add support to pass on info field

Author: junjun-zhang

payload-gen-dna-alignment/main.py

@@ -135,6 +135,7 @@ def main(args):
             'name': 'sequencing_alignment'
         },
         'studyId': seq_experiment_analysis_dict.get('studyId'),
+        'info': {},
         'workflow': {
             'workflow_name': workflow_full_name.get(args.wf_name, args.wf_name),
             'workflow_version': args.wf_version,
@@ -155,6 +156,12 @@ def main(args):
         'read_groups': seq_experiment_analysis_dict.get('read_groups')
     }
 
+    # pass `info` dict from seq_experiment payload to new payload
+    if 'info' in seq_experiment_analysis_dict and isinstance(seq_experiment_analysis_dict['info'], dict):
+        payload['info'] = seq_experiment_analysis_dict['info']
+    else:
+        payload.pop('info')
+
     payload['experiment'].update(seq_experiment_analysis_dict.get('experiment', {}))
 
     if 'library_strategy' in payload['experiment']:

payload-gen-dna-alignment/tests/checker.nf

@@ -74,13 +74,13 @@ process file_smart_diff {
     cat ${output_file} \
       | sed -e 's/"run_id": ".*"/"run_id": "run_id"/' \
       | sed -e 's/"session_id": ".*"/"session_id": "session_id"/' \
-      | sed -e 's/"fileName": ".*.DO.*.SA.*.*"/"fileName": "_study_.DO_id_.SA_id_._normalized_file_name_"/' \
+      | sed -e 's/"fileName": ".*"/"fileName": "_normalized_file_name_"/' \
       > normalized_output
 
     ([[ '${expected_file}' == *.gz ]] && gunzip -c ${expected_file} || cat ${expected_file}) \
       | sed -e 's/"run_id": ".*"/"run_id": "run_id"/' \
       | sed -e 's/"session_id": ".*"/"session_id": "session_id"/' \
-      | sed -e 's/"fileName": ".*.DO.*.SA.*.*"/"fileName": "_study_.DO_id_.SA_id_._normalized_file_name_"/' \
+      | sed -e 's/"fileName": ".*"/"fileName": "_normalized_file_name_"/' \
       > normalized_expected
 
     diff normalized_output normalized_expected \

tests/data/0ae2c59b-2976-485c-a2c5-9b2976085cbf.fq.sequencing_experiment.song-analysis.json

@@ -1,6 +1,9 @@
 {
   "analysisId": "0ae2c59b-2976-485c-a2c5-9b2976085cbf",
   "studyId": "TEST-PRO",
+  "info": {
+    "anything": "any value"
+  },
   "analysisState": "PUBLISHED",
   "samples": [
     {

tests/data/dc934840-98a2-4471-8655-deaaad226180.dna_alignment.payload.json

@@ -3,6 +3,9 @@
     "name": "sequencing_alignment"
   },
   "studyId": "TEST-PRO",
+  "info": {
+    "anything": "any value"
+  },
   "workflow": {
     "workflow_name": "DNA Seq Alignment",
     "workflow_version": "0.4.0",

tests/data/ebf6a3ab-05d5-4a19-bc36-5fd4abac58ff.dna_alignment.payload.json

@@ -3,6 +3,9 @@
     "name": "sequencing_alignment"
   },
   "studyId": "TEST-PRO",
+  "info": {
+    "anything": "any value"
+  },
   "workflow": {
     "workflow_name": "DNA Seq Alignment",
     "workflow_version": "0.4.0",