1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/29c1b1b78ea5/ changeset: 29c1b1b78ea5 user: greg date: 2013-02-13 20:39:44 summary: Enhance the process for setting metadata on tool shed repositories to better accommodate recently introduced support for the repository dependecny definition and tool dependency definition Galaxy utilities. affected #: 1 file

diff -r b6241599d1d0bbb4b9ba670bde9fbb421ef6c396 -r 29c1b1b78ea55bbcff28cd33338e2a765efb2e08 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -631,38 +631,51 @@ ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] ancestor_guids.sort() + ancestor_readme_files = ancestor_metadata_dict.get( 'readme_files', [] ) ancestor_repository_dependencies_dict = ancestor_metadata_dict.get( 'repository_dependencies', {} ) ancestor_repository_dependencies = ancestor_repository_dependencies_dict.get( 'repository_dependencies', [] ) - ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', [] ) + ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) current_datatypes = current_metadata_dict.get( 'datatypes', [] ) current_tools = current_metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() + current_readme_files = current_metadata_dict.get( 'readme_files', [] ) current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', [] ) + current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) current_workflows = current_metadata_dict.get( 'workflows', [] ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes + no_readme_files = not ancestor_readme_files and not current_readme_files no_repository_dependencies = not ancestor_repository_dependencies and not current_repository_dependencies - # Note: we currently don't need to check tool_dependencies since we're checking for guids - tool_dependencies always require tools (currently). + # Tool dependencies can define orphan dependencies in the tool shed. no_tool_dependencies = not ancestor_tool_dependencies and not current_tool_dependencies no_tools = not ancestor_guids and not current_guids no_workflows = not ancestor_workflows and not current_workflows - if no_datatypes and no_repository_dependencies and no_tool_dependencies and no_tools and no_workflows: + if no_datatypes and no_readme_files and no_repository_dependencies and no_tool_dependencies and no_tools and no_workflows: return 'no metadata' + # Uncomment the following if we decide that README files should affect how installable repository revisions are defined. See the NOTE in the + # compare_readme_files() method. + # readme_file_comparision = compare_readme_files( ancestor_readme_files, current_readme_files ) repository_dependency_comparison = compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ) + tool_dependency_comparison = compare_tool_dependencies( ancestor_tool_dependencies, current_tool_dependencies ) workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) # Handle case where all metadata is the same. - if ancestor_guids == current_guids and repository_dependency_comparison == 'equal' and workflow_comparison == 'equal' and datatype_comparison == 'equal': + if ancestor_guids == current_guids and \ + repository_dependency_comparison == 'equal' and \ + tool_dependency_comparison == 'equal' and \ + workflow_comparison == 'equal' and \ + datatype_comparison == 'equal': return 'equal' # Handle case where ancestor metadata is a subset of current metadata. + # readme_file_is_subset = readme_file_comparision in [ 'equal', 'subset' ] repository_dependency_is_subset = repository_dependency_comparison in [ 'equal', 'subset' ] + tool_dependency_is_subset = tool_dependency_comparison in [ 'equal', 'subset' ] workflow_dependency_is_subset = workflow_comparison in [ 'equal', 'subset' ] datatype_is_subset = datatype_comparison in [ 'equal', 'subset' ] - if repository_dependency_is_subset and workflow_dependency_is_subset and datatype_is_subset: + if repository_dependency_is_subset and tool_dependency_is_subset and workflow_dependency_is_subset and datatype_is_subset: is_subset = True for guid in ancestor_guids: if guid not in current_guids: @@ -694,6 +707,25 @@ else: return 'subset' return 'not equal and not subset' +def compare_readme_files( ancestor_readme_files, current_readme_files ): + """Determine if ancestor_readme_files is equal to or a subset of current_readme_files.""" + # NOTE: Although repository README files are considered a Galaxy utility similar to tools, repository dependency definition files, etc., + # we don't define installable repository revisions based on changes to README files. To understand why, consider the following scenario: + # 1. Upload the filtering tool to a new repository - this will result in installable revision 0. + # 2. Upload a README file to the repository - this will move the installable revision from revision 0 to revision 1. + # 3. Delete the README file from the repository - this will move the installable revision from revision 1 to revision 2. + # The above scenario is the current behavior, and that is why this method is not currently called. This method exists only in case we decide + # to change this current behavior. + # The lists of readme files looks something like: ["database/community_files/000/repo_2/readme.txt"] + if len( ancestor_readme_files ) <= len( current_readme_files ): + for ancestor_readme_file in ancestor_readme_files: + if ancestor_readme_file not in current_readme_files: + return 'not equal and not subset' + if len( ancestor_readme_files ) == len( current_readme_files ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' def compare_repository_dependencies( ancestor_repository_dependencies, current_repository_dependencies ): """Determine if ancestor_repository_dependencies is the same as or a subset of current_repository_dependencies.""" # The list of repository_dependencies looks something like: [["http://localhost:9009", "emboss_datatypes", "test", "ab03a2a5f407"]]. @@ -717,6 +749,25 @@ else: return 'subset' return 'not equal and not subset' +def compare_tool_dependencies( ancestor_tool_dependencies, current_tool_dependencies ): + """Determine if ancestor_tool_dependencies is the same as or a subset of current_tool_dependencies.""" + # The tool_dependencies dictionary looks something like: + # {'bwa/0.5.9': {'readme': 'some string', 'version': '0.5.9', 'type': 'package', 'name': 'bwa'}} + if len( ancestor_tool_dependencies ) <= len( current_tool_dependencies ): + for ancestor_td_key, ancestor_requirements_dict in ancestor_tool_dependencies.items(): + if ancestor_td_key in current_tool_dependencies: + # The only values that could have changed between the 2 dictionaries are the "readme" or "type" values. Changing the readme value + # makes no difference. Changing the type will change the installation process, but for now we'll assume it was a typo, so new metadata + # shouldn't be generated. + continue + else: + return 'not equal and not subset' + # At this point we know that ancestor_tool_dependencies is at least a subset of current_tool_dependencies. + if len( ancestor_tool_dependencies ) == len( current_tool_dependencies ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' def compare_workflows( ancestor_workflows, current_workflows ): """Determine if ancestor_workflows is the same as current_workflows or if ancestor_workflows is a subset of current_workflows.""" if len( ancestor_workflows ) <= len( current_workflows ): @@ -730,9 +781,7 @@ found_in_current = False for current_workflow_tup in current_workflows: current_workflow_dict = current_workflow_tup[1] - # Assume that if the name and number of steps are euqal, - # then the workflows are the same. Of course, this may - # not be true... + # Assume that if the name and number of steps are euqal, then the workflows are the same. Of course, this may not be true... if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps: found_in_current = True break @@ -1070,7 +1119,11 @@ else: original_repository_metadata = None readme_file_names = get_readme_file_names( repository.name ) - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + if app.name == 'galaxy': + # Shed related tool panel configs are only relevant to Galaxy. + metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + else: + metadata_dict = {} readme_files = [] invalid_file_tups = [] invalid_tool_configs = [] @@ -2862,42 +2915,158 @@ containers_dict[ 'tool_dependencies' ] = root_container containers_dict[ 'missing_tool_dependencies' ] = None return containers_dict -def new_repository_dependency_metadata_required( trans, repository, metadata_dict ): +def new_datatypes_metadata_required( trans, repository_metadata, metadata_dict ): """ - Compare the last saved metadata for each repository dependency in the repository with the new metadata in metadata_dict to determine if a new - repository_metadata table record is required or if the last saved metadata record can be updated instead. + Compare the last saved metadata for each datatype in the repository with the new metadata in metadata_dict to determine if a new + repository_metadata table record is required or if the last saved metadata record can be updated for datatypes instead. """ - if 'repository_dependencies' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) + # Datatypes are stored in metadata as a list of dictionaries that looks like: + # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] + if 'datatypes' in metadata_dict: + current_datatypes = metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: - if 'repository_dependencies' in metadata: - saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + if 'datatypes' in metadata: + ancestor_datatypes = metadata[ 'datatypes' ] # The saved metadata must be a subset of the new metadata. - for new_repository_dependency_metadata in new_repository_dependencies: - if new_repository_dependency_metadata not in saved_repository_dependencies: - return True - for saved_repository_dependency_metadata in saved_repository_dependencies: - if saved_repository_dependency_metadata not in new_repository_dependencies: - return True + datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) + if datatype_comparison == 'not equal and not subset': + return True + else: + return False + else: + # The new metadata includes datatypes, but the stored metadata does not, so we can update the stored metadata. + return False else: - # We have repository metadata that does not include metadata for any repository dependencies in the - # repository, so we can update the existing repository metadata. + # There is no stored metadata, so we can update the metadata column in the repository_metadata table. return False else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. + # There is no stored repository metadata, so we need to create a new repository_metadata table record. return True - # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed. + # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata table record is not needed. return False -def new_tool_metadata_required( trans, repository, metadata_dict ): +def new_metadata_required_for_utilities( trans, repository, new_tip_metadata_dict ): + """ + Galaxy utilities currently consist of datatypes, repository_dependency definitions, tools, tool_dependency definitions and exported + Galaxy workflows. This method compares the last stored repository_metadata record associated with the received repository against the + contents of the received new_tip_metadata_dict and returns True or False for the union set of Galaxy utilities contained in both metadata + dictionaries. The metadata contained in new_tip_metadata_dict may not be a subset of that contained in the last stored repository_metadata + record associated with the received repository because one or more Galaxy utilities may have been deleted from the repository in the new tip. + """ + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + datatypes_required = new_datatypes_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + # Uncomment the following if we decide that README files should affect how installable repository revisions are defined. See the NOTE in the + # compare_readme_files() method. + # readme_files_required = new_readme_files_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + repository_dependencies_required = new_repository_dependency_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + tools_required = new_tool_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + tool_dependencies_required = new_tool_dependency_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + workflows_required = new_workflow_metadata_required( trans, repository_metadata, new_tip_metadata_dict ) + if datatypes_required or repository_dependencies_required or tools_required or tool_dependencies_required or workflows_required: + return True + return False +def new_readme_files_metadata_required( trans, repository_metadata, metadata_dict ): + """ + Compare the last saved metadata for each readme file in the repository with the new metadata in metadata_dict to determine if a new + repository_metadata table record is required or if the last saved metadata record can be updated for readme files instead. + """ + # Repository README files are kind of a special case because they have no effect on reproducibility. We'll simply inspect the file names to + # determine if any that exist in the saved metadata are eliminated from the new metadata in the received metadata_dict. + if 'readme_files' in metadata_dict: + current_readme_files = metadata_dict[ 'readme_files' ] + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'readme_files' in metadata: + ancestor_readme_files = metadata[ 'readme_files' ] + # The saved metadata must be a subset of the new metadata. + readme_file_comparison = compare_readme_files( ancestor_readme_files, current_readme_files ) + if readme_file_comparison == 'not equal and not subset': + return True + else: + return False + else: + # The new metadata includes readme_files, but the stored metadata does not, so we can update the stored metadata. + return False + else: + # There is no stored metadata, so we can update the metadata column in the repository_metadata table. + return False + else: + # There is no stored repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata table record is not needed. + return False +def new_repository_dependency_metadata_required( trans, repository_metadata, metadata_dict ): + """ + Compare the last saved metadata for each repository dependency in the repository with the new metadata in metadata_dict to determine if a new + repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. + """ + if repository_metadata: + metadata = repository_metadata.metadata + if 'repository_dependencies' in metadata: + saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + if new_repository_dependencies_metadata: + new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + # The saved metadata must be a subset of the new metadata. + for new_repository_dependency_metadata in new_repository_dependencies: + if new_repository_dependency_metadata not in saved_repository_dependencies: + return True + for saved_repository_dependency_metadata in saved_repository_dependencies: + if saved_repository_dependency_metadata not in new_repository_dependencies: + return True + else: + # The repository_dependencies.xml file must have been deleted, so create a new repository_metadata record so we always have + # access to the deleted file. + return True + else: + if 'repository_dependencies' in metadata_dict: + # There is no saved repository metadata, so we need to create a new repository_metadata record. + return True + else: + # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata record is not needed. + return False +def new_tool_dependency_metadata_required( trans, repository_metadata, metadata_dict ): + """ + Compare the last saved metadata for each tool dependency in the repository with the new metadata in metadata_dict to determine if a new + repository_metadata table record is required or if the last saved metadata record can be updated for tool_dependencies instead. + """ + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tool_dependencies' in metadata: + saved_tool_dependencies = metadata[ 'tool_dependencies' ] + new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + if new_tool_dependencies: + # The saved metadata must be a subset of the new metadata. + for new_repository_dependency_metadata in new_tool_dependencies: + if new_repository_dependency_metadata not in saved_tool_dependencies: + return True + for saved_repository_dependency_metadata in saved_tool_dependencies: + if saved_repository_dependency_metadata not in new_tool_dependencies: + return True + else: + # The tool_dependencies.xml file must have been deleted, so create a new repository_metadata record so we always have + # access to the deleted file. + return True + else: + # We have repository metadata that does not include metadata for any tool dependencies in the repository, so we can update + # the existing repository metadata. + return False + else: + if 'tool_dependencies' in metadata_dict: + # There is no saved repository metadata, so we need to create a new repository_metadata record. + return True + else: + # The received metadata_dict includes no metadata for tool dependencies, so a new repository_metadata record is not needed. + return False +def new_tool_metadata_required( trans, repository_metadata, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ if 'tools' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -2921,22 +3090,23 @@ for new_tool_metadata_dict in metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True + else: + # The new metadata includes tools, but the stored metadata does not, so we can update the stored metadata. + return False else: - # We have repository metadata that does not include metadata for any tools in the - # repository, so we can update the existing repository metadata. + # There is no stored metadata, so we can update the metadata column in the repository_metadata table. return False else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. + # There is no stored repository metadata, so we need to create a new repository_metadata table record. return True # The received metadata_dict includes no metadata for tools, so a new repository_metadata table record is not needed. return False -def new_workflow_metadata_required( trans, repository, metadata_dict ): +def new_workflow_metadata_required( trans, repository_metadata, metadata_dict ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: # The repository has metadata, so update the workflows value - no new record is needed. return False @@ -3206,9 +3376,9 @@ persist=False ) # We'll only display error messages for the repository tip (it may be better to display error messages for each installable changeset revision). if current_changeset_revision == repository.tip( trans.app ): - invalid_file_tups.extend( invalid_tups ) + invalid_file_tups.extend( invalid_tups ) if current_metadata_dict: - if not metadata_changeset_revision and not metadata_dict: + if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. metadata_changeset_revision = current_changeset_revision metadata_dict = current_metadata_dict @@ -3344,17 +3514,15 @@ updating_installed_repository=False, persist=False ) if metadata_dict: - downloadable = is_downloadable( metadata_dict ) repository_metadata = None - if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \ - new_tool_metadata_required( trans, repository, metadata_dict ) or \ - new_workflow_metadata_required( trans, repository, metadata_dict ): + if new_metadata_required_for_utilities( trans, repository, metadata_dict ): # Create a new repository_metadata table row. repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. if len( repository.downloadable_revisions ) == 1: handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: + # Update the latest stored repository metadata with the contents and attributes of metadata_dict. repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: downloadable = is_downloadable( metadata_dict ) @@ -3365,7 +3533,7 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - # There are no tools in the repository, and we're setting metadata on the repository tip. + # There are no metadata records associated with the repository. repository_metadata = create_or_update_repository_metadata( trans, encoded_id, repository, repository.tip( trans.app ), metadata_dict ) if 'tools' in metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog.

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