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

commonmeta/metadata.py

@@ -0,0 +1,320 @@
+"""Metadata"""
+
+from os import path
+import orjson as json
+from typing import Optional, Union
+import yaml
+from pydash import py_
+
+from .readers.crossref_reader import (
+    get_crossref,
+    read_crossref,
+)
+from .readers.datacite_reader import (
+    get_datacite,
+    read_datacite,
+)
+from .readers.datacite_xml_reader import read_datacite_xml
+from .readers.crossref_xml_reader import (
+    get_crossref_xml,
+    read_crossref_xml,
+)
+from .readers.schema_org_reader import (
+    get_schema_org,
+    read_schema_org,
+)
+from .readers.codemeta_reader import (
+    get_codemeta,
+    read_codemeta,
+)
+from .readers.csl_reader import read_csl
+from .readers.cff_reader import get_cff, read_cff
+from .readers.json_feed_reader import get_json_feed_item, read_json_feed_item
+from .readers.inveniordm_reader import (
+    get_inveniordm,
+    read_inveniordm,
+)
+from .readers.kbase_reader import read_kbase
+from .readers.commonmeta_reader import read_commonmeta
+from .readers.ris_reader import read_ris
+from .writers.datacite_writer import write_datacite
+from .writers.bibtex_writer import write_bibtex, write_bibtex_list
+from .writers.citation_writer import write_citation, write_citation_list
+from .writers.crossref_xml_writer import write_crossref_xml, write_crossref_xml_list
+from .writers.csl_writer import write_csl, write_csl_list
+from .writers.ris_writer import write_ris, write_ris_list
+from .writers.schema_org_writer import write_schema_org
+from .writers.commonmeta_writer import write_commonmeta, write_commonmeta_list
+from .writers.inveniordm_writer import write_inveniordm
+from .utils import normalize_id, find_from_format
+from .base_utils import parse_xml, wrap
+from .doi_utils import doi_from_url
+from .schema_utils import json_schema_errors
+from .constants import CM_TO_CR_TRANSLATIONS
+
+
+# pylint: disable=R0902
+class Metadata:
+    """Metadata"""
+
+    def __init__(self, string: Optional[Union[str, dict]], **kwargs):
+        if string is None or not isinstance(string, (str, dict)):
+            raise ValueError("No input found")
+        self.via = kwargs.get("via", None)
+        if isinstance(string, dict):
+            data = string
+        elif isinstance(string, str):
+            pid = normalize_id(string)
+            if pid is not None and self.via is None:
+                self.via = find_from_format(pid=pid)
+            elif path.exists(string):
+                with open(string, encoding="utf-8") as file:
+                    string = file.read()
+                if self.via is None:
+                    self.via = find_from_format(string=string)
+            if self.via is None:
+                self.via = "commonmeta"
+            data = self.get_metadata(pid=pid, string=string)
+        meta = self.read_metadata(data=data, **kwargs)
+
+        # required properties
+        self.id = meta.get("id")  # pylint: disable=C0103
+        self.type = meta.get("type")
+        # recommended and optional properties
+        self.additional_type = meta.get("additionalType")
+        self.archive_locations = meta.get("archiveLocations")
+        self.container = meta.get("container")
+        self.contributors = meta.get("contributors")
+        self.date = meta.get("date")
+        self.descriptions = meta.get("descriptions")
+        self.files = meta.get("files")
+        self.funding_references = meta.get("fundingReferences")
+        self.geo_locations = meta.get("geoLocations")
+        self.identifiers = meta.get("identifiers")
+        self.language = meta.get("language")
+        self.license = meta.get("license")
+        self.provider = meta.get("provider")
+        self.publisher = meta.get("publisher")
+        self.references = meta.get("references")
+        self.relations = meta.get("relations")
+        self.subjects = meta.get("subjects")
+        self.titles = meta.get("titles")
+        self.url = meta.get("url")
+        self.version = meta.get("version")
+        # other properties
+        self.date_created = meta.get("date_created")
+        self.date_registered = meta.get("date_registered")
+        self.date_published = meta.get("date_published")
+        self.date_updated = meta.get("date_updated")
+        self.state = meta.get("state")
+
+        # Catch errors in the reader, then validate against JSON schema for Commonmeta
+        self.errors = meta.get("errors", None) or json_schema_errors(
+            json.loads(self.write())
+        )
+        self.write_errors = None
+        self.is_valid = (
+            meta.get("state", None) not in ["not_found", "forbidden", "bad_request"]
+            and self.errors is None
+            and self.write_errors is None
+        )
+
+    def get_metadata(self, pid, string) -> dict:
+        via = self.via
+        if pid is not None:
+            if via == "schema_org":
+                return get_schema_org(pid)
+            elif via == "datacite":
+                return get_datacite(pid)
+            elif via in ["crossref", "op"]:
+                return get_crossref(pid)
+            elif via == "crossref_xml":
+                return get_crossref_xml(pid)
+            elif via == "codemeta":
+                return get_codemeta(pid)
+            elif via == "cff":
+                return get_cff(pid)
+            elif via == "json_feed_item":
+                return get_json_feed_item(pid)
+            elif via == "inveniordm":
+                return get_inveniordm(pid)
+        elif string is not None:
+            if via == "datacite_xml":
+                return parse_xml(string)
+            elif via == "crossref_xml":
+                return parse_xml(string, dialect="crossref")
+            elif via == "cff":
+                return yaml.safe_load(string)
+            elif via == "bibtex":
+                raise ValueError("Bibtex not supported")
+            elif via == "ris":
+                return string
+            elif via in [
+                "commonmeta",
+                "crossref",
+                "datacite",
+                "schema_org",
+                "csl",
+                "json_feed_item",
+                "codemeta",
+                "kbase",
+                "inveniordm",
+            ]:
+                return json.loads(string)
+            else:
+                raise ValueError("No input format found")
+        else:
+            raise ValueError("No metadata found")
+
+    def read_metadata(self, data: dict, **kwargs) -> dict:
+        """get_metadata"""
+        via = isinstance(data, dict) and data.get("via", None) or self.via
+        if via == "commonmeta":
+            return read_commonmeta(data, **kwargs)
+        elif via == "schema_org":
+            return read_schema_org(data)
+        elif via == "datacite":
+            return read_datacite(data)
+        elif via == "datacite_xml":
+            return read_datacite_xml(data)
+        elif via in ["crossref", "op"]:
+            return read_crossref(data)
+        elif via == "crossref_xml":
+            return read_crossref_xml(data)
+        elif via == "csl":
+            return read_csl(data, **kwargs)
+        elif via == "codemeta":
+            return read_codemeta(data)
+        elif via == "cff":
+            return read_cff(data)
+        elif via == "json_feed_item":
+            return read_json_feed_item(data, **kwargs)
+        elif via == "inveniordm":
+            return read_inveniordm(data)
+        elif via == "kbase":
+            return read_kbase(data)
+        elif via == "ris":
+            return read_ris(data)
+        else:
+            raise ValueError("No input format found")
+
+    def write(self, to: str = "commonmeta", **kwargs) -> str:
+        """convert metadata into different formats"""
+        try:
+            if to == "commonmeta":
+                return write_commonmeta(self)
+            elif to == "bibtex":
+                return write_bibtex(self)
+            elif to == "csl":
+                instance = py_.omit(json.loads(write_csl(self)), [])
+                self.errors = json_schema_errors(instance, schema="csl")
+                return write_csl(self)
+            elif to == "citation":
+                self.style = kwargs.get("style", "apa")
+                self.locale = kwargs.get("locale", "en-US")
+                return write_citation(self)
+            elif to == "ris":
+                return write_ris(self)
+            elif to == "schema_org":
+                return write_schema_org(self)
+            elif to == "inveniordm":
+                return write_inveniordm(self)
+            elif to == "datacite":
+                instance = json.loads(write_datacite(self))
+                self.write_errors = json_schema_errors(instance, schema="datacite")
+                print(self.write_errors)
+                return write_datacite(self)
+            elif to == "crossref_xml":
+                doi = doi_from_url(self.id)
+                _type = CM_TO_CR_TRANSLATIONS.get(self.type, None)
+                url = self.url
+                instance = {"doi": doi, "type": _type, "url": url}
+                self.depositor = kwargs.get("depositor", None)
+                self.email = kwargs.get("email", None)
+                self.registrant = kwargs.get("registrant", None)
+                self.write_errors = json_schema_errors(instance, schema="crossref")
+                return write_crossref_xml(self)
+            else:
+                raise ValueError("No output format found")
+        except json.JSONDecodeError:
+            raise ValueError("Invalid JSON")
+
+
+class MetadataList:
+    """MetadataList"""
+
+    def __init__(
+        self, dct: Optional[Union[str, dict]] = None, **kwargs
+    ) -> Optional[dict]:
+        if dct is None or not isinstance(dct, (str, bytes, dict)):
+            raise ValueError("No input found")
+        if isinstance(dct, dict):
+            meta = dct
+        elif isinstance(dct, (str, bytes)):
+            if path.exists(dct):
+                with open(dct, encoding="utf-8") as file:
+                    dct = file.read()
+            self.via = kwargs.get("via", None) or find_from_format(string=dct)
+            meta = self.get_metadata_list(dct)
+
+        self.id = meta.get("id", None)
+        self.type = meta.get("type", None)
+        self.title = meta.get("title", None)
+        self.description = meta.get("description", None)
+
+        # options needed for Crossref DOI registration
+        self.depositor = kwargs.get("depositor", None)
+        self.email = kwargs.get("email", None)
+        self.registrant = kwargs.get("registrant", None)
+
+        self.items = self.read_metadata_list(wrap(meta.get("items", None)), **kwargs)
+        self.errors = [i.errors for i in self.items if i.errors is not None]
+        self.write_errors = [
+            i.write_errors for i in self.items if i.write_errors is not None
+        ]
+        self.is_valid = all([i.is_valid for i in self.items])
+
+        # other options
+        self.jsonlines = kwargs.get("jsonlines", False)
+        self.filename = kwargs.get("filename", None)
+
+    def get_metadata_list(self, string) -> list:
+        if string is None or not isinstance(string, (str, bytes)):
+            raise ValueError("No input found")
+        if self.via in [
+            "commonmeta",
+            "crossref",
+            "datacite",
+            "schema_org",
+            "csl",
+            "json_feed_item",
+        ]:
+            return json.loads(string)
+        else:
+            raise ValueError("No input format found")
+
+    def read_metadata_list(self, data: list, **kwargs) -> list:
+        """read_metadata_list"""
+        kwargs["via"] = kwargs.get("via", None) or self.via
+        return [Metadata(i, **kwargs) for i in data]
+
+    def write(self, to: str = "commonmeta", **kwargs) -> str:
+        """convert metadata list into different formats"""
+        if to == "commonmeta":
+            return write_commonmeta_list(self)
+        elif to == "bibtex":
+            return write_bibtex_list(self)
+        elif to == "csl":
+            return write_csl_list(self)
+        elif to == "citation":
+            return write_citation_list(self, **kwargs)
+        elif to == "ris":
+            return write_ris_list(self)
+        elif to == "schema_org":
+            raise ValueError("Schema.org not supported for metadata lists")
+        elif to == "datacite":
+            raise ValueError("Datacite not supported for metadata lists")
+        elif to == "crossref_xml":
+            return write_crossref_xml_list(self)
+        else:
+            raise ValueError("No output format found")

commonmeta/readers/__init__.py

@@ -0,0 +1 @@
+"""Readers for different metadata formats"""

commonmeta/readers/cff_reader.py

@@ -0,0 +1,199 @@
+"""cff reader for commonmeta-py"""
+from typing import Optional
+from urllib.parse import urlparse
+import httpx
+import yaml
+
+from ..utils import (
+    normalize_id,
+    name_to_fos,
+    dict_to_spdx,
+    normalize_orcid,
+    github_as_cff_url,
+    github_as_repo_url,
+)
+from ..base_utils import compact, wrap, presence, sanitize, parse_attributes
+from ..date_utils import get_iso8601_date
+from ..constants import Commonmeta
+
+
+def get_cff(pid: str, **kwargs) -> dict:
+    """get_cff"""
+    url = github_as_cff_url(pid)
+    response = httpx.get(url, timeout=10, **kwargs)
+    if response.status_code != 200:
+        return {"state": "not_found"}
+    text = response.text
+    repo_url = github_as_repo_url(url)
+    data = yaml.safe_load(text)
+
+    # collect metadata not included in the CFF file
+    if data.get("repository-code", None) is None:
+        data["repository-code"] = repo_url
+
+    return data
+
+
+def read_cff(data: Optional[dict], **kwargs) -> Commonmeta:
+    """read_cff"""
+    if data is None:
+        return {"state": "not_found"}
+    meta = data
+
+    read_options = kwargs or {}
+
+    # read_options = ActiveSupport::HashWithIndifferentAccess.new(options.except(:doi, :id, :url, :sandbox, :validate, :ra))
+
+    # identifiers = Array.wrap(meta.fetch('identifiers', nil)).map do |r|
+    #   r = normalize_id(r) if r.is_a?(String)
+    #   if r.is_a?(String) && URI(r).host != 'doi.org'
+    #     { 'identifierType' => 'URL', 'identifier' => r }
+    #   elsif r.is_a?(Hash)
+    #     { 'identifierType' => get_identifier_type(r['propertyID']), 'identifier' => r['value'] }
+    #   end
+    # end.compact.uniq
+
+    _id = normalize_id(kwargs.get("doi", None) or meta.get("doi", None))
+    # Array.wrap(meta.fetch('identifiers', nil)).find do |i|
+    #                                                     i['type'] == 'doi'
+    #                                                   end.fetch('value', nil))
+    _type = "Software"
+    url = normalize_id(meta.get("repository-code", None))
+    contributors = cff_contributors(wrap(meta.get("authors", None)))
+
+    if meta.get("title", None):
+        titles = [{"title": meta.get("title", None)}]
+    else:
+        titles = []
+
+    date = {
+        "published": get_iso8601_date(meta.get("date-released"))
+        if meta.get("date-released", None)
+        else None
+    }
+
+    publisher = (
+        {"name": "GitHub"} if url and urlparse(url).hostname == "github.com" else None
+    )
+
+    if meta.get("abstract", None):
+        descriptions = [
+            {
+                "description": sanitize(meta.get("abstract")),
+                "type": "Abstract",
+            }
+        ]
+    else:
+        descriptions = []
+
+    subjects = [name_to_fos(i) for i in wrap(meta.get("keywords", None))]
+
+    license_ = meta.get("license", None)
+    if license_ is not None:
+        license_ = dict_to_spdx({"id": meta.get("license")})
+
+    references = cff_references(wrap(meta.get("references", None)))
+
+    state = "findable" if meta or read_options else "not_found"
+
+    return {
+        "id": _id,
+        "type": _type,
+        # 'identifiers' => identifiers,
+        "url": url,
+        "titles": titles,
+        "contributors": presence(contributors),
+        "publisher": publisher,
+        "references": presence(references),
+        "date": date,
+        "descriptions": presence(descriptions),
+        "license": license_,
+        "version": meta.get("version", None),
+        "subjects": presence(subjects),
+        "provider": "DataCite" if _id else "GitHub",
+        "state": state,
+    } | read_options
+
+
+def cff_contributors(contributors):
+    """cff_contributors"""
+
+    def format_affiliation(affiliation):
+        """format_affiliation"""
+        if isinstance(affiliation, str):
+            return {"name": affiliation}
+        if isinstance(affiliation, dict):
+            return compact(affiliation)
+        return None
+        #         if a.is_a?(Hash)
+        #   a
+        # elsif a.is_a?(Hash) && a.key?('#text_') && a['#text'].strip.blank?
+        #   nil
+        # elsif a.is_a?(Hash) && a.key?('#text')
+        #   { 'name' => a['#text'] }
+        # elsif a.strip.blank
+
+    def format_element(i):
+        """format_element"""
+        if normalize_orcid(parse_attributes(i.get("orcid", None))):
+            _id = normalize_orcid(parse_attributes(i.get("orcid", None)))
+        else:
+            _id = None
+        if i.get("given-names", None) or i.get("family-names", None) or _id:
+            given_name = parse_attributes(i.get("given-names", None))
+            family_name = parse_attributes(i.get("family-names", None))
+            affiliation = compact(
+                [format_affiliation(a) for a in wrap(i.get("affiliation", None))]
+            )
+
+            return compact(
+                {
+                    "id": _id,
+                    "contributorRoles": ["Author"],
+                    "type": "Person",
+                    "givenName": given_name,
+                    "familyName": family_name,
+                    "affiliation": affiliation,
+                }
+            )
+        return {
+            "contributorRoles": ["Author"],
+            "type": "Organization",
+            "name": i.get("name", None) or i.get("#text", None),
+        }
+
+    return [format_element(i) for i in contributors]
+
+
+def cff_references(references):
+    """cff_references"""
+
+    def is_reference(i):
+        """is_reference"""
+        return (
+            next(
+                (
+                    item
+                    for item in wrap(i.get("identifers", None))
+                    if item.get("type", None) == "doi"
+                ),
+                None,
+            )
+            is not None
+        )
+
+    def map_reference(i):
+        """map_element"""
+        identifier = next(
+            (
+                item
+                for item in wrap(i.get("identifers", None))
+                if item.get("type", None) == "doi"
+            ),
+            None,
+        )
+        return compact(
+            {"doi": normalize_id(parse_attributes(identifier.get("value", None)))}
+        )
+
+    return [map_reference(i) for i in references if is_reference(i)]

commonmeta/readers/codemeta_reader.py

@@ -0,0 +1,112 @@
+"""codemeta reader for commonmeta-py"""
+from typing import Optional
+from collections import defaultdict
+import httpx
+
+from ..utils import (
+    normalize_id,
+    from_schema_org_creators,
+    name_to_fos,
+    dict_to_spdx,
+    github_as_codemeta_url,
+    github_as_repo_url,
+    doi_from_url,
+)
+from ..base_utils import wrap, presence, compact, sanitize
+from ..author_utils import get_authors
+from ..constants import (
+    Commonmeta,
+    SO_TO_CM_TRANSLATIONS,
+)
+
+
+def get_codemeta(pid: str, **kwargs) -> dict:
+    """get_codemeta"""
+    url = str(github_as_codemeta_url(pid))
+    response = httpx.get(url, timeout=10, **kwargs)
+    if response.status_code != 200:
+        return {"state": "not_found"}
+    data = response.json()
+    if data.get("codeRepository", None) is None:
+        data["codeRepository"] = github_as_repo_url(url)
+
+    return data
+
+
+def read_codemeta(data: Optional[dict], **kwargs) -> Commonmeta:
+    """read_codemeta"""
+    if data is None:
+        return {"state": "not_found"}
+    meta = data
+
+    read_options = kwargs or {}
+    # ActiveSupport: : HashWithIndifferentAccess.new(options.except(: doi, : id, : url,
+    # : sandbox, : validate, : ra)
+
+    _id = normalize_id(meta.get("id", None) or meta.get("identifier", None))
+    # id = normalize_id(options[:doi] | | meta.get('@id', None) | | meta.get('identifier', None))
+    _type = SO_TO_CM_TRANSLATIONS.get(meta.get("@type", "Software"))
+    # identifiers = Array.wrap(meta.get('identifier', None)).map do | r|
+    #   r = normalize_id(r) if r.is_a?(String)
+    #   if r.is_a?(String) & & URI(r) != 'doi.org'
+    #     {'identifierType': 'URL', 'identifier': r}
+    #   elsif r.is_a?(Hash)
+    #     {'identifierType': get_identifier_type(
+    #         r['propertyID']), 'identifier': r['value']}
+    #   end
+    # end.compact.uniq
+
+    has_agents = meta.get("agents", None)
+    authors = meta.get("authors", None) if has_agents is None else has_agents
+    contributors = get_authors(from_schema_org_creators(wrap(authors)))
+    contrib = get_authors(from_schema_org_creators(wrap(meta.get("editor", None))))
+    if contrib:
+        contributors += contrib
+    date: dict = defaultdict(list)
+    date["created"] = meta.get("dateCreated", None)
+    date["published"] = meta.get("datePublished", None)
+    date["updated"] = meta.get("dateModified", None)
+
+    publisher = {"name": meta.get("publisher", None)}
+
+    if meta.get("description", None):
+        descriptions = [
+            {
+                "description": sanitize(str(meta.get("description"))),
+                "descriptionType": "Abstract",
+            }
+        ]
+    else:
+        descriptions = None
+
+    subjects = [name_to_fos(i) for i in wrap(meta.get("keywords", None))]
+
+    has_title = meta.get("title", None)
+    if has_title is None:
+        titles = [{"title": meta.get("name", None)}]
+    else:
+        titles = [{"title": has_title}]
+
+    license_ = meta.get("licenseId", None)
+    if license_:
+        license_ = dict_to_spdx({"id": meta.get("licenseId")})
+
+    provider = "DataCite" if doi_from_url(_id) else "GitHub"
+    state = "findable" if meta or read_options else "not_found"
+
+    return {
+        "id": _id,
+        "type": _type,
+        "url": normalize_id(meta.get("codeRepository", None)),
+        "identifiers": None,
+        "titles": titles,
+        "contributors": presence(contributors),
+        "publisher": publisher,
+        "date": compact(date),
+        "descriptions": descriptions,
+        "license": license_,
+        "version": meta.get("version", None),
+        "subjects": presence(subjects),
+        "provider": provider,
+        "state": state,
+    } | read_options

commonmeta/readers/commonmeta_reader.py

@@ -0,0 +1,13 @@
+"""Commonmeta reader for commonmeta-py"""
+from ..constants import Commonmeta
+
+
+def read_commonmeta(data: dict, **kwargs) -> Commonmeta:
+    """read_commonmeta"""
+    if data is None:
+        return {"state": "not_found"}
+    meta = data
+
+    read_options = kwargs or {}
+
+    return meta | read_options