commonmeta-py 0.101__py3-none-any.whl → 0.104__py3-none-any.whl

commonmeta/readers/openalex_reader.py

@@ -0,0 +1,380 @@
+"""OpenAlex reader for commonmeta-py"""
+
+from typing import Optional
+
+import httpx
+from pydash import py_
+
+from ..author_utils import get_authors
+from ..base_utils import compact, presence, sanitize, wrap
+from ..constants import (
+    CR_TO_CM_TRANSLATIONS,
+    OA_TO_CM_CONTAINER_TRANLATIONS,
+    OA_TO_CM_TRANSLATIONS,
+    Commonmeta,
+)
+from ..doi_utils import (
+    normalize_doi,
+    openalex_api_sample_url,
+    openalex_api_url,
+)
+from ..utils import (
+    dict_to_spdx,
+    normalize_url,
+    validate_openalex,
+)
+
+# Map OpenAlex license strings to SPDX licenceId. May not be the correct license version.
+OA_LICENSES = {"cc-by": "CC-BY-4.0", "cc0": "CC0-1.0"}
+OA_IDENTIFIER_TYPES = {
+    "openalex": "OpenAlex",
+    "doi": "DOI",
+    "mag": "MAG",
+    "pmid": "PMID",
+    "pmcid": "PMCID",
+}
+
+
+def get_openalex(pid: str, **kwargs) -> dict:
+    """get_openalex"""
+    doi = normalize_doi(pid)
+    if doi is None:
+        return {"state": "not_found"}
+    url = openalex_api_url(doi)
+    response = httpx.get(url, timeout=10, **kwargs)
+    if response.status_code != 200:
+        return {"state": "not_found"}
+    return response.json() | {"via": "openalex"}
+
+
+def read_openalex(data: Optional[dict], **kwargs) -> Commonmeta:
+    """read_openalex"""
+    if data is None:
+        return {"state": "not_found"}
+    meta = data
+    read_options = kwargs or {}
+
+    doi = meta.get("doi", None)
+    _id = normalize_doi(doi)
+    _type = CR_TO_CM_TRANSLATIONS.get(meta.get("type_crossref", None)) or "Other"
+    additional_type = OA_TO_CM_TRANSLATIONS.get(meta.get("type", None))
+    if additional_type == _type:
+        additional_type = None
+
+    archive_locations = []
+    contributors = get_contributors(wrap(meta.get("authorships")))
+    contributors = get_authors(contributors)
+
+    url = normalize_url(
+        py_.get(meta, "primary_location.landing_page_url") or py_.get(meta, "id")
+    )
+    title = meta.get("title", None)
+    if title is not None:
+        titles = [{"title": sanitize(title)}]
+    else:
+        titles = None
+    publisher = compact(
+        {"name": py_.get(meta, "primary_location.source.host_organization_name")}
+    )
+    date = compact(
+        {
+            "published": py_.get(meta, "publication_date")
+            or py_.get(meta, "created_date")
+        }
+    )
+    identifiers = [
+        {
+            "identifier": uid,
+            "identifierType": OA_IDENTIFIER_TYPES[uidType],
+        }
+        for uidType, uid in (meta.get("ids", {})).items()
+    ]
+
+    license_ = py_.get(meta, "best_oa_location.license")
+    if license_ is not None:
+        license_ = OA_LICENSES.get(license_, license_)
+        license_ = dict_to_spdx({"id": license_})
+    container = get_container(meta)
+    relations = []
+    references = [
+        get_related(i) for i in get_references(meta.get("referenced_works", []))
+    ]
+    funding_references = from_openalex_funding(wrap(meta.get("grants", None)))
+
+    description = get_abstract(meta)
+    if description is not None:
+        descriptions = [{"description": sanitize(description), "type": "Abstract"}]
+    else:
+        descriptions = None
+
+    subjects = py_.uniq(
+        [
+            {"subject": py_.get(i, "subfield.display_name")}
+            for i in wrap(meta.get("topics", None))
+        ]
+    )
+    files = get_files(meta)
+
+    return {
+        # required properties
+        "id": _id,
+        "type": _type,
+        # recommended and optional properties
+        "additionalType": additional_type,
+        "archiveLocations": presence(archive_locations),
+        "container": presence(container),
+        "contributors": presence(contributors),
+        "date": presence(date),
+        "descriptions": presence(descriptions),
+        "files": presence(files),
+        "fundingReferences": presence(funding_references),
+        "geoLocations": None,
+        "identifiers": identifiers,
+        "language": meta.get("language", None),
+        "license": license_,
+        "provider": "OpenAlex",
+        "publisher": presence(publisher),
+        "references": presence(references),
+        "relations": presence(relations),
+        "subjects": presence(subjects),
+        "titles": presence(titles),
+        "url": url,
+        "version": meta.get("version", None),
+    } | read_options
+
+
+def get_abstract(meta):
+    """Parse abstract from OpenAlex abstract_inverted_index"""
+    abstract_inverted_index = py_.get(meta, "abstract_inverted_index")
+
+    if abstract_inverted_index:
+        # Determine the length of the abstract
+        max_pos = max(
+            p for positions in abstract_inverted_index.values() for p in positions
+        )
+        abstract_words = [""] * (max_pos + 1)
+
+        for word, positions in abstract_inverted_index.items():
+            for p in positions:
+                abstract_words[p] = word
+
+        abstract = " ".join(abstract_words)
+    else:
+        abstract = None
+    return abstract
+
+
+def get_contributors(contributors: list) -> list:
+    """Parse contributor"""
+
+    def parse_contributor(c):
+        affiliations = []
+        for affiliation in c.get("institutions", []):
+            affiliations.append(
+                compact(
+                    {
+                        "id": affiliation.get("ror", None),
+                        "name": affiliation.get("display_name", None),
+                    }
+                )
+            )
+
+        return compact(
+            {
+                "id": py_.get(c, "author.orcid"),
+                "name": py_.get(c, "author.display_name"),
+                "affiliations": affiliations,
+            }
+        )
+
+    return [parse_contributor(i) for i in contributors]
+
+
+def get_references(pids: list, **kwargs) -> list:
+    """Get related articles from OpenAlex using their pid
+    Used for retrieving metadata for citations and references which are not included in the OpenAlex record
+    """
+    references = get_openalex_works(pids)
+    return references
+
+
+def get_citations(citation_url: str, **kwargs) -> list:
+    response = httpx.get(citation_url, timeout=10, **kwargs)
+    if response.status_code != 200:
+        return {"state": "not_found"}
+    response = response.json()
+    return response.json().get("results", [])
+
+
+def get_related(related: Optional[dict]) -> Optional[dict]:
+    """Get reference from OpenAlex reference"""
+    if related is None or not isinstance(related, dict):
+        return None
+    doi = related.get("doi", None)
+    metadata = {
+        "id": normalize_doi(doi) if doi else None,
+        "contributor": related.get("author", None),
+        "title": related.get("display_name", None),
+        "publisher": related.get(
+            "primary_location.source.host_organization_name", None
+        ),
+        "publicationYear": related.get("publication_year", None),
+        "volume": py_.get(related, "biblio.volume"),
+        "issue": py_.get(related, "biblio.issue"),
+        "firstPage": py_.get(related, "biblio.first_page"),
+        "lastPage": py_.get(related, "biblio.last_page"),
+        "containerTitle": related.get("primary_location.source.display_name", None),
+    }
+    return compact(metadata)
+
+
+def get_openalex_works(pids: list, **kwargs) -> list:
+    """Get OpenAlex works, use batches of 49 to honor API limit."""
+    pid_batches = [pids[i : i + 49] for i in range(0, len(pids), 49)]
+    works = []
+    for pid_batch in pid_batches:
+        ids = "|".join(pid_batch)
+        url = f"https://api.openalex.org/works?filter=ids.openalex:{ids}"
+        response = httpx.get(url, timeout=10, **kwargs)
+        if response.status_code != 200:
+            return {"state": "not_found"}
+        response = response.json()
+        if py_.get(response, "count") == 0:
+            return {"state": "not_found"}
+
+        works.extend(response.get("results"))
+
+    return works
+
+
+def get_openalex_funders(pids: list, **kwargs) -> list:
+    """Get ROR id and name from OpenAlex funders.
+    use batches of 49 to honor API limit."""
+    pid_batches = [pids[i : i + 49] for i in range(0, len(pids), 49)]
+    funders = []
+    for pid_batch in pid_batches:
+        ids = "|".join(pid_batch)
+        url = f"https://api.openalex.org/funders?filter=ids.openalex:{ids}"
+        response = httpx.get(url, timeout=10, **kwargs)
+        if response.status_code != 200:
+            return {"state": "not_found"}
+        response = response.json()
+        if py_.get(response, "count") == 0:
+            return {"state": "not_found"}
+
+        def format_funder(funder):
+            return compact(
+                {
+                    "id": py_.get(funder, "id"),
+                    "ror": py_.get(funder, "ids.ror"),
+                    "name": py_.get(funder, "display_name"),
+                }
+            )
+
+        f = [format_funder(i) for i in response.get("results")]
+        funders.extend(f)
+
+    return funders
+
+
+def get_openalex_source(str: Optional[str], **kwargs) -> Optional[dict]:
+    """Get issn, name, homepage_url and type from OpenAlex source."""
+    id = validate_openalex(str)
+    if not id:
+        return None
+
+    url = f"https://api.openalex.org/sources/{id}"
+    response = httpx.get(url, timeout=10, **kwargs)
+    if response.status_code != 200:
+        return {"state": "not_found"}
+    response = response.json()
+    if py_.get(response, "count") == 0:
+        return {"state": "not_found"}
+
+    return compact(
+        {
+            "id": py_.get(response, "id"),
+            "url": py_.get(response, "homepage_url"),
+            "issn": py_.get(response, "issn_l"),
+            "title": py_.get(response, "display_name"),
+            "type": py_.get(response, "type"),
+        }
+    )
+
+
+def get_files(meta) -> Optional[list]:
+    """get file links"""
+    pdf_url = py_.get(meta, "best_oa_location.pdf_url")
+    if pdf_url is None:
+        return None
+    return [
+        {"mimeType": "application/pdf", "url": pdf_url},
+    ]
+
+
+def get_container(meta: dict) -> dict:
+    """Get container from OpenAlex"""
+    source = get_openalex_source(py_.get(meta, "primary_location.source.id"))
+    print(source)
+    container_type = py_.get(source, "type")
+    if container_type:
+        container_type = OA_TO_CM_CONTAINER_TRANLATIONS.get(
+            container_type, container_type
+        )
+    issn = py_.get(source, "issn")
+    container_title = py_.get(source, "title")
+    url_ = py_.get(source, "url")
+
+    return compact(
+        {
+            "type": container_type,
+            "identifier": issn or url_,
+            "identifierType": "ISSN" if issn else "URL" if url_ else None,
+            "title": container_title,
+            "volume": py_.get(meta, "biblio.volume"),
+            "issue": py_.get(meta, "biblio.issue"),
+            "firstPage": py_.get(meta, "biblio.first_page"),
+            "lastPage": py_.get(meta, "biblio.last_page"),
+        }
+    )
+
+
+def from_openalex_funding(funding_references: list) -> list:
+    """Get funding references from OpenAlex"""
+    funder_ids = [
+        validate_openalex(funding.get("funder"))
+        for funding in funding_references
+        if "funder" in funding
+    ]
+    funders = get_openalex_funders(funder_ids)
+    formatted_funding_references = []
+    for funding in funding_references:
+        funder = next(
+            item for item in funders if item["id"] == funding.get("funder", None)
+        )
+        f = compact(
+            {
+                "funderName": funder.get("name", None),
+                "funderIdentifier": funder.get("ror", None),
+                "funderIdentifierType": "ROR" if funder.get("ror", None) else None,
+                "awardNumber": funding.get("award_id", None),
+            }
+        )
+        formatted_funding_references.append(f)
+    return py_.uniq(formatted_funding_references)
+
+
+def get_random_id_from_openalex(number: int = 1, **kwargs) -> list:
+    """Get random ID from OpenAlex"""
+    number = min(number, 20)
+    url = openalex_api_sample_url(number, **kwargs)
+    try:
+        response = httpx.get(url, timeout=10)
+        if response.status_code != 200:
+            return []
+
+        items = py_.get(response.json(), "results")
+        print(items)
+        return [i.get("id") for i in items]
+    except (httpx.ReadTimeout, httpx.ConnectError):
+        return []

commonmeta/readers/ris_reader.py

@@ -1,4 +1,5 @@
 """RIS reader for commonmeta-py"""
+
 from typing import Optional
 
 from ..utils import compact, normalize_url, wrap

commonmeta/resources/commonmeta_v0.16.json

@@ -5,8 +5,7 @@
   "description": "JSON representation of the Commonmeta schema.",
   "commonmeta": {
     "anyOf": [
-      { "$ref": "#/definitions/commonmeta"
-      },
+      { "$ref": "#/definitions/commonmeta" },
       {
         "type": "array",
         "description": "An array of commonmeta objects.",
@@ -196,7 +195,13 @@
               "type": {
                 "description": "The type of the description.",
                 "type": "string",
-                "enum": ["Abstract", "Summary", "Methods", "TechnicalInfo", "Other"]
+                "enum": [
+                  "Abstract",
+                  "Summary",
+                  "Methods",
+                  "TechnicalInfo",
+                  "Other"
+                ]
               },
               "language": {
                 "description": "The language of the title. Use one of the language codes from the IETF BCP 47 standard.",
@@ -267,7 +272,9 @@
                       "items": { "$ref": "#/definitions/geoLocationPoint" },
                       "minItems": 4
                     },
-                    "inPolygonPoint": { "$ref": "#/definitions/geoLocationPoint" }
+                    "inPolygonPoint": {
+                      "$ref": "#/definitions/geoLocationPoint"
+                    }
                   },
                   "required": ["polygonPoints"]
                 },
@@ -294,6 +301,7 @@
                   "Handle",
                   "ISBN",
                   "ISSN",
+                  "OpenAlex",
                   "PMID",
                   "PMCID",
                   "PURL",
@@ -323,7 +331,15 @@
         "provider": {
           "description": "The provider of the resource. This can be a DOI registration agency or a repository.",
           "type": "string",
-          "enum": ["Crossref", "DataCite", "GitHub", "JaLC", "KISTI", "mEDRA", "OP"]
+          "enum": [
+            "Crossref",
+            "DataCite",
+            "GitHub",
+            "JaLC",
+            "KISTI",
+            "mEDRA",
+            "OP"
+          ]
         },
         "publisher": {
           "description": "The publisher of the resource.",

commonmeta/schema_utils.py

@@ -1,4 +1,5 @@
 """Schema utils for commonmeta-py"""
+
 from os import path
 import orjson as json
 from jsonschema import Draft202012Validator, ValidationError

commonmeta/utils.py

@@ -1,22 +1,22 @@
 """Utils module for commonmeta-py"""
 
 import os
-import orjson as json
 import re
 import time
 from typing import Optional
 from urllib.parse import urlparse
-import yaml
-from furl import furl
+
 import bibtexparser
+import orjson as json
+import pycountry
+import yaml
 from bs4 import BeautifulSoup
+from furl import furl
 from pydash import py_
-import pycountry
 
-from .base_utils import wrap, compact, parse_attributes
-from .doi_utils import normalize_doi, doi_from_url, get_doi_ra, validate_doi, doi_as_url
+from .base_utils import compact, parse_attributes, wrap
 from .constants import DATACITE_CONTRIBUTOR_TYPES
-
+from .doi_utils import doi_as_url, doi_from_url, get_doi_ra, normalize_doi, validate_doi
 
 NORMALIZED_LICENSES = {
     "https://creativecommons.org/licenses/by/1.0": "https://creativecommons.org/licenses/by/1.0/legalcode",
@@ -144,17 +144,13 @@ def normalize_id(pid: Optional[str], **kwargs) -> Optional[str]:
         return doi
 
     # check for valid HTTP uri and ensure https
-    uri = urlparse(pid)
-    if not uri.netloc or uri.scheme not in ["http", "https"]:
+    f = furl(pid)
+    if not f.host or f.scheme not in ["http", "https"]:
         return None
-    if uri.scheme == "http":
-        pid = pid.replace(HTTP_SCHEME, HTTPS_SCHEME)
+    if f.scheme == "http":
+        f.scheme = "https"
 
-    # remove trailing slash
-    if pid.endswith("/"):
-        pid = pid.strip("/")
-
-    return pid
+    return f.url
 
 
 def normalize_ids(ids: list, relation_type=None) -> list:
@@ -289,6 +285,115 @@ def validate_isni(isni: Optional[str]) -> Optional[str]:
     return isni
 
 
+def validate_mag(mag: Optional[str]) -> Optional[str]:
+    """Validate Microsoft Academic Graph ID (mag)"""
+    if mag is None or not isinstance(mag, str):
+        return None
+    match = re.search(
+        r"\A(\d{4,10})\Z",
+        mag,
+    )
+    if match is None:
+        return None
+    return match.group(1)
+
+
+def validate_openalex(openalex: Optional[str]) -> Optional[str]:
+    """Validate OpenAlex ID"""
+    if openalex is None or not isinstance(openalex, str):
+        return None
+    match = re.search(
+        r"\A(?:(?:http|https)://openalex\.org/)?([AFIPSW]\d{8,10})\Z",
+        openalex,
+    )
+    if match is None:
+        return None
+    return match.group(1)
+
+
+def validate_pmid(pmid: Optional[str]) -> Optional[str]:
+    """Validate PubMed ID (pmid)"""
+    if pmid is None or not isinstance(pmid, str):
+        return None
+    match = re.search(
+        r"\A(?:(?:http|https)://pubmed\.ncbi\.nlm\.nih\.gov/)?(\d{4,8})\Z",
+        pmid,
+    )
+    if match is None:
+        return None
+    return match.group(1)
+
+
+def validate_pmcid(pmcid: Optional[str]) -> Optional[str]:
+    """Validate PubMed Central ID (pmcid)"""
+    if pmcid is None or not isinstance(pmcid, str):
+        return None
+    match = re.search(
+        r"\A(?:(?:http|https)://www\.ncbi\.nlm\.nih\.gov/pmc/articles/)?(\d{4,8})\Z",
+        pmcid,
+    )
+    if match is None:
+        return None
+    return match.group(1)
+
+
+def validate_id(id: Optional[str]) -> tuple[Optional[str], Optional[str]]:
+    """
+    Validate an identifier and return the validated identifier and its type.
+
+    Args:
+        id: The identifier string to validate
+
+    Returns:
+        A tuple containing (validated_id, id_type) or (None, None) if invalid
+    """
+    if id is None:
+        return None, None
+
+    # Check if it's a DOI
+    doi = validate_doi(id)
+    if doi:
+        return normalize_doi(id), "DOI"
+
+    # Check if it's an ORCID
+    orcid = validate_orcid(id)
+    if orcid:
+        return normalize_orcid(id), "ORCID"
+
+    # Check if it's a ROR
+    ror = validate_ror(id)
+    if ror:
+        return normalize_ror(id), "ROR"
+
+    # Check if it's an ISNI
+    isni = validate_isni(id)
+    if isni:
+        return normalize_isni(id), "ISNI"
+
+    # Check if it's an OpenAlex ID
+    openalex = validate_openalex(id)
+    if openalex:
+        return f"https://openalex.org/{openalex}", "OpenAlex"
+
+    # Check if it's a PubMed ID
+    pmid = validate_pmid(id)
+    if pmid:
+        return f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", "PMID"
+
+    # Check if it's a PubMed Central ID
+    pmcid = validate_pmcid(id)
+    if pmcid:
+        return f"https://www.ncbi.nlm.nih.gov/pmc/articles/{pmcid}", "PMCID"
+
+    # Check if it's a URL
+    url_type = validate_url(id)
+    if url_type:
+        return normalize_url(id), url_type
+
+    # No known valid identifier type was found
+    return None, None
+
+
 def normalize_isni(isni: Optional[str]) -> Optional[str]:
     """Normalize ISNI"""
     if isni is None or not isinstance(isni, str):

commonmeta/writers/bibtex_writer.py

@@ -1,4 +1,5 @@
 """Bibtex writer for commonmeta-py"""
+
 from bibtexparser.bwriter import BibTexWriter
 from bibtexparser.bibdatabase import BibDatabase
 from bibtexparser.customization import page_double_hyphen

commonmeta/writers/citation_writer.py

@@ -1,4 +1,5 @@
 """Citation writer for commonmeta-py"""
+
 import orjson as json
 import re
 from pydash import py_

commonmeta/writers/crossref_xml_writer.py

@@ -1,4 +1,5 @@
 """Crossref XML writer for commonmeta-py"""
+
 from typing import Optional
 from ..constants import Commonmeta
 from ..crossref_utils import generate_crossref_xml, generate_crossref_xml_list

commonmeta/writers/csl_writer.py

@@ -1,4 +1,5 @@
 """CSL-JSON writer for commonmeta-py"""
+
 import orjson as json
 from typing import Optional
 

commonmeta/writers/datacite_writer.py

@@ -1,4 +1,5 @@
 """DataCite writer for commonmeta-py"""
+
 import orjson as json
 from typing import Optional, Union
 

commonmeta/writers/ris_writer.py

@@ -1,4 +1,5 @@
 """RIS writer for commonmeta-py"""
+
 from ..utils import to_ris
 from ..base_utils import compact, wrap, presence, parse_attributes
 from ..doi_utils import doi_from_url

commonmeta/writers/schema_org_writer.py

@@ -1,4 +1,5 @@
 """Schema.org writer for commonmeta-py"""
+
 import orjson as json
 from ..utils import to_schema_org_creators, github_as_repo_url, get_language
 from ..base_utils import compact, wrap, presence, parse_attributes