diff options
Diffstat (limited to 'gn3/llms/process.py')
| -rw-r--r-- | gn3/llms/process.py | 96 |
1 files changed, 59 insertions, 37 deletions
diff --git a/gn3/llms/process.py b/gn3/llms/process.py index e38b73e..4725bcb 100644 --- a/gn3/llms/process.py +++ b/gn3/llms/process.py @@ -1,21 +1,53 @@ """this module contains code for processing response from fahamu client.py""" +# pylint: disable=C0301 import os import string import json - -from urllib.parse import urljoin -from urllib.parse import quote import logging -import requests +from urllib.parse import quote from gn3.llms.client import GeneNetworkQAClient -from gn3.llms.response import DocIDs BASE_URL = 'https://genenetwork.fahamuai.com/api/tasks' - - -# pylint: disable=C0301 +BASEDIR = os.path.abspath(os.path.dirname(__file__)) + + +class DocIDs(): + """ Class Method to Parse document id and names from files""" + def __init__(self): + """ + init method for Docids + * doc_ids.json: opens doc)ids for gn references + * sugar_doc_ids: open doci_ids for diabetes references + """ + self.doc_ids = self.load_file("doc_ids.json") + self.sugar_doc_ids = self.load_file("all_files.json") + self.format_doc_ids(self.sugar_doc_ids) + + def load_file(self, file_name): + """Method to load and read doc_id files""" + file_path = os.path.join(BASEDIR, file_name) + if os.path.isfile(file_path): + with open(file_path, "rb") as file_handler: + return json.load(file_handler) + else: + raise FileNotFoundError(f"{file_path}-- FIle does not exist\n") + + def format_doc_ids(self, docs): + """method to format doc_ids for list items""" + for _key, val in docs.items(): + if isinstance(val, list): + for doc_obj in val: + doc_name = doc_obj["filename"].removesuffix(".pdf").removesuffix(".txt").replace("_", "") + self.doc_ids.update({doc_obj["id"]: doc_name}) + + def get_info(self, doc_id): + """ interface to make read from doc_ids""" + if doc_id in self.doc_ids.keys(): + return self.doc_ids[doc_id] + else: + return doc_id def format_bibliography_info(bib_info): @@ -48,25 +80,6 @@ def parse_context(context, get_info_func, format_bib_func): 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}") @@ -92,27 +105,36 @@ 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(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: + 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", [] 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) + context, DocIDs().get_info, format_bibliography_info) + references = fetch_pubmed(references, "pubmed.json", data_dir) return task_id, answer, references else: - return task_id, "Please try to rephrase your question to receive feedback", [] + return task_id, "We couldn't provide a response,Please try to rephrase your question to receive feedback", [] def fetch_query_results(query, user_id, redis_conn): @@ -130,6 +152,6 @@ def fetch_query_results(query, user_id, redis_conn): def get_user_queries(user_id, redis_conn): """methos 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 != ""] + return [query for query in + [result.partition("-")[2] for result in results] if query != ""] |