commonmeta-py 0.22__py3-none-any.whl → 0.24__py3-none-any.whl

commonmeta/readers/datacite_reader.py

@@ -0,0 +1,390 @@
+"""datacite reader for Commonmeta"""
+
+from collections import defaultdict
+from typing import Optional
+import httpx
+from pydash import py_
+
+from ..utils import (
+    normalize_url,
+    normalize_doi,
+    normalize_cc_url,
+    dict_to_spdx,
+    format_name_identifier,
+)
+from ..base_utils import compact, wrap, presence
+from ..author_utils import get_authors
+from ..date_utils import normalize_date_dict
+from ..doi_utils import (
+    doi_as_url,
+    doi_from_url,
+    datacite_api_url,
+    datacite_api_sample_url,
+)
+from ..constants import (
+    DC_TO_CM_TRANSLATIONS,
+    DC_TO_CM_CONTAINER_TRANSLATIONS,
+    Commonmeta,
+)
+
+
+def get_datacite(pid: str, **kwargs) -> dict:
+    """get_datacite"""
+    doi = doi_from_url(pid)
+    if doi is None:
+        return {"state": "not_found"}
+    url = datacite_api_url(doi)
+    try:
+        response = httpx.get(url, timeout=10, **kwargs)
+        if response.status_code != 200:
+            return {"state": "not_found"}
+        return py_.get(response.json(), "data.attributes", {}) | {"via": "datacite"}
+    except httpx.ReadTimeout:
+        return {"state": "timeout"}
+
+
+def read_datacite(data: dict, **kwargs) -> Commonmeta:
+    """read_datacite"""
+    meta = data
+    if data is None:
+        return {"state": "not_found"}
+
+    read_options = kwargs or {}
+
+    _id = doi_as_url(meta.get("doi", None))
+    resource__typegeneral = py_.get(meta, "types.resourceTypeGeneral")
+    resource_type = py_.get(meta, "types.resourceType")
+    _type = DC_TO_CM_TRANSLATIONS.get(resource__typegeneral, "Other")
+    additional_type = DC_TO_CM_TRANSLATIONS.get(resource_type, None)
+    # if resource_type is one of the new resource__typegeneral types introduced in schema 4.3, use it
+    if additional_type:
+        _type = additional_type
+        additional_type = None
+    else:
+        additional_type = resource_type
+    titles = get_titles(wrap(meta.get("titles", None)))
+
+    contributors = get_authors(wrap(meta.get("creators", None)))
+    contrib = get_authors(wrap(meta.get("contributors", None)))
+    if contrib:
+        contributors = contributors + contrib
+
+    publisher = meta.get("publisher", None)
+    if isinstance(publisher, str):
+        publisher = {"name": publisher}
+    elif isinstance(publisher, dict):
+        publisher = get_publisher(publisher)
+    date = get_dates(wrap(meta.get("dates", None)), meta.get("publicationYear", None))
+    container = get_container(meta.get("container", None))
+    license_ = meta.get("rightsList", [])
+    if len(license_) > 0:
+        license_ = normalize_cc_url(license_[0].get("rightsUri", None))
+        license_ = dict_to_spdx({"url": license_}) if license_ else None
+
+    files = [get_file(i) for i in wrap(meta.get("content_url"))]
+
+    identifiers = get_identifiers(wrap(meta.get("alternateIdentifiers", None)))
+    identifiers.append(
+        compact(
+            {
+                "identifier": normalize_doi(_id),
+                "identifierType": "DOI",
+            }
+        )
+    )
+
+    references = get_references(
+        wrap(meta.get("relatedItems", None) or meta.get("relatedIdentifiers", None))
+    )
+    relations = get_relations(wrap(meta.get("relatedIdentifiers", None)))
+    descriptions = get_descriptions(wrap(meta.get("descriptions", None)))
+    geo_locations = get_geolocation(wrap(meta.get("geoLocations", None)))
+
+    def format_subject(subject):
+        """format_subject"""
+        return compact(
+            {
+                "subject": subject.get("subject", None),
+                "language": subject.get("lang", None),
+            }
+        )
+
+    subjects = py_.uniq([format_subject(i) for i in wrap(meta.get("subjects", None))])
+
+    return {
+        # required properties
+        "id": _id,
+        "type": _type,
+        # recommended and optional properties
+        "additionalType": additional_type,
+        "container": presence(container),
+        "contributors": presence(contributors),
+        "date": compact(date),
+        "descriptions": presence(descriptions),
+        "files": presence(files),
+        "fundingReferences": presence(meta.get("fundingReferences", None)),
+        "geoLocations": presence(geo_locations),
+        "identifiers": presence(identifiers),
+        "language": meta.get("language", None),
+        "license": presence(license_),
+        "provider": "DataCite",
+        "publisher": publisher,
+        "references": presence(references),
+        "relations": presence(relations),
+        "subjects": presence(subjects),
+        "titles": presence(titles),
+        "url": normalize_url(meta.get("url", None)),
+        "version": meta.get("version", None),
+    } | read_options
+
+
+def get_identifiers(identifiers: list) -> list:
+    """get_identifiers"""
+
+    def is_identifier(identifier):
+        """supported identifier types"""
+        return identifier.get("identifierType", None) in [
+            "ARK",
+            "arXiv",
+            "Bibcode",
+            "DOI",
+            "Handle",
+            "ISBN",
+            "ISSN",
+            "PMID",
+            "PMCID",
+            "PURL",
+            "URL",
+            "URN",
+            "Other",
+        ]
+
+    def format_identifier(identifier):
+        """format_identifier"""
+        if is_identifier(identifier):
+            type_ = identifier.get("identifierType")
+        else:
+            type_ = "Other"
+
+        return compact(
+            {
+                "identifier": identifier.get("alternateIdentifier", None),
+                "identifierType": type_,
+            }
+        )
+
+    return [format_identifier(i) for i in wrap(identifiers)]
+
+
+def get_references(references: list) -> list:
+    """get_references"""
+
+    def is_reference(reference):
+        """is_reference"""
+        return reference.get("relationType", None) in ["Cites", "References"]
+
+    def map_reference(reference, index):
+        """map_reference"""
+        identifier = reference.get("relatedIdentifier", None)
+        identifier_type = reference.get("relatedIdentifierType", None)
+        if identifier_type == "DOI":
+            id_ = normalize_doi(identifier)
+        elif identifier_type == "URL":
+            id_ = normalize_url(identifier)
+        else:
+            id_ = identifier
+        return compact(
+            {
+                "key": f"ref{index + 1}",
+                "id": id_,
+            }
+        )
+
+    return [
+        map_reference(i, index) for index, i in enumerate(references) if is_reference(i)
+    ]
+
+
+def get_relations(relations: list) -> list:
+    """get_relations"""
+
+    def is_relation(relation):
+        """relation"""
+        return relation.get("relationType", None) in [
+            "IsNewVersionOf",
+            "IsPreviousVersionOf",
+            "IsVersionOf",
+            "HasVersion",
+            "IsPartOf",
+            "HasPart",
+            "IsVariantFormOf",
+            "IsOriginalFormOf",
+            "IsIdenticalTo",
+            "IsTranslationOf",
+            "IsReviewedBy",
+            "Reviews",
+            "IsPreprintOf",
+            "HasPreprint",
+            "IsSupplementTo",
+        ]
+
+    def map_relation(relation):
+        """map_relation"""
+
+        identifier = normalize_doi(
+            relation.get("relatedIdentifier", None)
+        ) or relation.get("relatedIdentifier", None)
+        relation_type = relation.get("relationType", None)
+        return compact(
+            {
+                "id": identifier,
+                "type": relation_type,
+            }
+        )
+
+    return [map_relation(i) for i in relations if is_relation(i)]
+
+
+def get_file(file: str) -> dict:
+    """get_file"""
+    return compact({"url": file})
+
+
+def get_dates(dates: list, publication_year) -> dict:
+    """convert date list to dict, rename and/or remove some keys"""
+    date: dict = defaultdict(list)
+    for sub in dates:
+        date[sub.get("dateType", None)] = sub.get("date", None)
+    if date.get("Issued", None) is None and publication_year is not None:
+        date["Issued"] = str(publication_year)
+    return normalize_date_dict(date)
+
+
+def get_descriptions(descriptions: list) -> list:
+    """get_descriptions"""
+
+    def map_description(description):
+        """map_description"""
+        return compact(
+            {
+                "description": description.get("description", None),
+                "type": description.get("descriptionType")
+                if description.get("descriptionType", None)
+                in ["Abstract", "Methods", "TechnicalInfo", "Other"]
+                else "Other",
+                "language": description.get("lang", None),
+            }
+        )
+
+    return [
+        map_description(i)
+        for i in descriptions
+        if i.get("description", None) is not None
+    ]
+
+
+def get_titles(titles: list) -> list:
+    """get_titles"""
+
+    def map_title(title):
+        """map_title"""
+        return compact(
+            {
+                "title": title.get("title", None),
+                "type": title.get("titleType")
+                if title.get("titleType", None)
+                in ["AlternativeTitle", "Subtitle", "TranslatedTitle"]
+                else None,
+                "language": title.get("lang", None),
+            }
+        )
+
+    return [map_title(i) for i in titles if i.get("title", None) is not None]
+
+
+def get_publisher(publisher: dict) -> dict:
+    """get_publisher"""
+    return compact(
+        {"id": format_name_identifier(publisher), "name": publisher.get("name", None)}
+    )
+
+
+def get_geolocation(geolocations: list) -> list:
+    """get_geolocation"""
+
+    def geo_location_point(point: dict):
+        """geo_location_point, convert lat and long to int"""
+        return {
+            "pointLatitude": float(point.get("pointLatitude"))
+            if point.get("pointLatitude", None)
+            else None,
+            "pointLongitude": float(point.get("pointLongitude"))
+            if point.get("pointLongitude", None)
+            else None,
+        }
+
+    def geo_location_box(box: dict):
+        """geo_location_box, convert lat and long to int"""
+        return {
+            "eastBoundLongitude": float(box.get("eastBoundLongitude"))
+            if box.get("eastBoundLongitude", None)
+            else None,
+            "northBoundLatitude": float(box.get("northBoundLatitude"))
+            if box.get("northBoundLatitude", None)
+            else None,
+            "southBoundLatitude": float(box.get("southBoundLatitude"))
+            if box.get("southBoundLatitude", None)
+            else None,
+            "westBoundLongitude": float(box.get("westBoundLongitude"))
+            if box.get("westBoundLongitude", None)
+            else None,
+        }
+
+    return [
+        compact(
+            {
+                "geoLocationPoint": geo_location_point(location.get("geoLocationPoint"))
+                if location.get("geoLocationPoint", None)
+                else None,
+                "geoLocationBox": geo_location_box(location.get("geoLocationBox"))
+                if location.get("geoLocationBox", None)
+                else None,
+                "geoLocationPlace": location.get("geoLocationPlace", None),
+            }
+        )
+        for location in geolocations
+    ]
+
+
+def get_container(container: Optional[dict]) -> dict or None:
+    """get_container"""
+    if container is None:
+        return None
+    _type = (
+        DC_TO_CM_CONTAINER_TRANSLATIONS.get(container.get("type"), None)
+        if container.get("type", None)
+        else None
+    )
+
+    return compact(
+        {
+            "id": container.get("identifier", None),
+            "type": _type,
+            "title": container.get("title", None),
+        }
+    )
+
+
+def get_random_datacite_id(number: int = 1) -> list:
+    """Get random DOI from DataCite"""
+    number = 20 if number > 20 else number
+    url = datacite_api_sample_url(number)
+    try:
+        response = httpx.get(url, timeout=60)
+        if response.status_code != 200:
+            return []
+
+        items = py_.get(response.json(), "data")
+        return [i.get("id") for i in items]
+    except httpx.ReadTimeout:
+        return []