generic_ner.py

import logging
from transformers import Pipeline
import numpy as np
import torch
import nltk

nltk.download("averaged_perceptron_tagger")
nltk.download("averaged_perceptron_tagger_eng")
nltk.download("stopwords")
from nltk.chunk import conlltags2tree
from nltk import pos_tag
from nltk.tree import Tree
import torch.nn.functional as F
import re, string

stop_words = set(nltk.corpus.stopwords.words("english"))
DEBUG = False
punctuation = (
    string.punctuation
    + "«»—…“”"
    + "—."
    + "–"
    + "’"
    + "‘"
    + "´"
    + "•"
    + "°"
    + "»"
    + "“"
    + "”"
    + "–"
    + "—"
    + "‘’“”„«»•–—―‣◦…§¶†‡‰′″〈〉"
)

# List of additional "strange" punctuation marks
# additional_punctuation = "‘’“”„«»•–—―‣◦…§¶†‡‰′″〈〉"


WHITESPACE_RULES = {
    "fr": {
        "pct_no_ws_before": [".", ",", ")", "]", "}", "°", "...", ".-", "%"],
        "pct_no_ws_after": ["(", "[", "{"],
        "pct_no_ws_before_after": ["'", "-"],
        "pct_number": [".", ","],
    },
    "de": {
        "pct_no_ws_before": [
            ".",
            ",",
            ")",
            "]",
            "}",
            "°",
            "...",
            "?",
            "!",
            ":",
            ";",
            ".-",
            "%",
        ],
        "pct_no_ws_after": ["(", "[", "{"],
        "pct_no_ws_before_after": ["'", "-"],
        "pct_number": [".", ","],
    },
    "other": {
        "pct_no_ws_before": [
            ".",
            ",",
            ")",
            "]",
            "}",
            "°",
            "...",
            "?",
            "!",
            ":",
            ";",
            ".-",
            "%",
        ],
        "pct_no_ws_after": ["(", "[", "{"],
        "pct_no_ws_before_after": ["'", "-"],
        "pct_number": [".", ","],
    },
}


# def tokenize(text: str, language: str = "other") -> list[str]:
#     """Apply whitespace rules to the given text and language, separating it into tokens.
#
#     Args:
#         text (str): The input text to separate into a list of tokens.
#         language (str): Language of the text.
#
#     Returns:
#         list[str]: List of tokens with punctuation as separate tokens.
#     """
#     # text = add_spaces_around_punctuation(text)
#     if not text:
#         return []
#
#     if language not in WHITESPACE_RULES:
#         # Default behavior for languages without specific rules:
#         # tokenize using standard whitespace splitting
#         language = "other"
#
#     wsrules = WHITESPACE_RULES[language]
#     tokenized_text = []
#     current_token = ""
#
#     for char in text:
#         if char in wsrules["pct_no_ws_before_after"]:
#             if current_token:
#                 tokenized_text.append(current_token)
#             tokenized_text.append(char)
#             current_token = ""
#         elif char in wsrules["pct_no_ws_before"] or char in wsrules["pct_no_ws_after"]:
#             if current_token:
#                 tokenized_text.append(current_token)
#             tokenized_text.append(char)
#             current_token = ""
#         elif char.isspace():
#             if current_token:
#                 tokenized_text.append(current_token)
#                 current_token = ""
#         else:
#             current_token += char
#
#     if current_token:
#         tokenized_text.append(current_token)
#
#     return tokenized_text


def normalize_text(text):
    # Remove spaces and tabs for the search but keep newline characters
    return re.sub(r"[ \t]+", "", text)


def find_entity_indices(article_text, search_text):
    # Normalize texts by removing spaces and tabs
    normalized_article = normalize_text(article_text)
    normalized_search = normalize_text(search_text)

    # Initialize a list to hold all start and end indices
    indices = []

    # Find all occurrences of the search text in the normalized article text
    start_index = 0
    while True:
        start_index = normalized_article.find(normalized_search, start_index)
        if start_index == -1:
            break

        # Calculate the actual start and end indices in the original article text
        original_chars = 0
        original_start_index = 0
        for i in range(start_index):
            while article_text[original_start_index] in (" ", "\t"):
                original_start_index += 1
            if article_text[original_start_index] not in (" ", "\t", "\n"):
                original_chars += 1
            original_start_index += 1

        original_end_index = original_start_index
        search_chars = 0
        while search_chars < len(normalized_search):
            if article_text[original_end_index] not in (" ", "\t", "\n"):
                search_chars += 1
            original_end_index += 1  # Increment to include the last character

        # Append the found indices to the list
        if article_text[original_start_index] == " ":
            original_start_index += 1
        indices.append((original_start_index, original_end_index))

        # Move start_index to the next position to continue searching
        start_index += 1

    return indices


def get_entities(tokens, tags, confidences, text):

    tags = [tag.replace("S-", "B-").replace("E-", "I-") for tag in tags]
    pos_tags = [pos for token, pos in pos_tag(tokens)]

    for i in range(1, len(tags)):
        # If a 'B-' tag is followed by another 'B-' without an 'O' in between, change the second to 'I-'
        if tags[i].startswith("B-") and tags[i - 1].startswith("I-"):
            tags[i] = "I-" + tags[i][2:]  # Change 'B-' to 'I-' for the same entity type

    conlltags = [(token, pos, tg) for token, pos, tg in zip(tokens, pos_tags, tags)]
    ne_tree = conlltags2tree(conlltags)

    entities = []
    idx: int = 0
    already_done = []
    for subtree in ne_tree:
        # skipping 'O' tags
        if isinstance(subtree, Tree):
            original_label = subtree.label()
            original_string = " ".join([token for token, pos in subtree.leaves()])

            for indices in find_entity_indices(text, original_string):
                entity_start_position = indices[0]
                entity_end_position = indices[1]
                if (
                    "_".join(
                        [original_label, original_string, str(entity_start_position)]
                    )
                    in already_done
                ):
                    continue
                else:
                    already_done.append(
                        "_".join(
                            [
                                original_label,
                                original_string,
                                str(entity_start_position),
                            ]
                        )
                    )
                if len(text[entity_start_position:entity_end_position].strip()) < len(
                    text[entity_start_position:entity_end_position]
                ):
                    entity_start_position = (
                        entity_start_position
                        + len(text[entity_start_position:entity_end_position])
                        - len(text[entity_start_position:entity_end_position].strip())
                    )

                entities.append(
                    {
                        "type": original_label,
                        "confidence_ner": round(
                            np.average(confidences[idx : idx + len(subtree)]), 2
                        ),
                        "index": (idx, idx + len(subtree)),
                        "surface": text[
                            entity_start_position:entity_end_position
                        ],  # original_string,
                        "lOffset": entity_start_position,
                        "rOffset": entity_end_position,
                    }
                )

            idx += len(subtree)

            # Update the current character position
            # We add the length of the original string + 1 (for the space)
        else:
            token, pos = subtree
            # If it's not a named entity, we still need to update the character
            # position
            idx += 1

    return entities


def realign(word_ids, tokens, out_label_preds, softmax_scores, tokenizer, reverted_label_map):
    preds_list, words_list, confidence_list = [], [], []

    seen_word_ids = set()
    for i, word_id in enumerate(word_ids):
        if word_id is None or word_id in seen_word_ids:
            continue  # skip special tokens or repeated subwords

        seen_word_ids.add(word_id)

        try:
            preds_list.append(reverted_label_map[out_label_preds[i]])
            confidence_list.append(max(softmax_scores[i]))
        except Exception:
            preds_list.append("O")
            confidence_list.append(0.0)

        words_list.append(tokens[word_id])  # original word list index

    return words_list, preds_list, confidence_list

def add_spaces_around_punctuation(text):
    # Add a space before and after all punctuation
    all_punctuation = string.punctuation + punctuation
    return re.sub(r"([{}])".format(re.escape(all_punctuation)), r" \1 ", text)


def attach_comp_to_closest(entities):
    # Define valid entity types that can receive a "comp.function" or "comp.name" attachment
    valid_entity_types = {"org", "pers", "org.ent", "pers.ind"}

    # Separate "comp.function" and "comp.name" entities from other entities
    comp_entities = [ent for ent in entities if ent["type"].startswith("comp")]
    other_entities = [ent for ent in entities if not ent["type"].startswith("comp")]

    for comp_entity in comp_entities:
        closest_entity = None
        min_distance = float("inf")

        # Find the closest non-"comp" entity that is valid for attaching
        for other_entity in other_entities:
            # Calculate distance between the comp entity and the other entity
            if comp_entity["lOffset"] > other_entity["rOffset"]:
                distance = comp_entity["lOffset"] - other_entity["rOffset"]
            elif comp_entity["rOffset"] < other_entity["lOffset"]:
                distance = other_entity["lOffset"] - comp_entity["rOffset"]
            else:
                distance = 0  # They overlap or touch

            # Ensure the entity type is valid and check for minimal distance
            if (
                distance < min_distance
                and other_entity["type"].split(".")[0] in valid_entity_types
            ):
                min_distance = distance
                closest_entity = other_entity

        # Attach the "comp.function" or "comp.name" if a valid entity is found
        if closest_entity:
            suffix = comp_entity["type"].split(".")[
                -1
            ]  # Extract the suffix (e.g., 'name', 'function')
            closest_entity[suffix] = comp_entity["surface"]  # Attach the text

    return other_entities


def conflicting_context(comp_entity, target_entity):
    """
    Determines if there is a conflict between the comp_entity and the target entity.
    Prevents incorrect name and function attachments by using a rule-based approach.
    """
    # Case 1: Check for correct function attachment to person or organization entities
    if comp_entity["type"].startswith("comp.function"):
        if not ("pers" in target_entity["type"] or "org" in target_entity["type"]):
            return True  # Conflict: Function should only attach to persons or organizations

    # Case 2: Avoid attaching comp.* entities to non-person, non-organization types (like locations)
    if "loc" in target_entity["type"]:
        return True  # Conflict: comp.* entities should not attach to locations or similar types

    return False  # No conflict


def extract_name_from_text(text, partial_name):
    """
    Extracts the full name from the entity's text based on the partial name.
    This function assumes that the full name starts with capitalized letters and does not
    include any words that come after the partial name.
    """
    # Split the text and partial name into words
    words = text.split()
    partial_words = partial_name.split()

    if DEBUG:
        print("text:", text)
    if DEBUG:
        print("partial_name:", partial_name)

    # Find the position of the partial name in the word list
    for i, word in enumerate(words):
        if DEBUG:
            print(words, "---", words[i : i + len(partial_words)])
        if words[i : i + len(partial_words)] == partial_words:
            # Initialize full name with the partial name
            full_name = partial_words[:]

            if DEBUG:
                print("full_name:", full_name)

            # Check previous words and only add capitalized words (skip lowercase words)
            j = i - 1
            while j >= 0 and words[j][0].isupper():
                full_name.insert(0, words[j])
                j -= 1
                if DEBUG:
                    print("full_name:", full_name)

            # Return only the full name up to the partial name (ignore words after the name)
            return " ".join(full_name).strip()  # Join the words to form the full name

    # If not found, return the original text (as a fallback)
    return text.strip()


def repair_names_in_entities(entities):
    """
    This function repairs the names in the entities by extracting the full name
    from the text of the entity if a partial name (e.g., 'Washington') is incorrectly attached.
    """
    for entity in entities:
        if "name" in entity and "pers" in entity["type"]:
            name = entity["name"]
            text = entity["surface"]

            # Check if the attached name is part of the entity's text
            if name in text:
                # Extract the full name from the text by splitting around the attached name
                full_name = extract_name_from_text(entity["surface"], name)
                entity["name"] = (
                    full_name  # Replace the partial name with the full name
                )
        # if "name" not in entity:
        #     entity["name"] = entity["surface"]

    return entities


def clean_coarse_entities(entities):
    """
    This function removes entities that are not useful for the NEL process.
    """
    # Define a set of entity types that are considered useful for NEL
    useful_types = {
        "pers",  # Person
        "loc",  # Location
        "org",  # Organization
        "date",  # Product
        "time",  # Time
    }

    # Filter out entities that are not in the useful_types set unless they are comp.* entities
    cleaned_entities = [
        entity
        for entity in entities
        if entity["type"] in useful_types or "comp" in entity["type"]
    ]

    return cleaned_entities


def postprocess_entities(entities):
    # Step 1: Filter entities with the same text, keeping the one with the most dots in the 'entity' field
    entity_map = {}

    # Loop over the entities and prioritize the one with the most dots
    for entity in entities:
        entity_text = entity["surface"]
        num_dots = entity["type"].count(".")

        # If the entity text is new, or this entity has more dots, update the map
        if (
            entity_text not in entity_map
            or entity_map[entity_text]["type"].count(".") < num_dots
        ):
            entity_map[entity_text] = entity

    # Collect the filtered entities from the map
    filtered_entities = list(entity_map.values())

    # Step 2: Attach "comp.function" entities to the closest other entities
    filtered_entities = attach_comp_to_closest(filtered_entities)
    if DEBUG:
        print("After attach_comp_to_closest:", filtered_entities, "\n")
    filtered_entities = repair_names_in_entities(filtered_entities)
    if DEBUG:
        print("After repair_names_in_entities:", filtered_entities, "\n")

    # Step 3: Remove entities that are not useful for NEL
    # filtered_entities = clean_coarse_entities(filtered_entities)

    # filtered_entities = remove_blacklisted_entities(filtered_entities)

    return filtered_entities


def remove_included_entities(entities):
    # Loop through entities and remove those whose text is included in another with the same label
    final_entities = []
    for i, entity in enumerate(entities):
        is_included = False
        for other_entity in entities:
            if entity["surface"] != other_entity["surface"]:
                if "comp" in other_entity["type"]:
                    # Check if entity's text is a substring of another entity's text
                    if entity["surface"] in other_entity["surface"]:
                        is_included = True
                        break
                elif (
                    entity["type"].split(".")[0] in other_entity["type"].split(".")[0]
                    or other_entity["type"].split(".")[0]
                    in entity["type"].split(".")[0]
                ):
                    if entity["surface"] in other_entity["surface"]:
                        is_included = True
        if not is_included:
            final_entities.append(entity)
    return final_entities


def refine_entities_with_coarse(all_entities, coarse_entities):
    """
    Looks through all entities and refines them based on the coarse entities.
    If a surface match is found in the coarse entities and the types match,
    the entity's confidence_ner and type are updated based on the coarse entity.
    """
    # Create a dictionary for coarse entities based on surface and type for quick lookup
    coarse_lookup = {}
    for coarse_entity in coarse_entities:
        key = (coarse_entity["surface"], coarse_entity["type"].split(".")[0])
        coarse_lookup[key] = coarse_entity

    # Iterate through all entities and compare with the coarse entities
    for entity in all_entities:
        key = (
            entity["surface"],
            entity["type"].split(".")[0],
        )  # Use the coarse type for comparison

        if key in coarse_lookup:
            coarse_entity = coarse_lookup[key]
            # If a match is found, update the confidence_ner and type in the entity
            if entity["confidence_ner"] < coarse_entity["confidence_ner"]:
                entity["confidence_ner"] = coarse_entity["confidence_ner"]
                entity["type"] = coarse_entity[
                    "type"
                ]  # Update the type if the confidence is higher

    # No need to append to refined_entities, we're modifying in place
    for entity in all_entities:
        entity["type"] = entity["type"].split(".")[0]
    return all_entities


def remove_trailing_stopwords(entities):
    """
    This function removes stopwords and punctuation from both the beginning and end of each entity's text
    and repairs the lOffset and rOffset accordingly.
    """
    if DEBUG:
        print(f"Initial entities in remove_trailing_stopwords: {len(entities)}")
    new_entities = []
    for entity in entities:
        if "comp" not in entity["type"]:
            entity_text = entity["surface"]
            original_len = len(entity_text)

            # Initial offsets
            lOffset = entity.get("lOffset", 0)
            rOffset = entity.get("rOffset", original_len)

            # Remove stopwords and punctuation from the beginning
            # print('----', entity_text)
            if len(entity_text.split()) < 1:
                continue
            while entity_text and (
                entity_text.split()[0].lower() in stop_words
                or entity_text[0] in punctuation
            ):
                if entity_text.split()[0].lower() in stop_words:
                    stopword_len = (
                        len(entity_text.split()[0]) + 1
                    )  # Adjust length for stopword and following space
                    entity_text = entity_text[stopword_len:]  # Remove leading stopword
                    lOffset += stopword_len  # Adjust the left offset
                    if DEBUG:
                        print(
                            f"Removed leading stopword from entity: {entity['surface']} --> {entity_text} ({entity['type']}"
                        )
                elif entity_text[0] in punctuation:
                    entity_text = entity_text[1:]  # Remove leading punctuation
                    lOffset += 1  # Adjust the left offset
                    if DEBUG:
                        print(
                            f"Removed leading punctuation from entity: {entity['surface']} --> {entity_text} ({entity['type']}"
                        )

            # Remove stopwords and punctuation from the end
            if len(entity_text.strip()) > 1:
                while (
                    entity_text.strip().split()
                    and (
                        entity_text.strip().split()[-1].lower() in stop_words
                        or entity_text[-1] in punctuation
                    )
                ):
                    if entity_text.strip().split() and entity_text.strip().split()[-1].lower() in stop_words:
                        stopword_len = len(entity_text.strip().split()[-1]) + 1  # account for space
                        entity_text = entity_text[:-stopword_len]
                        rOffset -= stopword_len
                        if DEBUG:
                            print(
                                f"Removed trailing stopword from entity: {entity['surface']} --> {entity_text} ({entity['type']})"
                            )
                    if entity_text and entity_text[-1] in punctuation:
                        entity_text = entity_text[:-1]
                        rOffset -= 1
                        if DEBUG:
                            print(
                                f"Removed trailing punctuation from entity: {entity['surface']} --> {entity_text} ({entity['type']})"
                            )

            # Skip certain entities based on rules
            if entity_text in string.punctuation:
                if DEBUG:
                    print(f"Skipping entity: {entity_text}")
                # entities.remove(entity)
                continue
            # check now if its in stopwords
            if entity_text.lower() in stop_words:
                if DEBUG:
                    print(f"Skipping entity: {entity_text}")
                # entities.remove(entity)
                continue
            # check now if the entire entity is a list of stopwords:
            if all([word.lower() in stop_words for word in entity_text.split()]):
                if DEBUG:
                    print(f"Skipping entity: {entity_text}")
                # entities.remove(entity)
                continue
            # Check if the entire entity is made up of stopwords characters
            if all(
                [char.lower() in stop_words for char in entity_text if char.isalpha()]
            ):
                if DEBUG:
                    print(
                        f"Skipping entity: {entity_text} (all characters are stopwords)"
                    )
                # entities.remove(entity)
                continue
            # check now if all entity is in a list of punctuation
            if all([word in string.punctuation for word in entity_text.split()]):
                if DEBUG:
                    print(
                        f"Skipping entity: {entity_text} (all characters are punctuation)"
                    )
                # entities.remove(entity)
                continue
            if all(
                [
                    char.lower() in string.punctuation
                    for char in entity_text
                    if char.isalpha()
                ]
            ):
                if DEBUG:
                    print(
                        f"Skipping entity: {entity_text} (all characters are punctuation)"
                    )
                # entities.remove(entity)
                continue

            # if it's a number and "time" no in it, then continue
            if entity_text.isdigit() and "time" not in entity["type"]:
                if DEBUG:
                    print(f"Skipping entity: {entity_text}")
                # entities.remove(entity)
                continue

            if entity_text.startswith(" "):
                entity_text = entity_text[1:]
                # update lOffset, rOffset
                lOffset += 1
            if entity_text.endswith(" "):
                entity_text = entity_text[:-1]
                # update lOffset, rOffset
                rOffset -= 1

            # Update the entity surface and offsets
            entity["surface"] = entity_text
            entity["lOffset"] = lOffset
            entity["rOffset"] = rOffset

            # Remove the entity if the surface is empty after cleaning
            if len(entity["surface"].strip()) == 0:
                if DEBUG:
                    print(f"Deleted entity: {entity['surface']}")
                # entities.remove(entity)
            else:
                new_entities.append(entity)
        else:
            new_entities.append(entity)
    if DEBUG:
        print(f"Remained entities in remove_trailing_stopwords: {len(new_entities)}")
    return new_entities
    

class MultitaskTokenClassificationPipeline(Pipeline):

    def _sanitize_parameters(self, **kwargs):
        preprocess_kwargs = {}
        if "text" in kwargs:
            preprocess_kwargs["text"] = kwargs["text"]
        if "tokens" in kwargs:
            preprocess_kwargs["tokens"] = kwargs["tokens"]
        self.label_map = self.model.config.label_map
        self.id2label = {
            task: {id_: label for label, id_ in labels.items()}
            for task, labels in self.label_map.items()
        }
        return preprocess_kwargs, {}, {}

    def preprocess(self, text, **kwargs):

        tokens = kwargs["tokens"]
        tokenized_inputs = self.tokenizer(
            tokens,  # a list of strings
            is_split_into_words=True,
            padding="max_length",
            truncation=True,
            max_length=512,
        )
        word_ids = tokenized_inputs.word_ids()

        return tokenized_inputs, word_ids, text, tokens

    def _forward(self, inputs):
        inputs, word_ids, text, tokens = inputs

        input_ids = torch.tensor([inputs["input_ids"]], dtype=torch.long).to(
            self.model.device
        )
        attention_mask = torch.tensor([inputs["attention_mask"]], dtype=torch.long).to(
            self.model.device
        )
        with torch.no_grad():
            outputs = self.model(input_ids, attention_mask)
        return outputs, word_ids, text, tokens

    def is_within(self, entity1, entity2):
        """Check if entity1 is fully within the bounds of entity2."""
        return (
            entity1["lOffset"] >= entity2["lOffset"]
            and entity1["rOffset"] <= entity2["rOffset"]
        )

    def postprocess(self, outputs, **kwargs):
        """
        Postprocess the outputs of the model
        :param outputs:
        :param kwargs:
        :return:
        """
        tokens_result, word_ids, text, tokens = outputs

        predictions = {}
        confidence_scores = {}
        for task, logits in tokens_result.logits.items():
            predictions[task] = torch.argmax(logits, dim=-1).tolist()[0]
            confidence_scores[task] = F.softmax(logits, dim=-1).tolist()[0]

        entities = {}
        for task in predictions.keys():
            words_list, preds_list, confidence_list = realign(
                word_ids,
                tokens,
                predictions[task],
                confidence_scores[task],
                self.tokenizer,
                self.id2label[task],
            )

            entities[task] = get_entities(words_list, preds_list, confidence_list, text)

        # add titles to comp entities
        # from pprint import pprint

        # print("Before:")
        # pprint(entities)

        all_entities = []
        coarse_entities = []
        for key in entities:
            if key in ["NE-COARSE-LIT"]:
                coarse_entities = entities[key]
            all_entities.extend(entities[key])

        if DEBUG:
            print(all_entities)
        # print("After remove_included_entities:")
        all_entities = remove_included_entities(all_entities)
        if DEBUG:
            print("After remove_included_entities:", all_entities)
        all_entities = remove_trailing_stopwords(all_entities)
        if DEBUG:
            print("After remove_trailing_stopwords:", all_entities)
        all_entities = postprocess_entities(all_entities)
        if DEBUG:
            print("After postprocess_entities:", all_entities)
        all_entities = refine_entities_with_coarse(all_entities, coarse_entities)
        if DEBUG:
            print("After refine_entities_with_coarse:", all_entities)
        # print("After attach_comp_to_closest:")
        # pprint(all_entities)
        # print("\n")
        return all_entities