def get_installed_repositories_from_repository_dependencies( self, repository_dependencies_dict ):
installed_repositories = []
if repository_dependencies_dict and isinstance( repository_dependencies_dict, dict ):
for rd_key, rd_vals in repository_dependencies_dict.items():
if rd_key in [ 'root_key', 'description' ]:
continue
# rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ffb9c665__ESEP__True'
# rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']]
repository_components_tuple = container_util.get_components_from_key( rd_key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
tool_shed, name, owner, changeset_revision = components_list[ 0:4 ]
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app,
tool_shed,
name,
owner,
changeset_revision )
if installed_repository not in installed_repositories:
installed_repositories.append( installed_repository )
for rd_val in rd_vals:
tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ]
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app,
tool_shed,
name,
owner,
changeset_revision )
if installed_repository not in installed_repositories:
installed_repositories.append( installed_repository )
return installed_repositories
def get_installed_repositories_from_repository_dependencies(
self, repository_dependencies_dict):
installed_repositories = []
if repository_dependencies_dict and isinstance(
repository_dependencies_dict, dict):
for rd_key, rd_vals in repository_dependencies_dict.items():
if rd_key in ['root_key', 'description']:
continue
# rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ffb9c665__ESEP__True'
# rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']]
repository_components_tuple = container_util.get_components_from_key(
rd_key)
components_list = suc.extract_components_from_tuple(
repository_components_tuple)
tool_shed, name, owner, changeset_revision = components_list[
0:4]
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision(
self.app, tool_shed, name, owner, changeset_revision)
if installed_repository not in installed_repositories:
installed_repositories.append(installed_repository)
for rd_val in rd_vals:
tool_shed, name, owner, changeset_revision = rd_val[0:4]
installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision(
self.app, tool_shed, name, owner, changeset_revision)
if installed_repository not in installed_repositories:
installed_repositories.append(installed_repository)
return installed_repositories
def repair_repository_revision( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/repair_repository_revision
Repair a specified repository revision previously installed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository
"""
api_key = kwd.get( 'key', None )
# Get the information about the repository to be installed 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'." )
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'." )
tool_shed_repositories = []
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision )
repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository )
ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
if ordered_tsr_ids and ordered_repo_info_dicts:
repositories_for_repair = []
for index, tsr_id in enumerate( ordered_tsr_ids ):
repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) )
repo_info_dict = ordered_repo_info_dicts[ index ]
# TODO: handle errors in repair_dict.
repair_dict = repository_util.repair_tool_shed_repository( trans,
repository,
encoding_util.tool_shed_encode( repo_info_dict ) )
repository_dict = repository.get_api_value( value_mapper=default_tool_shed_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
if repair_dict:
errors = repair_dict.get( repository.name, [] )
repository_dict[ 'errors_attempting_repair' ] = ' '.join( errors )
tool_shed_repositories.append( repository_dict )
# Display the list of repaired repositories.
return tool_shed_repositories
def repair_repository_revision(self, trans, payload, **kwd):
"""
POST /api/tool_shed_repositories/repair_repository_revision
Repair a specified repository revision previously installed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed
: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
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(
payload, include_changeset=True)
tool_shed_repositories = []
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision(
trans.app, tool_shed_url, name, owner, changeset_revision)
rrm = RepairRepositoryManager(trans.app)
repair_dict = rrm.get_repair_dict(tool_shed_repository)
ordered_tsr_ids = repair_dict.get('ordered_tsr_ids', [])
ordered_repo_info_dicts = repair_dict.get('ordered_repo_info_dicts',
[])
if ordered_tsr_ids and ordered_repo_info_dicts:
for index, tsr_id in enumerate(ordered_tsr_ids):
repository = trans.install_model.context.query(
trans.install_model.ToolShedRepository).get(
trans.security.decode_id(tsr_id))
repo_info_dict = ordered_repo_info_dicts[index]
# TODO: handle errors in repair_dict.
repair_dict = rrm.repair_tool_shed_repository(
repository, encoding_util.tool_shed_encode(repo_info_dict))
repository_dict = repository.to_dict(
value_mapper=self.__get_value_mapper(trans, repository))
repository_dict['url'] = web.url_for(
controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id(repository.id))
if repair_dict:
errors = repair_dict.get(repository.name, [])
repository_dict['errors_attempting_repair'] = ' '.join(
errors)
tool_shed_repositories.append(repository_dict)
# Display the list of repaired repositories.
return tool_shed_repositories
def repair_repository_revision( self, trans, payload, **kwd ):
"""
POST /api/tool_shed_repositories/repair_repository_revision
Repair a specified repository revision previously installed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed
: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
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
tool_shed_repositories = []
tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app,
tool_shed_url,
name,
owner,
changeset_revision )
rrm = RepairRepositoryManager( trans.app )
repair_dict = rrm.get_repair_dict( tool_shed_repository )
ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
if ordered_tsr_ids and ordered_repo_info_dicts:
for index, tsr_id in enumerate( ordered_tsr_ids ):
repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) )
repo_info_dict = ordered_repo_info_dicts[ index ]
# TODO: handle errors in repair_dict.
repair_dict = rrm.repair_tool_shed_repository( repository,
encoding_util.tool_shed_encode( repo_info_dict ) )
repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id( repository.id ) )
if repair_dict:
errors = repair_dict.get( repository.name, [] )
repository_dict[ 'errors_attempting_repair' ] = ' '.join( errors )
tool_shed_repositories.append( repository_dict )
# Display the list of repaired repositories.
return tool_shed_repositories
