fix fetch token error from curent app

4 files changed, 54 insertions, 48 deletions

diff --git a/gn3/api/llm.py b/gn3/api/llm.py
index 83b5e85..68e6acc 100644
--- a/gn3/api/llm.py
+++ b/gn3/api/llm.py
@@ -2,7 +2,7 @@
 
 # pylint: skip-file
 
-from flask import jsonify, request, Blueprint
+from flask import jsonify, request, Blueprint, current_app
 
 from gn3.llms.process import getGNQA
 
@@ -16,7 +16,10 @@ def gnqa():
         return jsonify({"error": "querygnqa is missing in the request"}), 400
 
     try:
-        answer, refs = getGNQA(query)
+        auth_token = current_app.config.get("FAHAMU_AUTH_TOKEN")
+        answer, refs = getGNQA(
+            query, auth_token)
+
         return jsonify({
             "query": query,
             "answer": answer,
diff --git a/gn3/llms/client.py b/gn3/llms/client.py
index 6bcbf31..1c3acce 100644
--- a/gn3/llms/client.py
+++ b/gn3/llms/client.py
@@ -5,7 +5,7 @@ import os
 import datetime
 import time
 import requests
-from flask import current_app
+
 from requests import Session
 from urllib.parse import urljoin
 from requests.packages.urllib3.util.retry import Retry
@@ -59,7 +59,8 @@ class GeneNetworkQAClient(Session):
 
     def __init__(self, account, api_key, version="v3", timeout=5, total_retries=5, backoff_factor=30):
         super().__init__()
-        self.headers.update({"Authorization": "Bearer " + current_app.config.get("FAHAMU_AUTH_TOKEN","")})
+        self.headers.update(
+            {"Authorization": "Bearer " + api_key})
         self.answer_url = f"{self.BASE_URL}/answers"
         self.feedback_url = f"{self.BASE_URL}/feedback"
 
@@ -75,8 +76,6 @@ class GeneNetworkQAClient(Session):
         self.mount("https://", adapter)
         self.mount("http://", adapter)
 
-
-
     @staticmethod
     def format_bibliography_info(bib_info):
 
@@ -86,9 +85,9 @@ class GeneNetworkQAClient(Session):
         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', ''))
+                                                 bib_info.get('title', ''),
+                                                 bib_info.get('year', ''),
+                                                 bib_info.get('doi', ''))
         return bib_info
 
     @staticmethod
@@ -133,7 +132,7 @@ class GeneNetworkQAClient(Session):
         return res, 1
 
     def custom_request(self, method, url, *args, **kwargs):
-        max_retries = 3
+        max_retries = 5
         retry_delay = 10
 
         response = super().request(method, url, *args, **kwargs)
@@ -151,7 +150,7 @@ class GeneNetworkQAClient(Session):
                     raise exc
             if response.ok:
                 # Give time to get all the data
-                time.sleep(retry_delay*3)
+                time.sleep(retry_delay*1.5)
                 return response
             else:
                 time.sleep(retry_delay)
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index b8e7ded..58d565a 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -11,17 +11,9 @@ from gn3.llms.client import GeneNetworkQAClient
 from gn3.llms.response import DocIDs
 
 
-baseUrl           = 'https://genenetwork.fahamuai.com/api/tasks'
-answerUrl         = baseUrl + '/answers'
-basedir           = os.path.abspath(os.path.dirname(__file__))
-apiClient         = GeneNetworkQAClient(requests.Session(), api_key='')
-
-
-
-
-
-
-
+baseUrl = 'https://genenetwork.fahamuai.com/api/tasks'
+answerUrl = baseUrl + '/answers'
+basedir = os.path.abspath(os.path.dirname(__file__))
 
 
 def formatBibliographyInfo(bibInfo):
@@ -30,27 +22,29 @@ def formatBibliographyInfo(bibInfo):
         bibInfo = bibInfo.removesuffix('.txt')
     elif isinstance(bibInfo, dict):
         # format string bibliography information
-        bibInfo = "{0}.{1}.{2}.{3} ".format(bibInfo['author'], bibInfo['title'], bibInfo['year'], bibInfo['doi'])
+        bibInfo = "{0}.{1}.{2}.{3} ".format(
+            bibInfo['author'], bibInfo['title'], bibInfo['year'], bibInfo['doi'])
     return bibInfo
 
 
-def askTheDocuments( extendUrl, my_auth ):
+def askTheDocuments(extendUrl, my_auth):
     try:
-        res     = requests.post(baseUrl+extendUrl,
+        res = requests.post(baseUrl+extendUrl,
                             data={},
                             headers=my_auth)
         res.raise_for_status()
     except:
-        raise # what
+        raise  # what
     if (res.status_code != 200):
         return negativeStatusMsg(res), 0
-    task_id     = getTaskIDFromResult(res)
-    res         = getAnswerUsingTaskID(task_id, my_auth)
+    task_id = getTaskIDFromResult(res)
+    res = getAnswerUsingTaskID(task_id, my_auth)
     if (res.status_code != 200):
         return negativeStatusMsg(res), 0
     return res, 1
 
-def getAnswerUsingTaskID( extendUrl, my_auth ):
+
+def getAnswerUsingTaskID(extendUrl, my_auth):
     try:
         res = requests.get(answerUrl+extendUrl, data={}, headers=my_auth)
         res.raise_for_status()
@@ -58,8 +52,9 @@ def getAnswerUsingTaskID( extendUrl, my_auth ):
         raise
     return res
 
+
 def openAPIConfig():
-    f = open(os.path.join(basedir, "api.config.json") , "rb" )
+    f = open(os.path.join(basedir, "api.config.json"), "rb")
     result = json.load(f)
     f.close()
     return result
@@ -67,45 +62,50 @@ def openAPIConfig():
 
 def getTaskIDFromResult(res):
     task_id = json.loads(res.text)
-    result  = '?task_id=' + str(task_id['task_id'])
+    result = '?task_id=' + str(task_id['task_id'])
     return result
 
+
 def negativeStatusMsg(res):
-    return 'Problems\n\tStatus code => {0}\n\tReason=> {1}'.format(res.status_code, res.reason)  # mypy: ignore
+    # mypy: ignore
+    return 'Problems\n\tStatus code => {0}\n\tReason=> {1}'.format(res.status_code, res.reason)
+
 
 def filterResponseText(val):
     return json.loads(''.join([str(char) for char in val if char in string.printable]))
 
-def getGNQA(query):
-    res, task_id = apiClient.ask('?ask=' + query)
+
+def getGNQA(query, auth_token):
+    apiClient = GeneNetworkQAClient(requests.Session(), api_key=auth_token)
+    res, task_id = apiClient.ask('?ask=' + query, auth_token)
     res, success = apiClient.get_answer(task_id)
 
-    if ( success == 1 ):
-        respText       = filterResponseText(res.text)
+    if (success == 1):
+        respText = filterResponseText(res.text)
         if respText.get("data") is None:
-            return  "Unfortunately I have nothing on the query",[]
-        answer         = respText['data']['answer']
-        context        = respText['data']['context']
+            return "Unfortunately I have nothing on the query", []
+        answer = respText['data']['answer']
+        context = respText['data']['context']
         references = parse_context(context)
-        return answer,references
+        return answer, references
     else:
         return res, "Unfortunately I have nothing."
 
 
-
 def parse_context(context):
     """parse content map id to reference"""
     result = []
-    for doc_ids,summary in context.items():
+    for doc_ids, summary in context.items():
         comboTxt = ""
-        for entry  in summary:
+        for entry in summary:
             comboTxt += '\t' + entry['text']
 
         docInfo = DocIDs().getInfo(doc_ids)
-        if doc_ids !=docInfo:
+        if doc_ids != docInfo:
             bibInfo = formatBibliographyInfo(docInfo)
 
         else:
             bibInfo = doc_ids
-        result.append({"doc_id":doc_ids,"bibInfo":bibInfo,"comboTxt":comboTxt})
-    return result
\ No newline at end of file
+        result.append(
+            {"doc_id": doc_ids, "bibInfo": bibInfo, "comboTxt": comboTxt})
+    return result
diff --git a/gn3/settings.py b/gn3/settings.py
index ca4d271..15baae2 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -34,6 +34,7 @@ SECRET_KEY = "password"
 # gn2 results only used in fetching dataset info
 
 # FAHAMU API TOKEN
+FAHAMU_AUTH_TOKEN = ""
 
 GN2_BASE_URL = "http://www.genenetwork.org/"
 
@@ -54,6 +55,8 @@ GENOTYPE_FILES = os.environ.get(
 XAPIAN_DB_PATH = "xapian"
 
 # CROSS-ORIGIN SETUP
+
+
 def parse_env_cors(default):
     """Parse comma-separated configuration into list of strings."""
     origins_str = os.environ.get("CORS_ORIGINS", None)
@@ -62,6 +65,7 @@ def parse_env_cors(default):
             origin.strip() for origin in origins_str.split(",") if origin != ""]
     return default
 
+
 CORS_ORIGINS = parse_env_cors("*")
 
 CORS_HEADERS = [
@@ -75,9 +79,9 @@ TEXTDIR = f"{GNSHARE}/web/ProbeSetFreeze_DataMatrix"
 
 ROUND_TO = 10
 
-MULTIPROCESSOR_PROCS = 6 # Number of processes to spawn
+MULTIPROCESSOR_PROCS = 6  # Number of processes to spawn
 
-AUTH_SERVER_URL=""
+AUTH_SERVER_URL = ""
 AUTH_MIGRATIONS = "migrations/auth"
 AUTH_DB = os.environ.get(
     "AUTH_DB", f"{os.environ.get('HOME')}/genenetwork/gn3_files/db/auth.db")