app.py

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

import gradio as gr
import pandas as pd
import torch
from document_store import DocumentStore, get_annotation_from_document
from embedding import EmbeddingModel
from model_utils import annotate_document, create_document, load_models
from pie_modules.taskmodules import PointerNetworkTaskModuleForEnd2EndRE
from pytorch_ie import Pipeline
from pytorch_ie.documents import TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions
from rendering_utils import render_displacy, render_pretty_table
from transformers import PreTrainedModel, PreTrainedTokenizer
from vector_store import QdrantVectorStore, SimpleVectorStore

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"
DEFAULT_DEVICE = "cuda" if torch.cuda.is_available() else "cpu"
DEFAULT_EMBEDDING_MAX_LENGTH = 512
DEFAULT_EMBEDDING_BATCH_SIZE = 32
DEFAULT_SPLIT_REGEX = "\n\n\n+"


def escape_regex(regex: str) -> str:
    # "double escape" the backslashes
    result = regex.encode("unicode_escape").decode("utf-8")
    return result


def unescape_regex(regex: str) -> str:
    # reverse of escape_regex
    result = regex.encode("utf-8").decode("unicode_escape")
    return result


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[EmbeddingModel]],
    document_store: DocumentStore,
    split_regex_escaped: str,
) -> Tuple[dict, TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions]:
    try:
        document = create_document(
            text=text,
            doc_id=doc_id,
            split_regex=unescape_regex(split_regex_escaped)
            if len(split_regex_escaped) > 0
            else None,
        )
        annotate_document(
            document=document,
            annotation_pipeline=models[0],
            embedding_model=models[1],
        )
        document_store.add_document(document)
    except Exception as e:
        raise gr.Error(f"Failed to process text: {e}")
    # remove the embeddings because they are very large
    if document.metadata.get("embeddings"):
        document.metadata = {k: v for k, v in document.metadata.items() if k != "embeddings"}
    # 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[EmbeddingModel]],
    document_store: DocumentStore,
    split_regex_escaped: str,
    show_max_cross_doc_sims: bool = False,
) -> pd.DataFrame:
    try:
        new_documents = []
        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}' ...")
                new_document = create_document(
                    text=text,
                    doc_id=base_file_name,
                    split_regex=unescape_regex(split_regex_escaped)
                    if len(split_regex_escaped) > 0
                    else None,
                )
                annotate_document(
                    document=new_document,
                    annotation_pipeline=models[0],
                    embedding_model=models[1],
                )
                new_documents.append(new_document)
            else:
                raise gr.Error(f"Unsupported file format: {file_name}")
        document_store.add_documents(new_documents)
    except Exception as e:
        raise gr.Error(f"Failed to process uploaded files: {e}")

    return document_store.overview(with_max_cross_doc_sims=show_max_cross_doc_sims)


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


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


def select_processed_document(
    evt: gr.SelectData,
    processed_documents_df: pd.DataFrame,
    document_store: DocumentStore,
) -> TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions:
    row_idx, col_idx = evt.index
    doc_id = processed_documents_df.iloc[row_idx]["doc_id"]
    doc = document_store.get_document(doc_id, with_embeddings=False)
    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="Argumentative Relation Types",
        value=default,
        multiselect=True,
    )


def download_processed_documents(
    document_store: DocumentStore,
    file_name: str = "processed_documents.json",
) -> str:
    file_path = os.path.join(tempfile.gettempdir(), file_name)
    document_store.save_to_file(file_path, indent=2)
    return file_path


def upload_processed_documents(
    file_name: str,
    document_store: DocumentStore,
) -> pd.DataFrame:
    document_store.add_documents_from_file(file_name)
    return document_store.overview()


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 = load_models(
        model_name=DEFAULT_MODEL_NAME,
        revision=DEFAULT_MODEL_REVISION,
        embedding_model_name=DEFAULT_EMBEDDING_MODEL_NAME,
        embedding_max_length=DEFAULT_EMBEDDING_MAX_LENGTH,
        embedding_batch_size=DEFAULT_EMBEDDING_BATCH_SIZE,
        device=DEFAULT_DEVICE,
    )

    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:
        document_store_state = gr.State(
            DocumentStore(
                span_annotation_caption="adu",
                relation_annotation_caption="relation",
                vector_store=QdrantVectorStore(),
            )
        )
        # 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))
        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,
                    )
                    embedding_max_length = gr.Slider(
                        label="Embedding Model Max Length",
                        minimum=16,
                        maximum=2048,
                        step=8,
                        value=DEFAULT_EMBEDDING_MAX_LENGTH,
                    )
                    embedding_batch_size = gr.Slider(
                        label="Embedding Model Batch Size",
                        minimum=1,
                        maximum=128,
                        step=1,
                        value=DEFAULT_EMBEDDING_BATCH_SIZE,
                    )
                    device = gr.Textbox(
                        label="Device (e.g. 'cuda' or 'cpu')",
                        value=DEFAULT_DEVICE,
                    )
                    load_models_btn = gr.Button("Load Models")
                    load_models_btn.click(
                        fn=load_models,
                        inputs=[
                            model_name,
                            model_revision,
                            embedding_model_name,
                            embedding_max_length,
                            embedding_batch_size,
                            device,
                        ],
                        outputs=models_state,
                    )
                    split_regex_escaped = gr.Textbox(
                        label="Regex to partition the text",
                        placeholder="Regular expression pattern to split the text into partitions",
                        value=escape_regex(DEFAULT_SPLIT_REGEX),
                    )

                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")

            with gr.Column(scale=1):
                with gr.Accordion(
                    "Indexed Documents", open=False
                ) as processed_documents_accordion:
                    processed_documents_df = gr.DataFrame(
                        headers=["id", "num_adus", "num_relations"],
                        interactive=False,
                    )
                    show_max_cross_docu_sims = gr.Checkbox(
                        label="Show max cross-document similarities", value=False
                    )
                    gr.Markdown("Data Snapshot:")
                    with gr.Row():
                        download_processed_documents_btn = gr.DownloadButton("Download")
                        upload_processed_documents_btn = gr.UploadButton(
                            "Upload", file_types=["json"]
                        )

                upload_btn = gr.UploadButton(
                    "Upload & Analyse Reference Documents",
                    file_types=["text"],
                    file_count="multiple",
                )

                with gr.Accordion("Selected ADU", open=False):
                    selected_adu_id = gr.Textbox(label="ID", elem_id="selected_adu_id")
                    selected_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=0.95,
                    )
                    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"])

                    all2all_adu_similarities_button = gr.Button(
                        "Compute all ADU-to-ADU similarities"
                    )
                    all2all_adu_similarities = gr.DataFrame(
                        headers=["sim_score", "doc_id", "other_doc_id", "text", "other_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=[
                        "relation",
                        "adu",
                        "reference_adu",
                        "doc_id",
                        "sim_score",
                        "rel_score",
                    ],
                    interactive=False,
                )

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

        show_overview_kwargs = dict(
            fn=lambda document_store, show_max_sims, min_sim: document_store.overview(
                with_max_cross_doc_sims=show_max_sims
            ),
            inputs=[document_store_state, show_max_cross_docu_sims, min_similarity],
            outputs=[processed_documents_df],
        )
        predict_btn.click(fn=open_accordion, inputs=[], outputs=[output_accordion]).then(
            fn=wrapped_process_text,
            inputs=[doc_text, doc_id, models_state, document_store_state, split_regex_escaped],
            outputs=[document_json, document_state],
            api_name="predict",
        ).success(**show_overview_kwargs)
        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=open_accordion, inputs=[], outputs=[processed_documents_accordion]
        ).then(
            fn=process_uploaded_files,
            inputs=[
                upload_btn,
                models_state,
                document_store_state,
                split_regex_escaped,
                show_max_cross_docu_sims,
            ],
            outputs=[processed_documents_df],
        )
        processed_documents_df.select(
            select_processed_document,
            inputs=[processed_documents_df, document_store_state],
            outputs=[document_state],
        )
        show_max_cross_docu_sims.change(**show_overview_kwargs)

        download_processed_documents_btn.click(
            fn=partial(download_processed_documents, file_name="processed_documents.zip"),
            inputs=[document_store_state],
            outputs=[download_processed_documents_btn],
        )
        upload_processed_documents_btn.upload(
            fn=upload_processed_documents,
            inputs=[upload_processed_documents_btn, document_store_state],
            outputs=[processed_documents_df],
        )

        retrieve_relevant_adus_event_kwargs = dict(
            fn=partial(
                DocumentStore.get_related_annotations_from_other_documents_df,
                columns=relevant_adus.headers,
            ),
            inputs=[
                document_store_state,
                selected_adu_id,
                document_state,
                min_similarity,
                top_k,
                relation_types,
            ],
            outputs=[relevant_adus],
        )

        selected_adu_id.change(
            fn=partial(
                get_annotation_from_document,
                annotation_layer="labeled_spans",
                use_predictions=True,
            ),
            inputs=[document_state, selected_adu_id],
            outputs=[selected_adu_text],
        ).success(**retrieve_relevant_adus_event_kwargs)

        retrieve_similar_adus_btn.click(
            fn=lambda document_store, ann_id, document, min_sim, k: document_store.get_similar_annotations_df(
                ref_annotation_id=ann_id,
                ref_document=document,
                min_similarity=min_sim,
                top_k=k,
                annotation_layer="labeled_spans",
            ),
            inputs=[
                document_store_state,
                selected_adu_id,
                document_state,
                min_similarity,
                top_k,
            ],
            outputs=[similar_adus],
        )

        models_state.change(
            fn=set_relation_types,
            inputs=[models_state],
            outputs=[relation_types],
        )
        all2all_adu_similarities_button.click(
            fn=partial(
                DocumentStore.get_all2all_adu_similarities,
                columns=all2all_adu_similarities.headers,
            ),
            inputs=[document_store_state, min_similarity],
            outputs=[all2all_adu_similarities],
        )

        # 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('#selected_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()