1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8b3dbe32435/ Changeset: f8b3dbe32435 User: greg Date: 2013-08-27 20:51:33 Summary: Enhance the installed repositories container on the Manage repository page in Galaxy to properly display mising repositroy and tool dependencies for an installed repository. Affected #: 1 file diff -r 6dfd50e1cfd1e2b9f356cb9e9319f85caf6a74f3 -r f8b3dbe32435516af63e449cedb2e2fc9eb5bf26 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1265,6 +1265,35 @@ return get_folder( sub_folder, key ) return None +def get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ): + """ + Parse a repository dependency and return components necessary for proper display in Galaxy on the Manage repository page. + """ + if len( repository_dependency ) == 6: + # Metadata should have been reset on this installed repository, but it wasn't. + tool_shed_repository_id = repository_dependency[ 4 ] + installation_status = repository_dependency[ 5 ] + tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ] + # Default prior_installation_required to False. + prior_installation_required = False + repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required ] + elif len( repository_dependency ) == 7: + # We have a repository dependency tuple that includes a prior_installation_required value. + tool_shed_repository_id = repository_dependency[ 5 ] + installation_status = repository_dependency[ 6 ] + repository_dependency = repository_dependency[ 0:5 ] + else: + tool_shed_repository_id = None + installation_status = 'unknown' + if tool_shed_repository_id: + tool_shed_repository = suc.get_tool_shed_repository_by_id( trans, trans.security.encode_id( tool_shed_repository_id ) ) + if tool_shed_repository: + if tool_shed_repository.missing_repository_dependencies: + installation_status = '%s, missing repository dependencies' % installation_status + elif tool_shed_repository.missing_tool_dependencies: + installation_status = '%s, missing tool dependencies' % installation_status + return tool_shed_repository_id, installation_status, repository_dependency + def get_components_from_key( key ): # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. items = key.split( STRSEP ) @@ -1315,22 +1344,8 @@ sub_folder.repository_dependencies.append( repository_dependency ) for repository_dependency in rd_value: if trans.webapp.name == 'galaxy': - if len( repository_dependency ) == 6: - # Metadata should have been reset on this installed repository, but it wasn't. - tool_shed_repository_id = repository_dependency[ 4 ] - installation_status = repository_dependency[ 5 ] - tool_shed, name, owner, changeset_revision = repository_dependency[ 0:4 ] - # Default prior_installation_required to False. - prior_installation_required = False - repository_dependency = [ tool_shed, name, owner, changeset_revision, prior_installation_required ] - elif len( repository_dependency ) == 7: - # We have a repository dependency tuple that includes a prior_installation_required value. - tool_shed_repository_id = repository_dependency[ 5 ] - installation_status = repository_dependency[ 6 ] - repository_dependency = repository_dependency[ 0:5 ] - else: - tool_shed_repository_id = None - installation_status = 'unknown' + tool_shed_repository_id, installation_status, repository_dependency = \ + get_components_from_repository_dependency_for_installed_repository( trans, repository_dependency ) else: tool_shed_repository_id = None installation_status = None 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.