Merge pull request #188 from genenetwork/chores/merge-gnqa-api

Chores/merge gnqa api

1 files changed, 133 insertions, 111 deletions

diff --git a/gn3/api/llm.py b/gn3/api/llm.py
index 7d860d8..7e60271 100644
--- a/gn3/api/llm.py
+++ b/gn3/api/llm.py
@@ -1,128 +1,150 @@
-"""API for data used to generate menus"""
-
-# pylint: skip-file
+"""Api endpoints for gnqa"""
+import json
+from datetime import datetime
 
-from flask import jsonify, request, Blueprint, current_app
+from flask import Blueprint
+from flask import current_app
+from flask import jsonify
+from flask import request
 
-from functools import wraps
 from gn3.llms.process import get_gnqa
-from gn3.llms.process import get_user_queries
-from gn3.llms.process import fetch_query_results
+from gn3.llms.errors import LLMError
 from gn3.auth.authorisation.oauth2.resource_server import require_oauth
 from gn3.auth import db
-from redis import Redis
-import json
-import sqlite3
-from datetime import timedelta
-
-GnQNA = Blueprint("GnQNA", __name__)
 
 
-def handle_errors(func):
-    @wraps(func)
-    def decorated_function(*args, **kwargs):
-        try:
-            return func(*args, **kwargs)
-        except Exception as error:
-            return jsonify({"error": str(error)}), 500
-    return decorated_function
+gnqa = Blueprint("gnqa", __name__)
 
 
-@GnQNA.route("/gnqna", methods=["POST"])
-def gnqa():
-    # todo  add auth
+@gnqa.route("/search", methods=["PUT"])
+def search():
+    """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
-
-    try:
-        fahamu_token = current_app.config.get("FAHAMU_AUTH_TOKEN")
-        if fahamu_token is None:
-            return jsonify({"query": query, "error": "Use of invalid fahamu auth token"}), 500
-        task_id, answer, refs = get_gnqa(
-            query, fahamu_token, current_app.config.get("DATA_DIR"))
-        response = {
-            "task_id": task_id,
-            "query": query,
-            "answer": answer,
-            "references": refs
-        }
-        with (Redis.from_url(current_app.config["REDIS_URI"],
-                             decode_responses=True) as redis_conn):
-            # The key will be deleted after 60 seconds
-            redis_conn.setex(f"LLM:random_user-{query}", timedelta(days=10), json.dumps(response))
-        return jsonify({
-            **response,
-            "prev_queries": get_user_queries("random_user", redis_conn)
-        })
-    except Exception as error:
-        return jsonify({"query": query, "error": f"Request failed-{str(error)}"}), 500
-
-
-@GnQNA.route("/rating/<task_id>", methods=["POST"])
+    fahamu_token = current_app.config.get("FAHAMU_AUTH_TOKEN")
+    if not fahamu_token:
+        raise LLMError(
+            "Request failed: an LLM authorisation token  is required ", query)
+    task_id, answer, refs = get_gnqa(
+        query, fahamu_token, current_app.config.get("DATA_DIR"))
+    response = {
+        "task_id": task_id,
+        "query": query,
+        "answer": answer,
+        "references": refs
+    }
+    with (db.connection(current_app.config["LLM_DB_PATH"]) as conn,
+          require_oauth.acquire("profile user") as token):
+        cursor = conn.cursor()
+        cursor.execute("""CREATE TABLE IF NOT EXISTS
+        history(user_id TEXT NOT NULL,
+        task_id TEXT NOT NULL,
+        query  TEXT NOT NULL,
+        results  JSONB,
+        created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+        PRIMARY KEY(task_id)) WITHOUT ROWID""")
+        cursor.execute(
+            """INSERT INTO history(user_id, task_id, query, results)
+            VALUES(?, ?, ?, ?)
+            """, (str(token.user.user_id), str(task_id["task_id"]),
+                  query,
+                  json.dumps(response))
+        )
+    return response
+
+
+@gnqa.route("/rating/<task_id>", methods=["POST"])
 @require_oauth("profile")
-def rating(task_id):
-    try:
-        llm_db_path = current_app.config["LLM_DB_PATH"]
-        with (require_oauth.acquire("profile") as token,
-              db.connection(llm_db_path) as conn):
-
-            results = request.json
-            user_id, query, answer, weight = (token.user.user_id,
-                                              results.get("query"),
-                                              results.get("answer"),
-                                              results.get("weight", 0))
-            cursor = conn.cursor()
-            create_table = """CREATE TABLE IF NOT EXISTS Rating(
-                  user_id TEXT NOT NULL,
-                  query TEXT NOT NULL,
-                  answer TEXT NOT NULL,
-                  weight INTEGER NOT NULL DEFAULT 0,
-                  task_id TEXT NOT NULL UNIQUE
-                  )"""
-            cursor.execute(create_table)
-            cursor.execute("""INSERT INTO Rating(user_id,query,answer,weight,task_id)
-            VALUES(?,?,?,?,?)
-            ON CONFLICT(task_id) DO UPDATE SET
-            weight=excluded.weight
-            """, (str(user_id), query, answer, weight, task_id))
+def rate_queries(task_id):
+    """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
+        user_id, query, answer, weight = (token.user.user_id,
+                                          results.get("query"),
+                                          results.get("answer"),
+                                          results.get("weight", 0))
+        cursor = conn.cursor()
+        create_table = """CREATE TABLE IF NOT EXISTS Rating(
+              user_id TEXT NOT NULL,
+              query TEXT NOT NULL,
+              answer TEXT NOT NULL,
+              weight INTEGER NOT NULL DEFAULT 0,
+              task_id TEXT NOT NULL UNIQUE,
+              created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+              PRIMARY KEY(task_id))"""
+        cursor.execute(create_table)
+        cursor.execute("""INSERT INTO Rating(user_id, query,
+        answer, weight, task_id)
+        VALUES(?, ?, ?, ?, ?)
+        ON CONFLICT(task_id) DO UPDATE SET
+        weight=excluded.weight
+        """, (str(user_id), query, answer, weight, task_id))
         return {
-                "message": "You have successfully rated this query:Thank you!!"
-            }, 200
-    except sqlite3.Error as error:
-        return jsonify({"error": str(error)}), 500
-    except Exception as error:
-        raise error
+            "message": "You have successfully rated this query. Thank you!"
+        }, 200
 
 
-@GnQNA.route("/history/<query>", methods=["GET"])
+@gnqa.route("/search/records", methods=["GET"])
 @require_oauth("profile user")
-@handle_errors
-def fetch_user_hist(query):
-
-    with (require_oauth.acquire("profile user") as the_token, Redis.from_url(current_app.config["REDIS_URI"],
-                                                                             decode_responses=True) as redis_conn):
-        return jsonify({
-            **fetch_query_results(query, the_token.user.id, redis_conn),
-            "prev_queries": get_user_queries("random_user", redis_conn)
-        })
-
-
-@GnQNA.route("/historys/<query>", methods=["GET"])
-@handle_errors
-def fetch_users_hist_records(query):
-    """method to fetch all users hist:note this is a test functionality to be replaced by fetch_user_hist"""
-
-    with Redis.from_url(current_app.config["REDIS_URI"], decode_responses=True) as redis_conn:
-        return jsonify({
-            **fetch_query_results(query, "random_user", redis_conn),
-            "prev_queries": get_user_queries("random_user", redis_conn)
-        })
-
-
-@GnQNA.route("/get_hist_names", methods=["GET"])
-@handle_errors
-def fetch_prev_hist_ids():
-
-    with (Redis.from_url(current_app.config["REDIS_URI"], decode_responses=True)) as redis_conn:
-        return jsonify({"prev_queries": get_user_queries("random_user", redis_conn)})
+def get_user_search_records():
+    """get all  history records for a given user using their
+    user id
+    """
+    with (require_oauth.acquire("profile user") as token,
+          db.connection(current_app.config["LLM_DB_PATH"]) as conn):
+        cursor = conn.cursor()
+        cursor.execute(
+            """SELECT task_id, query, created_at from history WHERE user_id=?""",
+            (str(token.user.user_id),))
+        results = [dict(item) for item in cursor.fetchall()]
+        return jsonify(sorted(results, reverse=True,
+                       key=lambda x: datetime.strptime(x.get("created_at"),
+                                                       '%Y-%m-%d %H:%M:%S')))
+
+
+@gnqa.route("/search/record/<task_id>", methods=["GET"])
+@require_oauth("profile user")
+def get_user_record_by_task(task_id):
+    """Get user previous search record by task id """
+    with (require_oauth.acquire("profile user") as token,
+          db.connection(current_app.config["LLM_DB_PATH"]) as conn):
+        cursor = conn.cursor()
+        cursor.execute(
+            """SELECT results from history
+            Where task_id=? and user_id=?""",
+            (task_id,
+             str(token.user.user_id),))
+        record = cursor.fetchone()
+        if record:
+            return dict(record).get("results")
+        return {}
+
+
+@gnqa.route("/search/record/<task_id>", methods=["DELETE"])
+@require_oauth("profile user")
+def delete_record(task_id):
+    """Delete user previous seach record by task-id"""
+    with (require_oauth.acquire("profile user") as token,
+          db.connection(current_app.config["LLM_DB_PATH"]) as conn):
+        cursor = conn.cursor()
+        query = """DELETE FROM history
+        WHERE task_id=? and user_id=?"""
+        cursor.execute(query, (task_id, token.user.user_id,))
+        return {"msg": f"Successfully Deleted the task {task_id}"}
+
+
+@gnqa.route("/search/records", methods=["DELETE"])
+@require_oauth("profile user")
+def delete_records():
+    """ Delete a users records using for all given task ids"""
+    with (require_oauth.acquire("profile user") as token,
+          db.connection(current_app.config["LLM_DB_PATH"]) as conn):
+        task_ids = list(request.json.values())
+        cursor = conn.cursor()
+        query = """DELETE FROM history
+        WHERE task_id IN ({})
+        and user_id=?""".format(",".join("?" * len(task_ids)))
+        cursor.execute(query, (*task_ids, str(token.user.user_id),))
+        return jsonify({})