**module_method_kwds)
def from_workflow_step(self, trans, repository_id, changeset_revision,
tools_metadata, step):
"""Return module initialized from the WorkflowStep object `step`."""
type = step.type
module_method_kwds = dict()
if type == "tool":
module_method_kwds['repository_id'] = repository_id
module_method_kwds['changeset_revision'] = changeset_revision
module_method_kwds['tools_metadata'] = tools_metadata
return self.module_types[type].from_workflow_step(
trans, step, **module_method_kwds)
tool_shed_module_types = module_types.copy()
tool_shed_module_types['tool'] = RepoToolModule
module_factory = RepoWorkflowModuleFactory(tool_shed_module_types)
def generate_workflow_image(trans,
workflow_name,
repository_metadata_id=None,
repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == 'tool_shed':
module_method_kwds[ 'repository_id' ] = repository_id
module_method_kwds[ 'changeset_revision' ] = changeset_revision
module_method_kwds[ 'tools_metadata' ] = tools_metadata
return self.module_types[ type ].from_dict( trans, step_dict, **module_method_kwds )
def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ):
"""Return module initialized from the WorkflowStep object `step`."""
type = step.type
module_method_kwds = dict( )
if type == "tool":
module_method_kwds[ 'repository_id' ] = repository_id
module_method_kwds[ 'changeset_revision' ] = changeset_revision
module_method_kwds[ 'tools_metadata' ] = tools_metadata
return self.module_types[ type ].from_workflow_step( trans, step, **module_method_kwds )
tool_shed_module_types = module_types.copy()
tool_shed_module_types[ 'tool' ] = RepoToolModule
module_factory = RepoWorkflowModuleFactory( tool_shed_module_types )
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode( workflow_name )
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
repository_id = trans.security.encode_id( repository_metadata.repository_id )