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import gradio as gr
import os
import json
import networkx as nx
import pandas as pd
import plotly.graph_objects as go
import re
import sys
import sqlite3
import time
import uvicorn
from fastapi import FastAPI, Request
from fastapi.middleware.cors import CORSMiddleware
from gradio.routes import mount_gradio_app
from plotly.subplots import make_subplots
from tabulate import tabulate
from typing import Optional
ROOT_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
if ROOT_DIR not in sys.path:
sys.path.insert(0, ROOT_DIR)
from scripts.create_db import ArxivDatabase
from config import (
DEFAULT_TABLES_DIR,
DEFAULT_INTERFACE_MODEL_ID,
COOCCURRENCE_QUERY,
canned_queries,
)
app = FastAPI()
# Add CORS middleware
app.add_middleware(
CORSMiddleware,
allow_origins=["*"],
allow_credentials=True,
allow_methods=["*"],
allow_headers=["*"],
)
db: Optional[ArxivDatabase] = None
def truncate_or_wrap_text(text, max_length=50, wrap=False):
"""Truncate text to a maximum length, adding ellipsis if truncated, or wrap if specified."""
if wrap:
return "\n".join(
text[i : i + max_length] for i in range(0, len(text), max_length)
)
return text[:max_length] + "..." if len(text) > max_length else text
def format_url(url):
"""Format URL to be more compact in the table."""
return url.split("/")[-1] if url.startswith("http") else url
def get_available_databases():
ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
tables_dir = os.path.join(ROOT, DEFAULT_TABLES_DIR)
return [f for f in os.listdir(tables_dir) if f.endswith(".db")]
def query_db(query, is_sql, limit=None, wrap=False):
global db
if db is None:
return pd.DataFrame({"Error": ["Please load a database first."]})
try:
cursor = db.conn.cursor()
query = " ".join(query.strip().split("\n")).rstrip(";")
if limit is not None:
if "LIMIT" in query.upper():
# Replace existing LIMIT clause
query = re.sub(
r"LIMIT\s+\d+", f"LIMIT {limit}", query, flags=re.IGNORECASE
)
else:
query += f" LIMIT {limit}"
cursor.execute(query)
column_names = [description[0] for description in cursor.description]
results = cursor.fetchall()
df = pd.DataFrame(results, columns=column_names)
for column in df.columns:
if df[column].dtype == "object":
df[column] = df[column].apply(
lambda x: (
format_url(x)
if column == "url"
else truncate_or_wrap_text(x, wrap=wrap)
)
)
return df
except sqlite3.Error as e:
return pd.DataFrame({"Error": [f"Database error: {str(e)}"]})
except Exception as e:
return pd.DataFrame({"Error": [f"An unexpected error occurred: {str(e)}"]})
def generate_concept_cooccurrence_graph(db_path):
conn = sqlite3.connect(db_path)
df = pd.read_sql_query(COOCCURRENCE_QUERY, conn)
conn.close()
G = nx.from_pandas_edgelist(df, "concept1", "concept2", "co_occurrences")
pos = nx.spring_layout(G)
edge_x = []
edge_y = []
for edge in G.edges():
x0, y0 = pos[edge[0]]
x1, y1 = pos[edge[1]]
edge_x.extend([x0, x1, None])
edge_y.extend([y0, y1, None])
edge_trace = go.Scatter(
x=edge_x,
y=edge_y,
line=dict(width=0.5, color="#888"),
hoverinfo="none",
mode="lines",
)
node_x = [pos[node][0] for node in G.nodes()]
node_y = [pos[node][1] for node in G.nodes()]
node_trace = go.Scatter(
x=node_x,
y=node_y,
mode="markers",
hoverinfo="text",
marker=dict(
showscale=True,
colorscale="YlGnBu",
size=10,
colorbar=dict(
thickness=15,
title="Node Connections",
xanchor="left",
titleside="right",
),
),
)
node_adjacencies = []
node_text = []
for node, adjacencies in G.adjacency():
node_adjacencies.append(len(adjacencies))
node_text.append(f"{node}<br># of connections: {len(adjacencies)}")
node_trace.marker.color = node_adjacencies
node_trace.text = node_text
fig = go.Figure(
data=[edge_trace, node_trace],
layout=go.Layout(
title="Concept Co-occurrence Network",
titlefont_size=16,
showlegend=False,
hovermode="closest",
margin=dict(b=20, l=5, r=5, t=40),
annotations=[
dict(
text="",
showarrow=False,
xref="paper",
yref="paper",
x=0.005,
y=-0.002,
)
],
xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
yaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
),
)
return fig
# def load_database_with_graphs(db_name):
# global db
# ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
# db_path = os.path.join(ROOT, DEFAULT_TABLES_DIR, db_name)
# if not os.path.exists(db_path):
# return f"Database {db_name} does not exist.", None
# db = ArxivDatabase(db_path)
# db.init_db()
# if db.is_db_empty:
# return (
# f"Database loaded from {db_path}, but it is empty. Please populate it with data.",
# None,
# )
# # Generate graph
# graph = generate_concept_cooccurrence_graph(db_path)
# return f"Database loaded from {db_path}", graph
def load_database_with_graphs(db_name):
global db
ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
db_path = os.path.join(ROOT, DEFAULT_TABLES_DIR, db_name)
if not os.path.exists(db_path):
return f"Database {db_name} does not exist.", None
if db is None or db.db_path != db_path:
db = ArxivDatabase(db_path)
db.init_db()
if db.is_db_empty:
return (
f"Database loaded from {db_path}, but it is empty. Please populate it with data.",
None,
)
graph = generate_concept_cooccurrence_graph(db_path)
return f"Database loaded from {db_path}", graph
css = """
#selected-query {
max-height: 100px;
overflow-y: auto;
white-space: pre-wrap;
word-break: break-word;
}
"""
def create_demo():
with gr.Blocks(css=css) as demo:
gr.Markdown("# ArXiv Database Query Interface")
with gr.Row():
db_dropdown = gr.Dropdown(
choices=get_available_databases(), label="Select Database"
)
load_db_btn = gr.Button("Load Database", size="sm")
status = gr.Textbox(label="Status")
with gr.Row():
graph_output = gr.Plot(label="Concept Co-occurrence Graph")
with gr.Row():
wrap_checkbox = gr.Checkbox(label="Wrap long text", value=False)
canned_query_dropdown = gr.Dropdown(
choices=[q[0] for q in canned_queries], label="Select Query", scale=3
)
limit_input = gr.Number(
label="Limit", value=10000, step=1, minimum=1, scale=1
)
selected_query = gr.Textbox(
label="Selected Query",
interactive=False,
scale=2,
show_label=True,
show_copy_button=True,
elem_id="selected-query",
)
canned_query_submit = gr.Button("Submit Query", size="sm", scale=1)
with gr.Row():
sql_input = gr.Textbox(label="Custom SQL Query", lines=3, scale=4)
sql_submit = gr.Button("Submit Custom SQL", size="sm", scale=1)
output = gr.DataFrame(label="Results", wrap=True)
def update_selected_query(query_description):
for desc, sql in canned_queries:
if desc == query_description:
return sql
return ""
def submit_canned_query(query_description, limit, wrap):
for desc, sql in canned_queries:
if desc == query_description:
return query_db(sql, True, limit, wrap)
return pd.DataFrame({"Error": ["Selected query not found."]})
load_db_btn.click(
load_database_with_graphs,
inputs=[db_dropdown],
outputs=[status, graph_output],
)
canned_query_dropdown.change(
update_selected_query,
inputs=[canned_query_dropdown],
outputs=[selected_query],
)
canned_query_submit.click(
submit_canned_query,
inputs=[canned_query_dropdown, limit_input, wrap_checkbox],
outputs=output,
)
sql_submit.click(
query_db,
inputs=[sql_input, gr.Checkbox(value=True), limit_input, wrap_checkbox],
outputs=output,
)
return demo
demo = create_demo()
def close_db():
global db
if db is not None:
db.close()
db = None
# def launch():
# print("Launching Gradio app...", flush=True)
# demo.launch(share=True)
# print(
# "Gradio app launched. If you don't see a URL above, there might be network restrictions.",
# flush=True,
# )
# close_db()
# if __name__ == "__main__":
# launch()
# Mount the Gradio app
app = mount_gradio_app(app, demo, path="/")
@app.exception_handler(Exception)
async def exception_handler(request: Request, exc: Exception):
print(f"An error occurred: {str(exc)}")
return {"error": str(exc)}
@app.on_event("startup")
async def startup_event():
# You can initialize the database here if needed
pass
@app.on_event("shutdown")
async def shutdown_event():
close_db()
if __name__ == "__main__":
uvicorn.run(app, host="0.0.0.0", port=7860)
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