app.py

import os
os.system("pip uninstall -y gradio")
os.system("pip install --upgrade gradio")



import spaces


from pathlib import Path
from fastapi import FastAPI
from fastapi.staticfiles import StaticFiles
import uvicorn
import gradio as gr
from datetime import datetime
import sys



gr.set_static_paths(paths=["static/"])



# create a FastAPI app
app = FastAPI()

# create a static directory to store the static files
static_dir = Path('./static')
static_dir.mkdir(parents=True, exist_ok=True)

# mount FastAPI StaticFiles server
app.mount("/static", StaticFiles(directory=static_dir), name="static")

# Gradio stuff



import datamapplot
import numpy as np
import requests
import io
import pandas as pd
from pyalex import Works, Authors, Sources, Institutions, Concepts, Publishers, Funders
from itertools import chain
from compress_pickle import load, dump



from transformers import AutoTokenizer
from adapters import AutoAdapterModel
import torch
from tqdm import tqdm














def query_records(search_term):
    def invert_abstract(inv_index):
        if inv_index is not None:
            l_inv = [(w, p) for w, pos in inv_index.items() for p in pos]
            return " ".join(map(lambda x: x[0], sorted(l_inv, key=lambda x: x[1])))
        else:
            return ' '

    def get_pub(x):
        try: 
            source = x['source']['display_name']
            if source not in ['parsed_publication','Deleted Journal']:
                return source
            else: 
                return ' '
        except:
            return ' '

    # Fetch records based on the search term
    query = Works().search_filter(abstract=search_term)

    records = []
    for record in chain(*query.paginate(per_page=200)):
        records.append(record)

    records_df = pd.DataFrame(records)
    records_df['abstract'] = [invert_abstract(t) for t in records_df['abstract_inverted_index']]
    records_df['parsed_publication'] = [get_pub(x) for x in records_df['primary_location']]

    
    return records_df




################# Setting up the model for specter2 embeddings ###################



device = torch.device("mps" if torch.backends.mps.is_available() else "cuda")
print(f"Using device: {device}")

tokenizer = AutoTokenizer.from_pretrained('allenai/specter2_aug2023refresh_base')
model = AutoAdapterModel.from_pretrained('allenai/specter2_aug2023refresh_base')


@spaces.GPU(duration=120)
def create_embeddings(texts_to_embedd):
    # Set up the device


    print(len(texts_to_embedd))

    # Load the proximity adapter and activate it
    model.load_adapter("allenai/specter2_aug2023refresh", source="hf", load_as="proximity", set_active=True)
    model.set_active_adapters("proximity")
 
    model.to(device)

    def batch_generator(data, batch_size):
        """Yield consecutive batches of data."""
        for i in range(0, len(data), batch_size):
            yield data[i:i + batch_size]

    
    def encode_texts(texts, device, batch_size=16):
        """Process texts in batches and return their embeddings."""
        model.eval()
        with torch.no_grad():
            all_embeddings = []
            count = 0
            for batch in tqdm(batch_generator(texts, batch_size)):
                inputs = tokenizer(batch, padding=True, truncation=True, return_tensors="pt", max_length=512).to(device)
                outputs = model(**inputs)
                embeddings = outputs.last_hidden_state[:, 0, :]  # Taking the [CLS] token representation
                
                all_embeddings.append(embeddings.cpu())  # Move to CPU to free GPU memory
                #torch.mps.empty_cache()  # Clear cache to free up memory
                if count == 100:
                    torch.mps.empty_cache()
                    count = 0
                
                count +=1
            
            all_embeddings = torch.cat(all_embeddings, dim=0)
        return all_embeddings

    # Concatenate title and abstract
    embeddings = encode_texts(texts_to_embedd, device, batch_size=32).cpu().numpy()  # Process texts in batches of 10

    return embeddings





def predict(text_input, progress=gr.Progress()):
    
    # get data.
    records_df = query_records(text_input)
    print(records_df)
    
    
    
    texts_to_embedd = [title + tokenizer.sep_token + publication + tokenizer.sep_token  + abstract for title, publication, abstract in zip(records_df['title'],records_df['parsed_publication'], records_df['abstract'])]
    
    embeddings = create_embeddings(texts_to_embedd)
    print(embeddings)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    file_name = f"{datetime.utcnow().strftime('%s')}.html"
    file_path = static_dir / file_name
    print(file_path)
 
   #
    
    progress(0.7, desc="Loading hover data...")

    plot = datamapplot.create_interactive_plot(
        basedata_df[['x','y']].values,
        np.array(basedata_df['cluster_1_labels']),
        hover_text=[str(ix) + ', ' + str(row['parsed_publication']) + str(row['title']) for ix, row in basedata_df.iterrows()],
        font_family="Roboto Condensed",
    )

    progress(0.9, desc="Saving plot...")
    plot.save(file_path)

    progress(1.0, desc="Done!")
    iframe = f"""<iframe src="/static/{file_name}" width="100%" height="500px"></iframe>"""
    link = f'<a href="/static/{file_name}" target="_blank">{file_name}</a>'
    return link, iframe

with gr.Blocks() as block:
    gr.Markdown("""
## Gradio + FastAPI + Static Server
This is a demo of how to use Gradio with FastAPI and a static server.
The Gradio app generates dynamic HTML files and stores them in a static directory. FastAPI serves the static files.
""")
    with gr.Row():
        with gr.Column():
            text_input = gr.Textbox(label="Name")
            markdown = gr.Markdown(label="Output Box")
            new_btn = gr.Button("New")
        with gr.Column():
            html = gr.HTML(label="HTML preview", show_label=True)

    new_btn.click(fn=predict, inputs=[text_input], outputs=[markdown, html])




def setup_basemap_data():
    # get data.
    print("getting basemap data...")
    basedata_file= requests.get(
        "https://www.maxnoichl.eu/full/oa_project_on_scimap_background_data/100k_filtered_OA_sample_cluster_and_positions.bz"
    )
    # Write the response content to a .bz file in the static directory
    static_dir = Path("static")
    static_dir.mkdir(exist_ok=True)
    bz_file_name = "100k_filtered_OA_sample_cluster_and_positions.bz"
    bz_file_path = static_dir / bz_file_name
    
    with open(bz_file_path, "wb") as f:
        f.write(basedata_file.content)
    
    # Load the data from the saved .bz file
    
    basedata_df = load(bz_file_path)
    
    
    return basedata_df

basedata_df = setup_basemap_data()


# mount Gradio app to FastAPI app
app = gr.mount_gradio_app(app, block, path="/")

# serve the app
if __name__ == "__main__":
    uvicorn.run(app, host="0.0.0.0", port=7860)

# run the app with
# python app.py
# or
# uvicorn "app:app" --host "0.0.0.0" --port 7860 --reload