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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/all_enrollments.py	Thu Sep 22 08:57:04 2016 -0400
@@ -0,0 +1,82 @@
+import csv, os, sys, argparse
+
+from bl.vl.kb import KnowledgeBase as KB
+import bl.vl.utils.ome_utils as vlu
+from bl.vl.utils import LOG_LEVELS, get_logger
+
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='Retrieve all enrollments')
+    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
+    parser.add_argument('--loglevel', type=str, choices = LOG_LEVELS,
+                        help='logger level', default='INFO')
+    parser.add_argument('--host', type=str, help='omero hostname')
+    parser.add_argument('--user', type=str, help='omero user')
+    parser.add_argument('--passwd', type=str, help='omero password')
+    parser.add_argument('--ofile', type=str, help='output file path',
+                        required=True)
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    # This is a temporary hack!!!
+    to_be_ignored = ['IMMUNOCHIP_DISCARDED', 'CASI_MS_CSM_TMP',
+                     'CASI_MS_CSM_CODES']
+
+    logger = get_logger('all_enrollments', 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)
+
+    try:
+        out_file_path = args.ofile
+    except IndexError:
+        logger.error('Mandatory field missing.')
+        parser.print_help()
+        sys.exit(2)
+
+    # Create the KnowledgeBase object
+    kb = KB(driver='omero')(host, user, passwd)
+
+    # Retrieve all studies from omero
+    studies = kb.get_objects(kb.Study)
+    studies = [s for s in studies if s.label not in to_be_ignored]
+    logger.info('Retrieved %d studies from database' % len(studies))
+
+    csv_header = ['individual_uuid']
+    enrolls_map = {}
+    # For each study, retrieve all enrollments
+    for s in studies:
+        logger.info('Retrieving enrollments for study %s' % s.label)
+        enrolls = kb.get_enrolled(s)
+        logger.info('%s enrollments retrieved' % len(enrolls))
+        if len(enrolls) > 0:
+            logger.debug('Building lookup dictionary....')
+            csv_header.append(s.label) # Add study label to CSV header
+            for e in enrolls:
+                enrolls_map.setdefault(e.individual.omero_id, {})['individual_uuid'] = e.individual.id
+                enrolls_map[e.individual.omero_id][s.label] = e.studyCode
+        else:
+            logger.debug('No enrollments found, skip study %s' % s.label)
+            
+    # Write to CSV file
+    logger.debug('Writing CSV file %s' % out_file_path)
+    with open(out_file_path, 'w') as f:
+        writer = csv.DictWriter(f, csv_header,
+                                delimiter='\t', quotechar='"',
+                                restval = 'None')
+        writer.writeheader()
+        for k, v in enrolls_map.iteritems():
+            writer.writerow(v)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])