Fix for running workflows with steps that don't have jobs

lib/galaxy/model/mapping.py

@@ -571,7 +571,7 @@ WorkflowInvocationStep.table = Table( "workflow_invocation_step", metadata,
     Column( "update_time", DateTime, default=now, onupdate=now ),
     Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
     Column( "workflow_step_id",  Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
-    Column( "job_id",  Integer, ForeignKey( "job.id" ), index=True, nullable=False )
+    Column( "job_id",  Integer, ForeignKey( "job.id" ), index=True, nullable=True )
     )
 
 StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata,

lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py

@@ -0,0 +1,62 @@
+"""
+Drop and readd workflow invocation tables, allowing null jobs
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+logging.basicConfig( level=logging.DEBUG )
+log = logging.getLogger( __name__ )
+
+import datetime
+now = datetime.datetime.utcnow
+
+def upgrade():
+    print __doc__
+    
+    metadata = MetaData( migrate_engine )
+    db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+    metadata.reflect()
+
+    # 1) Drop
+
+    for table_name in [ "workflow_invocation_step", "workflow_invocation" ]:
+        try:
+            t = Table( table_name, metadata, autoload=True ).drop()
+        except:
+            log.exception( "Failed to drop table '%s', ignoring (might result in wrong schema)" % table_name )
+        
+    # 2) Readd
+    
+    metadata = MetaData( migrate_engine )
+    db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+    metadata.reflect()
+        
+    WorkflowInvocation_table = Table( "workflow_invocation", metadata,
+        Column( "id", Integer, primary_key=True ),
+        Column( "create_time", DateTime, default=now ),
+        Column( "update_time", DateTime, default=now, onupdate=now ),
+        Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
+    )
+
+    WorkflowInvocationStep_table = Table( "workflow_invocation_step", metadata,
+        Column( "id", Integer, primary_key=True ),
+        Column( "create_time", DateTime, default=now ),
+        Column( "update_time", DateTime, default=now, onupdate=now ),
+        Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
+        Column( "workflow_step_id",  Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
+        Column( "job_id",  Integer, ForeignKey( "job.id" ), index=True, nullable=True ),
+    )
+    
+    for table in [ WorkflowInvocation_table, WorkflowInvocationStep_table ]:
+        try:
+            table.create()
+        except:
+            log.exception( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
+
+def downgrade():
+    # No downgrade
+    pass