Refactoring work to add in Workflow UUIDs

lib/galaxy/model/__init__.py

@@ -2974,6 +2974,7 @@ class StoredWorkflow( object, Dictifiable):
                 tag_str += ":" + tag.user_value
             tags_str_list.append( tag_str )
         rval['tags'] = tags_str_list
+        rval['latest_workflow_uuid'] = ( lambda uuid: str( uuid ) if self.latest_workflow.uuid else None )( self.latest_workflow.uuid )
         return rval
 
 
@@ -2982,12 +2983,16 @@ class Workflow( object, Dictifiable ):
     dict_collection_visible_keys = ( 'name', 'has_cycles', 'has_errors' )
     dict_element_visible_keys = ( 'name', 'has_cycles', 'has_errors' )
 
-    def __init__( self ):
+    def __init__( self, uuid=None ):
         self.user = None
         self.name = None
         self.has_cycles = None
         self.has_errors = None
         self.steps = []
+        if uuid is None:
+            self.uuid = uuid4()
+        else:
+            self.uuid = UUID(str(uuid))
 
     def has_outputs_defined(self):
         """
@@ -2998,6 +3003,11 @@ class Workflow( object, Dictifiable ):
                 return True
         return False
 
+    def to_dict( self, view='collection', value_mapper=None):
+        rval = super( Workflow, self ).to_dict( view=view, value_mapper = value_mapper )
+        rval['uuid'] = ( lambda uuid: str( uuid ) if uuid else None )( self.uuid )  
+        return rval
+
 
 
 class WorkflowStep( object ):

lib/galaxy/model/mapping.py

@@ -690,7 +690,8 @@ model.Workflow.table = Table( "workflow", metadata,
     Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ),
     Column( "name", TEXT ),
     Column( "has_cycles", Boolean ),
-    Column( "has_errors", Boolean )
+    Column( "has_errors", Boolean ),
+    Column( "uuid", UUIDType, nullable=True )
     )
 
 model.WorkflowStep.table = Table( "workflow_step", metadata,

lib/galaxy/model/migrate/versions/0121_workflow_uuids.py

@@ -0,0 +1,55 @@
+"""
+Add UUIDs to workflows
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.model.custom_types import UUIDType, TrimmedString
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData()
+
+
+
+"""
+Because both workflow and job requests can be determined 
+based the a fixed data structure, their IDs are based on
+hashing the data structure 
+"""
+workflow_uuid_column = Column( "uuid", UUIDType, nullable=True )
+
+
+def display_migration_details():
+    print "This migration script adds a UUID column to workflows"
+
+def upgrade(migrate_engine):
+    print __doc__
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    # Add the uuid colum to the workflow table
+    try:
+        workflow_table = Table( "workflow", metadata, autoload=True )
+        workflow_uuid_column.create( workflow_table )
+        assert workflow_uuid_column is workflow_table.c.uuid
+    except Exception, e:
+        print str(e)
+        log.error( "Adding column 'uuid' to workflow table failed: %s" % str( e ) )
+        return
+
+def downgrade(migrate_engine):
+    metadata.bind = migrate_engine
+    metadata.reflect()
+
+    # Drop the workflow table's uuid column.
+    try:
+        workflow_table = Table( "workflow", metadata, autoload=True )
+        workflow_uuid = workflow_table.c.uuid
+        workflow_uuid.drop()
+    except Exception, e:
+        log.debug( "Dropping 'uuid' column from workflow table failed: %s" % ( str( e ) ) )
+

lib/galaxy/web/base/controller.py

@@ -1791,6 +1791,8 @@ class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ):
         data['format-version'] = "0.1"
         data['name'] = workflow.name
         data['annotation'] = annotation_str
+        if workflow.uuid is not None:
+            data['uuid'] = str(workflow.uuid)  
         data['steps'] = {}
         # For each step, rebuild the form and encode the state
         for step in workflow.steps:

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

@@ -4,6 +4,7 @@ API operations for Workflows
 
 from __future__ import absolute_import
 
+import uuid
 import logging
 from sqlalchemy import desc, or_
 from galaxy import exceptions, util
@@ -437,6 +438,17 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHis
             query = trans.sa_session.query( trans.app.model.StoredWorkflow )
             stored_workflow = query.get( workflow_id )
         except Exception:
+            try:
+                #see if they have passed in the UUID for a workflow that is attached to a stored workflow
+                workflow_uuid = uuid.UUID(workflow_id)
+                stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
+                    trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
+                    trans.app.model.Workflow.uuid == workflow_uuid
+                )).first()            
+                if stored_workflow is None:
+                    raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
+            except:
+                pass #let the outer raise exception happen
             raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." )
         if stored_workflow is None:
             raise exceptions.ObjectNotFound( "No such workflow found." )

scripts/cleanup_datasets/populate_uuid.py

@@ -33,6 +33,12 @@ def main():
             row.uuid = uuid.uuid4()
             print "Setting dataset:", row.id, " UUID to ", row.uuid
     model.context.flush()
+    
+    for row in model.context.query( model.Workflow ):
+        if row.uuid is None:
+            row.uuid = uuid.uuid4()
+            print "Setting Workflow:", row.id, " UUID to ", row.uuid
+    model.context.flush()
 
 
 if __name__ == "__main__":