diff options
Diffstat (limited to 'gn3/llms')
| -rw-r--r-- | gn3/llms/client.py | 215 | ||||
| -rw-r--r-- | gn3/llms/errors.py | 31 | ||||
| -rw-r--r-- | gn3/llms/process.py | 179 | ||||
| -rw-r--r-- | gn3/llms/response.py | 75 |
4 files changed, 164 insertions, 336 deletions
diff --git a/gn3/llms/client.py b/gn3/llms/client.py index 042becd..ad6c400 100644 --- a/gn3/llms/client.py +++ b/gn3/llms/client.py @@ -1,72 +1,61 @@ -# pylint: skip-file +"""Module Contains code for making request to fahamu Api""" +# pylint: disable=C0301 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 +import requests 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 +from requests.adapters import Retry -basedir = os.path.join(os.path.dirname(__file__)) +from gn3.llms.errors import LLMError class TimeoutHTTPAdapter(HTTPAdapter): + """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, 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) + kwargs["timeout"] = ( + kwargs["timeout"] if kwargs.get("timeout") else self.timeout + ) + return super().send(*args, **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, + 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. + 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, api_key, 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" + self.query = "" adapter = TimeoutHTTPAdapter( timeout=timeout, @@ -80,141 +69,59 @@ 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(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( - base_url + extend_url, data={}, headers=my_auth) + response = requests.get( + self.answer_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 + return response + except requests.exceptions.RequestException as error: + raise error @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}" - # 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.negative_status_msg(res), 0 - task_id = self.getTaskIDFromResult(res) - return res, task_id + def ask(self, ex_url, query, *args, **kwargs): + """fahamu ask api interface""" + self.query = query + res = self.custom_request('POST', f"{self.base_url}{ex_url}", *args, **kwargs) + return res, json.loads(res.text) def get_answer(self, taskid, *args, **kwargs): - query = self.answer_url + self.extendTaskID(taskid) + """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 self.negative_status_msg(res), 0 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,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}") - raise error - - except requests.exceptions.RequestException as error: - raise error - - - - + response_msg = { + 404: "Api endpoint Does not exist", + 500: "Use of Invalid Token/or the Fahamu Api is currently down", + 400: "You sent a bad Fahamu request", + 401: "You do not have authorization to perform the request", + } + for _i in range(max_retries): + response = super().request(method, url, *args, **kwargs) if response.ok: - if method.lower() == "get" and response.json().get("data") is None: + if method.lower() == "get" and not response.json().get("data"): + # note this is a dirty trick to check if fahamu has returned the results + # the issue is that the api only returns 500 or 200 satus code + # TODO: fix this on their end time.sleep(retry_delay) continue - else: - return response + 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." + raise LLMError(f"Request error with code:\ + {response.status_code} occurred with reason:\ + {response_msg.get(response.status_code,response.reason)}", + self.query) + #time.sleep(retry_delay) + raise LLMError("Timeout error: We couldn't provide a response,Please try\ + to rephrase your question to receive feedback", + self.query) diff --git a/gn3/llms/errors.py b/gn3/llms/errors.py index e9f7c02..a3a47a3 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): @@ -56,7 +35,5 @@ class UnprocessableEntity(HTTPError): msg, request=request, response=response) -class LLMError(HTTPError): - def __init__(self, request, response, msg): - super(HTTPError, self).__init__( - msg, request=request, response=response) +class LLMError(Exception): + """custom exception for LLMErrorMIxins""" diff --git a/gn3/llms/process.py b/gn3/llms/process.py index e38b73e..55c27a0 100644 --- a/gn3/llms/process.py +++ b/gn3/llms/process.py @@ -1,25 +1,57 @@ """this module contains code for processing response from fahamu client.py""" +# pylint: disable=C0301 import os +import re 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 = load_file("doc_ids.json", BASEDIR) + self.sugar_doc_ids = load_file("all_files.json", BASEDIR) + self.format_doc_ids(self.sugar_doc_ids) + + def format_doc_ids(self, docs): + """method to format doc_ids for list items doc_id and doc_name""" + 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 + and extract info data else returns + doc_id + Args: + doc_id: str: a search key for doc_ids + Returns: + an object with doc_info if doc_id in 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): - """Function for formatting bibliography info""" + """Utility function for formatting bibliography info + """ if isinstance(bib_info, str): return bib_info.removesuffix('.txt') elif isinstance(bib_info, dict): @@ -27,14 +59,16 @@ def format_bibliography_info(bib_info): 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""" + """Function to parse doc_ids content + Args: + context: raw references from fahamu api + get_info_func: function to get doc_ids info + format_bib_func: function to foramt bibliography info + Returns: + an list with each item having (doc_id,bib_info, + combined reference text) + """ results = [] for doc_ids, summary in context.items(): combo_txt = "" @@ -43,32 +77,23 @@ def parse_context(context, get_info_func, format_bib_func): doc_info = get_info_func(doc_ids) bib_info = doc_ids if doc_ids == doc_info else format_bib_func( doc_info) + pattern = r'(https?://|www\.)[\w.-]+(\.[a-zA-Z]{2,})([/\w.-]*)*' + combo_text = re.sub(pattern, + lambda x: f"<a href='{x[0]}' target=_blank> {x[0]} </a>", + combo_txt) results.append( - {"doc_id": doc_ids, "bibInfo": bib_info, "comboTxt": combo_txt}) + {"doc_id": doc_ids, "bibInfo": bib_info, + "comboTxt": combo_text}) 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""" + """Utility function to read json file + Args: + filename: file name to read + dir_path: base directory for the file + Returns: json data read to a dict + """ 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") @@ -77,8 +102,19 @@ def load_file(filename, dir_path): def fetch_pubmed(references, file_name, data_dir=""): - """method to fetch and populate references with pubmed""" - + """ + Fetches PubMed data from a JSON file and populates the\ + references dictionary. + + Args: + references (dict): Dictionary with document IDs as keys\ + and reference data as values. + filename (str): Name of the JSON file containing PubMed data. + data_dir (str): Base directory where the data files are located. + + Returns: + dict: Updated references dictionary populated with the PubMed data. + """ try: pubmed = load_file(file_name, os.path.join(data_dir, "gn-meta/lit")) for reference in references: @@ -92,44 +128,27 @@ 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()""" - - 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 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): - """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 != ""] +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(api_key=auth_token) + res, task_id = api_client.ask('?ask=' + quote(query), query=query) + res, _status = api_client.get_answer(task_id) + resp_text = json.loads(''.join([str(char) + for char in res.text if char in string.printable])) + answer = re.sub(r'(https?://|www\.)[\w.-]+(\.[a-zA-Z]{2,})([/\w.-]*)*', + lambda x: f"<a href='{x[0]}' target=_blank> {x[0]} </a>", + resp_text["data"]["answer"]) + context = resp_text['data']['context'] + return task_id, answer, fetch_pubmed(parse_context( + context, DocIDs().get_info, + format_bibliography_info), + "pubmed.json", data_dir) diff --git a/gn3/llms/response.py b/gn3/llms/response.py deleted file mode 100644 index 11cbd94..0000000 --- a/gn3/llms/response.py +++ /dev/null @@ -1,75 +0,0 @@ - -# pylint: skip-file -import string -import json -import os - - -basedir = os.path.abspath(os.path.dirname(__file__)) - - -class DocIDs(): - 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): - 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 - 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): - if doc_id in self.doc_ids.keys(): - 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 - 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
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