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path: root/python/fatcat_tools/importers/grobid_metadata.py
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#!/usr/bin/env python3

import base64
import json
from typing import Any, Dict, List, Optional

import fatcat_openapi_client
from fatcat_openapi_client import ApiClient, FileEntity, ReleaseEntity

from fatcat_tools.normal import clean_doi

from .common import EntityImporter, clean, make_rel_url

MAX_ABSTRACT_BYTES = 4096


class GrobidMetadataImporter(EntityImporter):
    """
    This is a complex case: we need to parse and create both file and release entities.

    The "primary" entity here is really File, not Release. If a matching File
    exists, we bail in want(); if not we insert the Release during parsing, and
    insert both.

    TODO: should instead check if the File has any releases; if not, insert and update.
    TODO: relaxing 'None' constraint on parse_record() might make this refactor-able.
    """

    def __init__(self, api: ApiClient, **kwargs) -> None:

        eg_desc = kwargs.get(
            "editgroup_description",
            "Import of release and file metadata, as extracted from PDFs by GROBID.",
        )
        eg_extra = kwargs.get("editgroup_extra", dict())
        eg_extra["agent"] = eg_extra.get("agent", "fatcat_tools.GrobidMetadataImporter")
        super().__init__(api, editgroup_description=eg_desc, editgroup_extra=eg_extra, **kwargs)
        self.default_link_rel = kwargs.get("default_link_rel", "web")
        self.longtail_oa = kwargs.get("longtail_oa", False)

    def want(self, raw_record: Any) -> bool:
        return True

    def parse_record(self, row: str) -> Optional[FileEntity]:

        fields = row.split("\t")
        sha1_key = fields[0]
        cdx = json.loads(fields[1])
        mimetype = fields[2]
        file_size = int(fields[3])
        grobid_meta = json.loads(fields[4])
        fe = self.parse_file_metadata(sha1_key, cdx, mimetype, file_size)
        re = self.parse_grobid_json(grobid_meta)

        if not (fe and re):
            return None

        # lookup existing file SHA1
        existing = None
        try:
            existing = self.api.lookup_file(sha1=fe.sha1)
        except fatcat_openapi_client.rest.ApiException as err:
            if err.status != 404:
                raise err

        # if file is already in here, presumably not actually long-tail
        # HACK: this is doing an exists check in parse_record(), which is weird
        # TODO: this is where we should check if the file actually has
        # release_ids and/or URLs associated with it
        if existing and not self.bezerk_mode:
            self.counts["exists"] += 1
            self.counts["skip"] -= 1
            return None

        release_edit = self.create_release(re)
        fe.release_ids.append(release_edit.ident)
        return fe

    def parse_grobid_json(self, obj: Dict[str, Any]) -> Optional[ReleaseEntity]:

        if not obj.get("title"):
            return None

        extra_grobid: Dict[str, Any] = dict()

        abstract = obj.get("abstract")
        if abstract and len(abstract) < MAX_ABSTRACT_BYTES and len(abstract) > 10:
            abobj = fatcat_openapi_client.ReleaseAbstract(
                mimetype="text/plain", content=clean(obj.get("abstract"))
            )
            abstracts = [abobj]
        else:
            abstracts = []

        contribs = []
        for i, a in enumerate(obj.get("authors", [])):
            contribs.append(
                fatcat_openapi_client.ReleaseContrib(
                    index=i,
                    raw_name=clean(a["name"]),
                    given_name=clean(a.get("given_name")),
                    surname=clean(a.get("surname")),
                    role="author",
                    extra=None,
                )
            )

        refs = []
        for raw in obj.get("citations", []):
            cite_extra: Dict[str, Any] = dict()
            year = None
            if raw.get("date"):
                try:
                    year = int(raw["date"].strip()[:4])
                except (IndexError, ValueError):
                    pass
            for key in ("volume", "url", "issue", "publisher"):
                if raw.get(key):
                    cite_extra[key] = clean(raw[key])
            if raw.get("authors"):
                cite_extra["authors"] = [clean(a["name"]) for a in raw["authors"]]

            refs.append(
                fatcat_openapi_client.ReleaseRef(
                    key=clean(raw.get("id")),
                    year=year,
                    title=clean(raw["title"]),
                    extra=cite_extra or None,
                )
            )

        release_date = None
        release_year = None
        if obj.get("date"):
            # only returns year, ever?
            release_year = int(obj["date"][:4])

        extra: Dict[str, Any] = dict()
        doi = clean_doi(obj.get("doi"))
        if doi:
            extra["doi"] = doi
        if obj["journal"] and obj["journal"].get("name"):
            extra["container_name"] = clean(obj["journal"]["name"])

        # TODO: ISSN/eISSN handling? or just journal name lookup?

        if extra_grobid:
            extra["grobid"] = extra_grobid
        if self.longtail_oa:
            extra["longtail_oa"] = True

        clean_title = clean(obj["title"], force_xml=True)
        if not clean_title or len(clean_title) < 2:
            return None
        title = clean_title

        re = fatcat_openapi_client.ReleaseEntity(
            title=title,
            release_type="article-journal",
            release_date=release_date,
            release_year=release_year,
            contribs=contribs,
            refs=refs,
            publisher=clean(obj["journal"].get("publisher")),
            volume=clean(obj["journal"].get("volume")),
            issue=clean(obj["journal"].get("issue")),
            abstracts=abstracts or None,
            ext_ids=fatcat_openapi_client.ReleaseExtIds(),
            extra=extra or None,
        )
        return re

    def parse_file_metadata(
        self, sha1_key: str, cdx: Dict[str, Any], mimetype: str, file_size: int
    ) -> FileEntity:

        sha1 = (
            base64.b16encode(base64.b32decode(sha1_key.replace("sha1:", "")))
            .decode("ascii")
            .lower()
        )

        fe = fatcat_openapi_client.FileEntity(
            sha1=sha1,
            size=int(file_size),
            mimetype=mimetype,
            release_ids=[],
            urls=[],
        )

        # parse URLs and CDX
        original = cdx["url"]
        assert len(cdx["dt"]) >= 8
        wayback = "https://web.archive.org/web/{}/{}".format(cdx["dt"], original)
        fe.urls.append(fatcat_openapi_client.FileUrl(url=wayback, rel="webarchive"))
        original_url = make_rel_url(original, default_link_rel=self.default_link_rel)
        if original_url is not None:
            fe.urls.append(
                fatcat_openapi_client.FileUrl(rel=original_url[0], url=original_url[1])
            )

        return fe

    def try_update(self, re: FileEntity) -> bool:
        # did the exists check in 'parse_record()', because we needed to create a release
        return True

    def insert_batch(self, batch: List[FileEntity]) -> None:
        self.api.create_file_auto_batch(
            fatcat_openapi_client.FileAutoBatch(
                editgroup=fatcat_openapi_client.Editgroup(
                    description=self.editgroup_description, extra=self.editgroup_extra
                ),
                entity_list=batch,
            )
        )