app.py

import json
import logging
import os.path
from functools import partial
from typing import Dict, List, Optional, Tuple

import gradio as gr
import pandas as pd
from backend import get_annotation_from_document, get_relevant_adus, get_similar_adus, process_text
from pie_modules.taskmodules import PointerNetworkTaskModuleForEnd2EndRE
from pytorch_ie import Pipeline
from pytorch_ie.auto import AutoPipeline
from pytorch_ie.documents import TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
from rendering_utils import render_displacy, render_pretty_table
from transformers import AutoModel, AutoTokenizer, PreTrainedModel, PreTrainedTokenizer
from vector_store import SimpleVectorStore, VectorStore

logger = logging.getLogger(__name__)

RENDER_WITH_DISPLACY = "displaCy + highlighted arguments"
RENDER_WITH_PRETTY_TABLE = "Pretty Table"

DEFAULT_MODEL_NAME = "ArneBinder/sam-pointer-bart-base-v0.3"
DEFAULT_MODEL_REVISION = "76300f8e534e2fcf695f00cb49bba166739b8d8a"
# local path
# DEFAULT_MODEL_NAME = "models/dataset-sciarg/task-ner_re/v0.3/2024-05-28_23-33-46"
# DEFAULT_MODEL_REVISION = None
DEFAULT_EMBEDDING_MODEL_NAME = "allenai/scibert_scivocab_uncased"


def render_annotated_document(
    document: TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions,
    render_with: str,
    render_kwargs_json: str,
) -> str:
    render_kwargs = json.loads(render_kwargs_json)
    if render_with == RENDER_WITH_PRETTY_TABLE:
        html = render_pretty_table(document, **render_kwargs)
    elif render_with == RENDER_WITH_DISPLACY:
        html = render_displacy(document, **render_kwargs)
    else:
        raise ValueError(f"Unknown render_with value: {render_with}")

    return html


def wrapped_process_text(
    text: str,
    doc_id: str,
    models: Tuple[Pipeline, Optional[PreTrainedModel], Optional[PreTrainedTokenizer]],
    processed_documents: dict[
        str, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
    ],
    vector_store: VectorStore[Tuple[str, str]],
) -> Tuple[dict, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions]:
    document = process_text(
        text=text,
        doc_id=doc_id,
        models=models,
        processed_documents=processed_documents,
        vector_store=vector_store,
    )
    # Return as dict and document to avoid serialization issues
    return document.asdict(), document


def process_uploaded_files(
    file_names: List[str],
    models: Tuple[Pipeline, Optional[PreTrainedModel], Optional[PreTrainedTokenizer]],
    processed_documents: dict[
        str, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
    ],
    vector_store: VectorStore[Tuple[str, str]],
) -> None:
    try:
        for file_name in file_names:
            if file_name.lower().endswith(".txt"):
                # read the file content
                with open(file_name, "r", encoding="utf-8") as f:
                    text = f.read()
                base_file_name = os.path.basename(file_name)
                gr.Info(f"Processing file '{base_file_name}' ...")
                process_text(text, base_file_name, models, processed_documents, vector_store)
            else:
                raise gr.Error(f"Unsupported file format: {file_name}")
    except Exception as e:
        raise gr.Error(f"Failed to process uploaded files: {e}")


def open_accordion():
    return gr.Accordion(open=True)


def close_accordion():
    return gr.Accordion(open=False)


def load_argumentation_model(model_name: str, revision: Optional[str] = None) -> Pipeline:
    try:
        model = AutoPipeline.from_pretrained(
            model_name,
            device=-1,
            num_workers=0,
            taskmodule_kwargs=dict(revision=revision),
            model_kwargs=dict(revision=revision),
        )
    except Exception as e:
        raise gr.Error(f"Failed to load argumentation model: {e}")
    gr.Info(f"Loaded argumentation model: model_name={model_name}, revision={revision})")
    return model


def load_embedding_model(model_name: str) -> Tuple[PreTrainedModel, PreTrainedTokenizer]:
    try:
        embedding_model = AutoModel.from_pretrained(model_name)
        embedding_tokenizer = AutoTokenizer.from_pretrained(model_name)
    except Exception as e:
        raise gr.Error(f"Failed to load embedding model: {e}")
    gr.Info(f"Loaded embedding model: model_name={model_name})")
    return embedding_model, embedding_tokenizer


def load_models(
    model_name: str, revision: Optional[str] = None, embedding_model_name: Optional[str] = None
) -> Tuple[Pipeline, Optional[PreTrainedModel], Optional[PreTrainedTokenizer]]:
    argumentation_model = load_argumentation_model(model_name, revision)
    embedding_model = None
    embedding_tokenizer = None
    if embedding_model_name is not None and embedding_model_name.strip():
        embedding_model, embedding_tokenizer = load_embedding_model(embedding_model_name)

    return argumentation_model, embedding_model, embedding_tokenizer


def update_processed_documents_df(
    processed_documents: dict[str, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions]
) -> pd.DataFrame:
    df = pd.DataFrame(
        [
            (
                doc_id,
                len(document.labeled_spans.predictions),
                len(document.binary_relations.predictions),
            )
            for doc_id, document in processed_documents.items()
        ],
        columns=["doc_id", "num_adus", "num_relations"],
    )
    return df


def select_processed_document(
    evt: gr.SelectData,
    processed_documents_df: pd.DataFrame,
    processed_documents: Dict[
        str, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
    ],
) -> TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions:
    row_idx, col_idx = evt.index
    doc_id = processed_documents_df.iloc[row_idx]["doc_id"]
    gr.Info(f"Select document: {doc_id}")
    doc = processed_documents[doc_id]
    return doc


def set_relation_types(
    models: Tuple[Pipeline, Optional[PreTrainedModel], Optional[PreTrainedTokenizer]],
    default: Optional[List[str]] = None,
) -> gr.Dropdown:
    arg_pipeline = models[0]
    if isinstance(arg_pipeline.taskmodule, PointerNetworkTaskModuleForEnd2EndRE):
        relation_types = arg_pipeline.taskmodule.labels_per_layer["binary_relations"]
    else:
        raise gr.Error("Unsupported taskmodule for relation types")

    return gr.Dropdown(
        choices=relation_types,
        label="Relation Types",
        value=default,
        multiselect=True,
    )


def main():

    example_text = "Scholarly Argumentation Mining (SAM) has recently gained attention due to its potential to help scholars with the rapid growth of published scientific literature. It comprises two subtasks: argumentative discourse unit recognition (ADUR) and argumentative relation extraction (ARE), both of which are challenging since they require e.g. the integration of domain knowledge, the detection of implicit statements, and the disambiguation of argument structure. While previous work focused on dataset construction and baseline methods for specific document sections, such as abstract or results, full-text scholarly argumentation mining has seen little progress. In this work, we introduce a sequential pipeline model combining ADUR and ARE for full-text SAM, and provide a first analysis of the performance of pretrained language models (PLMs) on both subtasks. We establish a new SotA for ADUR on the Sci-Arg corpus, outperforming the previous best reported result by a large margin (+7% F1). We also present the first results for ARE, and thus for the full AM pipeline, on this benchmark dataset. Our detailed error analysis reveals that non-contiguous ADUs as well as the interpretation of discourse connectors pose major challenges and that data annotation needs to be more consistent."

    print("Loading models ...")
    argumentation_model, embedding_model, embedding_tokenizer = load_models(
        model_name=DEFAULT_MODEL_NAME,
        revision=DEFAULT_MODEL_REVISION,
        embedding_model_name=DEFAULT_EMBEDDING_MODEL_NAME,
    )

    default_render_kwargs = {
        "entity_options": {
            # we need to convert the keys to uppercase because the spacy rendering function expects them in uppercase
            "colors": {
                "own_claim".upper(): "#009933",
                "background_claim".upper(): "#99ccff",
                "data".upper(): "#993399",
            }
        },
        "colors_hover": {
            "selected": "#ffa",
            # "tail": "#aff",
            "tail": {
                # green
                "supports": "#9f9",
                # red
                "contradicts": "#f99",
                # do not highlight
                "parts_of_same": None,
            },
            "head": None,  # "#faf",
            "other": None,
        },
    }

    with gr.Blocks() as demo:
        processed_documents_state = gr.State(dict())
        vector_store_state = gr.State(SimpleVectorStore())
        # wrap the pipeline and the embedding model/tokenizer in a tuple to avoid that it gets called
        models_state = gr.State((argumentation_model, embedding_model, embedding_tokenizer))
        with gr.Row():
            with gr.Column(scale=1):
                doc_id = gr.Textbox(
                    label="Document ID",
                    value="user_input",
                )
                doc_text = gr.Textbox(
                    label="Text",
                    lines=20,
                    value=example_text,
                )
                with gr.Accordion("Model Configuration", open=False):
                    model_name = gr.Textbox(
                        label="Model Name",
                        value=DEFAULT_MODEL_NAME,
                    )
                    model_revision = gr.Textbox(
                        label="Model Revision",
                        value=DEFAULT_MODEL_REVISION,
                    )
                    embedding_model_name = gr.Textbox(
                        label=f"Embedding Model Name (e.g. {DEFAULT_EMBEDDING_MODEL_NAME})",
                        value=DEFAULT_EMBEDDING_MODEL_NAME,
                    )
                    load_models_btn = gr.Button("Load Models")
                    load_models_btn.click(
                        fn=load_models,
                        inputs=[model_name, model_revision, embedding_model_name],
                        outputs=models_state,
                    )

                predict_btn = gr.Button("Analyse")

                document_state = gr.State()

            with gr.Column(scale=1):

                with gr.Accordion("See plain result ...", open=False) as output_accordion:
                    document_json = gr.JSON(label="Model Output")

                with gr.Accordion("Render Options", open=False):
                    render_as = gr.Dropdown(
                        label="Render with",
                        choices=[RENDER_WITH_PRETTY_TABLE, RENDER_WITH_DISPLACY],
                        value=RENDER_WITH_DISPLACY,
                    )
                    render_kwargs = gr.Textbox(
                        label="Render Arguments",
                        lines=5,
                        value=json.dumps(default_render_kwargs, indent=2),
                    )
                render_btn = gr.Button("Re-render")

                rendered_output = gr.HTML(label="Rendered Output")

                # add_to_index_btn = gr.Button("Add current result to Index")
                upload_btn = gr.UploadButton(
                    "Upload & Analyse Documents", file_types=["text"], file_count="multiple"
                )

            with gr.Column(scale=1):
                with gr.Accordion("Indexed Documents", open=False):
                    processed_documents_df = gr.DataFrame(
                        headers=["id", "num_adus", "num_relations"],
                        interactive=False,
                    )

                with gr.Accordion("Reference ADU", open=False):
                    reference_adu_id = gr.Textbox(label="ID", elem_id="reference_adu_id")
                    reference_adu_text = gr.Textbox(label="Text")

                with gr.Accordion("Retrieval Configuration", open=False):
                    min_similarity = gr.Slider(
                        label="Minimum Similarity",
                        minimum=0.0,
                        maximum=1.0,
                        step=0.01,
                        value=0.8,
                    )
                    top_k = gr.Slider(
                        label="Top K",
                        minimum=2,
                        maximum=50,
                        step=1,
                        value=20,
                    )
                    retrieve_similar_adus_btn = gr.Button("Retrieve similar ADUs")
                    similar_adus = gr.DataFrame(headers=["doc_id", "adu_id", "score", "text"])
                    relation_types = set_relation_types(
                        models_state.value, default=["supports", "contradicts"]
                    )

                # retrieve_relevant_adus_btn = gr.Button("Retrieve relevant ADUs")
                relevant_adus = gr.DataFrame(
                    label="Relevant ADUs from other documents",
                    headers=[
                        "text",
                        "relation",
                        "doc_id",
                        "reference_adu",
                        "sim_score",
                        "rel_score",
                    ],
                )

        render_event_kwargs = dict(
            fn=render_annotated_document,
            inputs=[document_state, render_as, render_kwargs],
            outputs=rendered_output,
        )

        predict_btn.click(fn=open_accordion, inputs=[], outputs=[output_accordion]).then(
            fn=wrapped_process_text,
            inputs=[doc_text, doc_id, models_state, processed_documents_state, vector_store_state],
            outputs=[document_json, document_state],
            api_name="predict",
        ).success(
            fn=update_processed_documents_df,
            inputs=[processed_documents_state],
            outputs=[processed_documents_df],
        )
        render_btn.click(**render_event_kwargs, api_name="render")

        document_state.change(
            fn=lambda doc: doc.asdict(),
            inputs=[document_state],
            outputs=[document_json],
        ).success(close_accordion, inputs=[], outputs=[output_accordion]).then(
            **render_event_kwargs
        )

        upload_btn.upload(
            fn=process_uploaded_files,
            inputs=[upload_btn, models_state, processed_documents_state, vector_store_state],
            outputs=[],
        ).success(
            fn=update_processed_documents_df,
            inputs=[processed_documents_state],
            outputs=[processed_documents_df],
        )
        processed_documents_df.select(
            select_processed_document,
            inputs=[processed_documents_df, processed_documents_state],
            outputs=[document_state],
        )

        retrieve_relevant_adus_event_kwargs = dict(
            fn=get_relevant_adus,
            inputs=[
                reference_adu_id,
                document_state,
                vector_store_state,
                processed_documents_state,
                min_similarity,
                top_k,
                relation_types,
            ],
            outputs=[relevant_adus],
        )

        reference_adu_id.change(
            fn=partial(get_annotation_from_document, annotation_layer="labeled_spans"),
            inputs=[document_state, reference_adu_id],
            outputs=[reference_adu_text],
        ).success(**retrieve_relevant_adus_event_kwargs)

        retrieve_similar_adus_btn.click(
            fn=get_similar_adus,
            inputs=[
                reference_adu_id,
                document_state,
                vector_store_state,
                processed_documents_state,
                min_similarity,
                top_k,
            ],
            outputs=[similar_adus],
        )

        models_state.change(
            fn=set_relation_types,
            inputs=[models_state],
            outputs=[relation_types],
        )

        # retrieve_relevant_adus_btn.click(
        #     **retrieve_relevant_adus_event_kwargs
        # )

        js = """
        () => {
            function maybeSetColor(entity, colorAttributeKey, colorDictKey) {
                var color = entity.getAttribute('data-color-' + colorAttributeKey);
                // if color is a json string, parse it and use the value at colorDictKey
                try {
                    const colors = JSON.parse(color);
                    color = colors[colorDictKey];
                } catch (e) {}
                if (color) {
                    entity.style.backgroundColor = color;
                    entity.style.color = '#000';
                }
            }

            function highlightRelationArguments(entityId) {
                const entities = document.querySelectorAll('.entity');
                // reset all entities
                entities.forEach(entity => {
                    const color = entity.getAttribute('data-color-original');
                    entity.style.backgroundColor = color;
                    entity.style.color = '';
                });

                if (entityId !== null) {
                    var visitedEntities = new Set();
                    // highlight selected entity
                    const selectedEntity = document.getElementById(entityId);
                    if (selectedEntity) {
                        const label = selectedEntity.getAttribute('data-label');
                        maybeSetColor(selectedEntity, 'selected', label);
                        visitedEntities.add(selectedEntity);
                    }
                    // highlight tails
                    const relationTailsAndLabels = JSON.parse(selectedEntity.getAttribute('data-relation-tails'));
                    relationTailsAndLabels.forEach(relationTail => {
                        const tailEntity = document.getElementById(relationTail['entity-id']);
                        if (tailEntity) {
                            const label = relationTail['label'];
                            maybeSetColor(tailEntity, 'tail', label);
                            visitedEntities.add(tailEntity);
                        }
                    });
                    // highlight heads
                    const relationHeadsAndLabels = JSON.parse(selectedEntity.getAttribute('data-relation-heads'));
                    relationHeadsAndLabels.forEach(relationHead => {
                        const headEntity = document.getElementById(relationHead['entity-id']);
                        if (headEntity) {
                            const label = relationHead['label'];
                            maybeSetColor(headEntity, 'head', label);
                            visitedEntities.add(headEntity);
                        }
                    });
                    // highlight other entities
                    entities.forEach(entity => {
                        if (!visitedEntities.has(entity)) {
                            const label = entity.getAttribute('data-label');
                            maybeSetColor(entity, 'other', label);
                        }
                    });
                }
            }
            function setReferenceAduId(entityId) {
                // get the textarea element that holds the reference adu id
                let referenceAduIdDiv = document.querySelector('#reference_adu_id textarea');
                // set the value of the input field
                referenceAduIdDiv.value = entityId;
                // trigger an input event to update the state
                var event = new Event('input');
                referenceAduIdDiv.dispatchEvent(event);
            }

            const entities = document.querySelectorAll('.entity');
            entities.forEach(entity => {
                const alreadyHasListener = entity.getAttribute('data-has-listener');
                if (alreadyHasListener) {
                    return;
                }
                entity.addEventListener('mouseover', () => {
                    highlightRelationArguments(entity.id);
                    setReferenceAduId(entity.id);
                });
                entity.addEventListener('mouseout', () => {
                    highlightRelationArguments(null);
                });
                entity.setAttribute('data-has-listener', 'true');
            });
        }
        """

        rendered_output.change(fn=None, js=js, inputs=[], outputs=[])

    demo.launch()


if __name__ == "__main__":
    # configure logging
    logging.basicConfig()

    main()