commonmeta-py 0.107__py3-none-any.whl → 0.108__py3-none-any.whl

commonmeta/crossref_utils.py

@@ -1,662 +0,0 @@
-"""Crossref utils module for commonmeta-py"""
-
-import uuid
-from datetime import datetime
-from typing import Optional
-
-import pydash as py_
-from dateutil.parser import parse
-from furl import furl
-from lxml import etree
-
-from .constants import ROR_TO_CROSSREF_FUNDER_ID_TRANSLATIONS, Commonmeta
-from .doi_utils import doi_from_url, validate_doi
-from .utils import compact, normalize_id, normalize_orcid, validate_url, wrap
-
-
-def generate_crossref_xml(metadata: Commonmeta) -> Optional[str]:
-    """Generate Crossref XML. First checks for write errors (JSON schema validation)"""
-    xml = crossref_root()
-    head = etree.SubElement(xml, "head")
-    # we use a uuid as batch_id
-    etree.SubElement(head, "doi_batch_id").text = str(uuid.uuid4())
-    etree.SubElement(head, "timestamp").text = datetime.now().strftime("%Y%m%d%H%M%S")
-    depositor = etree.SubElement(head, "depositor")
-    etree.SubElement(depositor, "depositor_name").text = metadata.depositor
-    etree.SubElement(depositor, "email_address").text = metadata.email
-    etree.SubElement(head, "registrant").text = metadata.registrant
-
-    body = etree.SubElement(xml, "body")
-    body = insert_crossref_work(metadata, body)
-    return etree.tostring(
-        xml,
-        doctype='<?xml version="1.0" encoding="UTF-8"?>',
-        pretty_print=True,
-    )
-
-
-def insert_crossref_work(metadata, xml):
-    """Insert crossref work"""
-    if metadata.type not in ["JournalArticle", "Article", "BlogPost"]:
-        return xml
-    if doi_from_url(metadata.id) is None or metadata.url is None:
-        return xml
-    if metadata.type == "JournalArticle":
-        xml = insert_journal(metadata, xml)
-    elif metadata.type in ["Article", "BlogPost"]:
-        xml = insert_posted_content(metadata, xml)
-
-
-def insert_journal(metadata, xml):
-    """Insert journal"""
-    journal = etree.SubElement(xml, "journal")
-    if metadata.language is not None:
-        journal_metadata = etree.SubElement(
-            journal, "journal_metadata", {"language": metadata.language[:2]}
-        )
-    else:
-        journal_metadata = etree.SubElement(journal, "journal_metadata")
-    if (
-        metadata.container is not None
-        and metadata.container.get("title", None) is not None
-    ):
-        etree.SubElement(journal_metadata, "full_title").text = metadata.container.get(
-            "title"
-        )
-    journal_metadata = insert_group_title(metadata, journal_metadata)
-    journal_article = etree.SubElement(
-        journal, "journal_article", {"publication_type": "full_text"}
-    )
-    journal_article = insert_crossref_titles(metadata, journal_article)
-    journal_article = insert_crossref_contributors(metadata, journal_article)
-    journal_article = insert_crossref_publication_date(metadata, journal_article)
-    journal_article = insert_crossref_abstract(metadata, journal_article)
-    journal_article = insert_crossref_issn(metadata, journal_article)
-    journal_article = insert_item_number(metadata, journal_article)
-    journal_article = insert_funding_references(metadata, journal_article)
-    journal_article = insert_crossref_access_indicators(metadata, journal_article)
-    journal_article = insert_crossref_relations(metadata, journal_article)
-    journal_article = insert_archive_locations(metadata, journal_article)
-    journal_article = insert_doi_data(metadata, journal_article)
-    journal_article = insert_citation_list(metadata, journal_article)
-
-    return journal
-
-
-def insert_posted_content(metadata, xml):
-    """Insert posted content"""
-    if metadata.language is not None:
-        posted_content = etree.SubElement(
-            xml, "posted_content", {"type": "other", "language": metadata.language[:2]}
-        )
-    else:
-        posted_content = etree.SubElement(xml, "posted_content", {"type": "other"})
-
-    posted_content = insert_group_title(metadata, posted_content)
-    posted_content = insert_crossref_contributors(metadata, posted_content)
-    posted_content = insert_crossref_titles(metadata, posted_content)
-    posted_content = insert_posted_date(metadata, posted_content)
-    posted_content = insert_institution(metadata, posted_content)
-    posted_content = insert_item_number(metadata, posted_content)
-    posted_content = insert_crossref_abstract(metadata, posted_content)
-    posted_content = insert_funding_references(metadata, posted_content)
-    posted_content = insert_crossref_access_indicators(metadata, posted_content)
-    posted_content = insert_crossref_relations(metadata, posted_content)
-    posted_content = insert_archive_locations(metadata, posted_content)
-    posted_content = insert_doi_data(metadata, posted_content)
-    posted_content = insert_citation_list(metadata, posted_content)
-
-    return xml
-
-
-def insert_group_title(metadata, xml):
-    """Insert group title"""
-    if metadata.subjects is None or len(metadata.subjects) == 0:
-        return xml
-    group_title = metadata.subjects[0].get("subject", None)
-    # strip optional FOS (Field of Science) prefix
-    if group_title.startswith("FOS: "):
-        group_title = group_title[5:]
-    etree.SubElement(xml, "group_title").text = group_title
-    return xml
-
-
-def insert_crossref_contributors(metadata, xml):
-    """Insert crossref contributors"""
-    if metadata.contributors is None or len(metadata.contributors) == 0:
-        return xml
-    contributors = etree.SubElement(xml, "contributors")
-    con = [
-        c
-        for c in metadata.contributors
-        if c.get("contributorRoles", None) == ["Author"]
-        or c.get("contributorRoles", None) == ["Editor"]
-    ]
-    for num, contributor in enumerate(con):
-        contributor_role = (
-            "author" if "Author" in contributor.get("contributorRoles") else None
-        )
-        if contributor_role is None:
-            contributor_role = (
-                "editor" if "Editor" in contributor.get("contributorRoles") else None
-            )
-        sequence = "first" if num == 0 else "additional"
-        if (
-            contributor.get("type", None) == "Organization"
-            and contributor.get("name", None) is not None
-        ):
-            etree.SubElement(
-                contributors,
-                "organization",
-                {"contributor_role": contributor_role, "sequence": sequence},
-            ).text = contributor.get("name")
-        elif (
-            contributor.get("givenName", None) is not None
-            or contributor.get("familyName", None) is not None
-        ):
-            person_name = etree.SubElement(
-                contributors,
-                "person_name",
-                {"contributor_role": contributor_role, "sequence": sequence},
-            )
-            person_name = insert_crossref_person(contributor, person_name)
-        elif contributor.get("affiliations", None) is not None:
-            anonymous = etree.SubElement(
-                contributors,
-                "anonymous",
-                {"contributor_role": contributor_role, "sequence": sequence},
-            )
-            anonymous = insert_crossref_anonymous(contributor, anonymous)
-        else:
-            etree.SubElement(
-                contributors,
-                "anonymous",
-                {"contributor_role": contributor_role, "sequence": sequence},
-            )
-    return xml
-
-
-def insert_crossref_person(contributor, xml):
-    """Insert crossref person"""
-    if contributor.get("givenName", None) is not None:
-        etree.SubElement(xml, "given_name").text = contributor.get("givenName")
-    if contributor.get("familyName", None) is not None:
-        etree.SubElement(xml, "surname").text = contributor.get("familyName")
-
-    if contributor.get("affiliations", None) is not None:
-        affiliations = etree.SubElement(xml, "affiliations")
-        institution = etree.SubElement(affiliations, "institution")
-        if py_.get(contributor, "affiliations.0.name") is not None:
-            etree.SubElement(institution, "institution_name").text = py_.get(
-                contributor, "affiliations.0.name"
-            )
-        if py_.get(contributor, "affiliations.0.id") is not None:
-            etree.SubElement(
-                institution, "institution_id", {"type": "ror"}
-            ).text = py_.get(contributor, "affiliations.0.id")
-    orcid = normalize_orcid(contributor.get("id", None))
-    if orcid is not None:
-        etree.SubElement(xml, "ORCID").text = orcid
-    return xml
-
-
-def insert_crossref_anonymous(contributor, xml):
-    """Insert crossref anonymous"""
-    if contributor.get("affiliations", None) is None:
-        return xml
-    affiliations = etree.SubElement(xml, "affiliations")
-    institution = etree.SubElement(affiliations, "institution")
-    if py_.get(contributor, "affiliations.0.name") is not None:
-        etree.SubElement(institution, "institution_name").text = py_.get(
-            contributor, "affiliations.0.name"
-        )
-    return xml
-
-
-def insert_crossref_titles(metadata, xml):
-    """Insert crossref titles"""
-    titles = etree.SubElement(xml, "titles")
-    for title in wrap(metadata.titles):
-        if isinstance(title, dict):
-            etree.SubElement(titles, "title").text = title.get("title", None)
-        else:
-            etree.SubElement(titles, "title").text = title
-    return xml
-
-
-def insert_citation_list(metadata, xml):
-    """Insert citation list"""
-    if metadata.references is None or len(metadata.references) == 0:
-        return xml
-
-    citation_list = etree.SubElement(xml, "citation_list")
-    for i, ref in enumerate(metadata.references):
-        if ref.get("id", None) is None:
-            continue
-        citation = etree.SubElement(
-            citation_list, "citation", {"key": ref.get("key", f"ref{i + 1}")}
-        )
-        if ref.get("journal_title", None) is not None:
-            etree.SubElement(citation, "journal_article").text = ref.get(
-                "journal_title"
-            )
-        if ref.get("author", None) is not None:
-            etree.SubElement(citation, "author").text = ref.get("author")
-        if ref.get("volume", None) is not None:
-            etree.SubElement(citation, "volume").text = ref.get("volume")
-        if ref.get("first_page", None) is not None:
-            etree.SubElement(citation, "first_page").text = ref.get("first_page")
-        if ref.get("publicationYear", None) is not None:
-            etree.SubElement(citation, "cYear").text = ref.get("publicationYear")
-        if ref.get("title", None) is not None:
-            etree.SubElement(citation, "article_title").text = ref.get("title")
-        if ref.get("id", None) is not None:
-            etree.SubElement(citation, "doi").text = doi_from_url(ref.get("id"))
-        if ref.get("unstructured", None) is not None:
-            etree.SubElement(citation, "unstructured_citation").text = ref.get(
-                "unstructured"
-            )
-        print(xml)
-    return xml
-
-
-def insert_crossref_access_indicators(metadata, xml):
-    """Insert crossref access indicators"""
-    rights_uri = (
-        metadata.license.get("url", None) if metadata.license is not None else None
-    )
-    if rights_uri is None:
-        return xml
-    program = etree.SubElement(
-        xml,
-        "program",
-        {
-            "xmlns": "http://www.crossref.org/AccessIndicators.xsd",
-            "name": "AccessIndicators",
-        },
-    )
-    etree.SubElement(program, "license_ref", {"applies_to": "vor"}).text = rights_uri
-    etree.SubElement(program, "license_ref", {"applies_to": "tdm"}).text = rights_uri
-    return xml
-
-
-def insert_crossref_relations(metadata, xml):
-    """Insert crossref relations"""
-    if metadata.relations is None or len(metadata.relations) == 0:
-        return xml
-    program = etree.SubElement(
-        xml,
-        "program",
-        {
-            "xmlns": "http://www.crossref.org/relations.xsd",
-            "name": "relations",
-        },
-    )
-    for relation in metadata.relations:
-        if relation.get("type", None) in [
-            "IsPartOf",
-            "HasPart",
-            "IsReviewOf",
-            "HasReview",
-            "IsRelatedMaterial",
-            "HasRelatedMaterial",
-        ]:
-            group = "inter_work_relation"
-        elif relation.get("type", None) in [
-            "IsIdenticalTo",
-            "IsPreprintOf",
-            "HasPreprint",
-            "IsTranslationOf",
-            "HasTranslation",
-            "IsVersionOf",
-            "HasVersion",
-        ]:
-            group = "intra_work_relation"
-        else:
-            continue
-
-        related_item = etree.SubElement(program, "related_item")
-        f = furl(relation.get("id", None))
-        if validate_doi(relation.get("id", None)):
-            identifier_type = "doi"
-            _id = doi_from_url(relation.get("id", None))
-        elif f.host == "portal.issn.org":
-            identifier_type = "issn"
-            _id = f.path.segments[-1]
-        elif validate_url(relation.get("id", None)) == "URL":
-            identifier_type = "uri"
-            _id = relation.get("id", None)
-        else:
-            identifier_type = "other"
-            _id = relation.get("id", None)
-
-        etree.SubElement(
-            related_item,
-            group,
-            {
-                "relationship-type": py_.lower_first(relation.get("type"))
-                if relation.get("type", None) is not None
-                else None,
-                "identifier-type": identifier_type,
-            },
-        ).text = _id
-
-    return xml
-
-
-def insert_funding_references(metadata, xml):
-    """Insert funding references"""
-    if metadata.funding_references is None or len(metadata.funding_references) == 0:
-        return xml
-    program = etree.SubElement(
-        xml,
-        "program",
-        {
-            "xmlns": "http://www.crossref.org/fundref.xsd",
-            "name": "fundref",
-        },
-    )
-    for funding_reference in metadata.funding_references:
-        assertion = etree.SubElement(program, "assertion", {"name": "fundgroup"})
-        funder_name = etree.SubElement(
-            assertion,
-            "assertion",
-            {"name": "funder_name"},
-        )
-        if funding_reference.get("funderIdentifier", None) is not None:
-            funder_identifier = funding_reference.get("funderIdentifier", None)
-
-            # translate ROR to Crossref funder ID until Crossref supports ROR
-            funder_identifier = ROR_TO_CROSSREF_FUNDER_ID_TRANSLATIONS.get(
-                funder_identifier, funder_identifier
-            )
-
-            etree.SubElement(
-                funder_name,
-                "assertion",
-                {"name": "funder_identifier"},
-            ).text = funder_identifier
-        if funding_reference.get("awardNumber", None) is not None:
-            etree.SubElement(
-                assertion,
-                "assertion",
-                {"name": "award_number"},
-            ).text = funding_reference.get("awardNumber", None)
-        funder_name.text = funding_reference.get("funderName", None)
-    return xml
-
-
-def insert_crossref_subjects(metadata, xml):
-    """Insert crossref subjects"""
-    if metadata.subjects is None:
-        return xml
-    subjects = etree.SubElement(xml, "subjects")
-    for subject in metadata.subjects:
-        if isinstance(subject, dict):
-            etree.SubElement(subjects, "subject").text = subject.get("subject", None)
-        else:
-            etree.SubElement(subjects, "subject").text = subject
-    return xml
-
-
-def insert_crossref_language(metadata, xml):
-    """Insert crossref language"""
-    if metadata.language is None:
-        return xml
-    etree.SubElement(xml, "language").text = metadata.language
-    return xml
-
-
-def insert_crossref_publication_date(metadata, xml):
-    """Insert crossref publication date"""
-    pub_date = parse(metadata.date.get("published", None))
-    if pub_date is None:
-        return xml
-
-    publication_date = etree.SubElement(
-        xml, "publication_date", {"media_type": "online"}
-    )
-    etree.SubElement(publication_date, "month").text = f"{pub_date.month:d}"
-    etree.SubElement(publication_date, "day").text = f"{pub_date.day:d}"
-    etree.SubElement(publication_date, "year").text = str(pub_date.year)
-    return xml
-
-
-def insert_posted_date(metadata, xml):
-    """Insert posted date"""
-    pub_date = parse(metadata.date.get("published", None))
-    if pub_date is None:
-        return xml
-
-    posted_date = etree.SubElement(xml, "posted_date", {"media_type": "online"})
-    etree.SubElement(posted_date, "month").text = f"{pub_date.month:d}"
-    etree.SubElement(posted_date, "day").text = f"{pub_date.day:d}"
-    etree.SubElement(posted_date, "year").text = str(pub_date.year)
-    return xml
-
-
-def insert_institution(metadata, xml):
-    """Insert institution"""
-    if metadata.publisher.get("name", None) is None:
-        return xml
-    institution = etree.SubElement(xml, "institution")
-    etree.SubElement(institution, "institution_name").text = metadata.publisher.get(
-        "name"
-    )
-    return xml
-
-
-def insert_item_number(metadata, xml):
-    """Insert item number"""
-    if metadata.identifiers is None:
-        return xml
-    for identifier in metadata.identifiers:
-        if identifier.get("identifierType", None) == "UUID":
-            # strip hyphen from UUIDs, as item_number can only be 32 characters long (UUIDv4 is 36 characters long)
-            if identifier.get("identifierType", None) == "UUID":
-                identifier["identifier"] = identifier.get("identifier", "").replace(
-                    "-", ""
-                )
-            etree.SubElement(
-                xml,
-                "item_number",
-                {"item_number_type": identifier.get("identifierType", "").lower()},
-            ).text = identifier.get("identifier", None)
-        else:
-            continue
-    return xml
-
-
-def insert_archive_locations(metadata, xml):
-    """Insert archive locations"""
-    if metadata.archive_locations is None:
-        return xml
-    archive_locations = etree.SubElement(xml, "archive_locations")
-    for archive_location in metadata.archive_locations:
-        etree.SubElement(archive_locations, "archive", {"name": archive_location})
-    return xml
-
-
-def insert_doi_data(metadata, xml):
-    """Insert doi data"""
-    if doi_from_url(metadata.id) is None or metadata.url is None:
-        return xml
-    doi_data = etree.SubElement(xml, "doi_data")
-    etree.SubElement(doi_data, "doi").text = doi_from_url(metadata.id)
-    etree.SubElement(doi_data, "resource").text = metadata.url
-    collection = etree.SubElement(doi_data, "collection", {"property": "text-mining"})
-    item = etree.SubElement(collection, "item")
-    etree.SubElement(item, "resource", {"mime_type": "text/html"}).text = metadata.url
-    if metadata.files is None:
-        return xml
-    for file in metadata.files:
-        # Crossref schema currently doesn't support text/markdown
-        if file.get("mimeType", None) == "text/markdown":
-            file["mimeType"] = "text/plain"
-        item = etree.SubElement(collection, "item")
-        etree.SubElement(
-            item, "resource", {"mime_type": file.get("mimeType", "")}
-        ).text = file.get("url", None)
-    return xml
-
-
-def insert_crossref_license(metadata, xml):
-    """Insert crossref license"""
-    if metadata.license is None:
-        return xml
-    license_ = etree.SubElement(xml, "license")
-    if isinstance(metadata.license, dict):
-        r = metadata.license
-    else:
-        r = {}
-        r["rights"] = metadata.license
-        r["rightsUri"] = normalize_id(metadata.license)
-    attributes = compact(
-        {
-            "rightsURI": r.get("rightsUri", None),
-            "rightsIdentifier": r.get("rightsIdentifier", None),
-            "rightsIdentifierScheme": r.get("rightsIdentifierScheme"),
-            "schemeURI": r.get("schemeUri", None),
-            "xml:lang": r.get("lang", None),
-        }
-    )
-    etree.SubElement(license_, "rights", attributes).text = r.get("rights", None)
-    return xml
-
-
-def insert_crossref_issn(metadata, xml):
-    """Insert crossref issn"""
-    if (
-        metadata.container is None
-        or metadata.container.get("identifierType", None) != "ISSN"
-    ):
-        return xml
-    etree.SubElement(xml, "issn").text = metadata.container.get("identifier", None)
-    return xml
-
-
-def insert_crossref_abstract(metadata, xml):
-    """Insert crossref abstrac"""
-    if metadata.descriptions is None:
-        return xml
-    if isinstance(metadata.descriptions[0], dict):
-        d = metadata.descriptions[0]
-    else:
-        d = {}
-        d["description"] = metadata.descriptions[0]
-    abstract = etree.SubElement(
-        xml, "abstract", {"xmlns": "http://www.ncbi.nlm.nih.gov/JATS1"}
-    )
-    etree.SubElement(abstract, "p").text = d.get("description", None)
-    return xml
-
-
-def crossref_root():
-    """Crossref root with namespaces"""
-    doi_batch = """<doi_batch xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.crossref.org/schema/5.3.1" xmlns:jats="http://www.ncbi.nlm.nih.gov/JATS1" xmlns:fr="http://www.crossref.org/fundref.xsd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 https://www.crossref.org/schemas/crossref5.3.1.xsd" version="5.3.1"></doi_batch>"""
-    return etree.fromstring(doi_batch)
-
-
-def generate_crossref_xml_list(metalist) -> Optional[str]:
-    """Generate Crossref XML list."""
-    if not metalist.is_valid:
-        return None
-    xml = crossref_root()
-    head = etree.SubElement(xml, "head")
-    # we use a uuid as batch_id
-    etree.SubElement(head, "doi_batch_id").text = str(uuid.uuid4())
-    etree.SubElement(head, "timestamp").text = datetime.now().strftime("%Y%m%d%H%M%S")
-    depositor = etree.SubElement(head, "depositor")
-    etree.SubElement(depositor, "depositor_name").text = metalist.depositor or "test"
-    etree.SubElement(depositor, "email_address").text = (
-        metalist.email or "info@example.org"
-    )
-    etree.SubElement(head, "registrant").text = metalist.registrant or "test"
-
-    body = etree.SubElement(xml, "body")
-    body = [insert_crossref_work(item, body) for item in metalist.items]
-    return etree.tostring(
-        xml,
-        doctype='<?xml version="1.0" encoding="UTF-8"?>',
-        pretty_print=True,
-    )
-
-
-"""Errors for the Crossref XML API.
-
-Error responses will be converted into an exception from this module.
-"""
-
-
-class HttpError(Exception):
-    """Exception raised when a connection problem happens."""
-
-
-class CrossrefError(Exception):
-    """Exception raised when the server returns a known HTTP error code.
-
-    Known HTTP error codes include:
-
-    * 204 No Content
-    * 400 Bad Request
-    * 401 Unauthorized
-    * 403 Forbidden
-    * 404 Not Found
-    * 410 Gone (deleted)
-    """
-
-    @staticmethod
-    def factory(err_code, *args):
-        """Create exceptions through a Factory based on the HTTP error code."""
-        if err_code == 204:
-            return CrossrefNoContentError(*args)
-        elif err_code == 400:
-            return CrossrefBadRequestError(*args)
-        elif err_code == 401:
-            return CrossrefUnauthorizedError(*args)
-        elif err_code == 403:
-            return CrossrefForbiddenError(*args)
-        elif err_code == 404:
-            return CrossrefNotFoundError(*args)
-        else:
-            return CrossrefServerError(*args)
-
-
-class CrossrefServerError(CrossrefError):
-    """An internal server error happened on the Crossref end. Try later.
-
-    Base class for all 5XX-related HTTP error codes.
-    """
-
-
-class CrossrefRequestError(CrossrefError):
-    """A Crossref request error. You made an invalid request.
-
-    Base class for all 4XX-related HTTP error codes as well as 204.
-    """
-
-
-class CrossrefNoContentError(CrossrefRequestError):
-    """DOI is known to Crossref, but not resolvable.
-
-    This might be due to handle's latency.
-    """
-
-
-class CrossrefBadRequestError(CrossrefRequestError):
-    """Bad request error.
-
-    Bad requests can include e.g. invalid XML, wrong domain, wrong prefix.
-    """
-
-
-class CrossrefUnauthorizedError(CrossrefRequestError):
-    """Bad username or password."""
-
-
-class CrossrefForbiddenError(CrossrefRequestError):
-    """Login problem, record belongs to another party or quota exceeded."""
-
-
-class CrossrefNotFoundError(CrossrefRequestError):
-    """DOI does not exist in the database."""