diff galaxy-tools/biobank/utils/delete_flowcell_results.py @ 3:43be74e62bfe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/delete_flowcell_results.py	Thu Sep 22 08:57:04 2016 -0400
@@ -0,0 +1,97 @@
+import argparse, sys
+
+from bl.vl.kb import KnowledgeBase as KB
+from bl.vl.utils import get_logger, LOG_LEVELS
+import bl.vl.utils.ome_utils as vlu
+
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='remove datasamples connected to a specific sample of a flowcell')
+    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
+    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
+                        help='logging level (default=INFO)', default='INFO')
+    parser.add_argument('-H', '--host', type=str, help='omero server hostname')
+    parser.add_argument('-U', '--user', type=str, help='omero user')
+    parser.add_argument('-P', '--passwd', type=str, help='omero password')
+    parser.add_argument('--flowcell-label', type=str, required=True,
+                        help='flowcell label')
+    parser.add_argument('--sample-label', type=str, required=True,
+                        help='sample label')
+    parser.add_argument('--dry-run', action='store_true',
+                        help='run a simulation, don\'t delete anything')
+    return parser
+
+
+def get_flowcell_samples_map(flowcell, kb, logger):
+    fc = kb.get_by_label(kb.FlowCell, flowcell)
+    if not fc:
+        logger.info('No flowcell with label %s', flowcell)
+        sys.exit(0)
+    logger.info('Loading data for flowcell %s', flowcell)
+    dsamples = kb.dt.get_connected(fc, aklass = kb.SeqDataSample)
+    dsamples_map = {}
+    for ds in dsamples:
+        if ds.sample:
+            dsamples_map.setdefault(ds.sample.label, []).append(ds)
+        else:
+            dsamples_map.setdefault('NO_SAMPLE', []).append(ds)
+    return dsamples_map
+
+
+def print_report(dsamples_map, sample_label, kb, logger):
+    dsamples = dsamples_map.get(sample_label)
+    if not dsamples:
+        logger.info('No sample with label %s is related to the flowcell', sample_label)
+        sys.exit(0)
+    for ds in dsamples:
+        dobjs = kb.get_data_objects(ds)
+        logger.info('## data sample: %s', ds.label)
+        for dob in dobjs:
+            logger.info('### data object: %s --- mimetype: %s', dob.path, dob.mimetype)
+
+
+def delete(dsamples_map, sample_label, kb, logger):
+    for ds in dsamples_map[sample_label]:
+        # this is a hack specific for the automator workflow
+        if not ds.label.startswith('stage1'):
+            logger.info('Deleting data for %s', ds.label)
+            dobjs = kb.get_data_objects(ds)
+            for d in dobjs:
+                kb.delete(d)
+            a = ds.action
+            kb.delete(ds)
+            try:
+                kb.delete(a)
+            except:
+                pass
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('delete_flowcell_results', level=args.loglevel,
+                        filename=args.logfile)
+
+    try:
+        host = args.host or vlu.ome_host()
+        user = args.user or vlu.ome_user()
+        passwd = args.passwd or vlu.ome_passwd()
+    except ValueError, ve:
+        logger.critical(ve)
+        sys.exit(ve)
+
+    kb = KB(driver='omero')(host, user, passwd)
+
+    dsamples_map = get_flowcell_samples_map(args.flowcell_label, kb, logger)
+    print_report(dsamples_map, args.sample_label, kb, logger)
+    if not args.dry_run:
+        delete(dsamples_map, args.sample_label, kb. logger)
+        pass
+    else:
+        logger.debug('SIMULATION, exit now')
+    logger.info('Job completed')
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])