1) fix bug in validate_round2 code, 2) added Inf check (together with…

… NaN check) for validation

score_leaderboard.py

@@ -383,8 +383,8 @@ def score_submission(submission, status, args, syn,
             log.info('Scored: {}, {}, {}, {}'.format(
                 submission.id, submission.teamId, k, r))
             for m in r:
-                if math.isnan(m):
-                    raise Exception('NaN found in score {}'.format(r))
+                if math.isnan(m) or m == float('inf') or m == float('-inf'):
+                    raise Exception('NaN or +-Inf found in score {}'.format(r))
             score_outputs.append((k, r))
 
         # score to be shown on wiki (first bootstrap score)

validate.py

@@ -93,21 +93,24 @@ def validate(bw_file, window_size=25):
                     print(msg)
                     all_msg += msg + '\n'
                     valid = False
+                    break
                 if end > s:
                     msg = 'Invalid end interval in chromosome {}. '\
-                    'End must be equal to or smaller than chrom size. '
+                    'End must be equal to or smaller than chrom size. '\
                     'start: {}, end: {}, value: {}, chrsz: {}'.format(
                             c, start, end, v, s)
                     print(msg)
                     all_msg += msg + '\n'
                     valid = False
+                    break
                 if math.isnan(v) or v == float('inf') or v == float('-inf'):
-                    msg = 'Found NaN or Inf. '\
+                    msg = 'Found NaN or Inf in chromosome {}. '\
                     'start: {}, end: {}, value: {}, chrsz: {}'.format(
                             c, start, end, v, s)
                     print(msg)
                     all_msg += msg + '\n'
                     valid = False
+                    break
 
     except Exception as e:
         st = StringIO()

validate_round2.py

@@ -15,6 +15,8 @@
 import multiprocessing
 from validate import validate
 from io import StringIO
+from rank import get_team_name, parse_team_name_tsv
+from score import parse_submission_filename
 from score_leaderboard import mkdir_p, send_message
 from score_leaderboard import WIKI_TEMPLATE_SUBMISSION_STATUS, RE_PATTERN_SUBMISSION_FNAME
 from logger import log
@@ -133,7 +135,7 @@ def parse_arguments():
     p_syn.add_argument('--project-id', default='syn17083203',
                        help='Synapse project ID.')
     p_syn.add_argument('--round2-wiki-id',
-                       default='submission_status:594309',
+                       default='submission_status:594312',
                        help='Comma-delimited Synapse wiki ID for round2.')
     p_syn.add_argument('--submission-dir', default='./submissions',
                        help='Download submissions here.')
@@ -190,6 +192,7 @@ def validate_submission(submission, status, args, syn):
             status['status'] = 'VALIDATED'
             subject = 'Successfully validated submission %s %s %s:\n' % (
                 submission.name, submission.id, submission.teamId)
+            message += '\nSuccess!\n'
         else:
             subject = 'Invalid submission %s %s %s:\n' % (
                 submission.name, submission.id, submission.teamId)
@@ -255,16 +258,15 @@ def main():
                 for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
                     ret_vals.append(
                         pool.apply_async(validate_submission,
-                                         (submission, status, args, syn,
-                                          gene_annotations, enh_annotations)))
+                                         (submission, status, args, syn)))
                 # gather
                 for r in ret_vals:
                     r.get(BIG_INT)
 
                 pool.close()
                 pool.join()
 
-            update_wiki(syn, team_name_dict, args)
+            update_wiki_for_round2(syn, team_name_dict, args)
 
         except Exception as ex1:
             st = StringIO()