From 7aa31cf63e17efe194e501bc37068a2207ab8f38 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 25 Apr 2024 19:45:00 +0300
Subject: Pep8 formatting for response file.

---
 gn3/llms/response.py | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/gn3/llms/response.py b/gn3/llms/response.py
index 11cbd94..93320e9 100644
--- a/gn3/llms/response.py
+++ b/gn3/llms/response.py
@@ -1,11 +1,10 @@
 
 # pylint: skip-file
-import string
 import json
 import os
 
 
-basedir           = os.path.abspath(os.path.dirname(__file__))
+basedir = os.path.abspath(os.path.dirname(__file__))
 
 
 class DocIDs():
@@ -26,21 +25,20 @@ class DocIDs():
             return result
         else:
             raise Exception("\n{0} -- File does not exist\n".format(file_path))
-    
+
     def formatDocIDs(self, values):
         for _key, _val in values.items():
             if isinstance(_val, list):
                 for theObject in _val:
                     docName = self.formatDocumentName(theObject['filename'])
-                    docID   = theObject['id']
+                    docID = theObject['id']
                     self.doc_ids.update({docID: docName})
-                    
-    def formatDocumentName(self, val):
-       result = val.removesuffix('.pdf') 
-       result = result.removesuffix('.txt') 
-       result = result.replace('_', ' ')
-       return result
 
+    def formatDocumentName(self, val):
+        result = val.removesuffix('.pdf')
+        result = result.removesuffix('.txt')
+        result = result.replace('_', ' ')
+        return result
 
     def getInfo(self, doc_id):
         if doc_id in self.doc_ids.keys():
@@ -48,6 +46,7 @@ class DocIDs():
         else:
             return doc_id
 
+
 class RespContext():
     def __init__(self, context):
         self.cntxt = context
@@ -66,10 +65,9 @@ class RespContext():
 def createAccordionFromJson(theContext):
     result = ''
     # loop thru json array
-    ndx = 0
     for docID, summaryLst in theContext.items():
         # item is a key with a list
         comboTxt = ''
         for entry in summaryLst:
             comboTxt += '\t' + entry['text']
-    return result
\ No newline at end of file
+    return result
-- 
cgit v1.2.3


From f6acfd3d6024ad36ef82a8e27918b03f6538cccc Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 25 Apr 2024 19:14:12 +0300
Subject: Code refactoring   * this commit removes ununsed imports and also
 refactor    GenenetworkQAclient  Class

---
 gn3/llms/client.py | 67 +++++++++++++++++++++++++-----------------------------
 1 file changed, 31 insertions(+), 36 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 042becd..b843907 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -2,19 +2,13 @@
 import json
 import string
 import os
-import datetime
 import time
 import requests
 
 from requests import Session
-from urllib.parse import urljoin
 from requests.packages.urllib3.util.retry import Retry
-from requests import HTTPError
-from requests import Session
 from requests.adapters import HTTPAdapter
-from urllib.request import urlretrieve
 from urllib.parse import quote
-from gn3.llms.errors import UnprocessableEntity
 from gn3.llms.errors import LLMError
 
 basedir = os.path.join(os.path.dirname(__file__))
@@ -24,7 +18,8 @@ class TimeoutHTTPAdapter(HTTPAdapter):
     def __init__(self, timeout, *args, **kwargs):
         """TimeoutHTTPAdapter constructor.
         Args:
-            timeout (int): How many seconds to wait for the server to send data before
+            timeout (int): How many seconds to wait for the server to
+        send data before
                 giving up.
         """
         self.timeout = timeout
@@ -43,7 +38,8 @@ class GeneNetworkQAClient(Session):
     """GeneNetworkQA Client
 
     This class provides a client object interface to the GeneNetworkQA API.
-    It extends the `requests.Session` class and includes authorization, base URL,
+    It extends the `requests.Session` class and includes authorization,
+    base URL,
     request timeouts, and request retries.
 
     Args:
@@ -52,16 +48,19 @@ class GeneNetworkQAClient(Session):
         version (str, optional): API version, defaults to "v3".
         timeout (int, optional): Timeout value, defaults to 5.
         total_retries (int, optional): Total retries value, defaults to 5.
-        backoff_factor (int, optional): Retry backoff factor value, defaults to 30.
+        backoff_factor (int, optional): Retry backoff factor value,
+    defaults to 30.
 
     Usage:
         from genenetworkqa import GeneNetworkQAClient
-        gnqa = GeneNetworkQAClient(account="account-name", api_key="XXXXXXXXXXXXXXXXXXX...")
+        gnqa = GeneNetworkQAClient(account="account-name",
+    api_key="XXXXXXXXXXXXXXXXXXX...")
     """
 
     BASE_URL = 'https://genenetwork.fahamuai.com/api/tasks'
 
-    def __init__(self, account, api_key, version="v3", timeout=30, total_retries=5, backoff_factor=30):
+    def __init__(self, account, api_key, version="v3", timeout=30,
+                 total_retries=5, backoff_factor=30):
         super().__init__()
         self.headers.update(
             {"Authorization": "Bearer " + api_key})
@@ -95,31 +94,31 @@ class GeneNetworkQAClient(Session):
         return bib_info
 
     @staticmethod
-    def ask_the_documents(extend_url, my_auth):
+    def ask_the_documents(self, extend_url, my_auth):
         try:
             response = requests.post(
-                base_url + extend_url, data={}, headers=my_auth)
+                self.base_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
         except requests.exceptions.RequestException as e:
             # Handle the exception appropriately, e.g., log the error
             raise RuntimeError(f"Error making the request: {e}")
 
         if response.status_code != 200:
-            return negative_status_msg(response), 0
+            return GeneNetworkQAClient.negative_status_msg(response), 0
 
-        task_id = get_task_id_from_result(response)
-        response = get_answer_using_task_id(task_id, my_auth)
+        task_id = GeneNetworkQAClient.get_task_id_from_result(response)
+        response = GeneNetworkQAClient.get_answer_using_task_id(task_id,
+                                                                my_auth)
 
         if response.status_code != 200:
 
-            return negative_status_msg(response), 0
+            return GeneNetworkQAClient.negative_status_msg(response), 0
 
         return response, 1
 
     @staticmethod
     def negative_status_msg(response):
         return f"Error: Status code -{response.status_code}- Reason::{response.reason}"
-      #  return f"Problems\n\tStatus code => {response.status_code}\n\tReason => {response.reason}"
 
     def ask(self, exUrl, *args, **kwargs):
         askUrl = self.BASE_URL + exUrl
@@ -147,18 +146,13 @@ class GeneNetworkQAClient(Session):
                 response.raise_for_status()
 
             except requests.exceptions.HTTPError as error:
-                if error.response.status_code ==500:
-                    raise LLMError(error.request, error.response, f"Response Error,status_code:{error.response.status_code},Reason: Use of Invalid Token")
-                elif error.response.status_code ==404:
-                    raise LLMError(error.request,error.response,f"404 Client Error: Not Found for url: {self.BASE_URL}")
+                if error.response.status_code == 500:
+                    raise LLMError(error.request, error.response, f"Response Error with:status_code:{error.response.status_code},Reason for error: Use of Invalid Fahamu Token")
+                elif error.response.status_code == 404:
+                    raise LLMError(error.request, error.response, f"404 Client Error: Not Found for url: {self.BASE_URL}")
                 raise error
-
             except requests.exceptions.RequestException as error:
-                raise error 
-
-
-
-
+                raise error
             if response.ok:
                 if method.lower() == "get" and response.json().get("data") is None:
                     time.sleep(retry_delay)
@@ -175,11 +169,10 @@ class GeneNetworkQAClient(Session):
         result = f"?task_id={task_id.get('task_id', '')}"
         return result
 
-    @staticmethod
-    def get_answer_using_task_id(extend_url, my_auth):
+    def get_answer_using_task_id(self, extend_url, my_auth):
         try:
             response = requests.get(
-                answer_url + extend_url, data={}, headers=my_auth)
+               self.answer_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
             return response
         except requests.exceptions.RequestException as error:
@@ -189,7 +182,8 @@ class GeneNetworkQAClient(Session):
     @staticmethod
     def filter_response_text(val):
         """
-        Filters out non-printable characters from the input string and parses it as JSON.
+        Filters out non-printable characters from
+        the input string and parses it as JSON.
 
         Args:
             val (str): Input string to be filtered and parsed.
@@ -198,7 +192,8 @@ class GeneNetworkQAClient(Session):
             dict: Parsed JSON object.
         # remove  this
         """
-        return json.loads(''.join([str(char) for char in val if char in string.printable]))
+        return json.loads(''.join([str(char) for char in val if char
+                                   in string.printable]))
 
     def getTaskIDFromResult(self, res):
         return json.loads(res.text)
@@ -208,11 +203,11 @@ class GeneNetworkQAClient(Session):
 
     def get_gnqa(self, query):
         qstr = quote(query)
-        res, task_id = api_client.ask('?ask=' + qstr)
-        res, success = api_client.get_answer(task_id)
+        res, task_id = GeneNetworkQAClient.ask('?ask=' + qstr)
+        res, success = GeneNetworkQAClient.get_answer(task_id)
 
         if success == 1:
-            resp_text = filter_response_text(res.text)
+            resp_text = GeneNetworkQAClient.filter_response_text(res.text)
             answer = resp_text.get('data', {}).get('answer', '')
             context = resp_text.get('data', {}).get('context', '')
             return answer, context
-- 
cgit v1.2.3


From 852f5c65cdf78c92012afcf9790d272b4e3f4419 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 13:05:46 +0300
Subject: Pep8 Cleanup for llms/errors file

---
 gn3/llms/errors.py | 26 +++-----------------------
 1 file changed, 3 insertions(+), 23 deletions(-)

diff --git a/gn3/llms/errors.py b/gn3/llms/errors.py
index e9f7c02..af3d7b0 100644
--- a/gn3/llms/errors.py
+++ b/gn3/llms/errors.py
@@ -1,32 +1,11 @@
-
-# pylint: skip-file
+""" Error handlers for Fahamu Api"""
 import json
-
 from requests import HTTPError
 
 
 class UnprocessableEntity(HTTPError):
-    """An HTTP 422 Unprocessable Entity error occurred.
-
+    """Error for  HTTP 422 Unprocessable Entity
     https://help.helpjuice.com/en_US/api-v3/api-v3#errors
-
-    The request could not be processed, usually due to a missing or invalid parameter.
-
-    The response will also include an error object with an explanation of fields that
-    are missing or invalid. Here is an example:
-
-    .. code-block::
-
-        HTTP/1.1 422 Unprocessable Entity
-
-
-        {
-          "errors": [
-            {
-              "email": "is not valid."
-            }
-          ]
-        }
     """
 
     def __init__(self, request, response):
@@ -57,6 +36,7 @@ class UnprocessableEntity(HTTPError):
 
 
 class LLMError(HTTPError):
+    """Custom error from making Fahamu APi request """
     def __init__(self, request, response, msg):
         super(HTTPError, self).__init__(
             msg, request=request, response=response)
-- 
cgit v1.2.3


From 167706bb417627b1d9fcacb7cdcebeafe886c1ba Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 13:17:18 +0300
Subject: Remove unused imports for llm.response file

---
 gn3/llms/response.py | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gn3/llms/response.py b/gn3/llms/response.py
index 93320e9..7fce75b 100644
--- a/gn3/llms/response.py
+++ b/gn3/llms/response.py
@@ -45,29 +45,3 @@ class DocIDs():
             return self.doc_ids[doc_id]
         else:
             return doc_id
-
-
-class RespContext():
-    def __init__(self, context):
-        self.cntxt = context
-        self.theObj = {}
-
-    def parseIntoObject(self, info):
-        # check for obj, arr, or val
-        for key, val in info.items():
-            if isinstance(val, list):
-                self.parseIntoObject(val)
-            elif isinstance(val, str) or isinstance(val, int):
-                self.theObj[key] = val
-            self.theObj[key] = self.val
-
-
-def createAccordionFromJson(theContext):
-    result = ''
-    # loop thru json array
-    for docID, summaryLst in theContext.items():
-        # item is a key with a list
-        comboTxt = ''
-        for entry in summaryLst:
-            comboTxt += '\t' + entry['text']
-    return result
-- 
cgit v1.2.3


From 92ab53e9f0b10ebf7423626e37b3fe73eb8c0b65 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:05:02 +0300
Subject: Refactor code for llm:response

---
 gn3/llms/response.py | 60 ++++++++++++++++++++++++----------------------------
 1 file changed, 28 insertions(+), 32 deletions(-)

diff --git a/gn3/llms/response.py b/gn3/llms/response.py
index 7fce75b..2f00312 100644
--- a/gn3/llms/response.py
+++ b/gn3/llms/response.py
@@ -1,46 +1,42 @@
-
-# pylint: skip-file
+""" Module contains code for parsing references doc_ids """
+# pylint: disable=C0301
 import json
 import os
 
-
 basedir = os.path.abspath(os.path.dirname(__file__))
 
 
 class DocIDs():
+    """ Class Method to Parse document id and names"""
     def __init__(self):
-        # open doc ids for GN refs
-        self.doc_ids = self.loadFile("doc_ids.json")
-        # open doc ids for Diabetes references
-        self.sugar_doc_ids = self.loadFile("all_files.json")
-        # format is not what I prefer, it needs to be rebuilt
-        self.formatDocIDs(self.sugar_doc_ids)
-
-    def loadFile(self, file_name):
+        """
+        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):
-            f = open(file_path, "rb")
-            result = json.load(f)
-            f.close()
-            return result
+            with open(file_path, "rb") as file_handler:
+                return json.load(file_handler)
         else:
-            raise Exception("\n{0} -- File does not exist\n".format(file_path))
-
-    def formatDocIDs(self, values):
-        for _key, _val in values.items():
-            if isinstance(_val, list):
-                for theObject in _val:
-                    docName = self.formatDocumentName(theObject['filename'])
-                    docID = theObject['id']
-                    self.doc_ids.update({docID: docName})
-
-    def formatDocumentName(self, val):
-        result = val.removesuffix('.pdf')
-        result = result.removesuffix('.txt')
-        result = result.replace('_', ' ')
-        return result
-
-    def getInfo(self, doc_id):
+            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:
-- 
cgit v1.2.3


From 69013d298c869a42059af13bc63bef1bbdc7393d Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:05:30 +0300
Subject: Update file to use correct import from response file

---
 gn3/llms/process.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index e38b73e..4edc238 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -49,8 +49,9 @@ def parse_context(context, get_info_func, format_bib_func):
 
 
 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
+    """This method is used to provide
+    feedback for a document by making a rating
+    """
     try:
         url = urljoin(BASE_URL,
                       f"""/feedback?task_id={task_id}&document_id={doc_id}&feedback={rating}""")
@@ -107,7 +108,7 @@ def get_gnqa(query, auth_token, tmp_dir=""):
         answer = resp_text['data']['answer']
         context = resp_text['data']['context']
         references = parse_context(
-            context, DocIDs().getInfo, format_bibliography_info)
+            context, DocIDs().get_info, format_bibliography_info)
         references = fetch_pubmed(references, "pubmed.json", tmp_dir)
 
         return task_id, answer, references
-- 
cgit v1.2.3


From 75365bd88a720261a1b454f0ea11a840fb3be83e Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:20:00 +0300
Subject: Move Parsing Doc_Ids to process file     * Context: groups related
 items

---
 gn3/llms/process.py | 51 +++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 8 deletions(-)

diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index 4edc238..1881e92 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -1,21 +1,56 @@
 """this module contains code for processing response from fahamu client.py"""
+# pylint: disable=C0301
 import os
 import string
 import json
+import logging
+import requests
 
 from urllib.parse import urljoin
 from urllib.parse import quote
-import logging
-import requests
 
 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):
@@ -131,6 +166,6 @@ 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 != ""]
-- 
cgit v1.2.3


From f911db6b69b16ac5df57b27d213fa88a4c848f50 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:21:47 +0300
Subject: Delete response file   * File is obsolete functionality move to
 process.py file

---
 gn3/llms/response.py | 43 -------------------------------------------
 1 file changed, 43 deletions(-)
 delete mode 100644 gn3/llms/response.py

diff --git a/gn3/llms/response.py b/gn3/llms/response.py
deleted file mode 100644
index 2f00312..0000000
--- a/gn3/llms/response.py
+++ /dev/null
@@ -1,43 +0,0 @@
-""" Module contains code for parsing references doc_ids """
-# pylint: disable=C0301
-import json
-import os
-
-basedir = os.path.abspath(os.path.dirname(__file__))
-
-
-class DocIDs():
-    """ Class Method to Parse document id and names"""
-    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
-- 
cgit v1.2.3


From a5a6e319e85c28ff3ab9d6f2d8a869bc2ac77ac8 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:25:44 +0300
Subject: Delete function: only useful when training own llm model.

---
 gn3/llms/process.py | 20 --------------------
 1 file changed, 20 deletions(-)

diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index 1881e92..e47a997 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -83,26 +83,6 @@ 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
-    """
-    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}")
-- 
cgit v1.2.3


From 3913374700521647e93bf9afabb9943746ac5d5b Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 14:27:20 +0300
Subject: Pep8 formatting gn3:llm:process.

---
 gn3/llms/process.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index e47a997..d080acb 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -6,9 +6,7 @@ import json
 import logging
 import requests
 
-from urllib.parse import urljoin
 from urllib.parse import quote
-
 from gn3.llms.client import GeneNetworkQAClient
 
 
-- 
cgit v1.2.3


From f30300a82f605fa96130fbcbdcd17c53296d2372 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 16:34:34 +0300
Subject: Minor code refactoring related

---
 gn3/llms/process.py | 23 ++++++++++++++++-------
 1 file 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:
-- 
cgit v1.2.3


From fe23477126b482472f6193797f7d88f59421900c Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 16:35:03 +0300
Subject: Init code refactoring for clients fahamu interface

---
 gn3/llms/client.py | 66 +++++++++---------------------------------------------
 1 file changed, 11 insertions(+), 55 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index b843907..14dcef3 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -1,20 +1,19 @@
+"""Module  Contains code for making request to fahamu Api"""
 # pylint: skip-file
 import json
 import string
-import os
 import time
 import requests
-
 from requests import Session
 from requests.packages.urllib3.util.retry import Retry
 from requests.adapters import HTTPAdapter
 from urllib.parse import quote
 from gn3.llms.errors import LLMError
 
-basedir = os.path.join(os.path.dirname(__file__))
-
 
 class TimeoutHTTPAdapter(HTTPAdapter):
+    """HTTP TimeoutAdapter """
+    # todo rework on this
     def __init__(self, timeout, *args, **kwargs):
         """TimeoutHTTPAdapter constructor.
         Args:
@@ -79,48 +78,29 @@ class GeneNetworkQAClient(Session):
         self.mount("https://", adapter)
         self.mount("http://", adapter)
 
-    @staticmethod
-    def format_bibliography_info(bib_info):
-
-        if isinstance(bib_info, str):
-            # Remove '.txt'
-            bib_info = bib_info.removesuffix('.txt')
-        elif isinstance(bib_info, dict):
-            # Format string bibliography information
-            bib_info = "{0}.{1}.{2}.{3} ".format(bib_info.get('author', ''),
-                                                 bib_info.get('title', ''),
-                                                 bib_info.get('year', ''),
-                                                 bib_info.get('doi', ''))
-        return bib_info
-
-    @staticmethod
     def ask_the_documents(self, extend_url, my_auth):
         try:
             response = requests.post(
                 self.base_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
         except requests.exceptions.RequestException as e:
-            # Handle the exception appropriately, e.g., log the error
             raise RuntimeError(f"Error making the request: {e}")
-
         if response.status_code != 200:
             return GeneNetworkQAClient.negative_status_msg(response), 0
-
         task_id = GeneNetworkQAClient.get_task_id_from_result(response)
         response = GeneNetworkQAClient.get_answer_using_task_id(task_id,
                                                                 my_auth)
-
         if response.status_code != 200:
-
             return GeneNetworkQAClient.negative_status_msg(response), 0
-
         return response, 1
 
     @staticmethod
     def negative_status_msg(response):
+        """ handler for non 200 response from fahamu api"""
         return f"Error: Status code -{response.status_code}- Reason::{response.reason}"
 
     def ask(self, exUrl, *args, **kwargs):
+        """fahamu ask api interface"""
         askUrl = self.BASE_URL + exUrl
         res = self.custom_request('POST', askUrl, *args, **kwargs)
         if (res.status_code != 200):
@@ -129,6 +109,7 @@ class GeneNetworkQAClient(Session):
         return res, task_id
 
     def get_answer(self, taskid, *args, **kwargs):
+        """Fahamu get answer interface"""
         query = self.answer_url + self.extendTaskID(taskid)
         res = self.custom_request('GET', query, *args, **kwargs)
         if (res.status_code != 200):
@@ -136,15 +117,13 @@ class GeneNetworkQAClient(Session):
         return res, 1
 
     def custom_request(self, method, url, *args, **kwargs):
-
+        """ make custom request to fahamu api ask and get response"""
         max_retries = 50
         retry_delay = 3
-
         for i in range(max_retries):
             try:
                 response = super().request(method, url, *args, **kwargs)
                 response.raise_for_status()
-
             except requests.exceptions.HTTPError as error:
                 if error.response.status_code == 500:
                     raise LLMError(error.request, error.response, f"Response Error with:status_code:{error.response.status_code},Reason for error: Use of Invalid Fahamu Token")
@@ -165,33 +144,23 @@ class GeneNetworkQAClient(Session):
 
     @staticmethod
     def get_task_id_from_result(response):
+        """method to get task_id from response"""
         task_id = json.loads(response.text)
-        result = f"?task_id={task_id.get('task_id', '')}"
-        return result
+        return f"?task_id={task_id.get('task_id', '')}"
 
     def get_answer_using_task_id(self, extend_url, my_auth):
+        """call this method with task id to fetch response"""
         try:
             response = requests.get(
                self.answer_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
             return response
         except requests.exceptions.RequestException as error:
-            # Handle the exception appropriately, e.g., log the error
             raise error
 
     @staticmethod
     def filter_response_text(val):
-        """
-        Filters out non-printable characters from
-        the input string and parses it as JSON.
-
-        Args:
-            val (str): Input string to be filtered and parsed.
-
-        Returns:
-            dict: Parsed JSON object.
-        # remove  this
-        """
+        """method to filter out non-printable chacracters"""
         return json.loads(''.join([str(char) for char in val if char
                                    in string.printable]))
 
@@ -200,16 +169,3 @@ class GeneNetworkQAClient(Session):
 
     def extendTaskID(self, task_id):
         return '?task_id=' + str(task_id['task_id'])
-
-    def get_gnqa(self, query):
-        qstr = quote(query)
-        res, task_id = GeneNetworkQAClient.ask('?ask=' + qstr)
-        res, success = GeneNetworkQAClient.get_answer(task_id)
-
-        if success == 1:
-            resp_text = GeneNetworkQAClient.filter_response_text(res.text)
-            answer = resp_text.get('data', {}).get('answer', '')
-            context = resp_text.get('data', {}).get('context', '')
-            return answer, context
-        else:
-            return res, "Unfortunately, I have nothing."
-- 
cgit v1.2.3


From e0aadacbfc23f240c9dad1d0cd430ffcfa99d547 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 17:50:57 +0300
Subject: Pylint Fixes.

---
 gn3/llms/client.py | 83 ++++++++++++++++++++++--------------------------------
 1 file changed, 34 insertions(+), 49 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 14dcef3..2e9898f 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -1,13 +1,13 @@
 """Module  Contains code for making request to fahamu Api"""
-# pylint: skip-file
+# pylint: disable=C0301
 import json
-import string
 import time
+
 import requests
 from requests import Session
-from requests.packages.urllib3.util.retry import Retry
 from requests.adapters import HTTPAdapter
-from urllib.parse import quote
+
+from urllib3.util import Retry
 from gn3.llms.errors import LLMError
 
 
@@ -56,15 +56,14 @@ class GeneNetworkQAClient(Session):
     api_key="XXXXXXXXXXXXXXXXXXX...")
     """
 
-    BASE_URL = 'https://genenetwork.fahamuai.com/api/tasks'
-
     def __init__(self, account, api_key, version="v3", timeout=30,
                  total_retries=5, backoff_factor=30):
         super().__init__()
         self.headers.update(
             {"Authorization": "Bearer " + api_key})
-        self.answer_url = f"{self.BASE_URL}/answers"
-        self.feedback_url = f"{self.BASE_URL}/feedback"
+        self.base_url = "https://genenetwork.fahamuai.com/api/tasks"
+        self.answer_url = f"{self.base_url}/answers"
+        self.feedback_url = f"{self.base_url}/feedback"
 
         adapter = TimeoutHTTPAdapter(
             timeout=timeout,
@@ -83,8 +82,8 @@ class GeneNetworkQAClient(Session):
             response = requests.post(
                 self.base_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
-        except requests.exceptions.RequestException as e:
-            raise RuntimeError(f"Error making the request: {e}")
+        except requests.exceptions.RequestException as error:
+            raise RuntimeError(f"Error making the request: {error}") from error
         if response.status_code != 200:
             return GeneNetworkQAClient.negative_status_msg(response), 0
         task_id = GeneNetworkQAClient.get_task_id_from_result(response)
@@ -99,36 +98,50 @@ class GeneNetworkQAClient(Session):
         """ handler for non 200 response from fahamu api"""
         return f"Error: Status code -{response.status_code}- Reason::{response.reason}"
 
-    def ask(self, exUrl, *args, **kwargs):
+    def ask(self, ex_url, *args, **kwargs):
         """fahamu ask api interface"""
-        askUrl = self.BASE_URL + exUrl
-        res = self.custom_request('POST', askUrl, *args, **kwargs)
-        if (res.status_code != 200):
+        res = self.custom_request('POST', f"{self.base_url}{ex_url}", *args, **kwargs)
+        if res.status_code != 200:
             return self.negative_status_msg(res), 0
-        task_id = self.getTaskIDFromResult(res)
-        return res, task_id
+        return res, json.loads(res.text)
 
     def get_answer(self, taskid, *args, **kwargs):
         """Fahamu get answer interface"""
-        query = self.answer_url + self.extendTaskID(taskid)
+        query = f"{self.answer_url}?task_id={taskid['task_id']}"
         res = self.custom_request('GET', query, *args, **kwargs)
-        if (res.status_code != 200):
+        if res.status_code != 200:
             return self.negative_status_msg(res), 0
         return res, 1
 
+    @staticmethod
+    def get_task_id_from_result(response):
+        """method to get task_id from response"""
+        task_id = json.loads(response.text)
+        return f"?task_id={task_id.get('task_id', '')}"
+
+    def get_answer_using_task_id(self, extend_url, my_auth):
+        """call this method with task id to fetch response"""
+        try:
+            response = requests.get(
+               self.answer_url + extend_url, data={}, headers=my_auth)
+            response.raise_for_status()
+            return response
+        except requests.exceptions.RequestException as error:
+            raise error
+
     def custom_request(self, method, url, *args, **kwargs):
         """ make custom request to fahamu api ask and get response"""
         max_retries = 50
         retry_delay = 3
-        for i in range(max_retries):
+        for _i in range(max_retries):
             try:
                 response = super().request(method, url, *args, **kwargs)
                 response.raise_for_status()
             except requests.exceptions.HTTPError as error:
                 if error.response.status_code == 500:
-                    raise LLMError(error.request, error.response, f"Response Error with:status_code:{error.response.status_code},Reason for error: Use of Invalid Fahamu Token")
+                    raise LLMError(error.request, error.response, f"Response Error with:status_code:{error.response.status_code},Reason for error: Use of Invalid Fahamu Token") from error
                 elif error.response.status_code == 404:
-                    raise LLMError(error.request, error.response, f"404 Client Error: Not Found for url: {self.BASE_URL}")
+                    raise LLMError(error.request, error.response, f"404 Client Error: Not Found for url: {self.base_url}") from error
                 raise error
             except requests.exceptions.RequestException as error:
                 raise error
@@ -141,31 +154,3 @@ class GeneNetworkQAClient(Session):
             else:
                 time.sleep(retry_delay)
             return response
-
-    @staticmethod
-    def get_task_id_from_result(response):
-        """method to get task_id from response"""
-        task_id = json.loads(response.text)
-        return f"?task_id={task_id.get('task_id', '')}"
-
-    def get_answer_using_task_id(self, extend_url, my_auth):
-        """call this method with task id to fetch response"""
-        try:
-            response = requests.get(
-               self.answer_url + extend_url, data={}, headers=my_auth)
-            response.raise_for_status()
-            return response
-        except requests.exceptions.RequestException as error:
-            raise error
-
-    @staticmethod
-    def filter_response_text(val):
-        """method to filter out non-printable chacracters"""
-        return json.loads(''.join([str(char) for char in val if char
-                                   in string.printable]))
-
-    def getTaskIDFromResult(self, res):
-        return json.loads(res.text)
-
-    def extendTaskID(self, task_id):
-        return '?task_id=' + str(task_id['task_id'])
-- 
cgit v1.2.3


From 50c8500105912a6380ea8f971ccfb17ef0994279 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 16 May 2024 18:56:41 +0300
Subject: Refactor code for http request adapters.

---
 gn3/llms/client.py  | 43 +++++++++++--------------------------------
 gn3/llms/process.py |  2 +-
 2 files changed, 12 insertions(+), 33 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 2e9898f..810227f 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -1,5 +1,6 @@
 """Module  Contains code for making request to fahamu Api"""
 # pylint: disable=C0301
+# pylint: disable=R0913
 import json
 import time
 
@@ -24,13 +25,13 @@ class TimeoutHTTPAdapter(HTTPAdapter):
         self.timeout = timeout
         super().__init__(*args, **kwargs)
 
-    def send(self, request, **kwargs):
+    def send(self, *args, **kwargs):
         """Override :obj:`HTTPAdapter` send method to add a default timeout."""
         timeout = kwargs.get("timeout")
         if timeout is None:
             kwargs["timeout"] = self.timeout
 
-        return super().send(request, **kwargs)
+        return super().send(*args, **kwargs)
 
 
 class GeneNetworkQAClient(Session):
@@ -77,21 +78,15 @@ class GeneNetworkQAClient(Session):
         self.mount("https://", adapter)
         self.mount("http://", adapter)
 
-    def ask_the_documents(self, extend_url, my_auth):
+    def get_answer_using_task_id(self, extend_url, my_auth):
+        """call this method with task id to fetch response"""
         try:
-            response = requests.post(
-                self.base_url + extend_url, data={}, headers=my_auth)
+            response = requests.get(
+               self.answer_url + extend_url, data={}, headers=my_auth)
             response.raise_for_status()
+            return response
         except requests.exceptions.RequestException as error:
-            raise RuntimeError(f"Error making the request: {error}") from error
-        if response.status_code != 200:
-            return GeneNetworkQAClient.negative_status_msg(response), 0
-        task_id = GeneNetworkQAClient.get_task_id_from_result(response)
-        response = GeneNetworkQAClient.get_answer_using_task_id(task_id,
-                                                                my_auth)
-        if response.status_code != 200:
-            return GeneNetworkQAClient.negative_status_msg(response), 0
-        return response, 1
+            raise error
 
     @staticmethod
     def negative_status_msg(response):
@@ -102,7 +97,7 @@ class GeneNetworkQAClient(Session):
         """fahamu ask api interface"""
         res = self.custom_request('POST', f"{self.base_url}{ex_url}", *args, **kwargs)
         if res.status_code != 200:
-            return self.negative_status_msg(res), 0
+            return f"Error: Status code -{res.status_code}- Reason::{res.reason}", 0
         return res, json.loads(res.text)
 
     def get_answer(self, taskid, *args, **kwargs):
@@ -110,25 +105,9 @@ class GeneNetworkQAClient(Session):
         query = f"{self.answer_url}?task_id={taskid['task_id']}"
         res = self.custom_request('GET', query, *args, **kwargs)
         if res.status_code != 200:
-            return self.negative_status_msg(res), 0
+            return f"Error: Status code -{res.status_code}- Reason::{res.reason}", 0
         return res, 1
 
-    @staticmethod
-    def get_task_id_from_result(response):
-        """method to get task_id from response"""
-        task_id = json.loads(response.text)
-        return f"?task_id={task_id.get('task_id', '')}"
-
-    def get_answer_using_task_id(self, extend_url, my_auth):
-        """call this method with task id to fetch response"""
-        try:
-            response = requests.get(
-               self.answer_url + extend_url, data={}, headers=my_auth)
-            response.raise_for_status()
-            return response
-        except requests.exceptions.RequestException as error:
-            raise error
-
     def custom_request(self, method, url, *args, **kwargs):
         """ make custom request to fahamu api ask and get response"""
         max_retries = 50
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index 11961eb..9cb09a1 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -118,7 +118,7 @@ def get_gnqa(query, auth_token, data_dir=""):
          references: contains doc_name,reference,pub_med_info
     """
 
-    api_client = GeneNetworkQAClient(requests.Session(), auth_token)
+    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)}")
-- 
cgit v1.2.3


From 4d39c26b65aad3fa48d35fc11007f5f3afe1c112 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Fri, 17 May 2024 12:05:16 +0300
Subject: Timeout code refactoring.

---
 gn3/llms/client.py | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 810227f..05e3500 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -7,30 +7,23 @@ import time
 import requests
 from requests import Session
 from requests.adapters import HTTPAdapter
+from requests.adapters import Retry
 
-from urllib3.util import Retry
 from gn3.llms.errors import LLMError
 
 
 class TimeoutHTTPAdapter(HTTPAdapter):
-    """HTTP TimeoutAdapter """
-    # todo rework on this
+    """Set a default timeout for HTTP calls """
     def __init__(self, timeout, *args, **kwargs):
-        """TimeoutHTTPAdapter constructor.
-        Args:
-            timeout (int): How many seconds to wait for the server to
-        send data before
-                giving up.
-        """
+        """TimeoutHTTPAdapter constructor."""
         self.timeout = timeout
         super().__init__(*args, **kwargs)
 
     def send(self, *args, **kwargs):
         """Override :obj:`HTTPAdapter` send method to add a default timeout."""
-        timeout = kwargs.get("timeout")
-        if timeout is None:
-            kwargs["timeout"] = self.timeout
-
+        kwargs["timeout"] = (
+            kwargs["timeout"] if kwargs.get("timeout") else self.timeout
+        )
         return super().send(*args, **kwargs)
 
 
-- 
cgit v1.2.3


From d3bc323fe3a965ee5b6917987c4fe7662056e560 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Fri, 17 May 2024 13:34:37 +0300
Subject: Refactor custom  request codebase.

---
 gn3/llms/client.py  | 40 +++++++++++++++++++---------------------
 gn3/llms/process.py |  5 ++---
 2 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 05e3500..d57bca2 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -1,6 +1,5 @@
 """Module  Contains code for making request to fahamu Api"""
 # pylint: disable=C0301
-# pylint: disable=R0913
 import json
 import time
 
@@ -36,9 +35,7 @@ class GeneNetworkQAClient(Session):
     request timeouts, and request retries.
 
     Args:
-        account (str): Base address subdomain.
         api_key (str): API key.
-        version (str, optional): API version, defaults to "v3".
         timeout (int, optional): Timeout value, defaults to 5.
         total_retries (int, optional): Total retries value, defaults to 5.
         backoff_factor (int, optional): Retry backoff factor value,
@@ -50,7 +47,7 @@ class GeneNetworkQAClient(Session):
     api_key="XXXXXXXXXXXXXXXXXXX...")
     """
 
-    def __init__(self, account, api_key, version="v3", timeout=30,
+    def __init__(self, api_key, timeout=30,
                  total_retries=5, backoff_factor=30):
         super().__init__()
         self.headers.update(
@@ -95,11 +92,14 @@ class GeneNetworkQAClient(Session):
 
     def get_answer(self, taskid, *args, **kwargs):
         """Fahamu get answer interface"""
-        query = f"{self.answer_url}?task_id={taskid['task_id']}"
-        res = self.custom_request('GET', query, *args, **kwargs)
-        if res.status_code != 200:
-            return f"Error: Status code -{res.status_code}- Reason::{res.reason}", 0
-        return res, 1
+        try:
+            query = f"{self.answer_url}?task_id={taskid['task_id']}"
+            res = self.custom_request('GET', query, *args, **kwargs)
+            if res.status_code != 200:
+                return f"Error: Status code -{res.status_code}- Reason::{res.reason}", 0
+            return res, 1
+        except TimeoutError:
+            return "Timeout error occured:try to rephrase your query", 0
 
     def custom_request(self, method, url, *args, **kwargs):
         """ make custom request to fahamu api ask and get response"""
@@ -109,20 +109,18 @@ class GeneNetworkQAClient(Session):
             try:
                 response = super().request(method, url, *args, **kwargs)
                 response.raise_for_status()
+                if response.ok:
+                    if method.lower() == "get" and response.json().get("data") is None:
+                        time.sleep(retry_delay)
+                        continue
+                    return response
+                else:
+                    time.sleep(retry_delay)
             except requests.exceptions.HTTPError as error:
                 if error.response.status_code == 500:
                     raise LLMError(error.request, error.response, f"Response Error with:status_code:{error.response.status_code},Reason for error: Use of Invalid Fahamu Token") from error
-                elif error.response.status_code == 404:
-                    raise LLMError(error.request, error.response, f"404 Client Error: Not Found for url: {self.base_url}") from error
-                raise error
+                raise LLMError(error.request, error.response,
+            f"HTTP error occurred  with error status:{error.response.status_code}") from error
             except requests.exceptions.RequestException as error:
                 raise error
-            if response.ok:
-                if method.lower() == "get" and response.json().get("data") is None:
-                    time.sleep(retry_delay)
-                    continue
-                else:
-                    return response
-            else:
-                time.sleep(retry_delay)
-            return response
+        raise TimeoutError
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index 9cb09a1..4725bcb 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -5,7 +5,6 @@ import string
 import json
 import logging
 from urllib.parse import quote
-import requests
 
 from gn3.llms.client import GeneNetworkQAClient
 
@@ -118,7 +117,7 @@ def get_gnqa(query, auth_token, data_dir=""):
          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)}")
@@ -135,7 +134,7 @@ def get_gnqa(query, auth_token, 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):
-- 
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