -306,14 +306,19 @@ elif 'api' not in parts: parts.insert( 0, 'api' ) url = suc.url_join( base, *parts ) - if params: - url += '?%s' % params + if params is not None: + if 'key' not in params: + params[ 'key' ] = tool_shed_api_key + query_string = urllib.urlencode( params ) + url += '?%s' % query_string + else: + url += '?key=%s' % tool_shed_api_key return url def get_latest_downloadable_changeset_revision( url, name, owner ): error_message = '' parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = urllib.urlencode( dict( name=name, owner=owner ) ) + params = dict( name=name, owner=owner ) api_url = get_api_url( base=url, parts=parts, params=params ) changeset_revisions, error_message = json_from_url( api_url ) if error_message: @@ -336,7 +341,7 @@ def get_repository_dict( url, repository_dict ): error_message = '' parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts, params=None ) + api_url = get_api_url( base=url, parts=parts ) extended_dict, error_message = json_from_url( api_url ) if error_message: return None, error_message @@ -370,12 +375,12 @@ log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) repository_dicts = [] parts = [ 'repository_revisions' ] - params = urllib.urlencode( dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) ) + params = dict( do_not_test='false', + downloadable='true', + includes_tools='true', + malicious='false', + missing_test_components='false', + skip_tool_test='false' ) api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: @@ -462,7 +467,7 @@ """ error_message = '' parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] - api_url = get_api_url( base=tool_shed_url, parts=parts, params=None ) + api_url = get_api_url( base=tool_shed_url, parts=parts ) repository_metadata, error_message = json_from_url( api_url ) if error_message: return None, error_message https://bitbucket.org/galaxy/galaxy-central/commits/67b996a66ef9/ Changeset: 67b996a66ef9 User: inithello Date: 2013-12-13 20:32:11 Summary: Merge with 11729:46dd06fbc774. Affected #: 2 files diff -r 8ff39b398d5f3f275e55c42f69f6b5038e9d621d -r 67b996a66ef9f2de2381bfb66f11bba99b3552fd lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -212,13 +212,13 @@ tmp_dir=job_wrapper.working_directory, #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) - log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) if resolve_requirements: dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() if dependency_shell_commands: if isinstance( dependency_shell_commands, list ): dependency_shell_commands = "&&".join( dependency_shell_commands ) external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) + log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, env=os.environ, diff -r 8ff39b398d5f3f275e55c42f69f6b5038e9d621d -r 67b996a66ef9f2de2381bfb66f11bba99b3552fd 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 @@ -643,6 +643,11 @@ # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts # since it will be re-inserted later. tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + elif len( tool_test_results_dict ) == 2 and \ + 'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict: + # We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components". + # In this case, some tools are missing tests components while others are not. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. tool_test_results_dict = {} 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.