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Backend updates 2022 06 #652

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Merged
chreman merged 2 commits into from
Jun 3, 2022
Merged

Backend updates 2022 06 #652

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77afdfe
Merge pull request #651 from OpenKnowledgeMaps/dev
chreman Jun 3, 2022
0f79d7e
fix pubmed error handling
chreman Jun 3, 2022
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28 changes: 18 additions & 10 deletions server/workers/pubmed/src/pubmed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,12 +32,20 @@ def execute_search(self, params):
stdout, stderr = proc.communicate(json.dumps(data))
output = [o for o in stdout.split('\n') if len(o) > 0]
error = [o for o in stderr.split('\n') if len(o) > 0]
metadata = pd.DataFrame(json.loads(output[-2]))
text = pd.DataFrame(json.loads(output[-1]))
input_data = {}
input_data["metadata"] = metadata.to_json(orient='records')
input_data["text"] = text.to_json(orient='records')
return input_data
raw_metadata = json.loads(output[-2])
raw_text = json.loads(output[-1])
if isinstance(raw_metadata, dict) and raw_metadata.get('status') == "error":
res = raw_metadata
else:
metadata = pd.DataFrame(raw_metadata)
text = pd.DataFrame(raw_text)
input_data = {}
input_data["metadata"] = metadata.to_json(orient='records')
input_data["text"] = text.to_json(orient='records')
res = {}
res["input_data"] = input_data
res["params"] = params
return res
except Exception as e:
self.logger.error(e)
self.logger.error(error)
Expand All @@ -50,14 +58,14 @@ def run(self):
self.logger.debug(params)
if endpoint == "search":
try:
res = {}
res = self.execute_search(params)
res["id"] = k
res["input_data"] = self.execute_search(params)
res["params"] = params
if params.get('raw') is True:
if res.get("status") == "error" or params.get('raw') is True:
self.redis_store.set(k+"_output", json.dumps(res))
else:
self.redis_store.rpush("input_data", json.dumps(res).encode('utf8'))
except Exception as e:
self.logger.exception("Exception during data retrieval.")
self.logger.error(params)
self.logger.error(e)
self.logger.error(params)