section

autocorpus.section

Handles section processing for Auto-CORPus.

Modules used: - re: regular expression searching/replacing. - nltk: string tokenization - fuzzywuzzy: string-in-string ratio

Attributes

Classes

Functions

get_iao_term_mapping(section_heading)

Get the IAO term mapping for a given section heading.

Parameters:

Name	Type	Description	Default
section_heading	str	The name of the section heading.	required

Returns:

Type	Description
list[dict[str, str]]	The IAO term mapping for the section heading.

Source code in autocorpus/section.py

def get_iao_term_mapping(section_heading: str) -> list[dict[str, str]]:
    """Get the IAO term mapping for a given section heading.

    Args:
        section_heading: The name of the section heading.

    Returns:
        The IAO term mapping for the section heading.
    """
    mapping_dict = read_mapping_file()
    tokenized_section_heading = nltk.wordpunct_tokenize(section_heading)
    text = nltk.Text(tokenized_section_heading)
    words = [w.lower() for w in text]
    h2_tmp = " ".join(word for word in words)

    # TODO: check for best match, not the first
    mapping_result = []
    if h2_tmp != "":
        if any(x in h2_tmp for x in [" and ", "&", "/"]):
            h2_parts = re.split(r" and |\s?/\s?|\s?&\s?", h2_tmp)
            for h2_part in h2_parts:
                h2_part = re.sub(r"^\d*\s?[\(\.]]?\s?", "", h2_part)
                for IAO_term, heading_list in mapping_dict.items():
                    if any(
                        fuzz.ratio(h2_part, heading) >= 80 for heading in heading_list
                    ):
                        mapping_result.append(get_iao_term_to_id_mapping(IAO_term))
                        break

        else:
            for IAO_term, heading_list in mapping_dict.items():
                h2_tmp = re.sub(r"^\d*\s?[\(\.]]?\s?", "", h2_tmp)
                if any([fuzz.ratio(h2_tmp, heading) > 80 for heading in heading_list]):
                    mapping_result = [get_iao_term_to_id_mapping(IAO_term)]
                    break

    if mapping_result == []:
        return [{"iao_name": "document part", "iao_id": "IAO:0000314"}]

    return mapping_result

get_iao_term_to_id_mapping(iao_term)

Map IAO terms to IAO IDs.

Parameters:

Name	Type	Description	Default
iao_term	str	IAO term to map to an IAO ID.	required

Returns:

Type	Description
dict[str, str]	A dictionary containing the IAO term and its corresponding ID

Source code in autocorpus/section.py

def get_iao_term_to_id_mapping(iao_term: str) -> dict[str, str]:
    """Map IAO terms to IAO IDs.

    Args:
        iao_term: IAO term to map to an IAO ID.

    Returns:
        A dictionary containing the IAO term and its corresponding ID
    """
    mapping_result_id_version = read_iao_term_to_id_file().get(iao_term, "")

    return {"iao_name": iao_term, "iao_id": mapping_result_id_version}

get_section(config, section_dict)

Identifies a section using the provided configuration.

Parameters:

Name	Type	Description	Default
config	dict[str, dict[str, Any]]	AC configuration object.	required
section_dict	dict[str, Any]	Article section dictionary.	required

Source code in autocorpus/section.py

def get_section(
    config: dict[str, dict[str, Any]], section_dict: dict[str, Any]
) -> Iterable[Paragraph]:
    """Identifies a section using the provided configuration.

    Args:
        config: AC configuration object.
        section_dict: Article section dictionary.
    """
    section_heading = section_dict.get("headers", [""])[0]
    section_type = get_iao_term_mapping(section_heading)

    # Different processing for abbreviations and references section types
    if section_heading == "Abbreviations":
        if abbreviations_config := config.get("abbreviations-table", None):
            abbreviations = _get_abbreviations(
                abbreviations_config, section_dict["node"]
            )
            for body in abbreviations:
                yield Paragraph(section_heading, "", body, section_type)
            return

    if {
        "iao_name": "references section",
        "iao_id": "IAO:0000320",
    } in section_type:
        yield from _get_references(config, section_heading, section_dict["node"])
        return

    for child in _get_section(config, section_dict["node"]):
        yield Paragraph(
            section_heading,
            child.subheading,
            child.body,
            section_type,
        )

read_iao_term_to_id_file() cached

Parses the IAO_term_to_ID.txt file.

Returns:

Type	Description
dict[str, str]	Parsed IAO ids as a dictionary

Source code in autocorpus/section.py

@lru_cache
def read_iao_term_to_id_file() -> dict[str, str]:
    """Parses the IAO_term_to_ID.txt file.

    Returns:
        Parsed IAO ids as a dictionary
    """
    iao_term_to_no_dict = {}
    id_path = resources.files("autocorpus.IAO_dicts") / "IAO_term_to_ID.txt"
    with id_path.open(encoding="utf-8") as f:
        lines = f.readlines()
        for line in lines:
            iao_term, _, iao_no = line.rstrip("\n").partition("\t")
            iao_term_to_no_dict.update({iao_term: iao_no})
    return iao_term_to_no_dict

read_mapping_file() cached

Reads the IAO mapping file and parses it into a dictionary.

Returns:

Type	Description
dict[str, list[str]]	The parsed IAO mappings

Source code in autocorpus/section.py

@lru_cache
def read_mapping_file() -> dict[str, list[str]]:
    """Reads the IAO mapping file and parses it into a dictionary.

    Returns:
        The parsed IAO mappings
    """
    mapping_dict: dict[str, list[str]] = {}
    mapping_path = resources.files("autocorpus.IAO_dicts") / "IAO_FINAL_MAPPING.txt"
    with mapping_path.open(encoding="utf-8") as f:
        lines = f.readlines()
        for line in lines:
            heading, _, iao_term = line.rstrip("\n").lower().partition("\t")
            if iao_term != "":
                if "/" in iao_term:
                    iao_term_1 = iao_term.split("/")[0].strip(" ")
                    iao_term_2 = iao_term.split("/")[1].strip(" ")
                    if iao_term_1 in mapping_dict.keys():
                        mapping_dict[iao_term_1].append(heading)
                    else:
                        mapping_dict.update({iao_term_1: [heading]})

                    if iao_term_2 in mapping_dict.keys():
                        mapping_dict[iao_term_2].append(heading)
                    else:
                        mapping_dict.update({iao_term_2: [heading]})

                else:
                    if iao_term in mapping_dict.keys():
                        mapping_dict[iao_term].append(heading)
                    else:
                        mapping_dict.update({iao_term: [heading]})
    return mapping_dict