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authorAlexander_Kabui2024-05-27 14:09:02 +0300
committerAlexander_Kabui2024-05-27 14:09:02 +0300
commit105f2b36eb62b9b097e1cbf6fa815f98da77bc16 (patch)
treeeb1c94667f0a7f5a59db41353a70a07dd5808823
parent666461bcf6afc811e4c21dd23dbef2711a07049a (diff)
downloadgenenetwork3-105f2b36eb62b9b097e1cbf6fa815f98da77bc16.tar.gz
Update Docstrings for Api endpoints and functions.
-rw-r--r--gn3/api/llm.py6
-rw-r--r--gn3/llms/process.py48
2 files changed, 44 insertions, 10 deletions
diff --git a/gn3/api/llm.py b/gn3/api/llm.py
index ab33c7a..4b8ec52 100644
--- a/gn3/api/llm.py
+++ b/gn3/api/llm.py
@@ -17,7 +17,7 @@ gnqa = Blueprint("gnqa", __name__)
@gnqa.route("/search", methods=["POST"])
def search():
- """Main gnqa endpoint"""
+ """Api endpoint for searching queries in fahamu Api"""
query = request.json.get("querygnqa", "")
if not query:
return jsonify({"error": "querygnqa is missing in the request"}), 400
@@ -56,7 +56,7 @@ def search():
@gnqa.route("/rating/<task_id>", methods=["POST"])
@require_oauth("profile")
def rate_queries(task_id):
- """Endpoint for rating qnqa query and answer"""
+ """Api endpoint for rating GNQA query and answer"""
with (require_oauth.acquire("profile") as token,
db.connection(current_app.config["LLM_DB_PATH"]) as conn):
results = request.json
@@ -89,7 +89,7 @@ def rate_queries(task_id):
@gnqa.route("/history", methods=["GET"])
@require_oauth("profile user")
def fetch_prev_history():
- """ api method to fetch search query records"""
+ """Api endpoint to fetch GNQA previous search."""
with (require_oauth.acquire("profile user") as token,
db.connection(current_app.config["LLM_DB_PATH"]) as conn):
cursor = conn.cursor()
diff --git a/gn3/llms/process.py b/gn3/llms/process.py
index ab2a80e..ade4104 100644
--- a/gn3/llms/process.py
+++ b/gn3/llms/process.py
@@ -35,7 +35,7 @@ class DocIDs():
raise FileNotFoundError(f"{file_path}-- FIle does not exist\n")
def format_doc_ids(self, docs):
- """method to format doc_ids for list items"""
+ """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:
@@ -43,7 +43,14 @@ class DocIDs():
self.doc_ids.update({doc_obj["id"]: doc_name})
def get_info(self, doc_id):
- """ interface to make read from doc_ids"""
+ """ 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:
@@ -51,7 +58,8 @@ class DocIDs():
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):
@@ -66,7 +74,15 @@ def filter_response_text(val):
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 = ""
@@ -81,7 +97,12 @@ def parse_context(context, get_info_func, format_bib_func):
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")
@@ -90,8 +111,19 @@ 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:
@@ -123,4 +155,6 @@ def get_gnqa(query, auth_token, data_dir=""):
answer = 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)
+ context, DocIDs().get_info,
+ format_bibliography_info),
+ "pubmed.json", data_dir)