Merge pull request #1097 from jmchilton/cwl_refactoring

Small Tool and Workflow Cleanups from CWL Work.

lib/galaxy/managers/workflows.py

@@ -124,6 +124,9 @@ def build_invocations_query( self, trans, decoded_stored_workflow_id ):
 
 class WorkflowContentsManager(UsesAnnotations):
 
+    def __init__(self, app):
+        self.app = app
+
     def build_workflow_from_dict(
         self,
         trans,

lib/galaxy/tools/__init__.py

@@ -613,10 +613,6 @@ def parse( self, tool_source, guid=None ):
         """
         Read tool configuration from the element `root` and fill in `self`.
         """
-        # Get the (user visible) name of the tool
-        self.name = tool_source.parse_name()
-        if not self.name:
-            raise Exception( "Missing tool 'name'" )
         # Get the UNIQUE id for the tool
         self.old_id = tool_source.parse_id()
         if guid is None:
@@ -625,6 +621,12 @@ def parse( self, tool_source, guid=None ):
             self.id = guid
         if not self.id:
             raise Exception( "Missing tool 'id'" )
+
+        # Get the (user visible) name of the tool
+        self.name = tool_source.parse_name()
+        if not self.name:
+            raise Exception( "Missing tool 'name'" )
+
         self.version = tool_source.parse_version()
         if not self.version:
             # For backward compatibility, some tools may not have versions yet.

lib/galaxy/web/base/controller.py

@@ -1099,7 +1099,7 @@ def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publ
         Creates a workflow from a dict. Created workflow is stored in the database and returned.
         """
         # TODO: replace this method with direct access to manager.
-        workflow_contents_manager = workflows.WorkflowContentsManager()
+        workflow_contents_manager = workflows.WorkflowContentsManager( self.app )
         created_workflow = workflow_contents_manager.build_workflow_from_dict(
             trans,
             data,

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -30,7 +30,7 @@ def __init__( self, app ):
         super( WorkflowsAPIController, self ).__init__( app )
         self.history_manager = histories.HistoryManager( app )
         self.workflow_manager = workflows.WorkflowsManager( app )
-        self.workflow_contents_manager = workflows.WorkflowContentsManager()
+        self.workflow_contents_manager = workflows.WorkflowContentsManager( app )
 
     @expose_api
     def index(self, trans, **kwd):
@@ -300,8 +300,7 @@ def update( self, trans, id, payload, **kwds ):
         """
         stored_workflow = self.__get_stored_workflow( trans, id )
         if 'workflow' in payload:
-            workflow_contents_manager = workflows.WorkflowContentsManager()
-            workflow, errors = workflow_contents_manager.update_workflow_from_dict(
+            workflow, errors = self.workflow_contents_manager.update_workflow_from_dict(
                 trans,
                 stored_workflow,
                 payload['workflow'],

lib/galaxy/workflow/extract.py

@@ -106,6 +106,7 @@ def extract_steps( trans, history=None, job_ids=None, dataset_ids=None, dataset_
         step = model.WorkflowStep()
         step.type = 'tool'
         step.tool_id = job.tool_id
+        step.tool_version = job.tool_version
         step.tool_inputs = tool_inputs
         # NOTE: We shouldn't need to do two passes here since only
         #       an earlier job can be used as an input to a later

lib/galaxy/workflow/modules.py

@@ -222,6 +222,7 @@ def default_state( Class ):
     def save_to_step( self, step ):
         step.type = self.type
         step.tool_id = None
+        step.tool_version = None
         step.tool_inputs = self.state
 
     def get_state( self, secure=True ):