Source code for galaxy.webapps.tool_shed.api.repository_revisions

import logging

from sqlalchemy import and_

from galaxy import util
from galaxy import web
from galaxy.webapps.base.controller import BaseAPIController, HTTPBadRequest
from tool_shed.capsule import capsule_manager
from tool_shed.util import metadata_util
from tool_shed.util import repository_util

log = logging.getLogger(__name__)


[docs]class RepositoryRevisionsController(BaseAPIController):
    """RESTful controller for interactions with tool shed repository revisions."""

[docs]    @web.legacy_expose_api_anonymous
    def export(self, trans, payload, **kwd):
        """
        POST /api/repository_revisions/export
        Creates and saves a gzip compressed tar archive of a repository and optionally all of its repository dependencies.

        The following parameters are included in the payload.
        :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported
        :param name (required): the name of the Repository
        :param owner (required): the owner of the Repository
        :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
        :param export_repository_dependencies (optional): whether to export repository dependencies - defaults to False
        :param download_dir (optional): the local directory to which to download the archive - defaults to /tmp
        """
        tool_shed_url = payload.get('tool_shed_url', '')
        if not tool_shed_url:
            raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
        tool_shed_url = tool_shed_url.rstrip('/')
        name = payload.get('name', '')
        if not name:
            raise HTTPBadRequest(detail="Missing required parameter 'name'.")
        owner = payload.get('owner', '')
        if not owner:
            raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
        changeset_revision = payload.get('changeset_revision', '')
        if not changeset_revision:
            raise HTTPBadRequest(detail="Missing required parameter 'changeset_revision'.")
        export_repository_dependencies = payload.get('export_repository_dependencies', False)
        # We'll currently support only gzip-compressed tar archives.
        export_repository_dependencies = util.asbool(export_repository_dependencies)
        # Get the repository information.
        repository = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
        if repository is None:
            error_message = 'Cannot locate repository with name %s and owner %s,' % (str(name), str(owner))
            log.debug(error_message)
            return None, error_message
        erm = capsule_manager.ExportRepositoryManager(app=trans.app,
                                                      user=trans.user,
                                                      tool_shed_url=tool_shed_url,
                                                      repository=repository,
                                                      changeset_revision=changeset_revision,
                                                      export_repository_dependencies=export_repository_dependencies,
                                                      using_api=True)
        return erm.export_repository()

    def __get_value_mapper(self, trans):
        value_mapper = {'id' : trans.security.encode_id,
                        'repository_id' : trans.security.encode_id,
                        'user_id' : trans.security.encode_id}
        return value_mapper

[docs]    @web.legacy_expose_api_anonymous
    def index(self, trans, **kwd):
        """
        GET /api/repository_revisions
        Displays a collection (list) of repository revisions.
        """
        # Example URL: http://localhost:9009/api/repository_revisions
        repository_metadata_dicts = []
        # Build up an anded clause list of filters.
        clause_list = []
        # Filter by downloadable if received.
        downloadable = kwd.get('downloadable', None)
        if downloadable is not None:
            clause_list.append(trans.model.RepositoryMetadata.table.c.downloadable == util.asbool(downloadable))
        # Filter by malicious if received.
        malicious = kwd.get('malicious', None)
        if malicious is not None:
            clause_list.append(trans.model.RepositoryMetadata.table.c.malicious == util.asbool(malicious))
        # Filter by missing_test_components if received.
        missing_test_components = kwd.get('missing_test_components', None)
        if missing_test_components is not None:
            clause_list.append(trans.model.RepositoryMetadata.table.c.missing_test_components == util.asbool(missing_test_components))
        # Filter by includes_tools if received.
        includes_tools = kwd.get('includes_tools', None)
        if includes_tools is not None:
            clause_list.append(trans.model.RepositoryMetadata.table.c.includes_tools == util.asbool(includes_tools))
        for repository_metadata in trans.sa_session.query(trans.app.model.RepositoryMetadata) \
                                                   .filter(and_(*clause_list)) \
                                                   .order_by(trans.app.model.RepositoryMetadata.table.c.repository_id.desc()):
            repository_metadata_dict = repository_metadata.to_dict(view='collection',
                                                                   value_mapper=self.__get_value_mapper(trans))
            repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
                                                          action='show',
                                                          id=trans.security.encode_id(repository_metadata.id))
            repository_metadata_dicts.append(repository_metadata_dict)
        return repository_metadata_dicts

[docs]    @web.legacy_expose_api_anonymous
    def repository_dependencies(self, trans, id, **kwd):
        """
        GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies

        Returns a list of dictionaries that each define a specific downloadable revision of a
        repository in the Tool Shed.  This method returns dictionaries with more information in
        them than other methods in this controller.  The information about repository_metdata is
        enhanced to include information about the repository (e.g., name, owner, etc) associated
        with the repository_metadata record.

        :param id: the encoded id of the `RepositoryMetadata` object
        """
        # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
        repository_dependencies_dicts = []
        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
        if repository_metadata is None:
            log.debug('Invalid repository_metadata id received: %s' % str(id))
            return repository_dependencies_dicts
        metadata = repository_metadata.metadata
        if metadata is None:
            log.debug('The repository_metadata record with id %s has no metadata.' % str(id))
            return repository_dependencies_dicts
        if 'repository_dependencies' in metadata:
            rd_tups = metadata['repository_dependencies']['repository_dependencies']
            for rd_tup in rd_tups:
                tool_shed, name, owner, changeset_revision = rd_tup[0:4]
                repository_dependency = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
                if repository_dependency is None:
                    log.dbug('Cannot locate repository dependency %s owned by %s.' % (name, owner))
                    continue
                repository_dependency_id = trans.security.encode_id(repository_dependency.id)
                repository_dependency_repository_metadata = \
                    metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
                if repository_dependency_repository_metadata is None:
                    # The changeset_revision column in the repository_metadata table has been updated with a new
                    # value value, so find the changeset_revision to which we need to update.
                    new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(trans.app, repository_dependency, changeset_revision)
                    if new_changeset_revision != changeset_revision:
                        repository_dependency_repository_metadata = \
                            metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
                                                                                        repository_dependency_id,
                                                                                        new_changeset_revision)
                        changeset_revision = new_changeset_revision
                    else:
                        decoded_repository_dependency_id = trans.security.decode_id(repository_dependency_id)
                        debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
                            (decoded_repository_dependency_id, str(name), str(owner))
                        debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
                            (str(changeset_revision), str(new_changeset_revision))
                        log.debug(debug_msg)
                        continue
                repository_dependency_metadata_dict = \
                    repository_dependency_repository_metadata.to_dict(view='element',
                                                                      value_mapper=self.__get_value_mapper(trans))
                repository_dependency_dict = repository_dependency.to_dict(view='element',
                                                                           value_mapper=self.__get_value_mapper(trans))
                # We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
                # controller is working with repository_metadata records.  The above to_dict() method returns a dictionary
                # with an id entry for the repository record.  However, all of the other methods in this controller have
                # the id entry associated with a repository_metadata record id.  To avoid confusion, we'll update the
                # repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
                # Python dictionary update() method because we do not want to overwrite existing entries.
                for k, v in repository_dependency_dict.items():
                    if k not in repository_dependency_metadata_dict:
                        repository_dependency_metadata_dict[k] = v
                repository_dependency_metadata_dict['url'] = web.url_for(controller='repositories',
                                                                         action='show',
                                                                         id=repository_dependency_id)
                repository_dependencies_dicts.append(repository_dependency_metadata_dict)
        return repository_dependencies_dicts

[docs]    @web.legacy_expose_api_anonymous
    def show(self, trans, id, **kwd):
        """
        GET /api/repository_revisions/{encoded_repository_metadata_id}
        Displays information about a repository_metadata record in the Tool Shed.

        :param id: the encoded id of the `RepositoryMetadata` object
        """
        # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
        if repository_metadata is None:
            log.debug('Cannot locate repository_metadata with id %s' % str(id))
            return {}
        encoded_repository_id = trans.security.encode_id(repository_metadata.repository_id)
        repository_metadata_dict = repository_metadata.to_dict(view='element',
                                                               value_mapper=self.__get_value_mapper(trans))
        repository_metadata_dict['url'] = web.url_for(controller='repositories',
                                                      action='show',
                                                      id=encoded_repository_id)
        return repository_metadata_dict

[docs]    @web.legacy_expose_api
    def update(self, trans, payload, **kwd):
        """
        PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
        Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.

        :param id: the encoded id of the `RepositoryMetadata` object
        """
        repository_metadata_id = kwd.get('id', None)
        if repository_metadata_id is None:
            raise HTTPBadRequest(detail="Missing required parameter 'id'.")
        repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
        if repository_metadata is None:
            decoded_repository_metadata_id = trans.security.decode_id(repository_metadata_id)
            log.debug('Cannot locate repository_metadata with id %s' % str(decoded_repository_metadata_id))
            return {}
        else:
            decoded_repository_metadata_id = repository_metadata.id
        flush_needed = False
        for key, new_value in payload.items():
            if hasattr(repository_metadata, key):
                # log information when setting attributes associated with the Tool Shed's install and test framework.
                if key in ['includes_tools', 'missing_test_components']:
                    log.debug('Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.' %
                              (str(key), str(new_value), str(repository_metadata.changeset_revision)))
                setattr(repository_metadata, key, new_value)
                flush_needed = True
        if flush_needed:
            log.debug('Updating repository_metadata record with id %s and changeset_revision %s.' %
                      (str(decoded_repository_metadata_id), str(repository_metadata.changeset_revision)))
            trans.sa_session.add(repository_metadata)
            trans.sa_session.flush()
            trans.sa_session.refresh(repository_metadata)
        repository_metadata_dict = repository_metadata.to_dict(view='element',
                                                               value_mapper=self.__get_value_mapper(trans))
        repository_metadata_dict['url'] = web.url_for(controller='repository_revisions',
                                                      action='show',
                                                      id=repository_metadata_id)
        return repository_metadata_dict