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Added code for JSON oriented model approach
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prompts/__pycache__ | ||
rich_query_index | ||
.DS_Store | ||
.env | ||
__pycache__ | ||
__pycache__ | ||
src/query_index |
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import os | ||
import sys | ||
from flask import Flask, request, render_template, jsonify | ||
import urllib | ||
from index import load_index, query_engine | ||
Check failure on line 5 in src/app.py GitHub Actions / flake8 Lint
Check failure on line 5 in src/app.py GitHub Actions / flake8 Lint
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import json | ||
import logging | ||
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app = Flask("goat_nlp") | ||
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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) | ||
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def construct_url(json_output): | ||
base_url = "https://goat.genomehubs.org/" | ||
endpoint = "search?" | ||
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if json_output['intent'] == 'count': | ||
Check failure on line 23 in src/app.py GitHub Actions / flake8 Lint
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endpoint = "count?" | ||
elif json_output['intent'] == 'record': | ||
endpoint = "record?" | ||
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params = [] | ||
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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']}") | ||
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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" | ||
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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))) | ||
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@app.route('/') | ||
def home(): | ||
return render_template('chat.html') | ||
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@app.route('/rebuildIndex') | ||
def index(): | ||
load_index(force_reload=True) | ||
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@app.route('/chat', methods=['POST']) | ||
def chat(): | ||
user_message = request.form['user_input'] | ||
bot_message = chat_bot_rag(user_message) | ||
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try: | ||
bot_message = json.loads(bot_message)["url"] | ||
except Exception: | ||
pass | ||
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return jsonify({'response': str(bot_message)}) | ||
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if __name__ == '__main__': | ||
app.run(debug=True) |
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