app.py

import argparse
import html
import time

from extend import spacy_component  # this is needed to register the spacy component

import spacy
import streamlit as st
from annotated_text import annotation
from classy.utils.streamlit import get_md_200_random_color_generator


def main(
    model_checkpoint_path: str,
    inventory_path: str,
    cuda_device: int,
):
    # setup examples
    examples = [
        "Japan began the defence of their title with a lucky 2-1 win against Syria in a Group C championship match on Friday.",
        "The project was coded in Java.",
        "Rome is in Italy",
    ]

    # define load_resources

    @st.cache(allow_output_mutation=True)
    def load_resources(inventory_path):

        # load nlp
        nlp = spacy.load("en_core_web_sm")
        extend_config = dict(
            checkpoint_path=model_checkpoint_path,
            mentions_inventory_path=inventory_path,
            device=cuda_device,
            tokens_per_batch=10_000,
        )
        nlp.add_pipe("extend", after="ner", config=extend_config)

        # mock call to load resources
        nlp(examples[0])

        # return
        return nlp

    # preload default resources
    load_resources(inventory_path)

    # css rules
    st.write(
        """
            <style type="text/css">
                a {
                    text-decoration: none !important;
                }
            </style>
        """,
        unsafe_allow_html=True,
    )

    # setup header
    st.markdown(
        "<h1 style='text-align: center;'>ExtEnD: Extractive Entity Disambiguation</h1>",
        unsafe_allow_html=True,
    )
    st.write(
        """
            <div align="center">
                <a href="https://sunglasses-ai.github.io/classy/">
                    <img alt="Python" style="height: 3em; margin: 0em 1em 2em 1em;" src="data:image/svg+xml;base64,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">
                </a>
                <a href="https://spacy.io/" tyle="text-decoration: none">
                    <img alt="spaCy" style="height: 3em; margin: 0em 1em 2em 1em;" src="data:image/svg+xml;base64,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">
                </a>
            </div> 
        """,
        unsafe_allow_html=True,
    )

    # how it works
    def hiw():
        st.markdown("""
                ## How it works
    
                ExtEnD frames Entity Disambiguation as a text extraction problem:
            """)
        st.image(
            "data/repo-assets/extend_formulation.png", caption="ExtEnD Formulation"
        )
        st.markdown(
            """            
            Given the sentence *After a long fight Superman saved Metropolis*, where *Superman* is the mention
            to disambiguate, ExtEnD first concatenates the descriptions of all the possible candidates of *Superman* in the
            inventory and then selects the span whose description best suits the mention in its context.
            
            To use ExtEnD for full end2end entity linking, as we do in *Demo*, we just need to leverage a mention 
            identifier. Here [we use spaCy](https://github.com/SapienzaNLP/extend#spacy) (more specifically, its NER) and run ExtEnD on each named 
            entity spaCy identifies (if the corresponding mention is contained in the inventory).

            ##### Links:
             * [Full Paper](https://www.researchgate.net/publication/359392427_ExtEnD_Extractive_Entity_Disambiguation)
             * [GitHub](https://github.com/SapienzaNLP/extend)
        """
        )

    # demo
    def demo():
        st.markdown("## Demo")

        # read input
        placeholder = st.selectbox(
            "Examples",
            options=examples,
            index=0,
        )
        input_text = st.text_area("Input text to entity-disambiguate", placeholder)

        # button
        should_disambiguate = st.button("Disambiguate", key="classify")

        # load model and color generator
        nlp = load_resources(inventory_path)
        color_generator = get_md_200_random_color_generator()

        if should_disambiguate:

            # tag sentence
            time_start = time.perf_counter()
            doc = nlp(input_text)
            time_end = time.perf_counter()

            # extract entities
            entities = {}
            for ent in doc.ents:
                if ent._.disambiguated_entity is not None:
                    entities[ent.start_char] = (
                        ent.start_char,
                        ent.end_char,
                        ent.text,
                        ent._.disambiguated_entity,
                    )

            # create annotated html components

            annotated_html_components = []

            assert all(any(t.idx == _s for t in doc) for _s in entities)
            it = iter(list(doc))
            while True:
                try:
                    t = next(it)
                except StopIteration:
                    break
                if t.idx in entities:
                    _start, _end, _text, _entity = entities[t.idx]
                    while t.idx + len(t) != _end:
                        t = next(it)
                    annotated_html_components.append(
                        f"<a href=\"https://en.wikipedia.org/wiki/{_entity.lower().replace(' ', '_').capitalize()}\">{annotation(*(_text, _entity, color_generator()))}</a>"
                    )
                else:
                    annotated_html_components.append(str(html.escape(t.text)))

            st.markdown(
                "\n".join(
                    [
                        "<div>",
                        *annotated_html_components,
                        "<p></p>"
                        f'<div style="text-align: right"><p style="color: gray">Time: {(time_end - time_start):.2f}s</p></div>'
                        "</div>",
                    ]
                ),
                unsafe_allow_html=True,
            )

    demo()
    hiw()


if __name__ == "__main__":
    main(
        "experiments/extend-longformer-large/2021-10-22/09-11-39/checkpoints/best.ckpt",
        "data/inventories/le-and-titov-2018-inventory.min-count-2.sqlite3",
        cuda_device=-1,
    )