app.py

import logging
import os
import pathlib
import tempfile
from typing import List, Optional

import gradio as gr
import pandas as pd
from rdkit import Chem
from tqdm import tqdm

from configuration import GENE_EXPRESSION_METADATA
from submission import submission

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

site_mapper = {
    "central_nervous_system": "CNS",
    "haematopoietic_and_lymphoid_tissue": "Haema_lymph",
    "upper_aerodigestive_tract": "digestive",
    "autonomic_ganglia": "ganglia",
}


def run_inference(
    smiles: Optional[str],
    smiles_path: Optional[str],
    omic: Optional[str],
    confidence: bool,
):
    # Read SMILES
    if smiles == "" and smiles_path is None:
        raise TypeError("Pass either single SMILES or a file")
    elif smiles != "" and smiles_path is not None:
        raise TypeError("Pass either single SMILES or a file, not both")
    elif smiles != "":
        smiles = [smiles]
    elif smiles_path is not None:
        smiles_data = pd.read_csv(smiles_path.name, sep="\t", header=None)
        smiles = smiles_data[0]
        for smi in smiles:
            if Chem.MolFromSmiles(smi) is None:
                raise ValueError(f"Found invalid SMILES {smi}")

    # Read omics and otherwise load baseline
    if omic is not None:
        omic_path = omic.name
    else:
        omic_path = None

    result = pd.DataFrame({})
    for smi in tqdm(smiles, total=len(smiles)):
        output = submission(
            drug={"smiles": smi},
            workspace_id="emulated_workspace_id",
            task_id="emulated_task_id",
            estimate_confidence=confidence,
            omics_file=omic_path,
        )
        # For the moment no attention analysis
        output.pop("gene_attention")
        output.pop("smiles_attention", None)
        output.pop("IC50")

        result[f"IC50_{smi}"] = output["log_micromolar_IC50"].squeeze().round(3)
        if confidence:
            result[f"aleatoric_confidence_{smi}"] = (
                output["aleatoric_confidence"].squeeze().round(3)
            )
            result[f"epistemic_confidence_{smi}"] = (
                output["aleatoric_confidence"].squeeze().round(3)
            )
    predicted_df = result

    # Prepare DF to visualize
    if omic_path is None:
        df = GENE_EXPRESSION_METADATA.copy()
        df.drop(
            [
                "histology",
                "cell_line_name",
                "IC50 (min/max scaled)",
                "IC50 (log(μmol))",
            ],
            axis=1,
            inplace=True,
        )
        df["site"] = df["site"].apply(lambda x: site_mapper.get(x, x))
        df["cell_line"] = df["cell_line"].apply(lambda x: x.split("_")[0])
        if (not confidence) and "aleatoric_confidence" in df.columns:
            df.drop(
                ["aleatoric_confidence", "epistemic_confidence"], axis=1, inplace=True
            )
        if (not confidence) and "aleatoric_confidence" in predicted_df.columns:
            predicted_df.drop(
                ["aleatoric_confidence", "epistemic_confidence"], axis=1, inplace=True
            )
        # else:
        #     df = pd.read_csv(omic_path, low_memory=False)

        result_df = pd.concat(
            [df["cell_line"], predicted_df, df.drop(["cell_line"], axis=1)], axis=1
        )
    else:
        result_df = predicted_df

    # Save to temporary dir
    temp_path = os.path.join(tempfile.gettempdir(), "paccmann_result.csv")
    result_df.to_csv(temp_path)

    return temp_path, result_df.head(25)


if __name__ == "__main__":
    # Load metadata
    metadata_root = pathlib.Path(__file__).parent.joinpath("model_cards")

    examples = [
        ["COc1cc(O)c2c(c1)C=CCC(O)C(O)C(=O)C=CCC(C)OC2=O", None, None, False],
        ["COC1=C(C=C2C(=C1)N=CN=C2NC3=CC(=C(C=C3)F)Cl)OCCCN4CCOCC4", None, None, True],
        # [None, metadata_root.joinpath("molecules.smi"), None, False],
    ]
    with open(metadata_root.joinpath("article.md"), "r") as f:
        article = f.read()
    with open(metadata_root.joinpath("description.md"), "r") as f:
        description = f.read()

    demo = gr.Interface(
        fn=run_inference,
        title="PaccMann",
        inputs=[
            gr.Textbox(
                label="SMILES",
                placeholder="COc1cc(O)c2c(c1)C=CCC(O)C(O)C(=O)C=CCC(C)OC2=O",
                lines=1,
            ),
            gr.File(
                file_types=[".smi", ".tsv"],
                label="Multiple SMILES",
            ),
            gr.File(
                file_types=[".csv"],
                label="Transcriptomics data file",
            ),
            gr.Radio(choices=[True, False], label="Estimate confidence", value=False),
        ],
        outputs=[
            gr.File(label="Download full results"),
            gr.DataFrame(label="Preview of results for 25 cell lines"),
        ],
        article=article,
        description=description,
        examples=examples,
    )
    demo.launch(debug=True, show_error=True)