set job state to new in upload tool action so that track_jobs_in_database works

lib/galaxy/tools/actions/upload.py

@@ -144,6 +144,7 @@ class UploadToolAction( ToolAction ):
         job.add_parameter( 'paramfile', to_json_string( json_file_path ) )
         for i, dataset in enumerate( data_list ):
             job.add_output_dataset( i, dataset )
+        job.state = trans.app.model.Job.states.NEW
         trans.app.model.flush()
         
         # Queue the job for execution

tools/data_source/upload.py

@@ -206,6 +206,8 @@ def add_file( dataset, json_file ):
                         elif ext == 'scf' and dataset.file_type != 'scf':
                             file_err( "You must manually set the 'File Format' to 'Scf' when uploading scf files.", dataset, json_file )
                             return
+                    else:
+                        ext = 'binary'
                     data_type = 'binary'
         if not data_type:
             # We must have a text file