1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a41446bf66fd/ changeset: a41446bf66fd user: greg date: 2013-02-16 22:20:33 summary: Fix for handling a complex repository dependency defintiion and a bit of code cleanup. affected #: 1 file diff -r 2fc2d5ef636913bdb29c4f9ecea42e440a2c326a -r a41446bf66fda81772b6fe7d02f921a4955f7ce9 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1429,8 +1429,8 @@ # We have a complex repository dependency. If the retruned value of repository_dependency_is_valid is True, the tool # dependency definition will be set as invalid. This is currently the only case where a tool dependency definition is # considered invalid. - repository_dependencies_tup, repository_dependency_is_valid, error_message = handle_repository_elem( app=app, - repository_elem=sub_elem ) + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + handle_repository_elem( app=app, repository_elem=sub_elem ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -1490,19 +1490,6 @@ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ - """ - "{"orphan_tool_dependencies": - {"bwa/0.5.9": - {"name": "bwa", - "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", - "type": "package", "version": "0.5.9"}}, - "tool_dependencies": - {"bwa/0.5.9": - {"name": "bwa", - "readme": "\\nCompiling BWA requires zlib and libpthread to be present on your system.\\n ", - "type": "package", - "version": "0.5.9"}}}" - """ error_message = '' if original_repository_metadata: # Keep a copy of the original tool dependencies dictionary and the list of tool dictionaries in the metadata. @@ -1538,7 +1525,8 @@ # We have an invalid complex repository dependency, so mark the tool dependency as invalid. tool_dependency_is_valid = False # Append the error message to the invalid repository dependency tuple. - repository_dependency_tup.append( message ) + toolshed, name, owner, changeset_revision = repository_dependency_tup + repository_dependency_tup = ( toolshed, name, owner, changeset_revision, message ) invalid_repository_dependency_tups.append( repository_dependency_tup ) error_message = '%s %s' % ( error_message, message ) elif elem.tag == 'set_environment': 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.