Added code for JSON oriented model approach

.gitignore

@@ -1,5 +1,5 @@
 prompts/__pycache__
-rich_query_index
 .DS_Store
 .env
-__pycache__
+__pycache__
+src/query_index

src/app.py

@@ -0,0 +1,78 @@
+import os
+import sys
+from flask import Flask, request, render_template, jsonify
+import urllib
+from index import load_index, query_engine
+import json
+import logging
+
+
+app = Flask("goat_nlp")
+
+handler = logging.StreamHandler(sys.stdout)
+handler.setFormatter(logging.Formatter(
+    '%(asctime)s - %(name)s - %(levelname)s - %(message)s'))
+app.logger.addHandler(handler)
+app.logger.setLevel(logging.INFO)
+
+
+def construct_url(json_output):
+    base_url = "https://goat.genomehubs.org/"
+    endpoint = "search?"
+
+    if json_output['intent'] == 'count':
+        endpoint = "count?"
+    elif json_output['intent'] == 'record':
+        endpoint = "record?"
+
+    params = []
+
+    if 'taxon' in json_output:
+        params.append(f"tax_tree(* {json_output['taxon']})")
+    if 'rank' in json_output:
+        params.append(f"tax_rank({json_output['rank']})")
+    if 'field' in json_output:
+        params.append(f"{json_output['field']}")
+    if "time_frame_query" in json_output:
+        params.append(f"{json_output['time_frame_query']}")
+
+    query_string = " AND ".join(params)
+    return base_url + endpoint + "query=" + urllib.parse.quote_plus(query_string) + "&result=taxon&summaryValues=count&taxonomy=ncbi&offset=0&fields=assembly_level%2Cassembly_span%2Cgenome_size%2Cchromosome_number%2Chaploid_number&names=common_name&ranks=&includeEstimates=false&size=100"
+
+
+def chat_bot_rag(query):
+    # entity_taxon_map = fetch_related_taxons(query)
+    for _ in range(int(os.getenv("RETRY_COUNT", 3))):
+        try:
+            return construct_url(json.loads(query_engine.custom_query(query)))
+        except Exception as e:
+            app.logger.error(f"Error: {e}")
+            app.logger.error("Retrying...")
+    return construct_url(json.loads(query_engine.custom_query(query)))
+
+
+@app.route('/')
+def home():
+    return render_template('chat.html')
+
+
+@app.route('/rebuildIndex')
+def index():
+    load_index(force_reload=True)
+
+
+@app.route('/chat', methods=['POST'])
+def chat():
+    user_message = request.form['user_input']
+    bot_message = chat_bot_rag(user_message)
+
+    try:
+        bot_message = json.loads(bot_message)["url"]
+    except Exception:
+        pass
+
+    return jsonify({'response': str(bot_message)})
+
+
+if __name__ == '__main__':
+    app.run(debug=True)