Added code for JSON oriented model approach (#4)

* Added code for JSON oriented model approach

* chore: Update code formatting and editor settings
Refined logic for time based queries

* refactor: Reorganize imports and update code formatting

* chore: Refactor build_index function to simplify code

* Minor changes

* Minor changes

* Removed conflicting flake8 error

* Updated model in INSTALL.md

* Resolved PR Comments

.github/workflows/flake8.yml

@@ -20,7 +20,7 @@ jobs:
       - name: flake8 Lint
         uses: TrueBrain/actions-flake8@v2
         with:
-          ignore: E203,E701
+          ignore: E203,E701,W503,W504
           max_line_length: 88
           path: src
           plugins: flake8-black flake8-isort flake8-quotes

.gitignore

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

.vscode/settings.json

@@ -1,11 +1,14 @@
 {
   "git.ignoreLimitWarning": true,
   "editor.formatOnSave": true,
-  "flake8.args": ["--max-line-length=88"],
+  "flake8.args": [
+    "--max-line-length=88"
+  ],
   "[python]": {
     "editor.codeActionsOnSave": {
       "source.organizeImports.python": "explicit"
     },
-    "editor.defaultFormatter": "ms-python.black-formatter"
+    "editor.defaultFormatter": "ms-python.black-formatter",
+    "editor.formatOnSave": true,
   }
-}
+}

INSTALL.md

@@ -52,7 +52,7 @@ curl -fsSL https://ollama.com/install.sh | sh
 Run the Ollama application:
 
 ```bash
-ollama run llama3
+ollama run codellama
 ```
 
 ## Step 7: Start the Flask Application

setup.cfg

@@ -1,4 +1,4 @@
 [flake8]
 max-line-length = 88
-extend-ignore = E203,E701
+extend-ignore = E203,E701,W503,W504
 inline-quotes = double

src/app.py

@@ -0,0 +1,93 @@
+import json
+import logging
+import os
+import sys
+import urllib
+
+from flask import Flask, render_template, request
+
+from index import load_index, query_engine
+
+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?"
+    suffix = (
+        "&result=taxon&summaryValues=count&taxonomy=ncbi&offset=0"
+        + "&fields=assembly_level%2Cassembly_span%2Cgenome_size%2C"
+        + "chromosome_number%2Chaploid_number&names=common_name&ranks="
+        + "&includeEstimates=false&size=100"
+    )
+
+    if json_output["intent"] == "count":
+        endpoint = "api/v2/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']}")
+        suffix = (
+            "&result=assembly&summaryValues=count&taxonomy=ncbi&offset=0"
+            + "&fields=assembly_level%2Cassembly_span%2Cgenome_size%2C"
+            + "chromosome_number%2Chaploid_number&names=common_name&ranks="
+            + "&includeEstimates=false&size=100"
+        )
+
+    query_string = " AND ".join(params)
+    return base_url + endpoint + "query=" + urllib.parse.quote(query_string) + suffix
+
+
+def chat_bot_rag(query):
+    # entity_taxon_map = fetch_related_taxons(query)
+    for _ in range(int(os.getenv("RETRY_COUNT", 3))):
+        try:
+            model_response = json.loads(query_engine.custom_query(query))
+            return {
+                "json_debug": json.dumps(model_response, indent=2),
+                "url": construct_url(model_response),
+            }
+            # return construct_url(json.loads(query_engine.custom_query(query)))
+        except Exception as e:
+            app.logger.error(f"Error: {e}")
+            app.logger.error("Retrying...")
+    model_response = json.loads(query_engine.custom_query(query))
+    return {
+        "json_debug": json.dumps(model_response, indent=2),
+        "url": construct_url(model_response),
+    }
+
+
+@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():
+    return chat_bot_rag(request.form["user_input"])
+
+
+if __name__ == "__main__":
+    app.run(debug=True)