def import_capsule( self, trans, payload, **kwd ):
"""
POST /api/repositories/new/import_capsule
Import a repository capsule into the Tool Shed.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed into which the capsule should be imported.
:param capsule_file_name (required): the name of the capsule file.
"""
# Get the information about the capsule to be imported from the payload.
tool_shed_url = payload.get( 'tool_shed_url', '' )
if not tool_shed_url:
raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
capsule_file_name = payload.get( 'capsule_file_name', '' )
if not capsule_file_name:
raise HTTPBadRequest( detail="Missing required parameter 'capsule_file_name'." )
capsule_file_path = os.path.abspath( capsule_file_name )
capsule_dict = dict( error_message='',
encoded_file_path=None,
status='ok',
tar_archive=None,
uploaded_file=None,
capsule_file_name=None )
if os.path.getsize( os.path.abspath( capsule_file_name ) ) == 0:
log.debug( 'Your capsule file %s is empty.' % str( capsule_file_name ) )
return {}
try:
# Open for reading with transparent compression.
tar_archive = tarfile.open( capsule_file_path, 'r:*' )
except tarfile.ReadError, e:
log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) )
return {}
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.
file_type = 'gz'
export_repository_dependencies = util.asbool(
export_repository_dependencies)
# Get the repository information.
repository = suc.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
repository_id = trans.security.encode_id(repository.id)
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 __decode_library_content_id( self, content_id ):
if len( content_id ) % 16 == 0:
return 'LibraryDataset', content_id
elif content_id.startswith( 'F' ):
return 'LibraryFolder', content_id[ 1: ]
else:
raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) )
def add_repository_registry_entry(self, trans, payload, **kwd):
"""
POST /api/repositories/add_repository_registry_entry
Adds appropriate entries to the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin():
response_dict['status'] = 'error'
response_dict[
'message'] = "You are not authorized to add entries to this Tool Shed's repository registry."
return response_dict
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'.")
repository = suc.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)
response_dict['status'] = 'error'
response_dict['message'] = error_message
return response_dict
# Update the repository registry.
trans.app.repository_registry.add_entry(repository)
response_dict['status'] = 'ok'
response_dict[ 'message' ] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
% ( name, owner )
return response_dict
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 key == 'time_last_tested':
repository_metadata.time_last_tested = datetime.datetime.utcnow(
)
flush_needed = True
elif hasattr(repository_metadata, key):
# log information when setting attributes associated with the Tool Shed's install and test framework.
if key in [
'do_not_test', 'includes_tools',
'missing_test_components', 'test_install_error',
'tools_functionally_correct'
]:
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
