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# pylint: skip-file
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
basedir = os.path.join(os.path.dirname(__file__))
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
giving up.
"""
self.timeout = timeout
super().__init__(*args, **kwargs)
def send(self, request, **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)
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,
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, defaults to 30.
Usage:
from genenetworkqa import GeneNetworkQAClient
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):
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"
adapter = TimeoutHTTPAdapter(
timeout=timeout,
max_retries=Retry(
total=total_retries,
status_forcelist=[429, 500, 502, 503, 504],
backoff_factor=backoff_factor,
),
)
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(extend_url, my_auth):
try:
response = requests.post(
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
task_id = get_task_id_from_result(response)
response = get_answer_using_task_id(task_id, my_auth)
if response.status_code != 200:
return negative_status_msg(response), 0
return response, 1
@staticmethod
def negative_status_msg(response):
return f"Problems\n\tStatus code => {response.status_code}\n\tReason => {response.reason}"
def ask(self, exUrl, *args, **kwargs):
askUrl = self.BASE_URL + exUrl
res = self.custom_request('POST', askUrl, *args, **kwargs)
if (res.status_code != 200):
return self.negativeStatusMsg(res), 0
task_id = self.getTaskIDFromResult(res)
return res, task_id
def get_answer(self, taskid, *args, **kwargs):
query = self.answer_url + self.extendTaskID(taskid)
res = self.custom_request('GET', query, *args, **kwargs)
if (res.status_code != 200):
return self.negativeStatusMsg(res), 0
return res, 1
def custom_request(self, method, url, *args, **kwargs):
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.RequestException as exc:
if exc.response.status_code == 422:
raise UnprocessableEntity(exc.request, exc.response)
# from exc
elif i == max_retries - 1:
raise exc
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
@staticmethod
def get_task_id_from_result(response):
task_id = json.loads(response.text)
result = f"?task_id={task_id.get('task_id', '')}"
return result
@staticmethod
def get_answer_using_task_id(extend_url, my_auth):
try:
response = requests.get(
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
"""
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'])
def get_gnqa(self, query):
qstr = quote(query)
res, task_id = api_client.ask('?ask=' + qstr)
res, success = api_client.get_answer(task_id)
if success == 1:
resp_text = 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."
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