migrator.py : add pre-process mapper

server/web2py/applications/vidjil/scripts/migrator.py

@@ -187,12 +187,13 @@ class SampleSetExtractor(Extractor):
 
 class Importer():
 
-    def __init__(self, groupid, db, log, config_mapper):
+    def __init__(self, groupid, db, log, config_mapper, pprocess_mapper):
         self.log = log
         self.log.info("initialising importer")
         self.groupid = groupid
         self.db = db
-        self.mappings = {'config': config_mapper}
+        self.mappings = {'config': config_mapper,
+                        'pre_process': pprocess_mapper}
         self.mappings['sample_set'] = IdMapper(self.log)
 
     def importSampleSets(self, stype, sets):
@@ -326,7 +327,7 @@ def export_sample_set_data(filesrc, filepath, sample_type, sample_ids, log=Migra
 
     log.info("done")
 
-def import_data(filesrc, filedest, groupid, config=None, dry_run=False, log=MigrateLogger()):
+def import_data(filesrc, filedest, groupid, config=None, pprocess=None, dry_run=False, log=MigrateLogger()):
     log.info("importing data")
     data = {}
     with open(filesrc + '/export.json', 'r') as infile:
@@ -336,7 +337,12 @@ def import_data(filesrc, filedest, groupid, config=None, dry_run=False, log=Migr
     config_mapper = ConfigMapper(log)
     if config:
         config_mapper.load(config)
-    imp = Importer(groupid, db, log, config_mapper)
+
+    pprocess_mapper = ConfigMapper(log)
+    if pprocess_mapper:
+        pprocess_mapper.load(pprocess)
+
+    imp = Importer(groupid, db, log, config_mapper, pprocess_mapper)
 
     try:
         set_types = ['patient', 'run', 'generic']
@@ -350,6 +356,8 @@ def import_data(filesrc, filedest, groupid, config=None, dry_run=False, log=Migr
 
         for row in data['fused_file']:
             data['fused_file'][row]['patient_id'] = None
+
+        imp.importTable('sequence_file', data['sequence_file'], {'pre_process': 'pre_process_id'}, map_val=True)
         imp.importTable('sample_set_membership', data['membership'], {'sample_set': 'sample_set_id', 'sequence_file': 'sequence_file_id'})
         imp.importTable('scheduler_task', data['scheduler_task'], map_val=True)
         imp.importTable('scheduler_run', data['scheduler_run'], {'scheduler_task': 'task_id'})
@@ -388,6 +396,7 @@ def main():
     import_parser = subparsers.add_parser('import', help='Import data from JSON into the DB')
     import_parser.add_argument('--dry-run', dest='dry', action='store_true', help='With a dry run, the data will not be saved to the database')
     import_parser.add_argument('--config', type=str, dest='config', help='Select the config mapping file')
+    import_parser.add_argument('--pre-process', type=str, dest='pprocess', help='Select the pre-process mapping file')
     import_parser.add_argument('groupid', type=long, help='The long ID of the receiver group')
 
     parser.add_argument('-p', type=str, dest='filepath', default='./', help='Select the file destination')
@@ -408,7 +417,7 @@ def main():
     elif args.command == 'import':
         if args.dry:
             log.log.setLevel(logging.DEBUG)
-        import_data(args.filesrc, args.filepath, args.groupid, args.config, args.dry, log)
+        import_data(args.filesrc, args.filepath, args.groupid, args.config, args.pprocess, args.dry, log)
 
 if __name__ == '__main__':
     main()