citation.py

import html

from citeproc import formatter, CitationStylesBibliography, Citation, CitationItem
from citeproc.source.json import CiteProcJSON

from enhanced_citation_style import EnhancedCitationStyle, get_style_name
from steps.utils import author_name_as_dict


def display_citation(bibtex_metadata, bib_stylename, formatter=formatter.html):
    # valid style names: plos, apa, pnas, nature, bmj, harvard1
    # full list is here: https://github.com/citation-style-language/styles

    bib_style = EnhancedCitationStyle(bib_stylename)
    bibliography = CitationStylesBibliography(
        bib_style, bibtex_metadata, formatter
    )  # could be formatter.html
    citation = Citation([CitationItem("ITEM-1")])
    bibliography.register(citation)

    citation_parts = "".join(bibliography.bibliography()[0])
    citation_text = "".join(citation_parts)

    if bib_stylename == "apa":
        # strip extra periods and spaces that can occur in APA format
        citation_text = citation_text.replace("..", ".")
        citation_text = citation_text.replace("  ", " ")

        citation_text = citation_text.strip()

        # strip leading comma
        if citation_text.startswith(","):
            citation_text = citation_text.lstrip(",").strip()

        citation_text = strip_duplicate_apa_title(bibtex_metadata, citation_text)

    citation_text = html.unescape(citation_text)
    return citation_text


def get_author_list(data_author):
    author_list = []
    for name_dict in data_author:
        new_name_dict = {}
        if "family" not in name_dict:
            if "name" in name_dict:
                new_name_dict["family"] = name_dict["name"]
            else:
                new_name_dict["family"] = ""
        for name_k, name_v in name_dict.items():
            if name_k == "literal":
                new_name_dict = author_name_as_dict(name_v)
            else:
                new_name_dict[name_k] = name_v
        author_list.append(new_name_dict)
    return author_list


def build_bibtex_author_list(authors):
    author_list = ""
    for i, author in enumerate(authors):
        if i > 0:
            author_list += " and "

        if author.get("family"):
            author_list += author.get("family")

        if author.get("given"):
            author_list += ", " + author.get("given")

    return author_list


def bibtex_pages_format(pages):
    return pages.replace("-", "--")


def get_bib_source_from_dict(data):
    data["id"] = "ITEM-1"

    if "author" in data:
        data["author"] = get_author_list(data["author"])

    if "type" not in data:
        data["type"] = "misc"

    if data["type"] != "software":
        for k, val in data.items():
            if val and (k in ["title", "container-title"]):
                num_upper = sum([1 for c in val if c.isupper()])
                if num_upper > 0.75 * len(val):
                    data[k] = val.title()

    if "page" in data and data["page"] == "-":
        del data["page"]

    if "bibtex" in data:
        del data["bibtex"]

    if "issued" in data:
        if data["issued"]["date-parts"][0][0] is None:
            del data["issued"]

    bib_source = CiteProcJSON([data])

    return bib_source


def strip_duplicate_apa_title(bibtex_metadata, citation_text):
    item = bibtex_metadata.get("item-1")
    title = item.get("title")
    if title and "Retrieved from https://github.com" not in citation_text:
        title = "".join(title).replace("  ", " ")
        if citation_text.count(title) == 2:
            citation_text = citation_text.replace(title, "", 1)
        if citation_text[0] == ".":
            citation_text = citation_text.replace(".", "", 1)
            citation_text = citation_text.lstrip()
    return citation_text


def citations(bibtex_metadata):
    response = []
    # full list of possible citation formats is here: https://github.com/citation-style-language/styles
    for bib_stylename in [
        "apa",
        "harvard1",
        "nature",
        "modern-language-association-with-url",
        "chicago-author-date",
        "vancouver",
    ]:
        citation_style_object = {
            "style_shortname": bib_stylename,
            "citation": display_citation(bibtex_metadata, bib_stylename),
            "style_fullname": get_style_name(bib_stylename),
        }
        response.append(citation_style_object)
    return response


def export_contents(export_type, metadata_dict):
    if export_type == "csv":
        items = list(metadata_dict.items())
        header_row = ",".join([name for (name, value) in items])
        try:
            value_row = ",".join([str(value) for (name, value) in items])
        except UnicodeEncodeError:
            value_row = ""
        response = "{}\n{}".format(header_row, value_row)
        return response
    elif export_type == "ris":
        response_list = []
        response_list.append(("TY", "JOUR"))
        response_list.append(("T1", metadata_dict.get("title", "")))
        response_list.append(("JO", metadata_dict.get("container-title", "")))
        response_list.append(("VL", metadata_dict.get("volume", "")))
        response_list.append(("IS", metadata_dict.get("issue", "")))
        response_list.append(("SP", metadata_dict.get("page", "")))
        response_list.append(("V1", metadata_dict.get("year", "")))
        response_list.append(("PB", metadata_dict.get("publisher", "")))
        for author in metadata_dict.get("author", []):
            response_list.append(
                ("A1", ", ".join([author.get("family", ""), author.get("given", "")]))
            )
        response = "\n".join("{} - {}".format(k, v) for (k, v) in response_list)
        response += "\nER - "
        return response
    elif export_type == "enw":
        response_list = []
        response_list.append(("%T", metadata_dict.get("title", "")))
        response_list.append(("%J", metadata_dict.get("container-title", "")))
        response_list.append(("%V", metadata_dict.get("volume", "")))
        response_list.append(("%N", metadata_dict.get("issue", "")))
        response_list.append(("%P", metadata_dict.get("page", "")))
        response_list.append(("%D", metadata_dict.get("year", "")))
        response_list.append(("%I", metadata_dict.get("publisher", "")))
        response_list.append(("0%", "Journal Article"))
        for author in metadata_dict.get("author", []):
            response_list.append(
                ("%A", ", ".join([author.get("family", ""), author.get("given", "")]))
            )
        response = "\n".join("{} {}".format(k, v) for (k, v) in response_list)
        return response
    elif export_type == "bibtex":
        if metadata_dict.get("type"):
            response = "@" + metadata_dict.get("type") + "{ITEM1, "
        else:
            response = "@article{ITEM1, "

        response_list = []

        response_list.append(("title", metadata_dict.get("title", "")))

        # handle book type differently
        if metadata_dict.get("type") == "book":
            response_list.append(("isbn", metadata_dict.get("isbn", "")))
        elif metadata_dict.get("type") == "software":
            response_list.append(("url", metadata_dict.get("URL", "")))
            response_list.append(("journal", metadata_dict.get("container-title", "")))
            response_list.append(("volume", metadata_dict.get("volume", "")))
            response_list.append(("number", metadata_dict.get("number", "")))
        else:
            response_list.append(("journal", metadata_dict.get("container-title", "")))
            response_list.append(("volume", metadata_dict.get("volume", "")))
            response_list.append(("number", metadata_dict.get("number", "")))

        response_list.append(
            ("pages", bibtex_pages_format(metadata_dict.get("page", "")))
        )
        response_list.append(("year", metadata_dict.get("year", "")))
        response_list.append(("publisher", metadata_dict.get("publisher", "")))
        author_list = build_bibtex_author_list(metadata_dict.get("author", []))
        response_list.append(("author", author_list))

        response += ",\n".join("{}={{{}}}".format(k, v) for (k, v) in response_list)
        response += "}"

        return response

    return None


def reference_manager_exports(metadata_dict):
    response = []
    for export_name in ["csv", "enw", "ris", "bibtex"]:
        export_object = {
            "export_name": export_name,
            "export": export_contents(export_name, metadata_dict),
        }
        response.append(export_object)
    return response