app.py

import functools
import html
import logging
import textwrap
import traceback
from pathlib import Path
from typing import List

import gradio as gr
import pandas as pd
from rxn.utilities.logging import setup_console_logger
from rxn.utilities.strings import remove_postfix

from utils import TranslatorWithSentencePiece, download_cde_data, split_into_sentences

logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())

_SAC_MODEL_TAG = "Heterogenous SAC model (ACE)"
_ORGANIC_MODEL_TAG = "Organic chemistry model"
_PRETRAINED_MODEL_TAG = "Pretrained model"

model_type_to_models = {
    _SAC_MODEL_TAG: ["sac.pt"],
    _ORGANIC_MODEL_TAG: ["organic-1.pt", "organic-2.pt", "organic-3.pt"],
    _PRETRAINED_MODEL_TAG: ["pretrained.pt"],
}

SYNTHESIS_TEXT_PLACEHOLDER = (
    "Enter the synthesis procedure here, or click on one of the examples below."
)

@functools.lru_cache
def load_model(model_type: str) -> TranslatorWithSentencePiece:
    logger.info(f"Loading model {model_type}... ")

    model_files = model_type_to_models[model_type]
    sp_model = "sp_model.model"

    model = TranslatorWithSentencePiece(
        translation_model=model_files,
        sentencepiece_model=sp_model,
    )
    logger.info(f"Loading model {model_type}... Done.")

    return model


def sentence_and_actions_to_html(
    sentence: str, action_string: str, show_sentences: bool
) -> str:
    output = ""
    li_start = '<li style="margin-left: 12px;">' if show_sentences else "<li>"
    li_end = "</li>"

    action_string = remove_postfix(action_string, ".")

    if show_sentences:
        output += f"<p>{sentence}</p>"

    actions = [f"{li_start}{action}{li_end}" for action in action_string.split("; ")]
    output += "".join(actions)

    if show_sentences:
        # If we show the sentence, we need the list/enumeration delimiters,
        # as there is one list per sentence.
        output = f"<ol>{output}</ol>"

    return output


def try_action_extraction(model_type: str, text: str, show_sentences: bool) -> str:
    logger.info(f'Extracting actions from paragraph "{textwrap.shorten(text, 60)}"...')

    download_cde_data()

    model = load_model(model_type)

    logger.info(f"Splitting paragraph into sentences...")
    sentences = split_into_sentences(text)
    logger.info(f"Splitting paragraph into sentences... Done.")

    logger.info(f"Translation with OpenNMT...")
    action_strings = model.translate(sentences)
    logger.info(f"Translation with OpenNMT... Done.")

    output = ""
    for sentence, action_string in zip(sentences, action_strings):
        output += sentence_and_actions_to_html(sentence, action_string, show_sentences)

    if not show_sentences:
        # If the sentences were not shown, we need to add the list/enumeration
        # delimiters here (globally)
        output = f"<ol>{output}</ol>"

    # PostTreatment was renamed to ThermalTreatment, old model still relies on the former
    output = output.replace("POSTTREATMENT", "THERMALTREATMENT")

    logger.info(
        f'Extracting actions from paragraph "{textwrap.shorten(text, 60)}"... Done.'
    )
    return output


def action_extraction(model_type: str, text: str, show_sentences: bool) -> str:
    try:
        return try_action_extraction(model_type, text, show_sentences)
    except Exception as e:
        tb = "".join(traceback.TracebackException.from_exception(e).format())
        tb_html = f"<pre>{html.escape(tb)}</pre>"
        return f"<p><b>Error!</b> The action extraction failed: {e}</p>{tb_html}"


def launch() -> gr.Interface:
    logger.info("Launching the Gradio app")

    metadata_dir = Path(__file__).parent / "model_cards"

    examples_df: pd.DataFrame = pd.read_csv(
        metadata_dir / "sac_synthesis_mining_examples.csv", header=None
    ).fillna("")
    examples: List[List[str]] = examples_df.to_numpy().tolist()

    with open(metadata_dir / "sac_synthesis_mining_article.md", "r") as f:
        article = f.read()
    with open(metadata_dir / "sac_synthesis_mining_description.md", "r") as f:
        description = f.read()

    demo = gr.Interface(
        fn=action_extraction,
        title="Extraction of synthesis protocols from paragraphs in machine readable format",
        inputs=[
            gr.Dropdown(
                [_SAC_MODEL_TAG, _ORGANIC_MODEL_TAG, _PRETRAINED_MODEL_TAG],
                label="Model",
                value=_SAC_MODEL_TAG,
            ),
            gr.Textbox(label="Synthesis text", lines=7, placeholder=SYNTHESIS_TEXT_PLACEHOLDER),
            gr.Checkbox(label="Show sentences in the output"),
        ],
        outputs=gr.HTML(label="Output"),
        article=article,
        description=description,
        examples=examples,
        allow_flagging="never",
        theme="gradio/base",
    )
    demo.launch(debug=True, show_error=True)
    return demo


setup_console_logger(level="INFO")
demo = launch()