Fixed challenges hyphen parsing. 2.4.0

Author: ESapenaVentura

lrgasp_metrics/JSON_templates/write_dataset.py

@@ -55,7 +55,7 @@ def metric_to_filename(metric):
     return metric
 
 def main(experiment_path, rdata_path, output_path, challenge):
-    match = challenge.split("_")[0].upper()
+    match = challenge.split("_")[1].replace('sirvs', 'SIRV')
     # Set the values to pass to write_assessment_dataset contained in experiment metadata
     experiment = json.load(open(experiment_path, 'r'))
     community = "OEBC010"

lrgasp_validation/validation.py

@@ -167,12 +167,13 @@ def validate_library_to_metadata(experiment_json):
 
 def challenges_are_valid(challenges, experiment_json):
     for challenge in challenges:
-        split_challenge = challenge.split("_")
-        if experiment_json['library_preps'] not in split_challenge[2]:
+        split_challenge = challenge.split('_')[:2]
+        split_challenge.extend(challenge.split('_')[2].split('-'))
+        if experiment_json.get('library_preps', '') not in split_challenge[2]:
             ERRORS.append(f'Library preparation in challenge {challenge} and metadata provided in experiment.json is not consistent; please ensure you selected the proper library preparation.')
-        if experiment_json['platforms'] not in split_challenge[3]:
+        if experiment_json.get('platforms', '') not in split_challenge[3]:
             ERRORS.append(f'Sequencing platform in challenge {challenge} and metadata provided in experiment.json is not consistent; please ensure you selected the proper sequencing platform.')
-        length = experiment_json['data_category'].split("_")
+        length = experiment_json.get('data_category', 'N_N').split("_")
         length = f"{length[0][0]}{length[1][0]}".upper()
         if length not in split_challenge[4]:
             ERRORS.append(f'Read length in challenge {challenge} and metadata provided in experiment.json is not consistent; please ensure you selected the proper read length.')