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"""this module contains code for processing response from fahamu client.py"""
import os
import string
import json
from urllib.parse import urljoin
from urllib.parse import quote
import logging
import requests
from apis.gnqaclient import GeneNetworkQAClient
from apis.resp import DocIDs
BASE_URL = 'https://genenetwork.fahamuai.com/api/tasks'
# pylint: disable=C0301
def format_bibliography_info(bib_info):
"""Function for formatting bibliography info"""
if isinstance(bib_info, str):
return bib_info.removesuffix('.txt')
elif isinstance(bib_info, dict):
return f"{bib_info['author']}.{bib_info['title']}.{bib_info['year']}.{bib_info['doi']} "
return bib_info
def filter_response_text(val):
"""helper function for filtering non-printable chars"""
return json.loads(''.join([str(char)
for char in val if char in string.printable]))
def parse_context(context, get_info_func, format_bib_func):
"""function to parse doc_ids content"""
results = []
for doc_ids, summary in context.items():
combo_txt = ""
for entry in summary:
combo_txt += "\t" + entry["text"]
doc_info = get_info_func(doc_ids)
bib_info = doc_ids if doc_ids == doc_info else format_bib_func(
doc_info)
results.append(
{"doc_id": doc_ids, "bibInfo": bib_info, "comboTxt": combo_txt})
return results
def rate_document(task_id, doc_id, rating, auth_token):
"""This method is used to provide feedback for a document by making a rating."""
# todo move this to clients
try:
url = urljoin(BASE_URL,
f"""/feedback?task_id={task_id}&document_id={doc_id}&feedback={rating}""")
headers = {"Authorization": f"Bearer {auth_token}"}
resp = requests.post(url, headers=headers)
resp.raise_for_status()
return {"status": "success", **resp.json()}
except requests.exceptions.HTTPError as http_error:
raise RuntimeError(f"HTTP Error Occurred:\
{http_error.response.text} -with status code- {http_error.response.status_code}") from http_error
except Exception as error:
raise RuntimeError(f"An error occurred: {str(error)}") from error
def load_file(filename, dir_path):
"""function to open and load json file"""
file_path = os.path.join(dir_path, f"{filename}")
if not os.path.isfile(file_path):
raise FileNotFoundError(f"{filename} was not found or is a directory")
with open(file_path, "rb") as file_handler:
return json.load(file_handler)
def fetch_pubmed(references, file_name, data_dir=""):
"""method to fetch and populate references with pubmed"""
try:
pubmed = load_file(file_name, os.path.join(data_dir, "gn-meta/lit"))
for reference in references:
if pubmed.get(reference["doc_id"]):
reference["pubmed"] = pubmed.get(reference["doc_id"])
return references
except FileNotFoundError:
logging.error("failed to find pubmed_path for %s/%s",
data_dir, file_name)
return references
def get_gnqa(query, auth_token, tmp_dir=""):
"""entry function for the gn3 api endpoint()"""
api_client = GeneNetworkQAClient(requests.Session(), api_key=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:
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", []
answer = resp_text['data']['answer']
context = resp_text['data']['context']
references = parse_context(
context, DocIDs().getInfo, format_bibliography_info)
#references = fetch_pubmed(references, "pubmed.json", tmp_dir)
return task_id, answer, references
else:
return task_id, "Please try to rephrase your question to receive feedback", []
def get_response_from_taskid(auth_token, task_id):
api_client = GeneNetworkQAClient(requests.Session(), api_key=auth_token)
res, success = api_client.answer(task_id)
if success == 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", []
answer = resp_text['data']['answer']
context = resp_text['data']['context']
references = parse_context(
context, DocIDs().getInfo, format_bibliography_info)
#references = fetch_pubmed(references, "pubmed.json", tmp_dir)
return task_id, answer, references
else:
return task_id, "Please try to rephrase your question to receive feedback", []
def fetch_query_results(query, user_id, redis_conn):
"""this method fetches prev user query searches"""
result = redis_conn.get(f"LLM:{user_id}-{query}")
if result:
return json.loads(result)
return {
"query": query,
"answer": "Sorry No answer for you",
"references": [],
"task_id": None
}
def get_user_queries(user_id, redis_conn):
"""methods to fetch all queries for a specific user"""
results = redis_conn.keys(f"LLM:{user_id}*")
return [query for query in [result.partition("-")[2] for result in results] if query != ""]
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