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authorAlexander_Kabui2024-05-16 16:34:34 +0300
committerAlexander_Kabui2024-05-16 16:34:34 +0300
commitf30300a82f605fa96130fbcbdcd17c53296d2372 (patch)
tree46739a71836cc7b36cc2c61d84607fd453c3b08b /gn3
parent3913374700521647e93bf9afabb9943746ac5d5b (diff)
downloadgenenetwork3-f30300a82f605fa96130fbcbdcd17c53296d2372.tar.gz
Minor code refactoring related
Diffstat (limited to 'gn3')
-rw-r--r--gn3/llms/process.py23
1 files changed, 16 insertions, 7 deletions
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index d080acb..11961eb 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -4,9 +4,9 @@ import os
import string
import json
import logging
+from urllib.parse import quote
import requests
-from urllib.parse import quote
from gn3.llms.client import GeneNetworkQAClient
@@ -106,15 +106,24 @@ def fetch_pubmed(references, file_name, data_dir=""):
return references
-def get_gnqa(query, auth_token, tmp_dir=""):
- """entry function for the gn3 api endpoint()"""
+def get_gnqa(query, auth_token, data_dir=""):
+ """entry function for the gn3 api endpoint()
+ ARGS:
+ query: what is a gene
+ auth_token: token to connect to api_client
+ data_dir: base datirectory for gn3 data
+ Returns:
+ task_id: fahamu unique identifier for task
+ answer
+ references: contains doc_name,reference,pub_med_info
+ """
- api_client = GeneNetworkQAClient(requests.Session(), api_key=auth_token)
+ api_client = GeneNetworkQAClient(requests.Session(), auth_token)
res, task_id = api_client.ask('?ask=' + quote(query), auth_token)
if task_id == 0:
raise RuntimeError(f"Error connecting to Fahamu Api: {str(res)}")
- res, success = api_client.get_answer(task_id)
- if success == 1:
+ res, status = api_client.get_answer(task_id)
+ if status == 1:
resp_text = filter_response_text(res.text)
if resp_text.get("data") is None:
return task_id, "Please try to rephrase your question to receive feedback", []
@@ -122,7 +131,7 @@ def get_gnqa(query, auth_token, tmp_dir=""):
context = resp_text['data']['context']
references = parse_context(
context, DocIDs().get_info, format_bibliography_info)
- references = fetch_pubmed(references, "pubmed.json", tmp_dir)
+ references = fetch_pubmed(references, "pubmed.json", data_dir)
return task_id, answer, references
else: