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_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( 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_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( 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_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( 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_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( 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 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_installed_repository(
trans.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=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 load_from_element( self, elem, tool_path ):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % ( elem.tag )
self.declared_id = elem.get( 'id', None )
self.guid = elem.get( 'guid', None )
path = elem.get( 'tool_file', None )
self.version = elem.get( 'version', self.version )
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find( 'tool' )
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % ( util.xml_to_string( elem ) )
path = tool_elem.get( "file", None )
tool_guid = tool_elem.get( "guid", None )
# need to determine repository info so that dependencies will work correctly
tool_shed_url = tool_elem.find( 'tool_shed' ).text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
repository_name = tool_elem.find( 'repository_name' ).text
repository_owner = tool_elem.find( 'repository_owner' ).text
installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text
self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
tool_shed_repository = \
suc.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
# we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path )
except Exception, e:
log.error( 'Error determining tool_path for Data Manager during testing: %s', e )
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id )
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get( "shed_conf_file", None )
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename( shed_conf_file, None )
if shed_conf:
tool_path = shed_conf.get( "tool_path", tool_path )
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_installed_repository( trans.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=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 load_from_element(self, elem, tool_path):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % (
elem.tag)
self.declared_id = elem.get('id', None)
self.guid = elem.get('guid', None)
path = elem.get('tool_file', None)
self.version = elem.get('version', self.version)
tool_shed_repository_id = None
tool_guid = None
if path is None:
tool_elem = elem.find('tool')
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % (
util.xml_to_string(elem))
path = tool_elem.get("file", None)
tool_guid = tool_elem.get("guid", None)
# need to determine repository info so that dependencies will work correctly
tool_shed_url = tool_elem.find('tool_shed').text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(
self.data_managers.app, tool_shed_url)
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url(
tool_shed_url)
repository_name = tool_elem.find('repository_name').text
repository_owner = tool_elem.find('repository_owner').text
installed_changeset_revision = tool_elem.find(
'installed_changeset_revision').text
self.tool_shed_repository_info_dict = dict(
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision)
tool_shed_repository = \
suc.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository is None:
log.warning(
'Could not determine tool shed repository from database. This should only ever happen when running tests.'
)
# we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml(
elem.get('shed_conf_file')).getroot().get(
'tool_path', tool_path)
except Exception, e:
log.error(
'Error determining tool_path for Data Manager during testing: %s',
e)
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id(
tool_shed_repository.id)
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get("shed_conf_file", None)
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename(
shed_conf_file, None)
if shed_conf:
tool_path = shed_conf.get("tool_path", tool_path)
