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Guard against invalid Salmon JSON output #1172

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Mar 26, 2019
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Guard against invalid Salmon JSON output #1172

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37 changes: 23 additions & 14 deletions workers/data_refinery_workers/processors/salmon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -990,20 +990,29 @@ def _run_salmon(job_context: Dict) -> Dict:
kv.is_public = True
kv.save()

with open(os.path.join(job_context['output_directory'], 'lib_format_counts.json')) as lfc_file:
format_count_data = json.load(lfc_file)
kv = ComputationalResultAnnotation()
kv.data = format_count_data
kv.result = result
kv.is_public = True
kv.save()
with open(os.path.join(job_context['output_directory'], 'aux_info', 'meta_info.json')) as mi_file:
meta_info = json.load(mi_file)
kv = ComputationalResultAnnotation()
kv.data = meta_info
kv.result = result
kv.is_public = True
kv.save()
try:
with open(os.path.join(job_context['output_directory'], 'lib_format_counts.json')) as lfc_file:
format_count_data = json.load(lfc_file)
kv = ComputationalResultAnnotation()
kv.data = format_count_data
kv.result = result
kv.is_public = True
kv.save()
except Exception:
# See: https://github.com/AlexsLemonade/refinebio/issues/1167
logger.exception("Error parsing Salmon lib_format_counts JSON output!", processor_job=job_context["job_id"])

try:
with open(os.path.join(job_context['output_directory'], 'aux_info', 'meta_info.json')) as mi_file:
meta_info = json.load(mi_file)
kv = ComputationalResultAnnotation()
kv.data = meta_info
kv.result = result
kv.is_public = True
kv.save()
except Exception:
# See: https://github.com/AlexsLemonade/refinebio/issues/1167
logger.exception("Error parsing Salmon meta_info JSON output!", processor_job=job_context["job_id"])

job_context["success"] = True

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