commonmeta-py 0.103__py3-none-any.whl → 0.105__py3-none-any.whl

commonmeta/__init__.py

@@ -10,7 +10,7 @@ commonmeta-py is a Python library to convert scholarly metadata
 """
 
 __title__ = "commonmeta-py"
-__version__ = "0.103"
+__version__ = "0.105"
 __author__ = "Martin Fenner"
 __license__ = "MIT"
 

commonmeta/cli.py

@@ -1,16 +1,18 @@
-import click
 import time
-import pydash as py_
+
+import click
 import orjson as json
+import pydash as py_
 
 from commonmeta import Metadata, MetadataList  # __version__
 from commonmeta.api_utils import update_ghost_post_via_api
-from commonmeta.doi_utils import validate_prefix, encode_doi, decode_doi
+from commonmeta.doi_utils import decode_doi, encode_doi, validate_prefix
+from commonmeta.readers.crossref_reader import get_random_crossref_id
+from commonmeta.readers.datacite_reader import get_random_datacite_id
 from commonmeta.readers.json_feed_reader import (
     get_json_feed_item_uuid,
 )
-from commonmeta.readers.crossref_reader import get_random_crossref_id
-from commonmeta.readers.datacite_reader import get_random_datacite_id
+from commonmeta.readers.openalex_reader import get_random_openalex_id
 
 
 @click.group()
@@ -130,6 +132,8 @@ def sample(provider, prefix, type, number, to, style, locale, show_errors):
         )
     elif provider == "datacite":
         string = json.dumps({"items": get_random_datacite_id(number)})
+    elif provider == "openalex":
+        string = json.dumps({"items": get_random_openalex_id(number)})
     else:
         output = "Provider not supported. Use 'crossref' or 'datacite' instead."
         click.echo(output)

commonmeta/doi_utils.py

@@ -302,16 +302,6 @@ def datacite_api_sample_url(number: int = 1, **kwargs) -> str:
     return f"https://api.datacite.org/dois?random=true&page[size]={number}"
 
 
-def openalex_api_url(doi: str, **kwargs) -> str:
-    """Return the OpenAlex API URL for a given DOI"""
-    return f"https://api.openalex.org/works/{doi}"
-
-
-def openalex_api_sample_url(number: int = 1, **kwargs) -> str:
-    """Return the OpenAlex API URL for a sample of dois"""
-    return f"https://api.openalex.org/works?sample={number}"
-
-
 def is_rogue_scholar_doi(doi: str) -> bool:
     """Return True if DOI is from Rogue Scholar"""
     prefix = validate_prefix(doi)

commonmeta/metadata.py

@@ -199,6 +199,7 @@ class Metadata:
                 "codemeta",
                 "kbase",
                 "inveniordm",
+                "openalex",
             ]:
                 return json.loads(string)
             else:
@@ -237,7 +238,7 @@ class Metadata:
         elif via == "kbase":
             return dict(read_kbase(data))
         elif via == "openalex":
-            return read_openalex(data)
+            return dict(read_openalex(data))
         elif via == "ris":
             return dict(read_ris(data["data"] if isinstance(data, dict) else data))
         else:
@@ -397,6 +398,7 @@ class MetadataList:
             "crossref",
             "datacite",
             "schema_org",
+            "openalex",
             "csl",
             "json_feed_item",
         ]:
@@ -425,6 +427,8 @@ class MetadataList:
             raise ValueError("Schema.org not supported for metadata lists")
         elif to == "datacite":
             raise ValueError("Datacite not supported for metadata lists")
+        elif to == "openalex":
+            raise ValueError("OpenAlex not supported for metadata lists")
         elif to == "crossref_xml":
             return write_crossref_xml_list(self)
         else:

commonmeta/readers/datacite_reader.py

@@ -2,29 +2,30 @@
 
 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 ..base_utils import compact, presence, wrap
+from ..constants import (
+    DC_TO_CM_CONTAINER_TRANSLATIONS,
+    DC_TO_CM_TRANSLATIONS,
+    Commonmeta,
+)
 from ..date_utils import normalize_date_dict
 from ..doi_utils import (
+    datacite_api_sample_url,
+    datacite_api_url,
     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,
+from ..utils import (
+    dict_to_spdx,
+    format_name_identifier,
+    normalize_cc_url,
+    normalize_doi,
+    normalize_url,
 )
 
 

commonmeta/readers/openalex_reader.py

@@ -15,12 +15,14 @@ from ..constants import (
 )
 from ..doi_utils import (
     normalize_doi,
-    openalex_api_sample_url,
-    openalex_api_url,
 )
 from ..utils import (
     dict_to_spdx,
     normalize_url,
+    openalex_api_query_url,
+    openalex_api_sample_url,
+    openalex_api_url,
+    validate_id,
     validate_openalex,
 )
 
@@ -35,15 +37,27 @@ OA_IDENTIFIER_TYPES = {
 }
 
 
+def get_openalex_list(query: dict, **kwargs) -> list[dict]:
+    """get_openalex list from OpenAlex API."""
+    url = openalex_api_query_url(query, **kwargs)
+    response = httpx.get(url, timeout=30, **kwargs)
+    if response.status_code != 200:
+        return []
+    return response.json().get("results", [])
+
+
 def get_openalex(pid: str, **kwargs) -> dict:
     """get_openalex"""
-    doi = normalize_doi(pid)
-    if doi is None:
+    id, identifier_type = validate_id(pid)
+    if identifier_type not in ["DOI", "MAG", "OpenAlex", "PMID", "PMCID"]:
         return {"state": "not_found"}
-    url = openalex_api_url(doi)
+    url = openalex_api_url(id, identifier_type, **kwargs)
     response = httpx.get(url, timeout=10, **kwargs)
     if response.status_code != 200:
         return {"state": "not_found"}
+    # OpenAlex returns record as list
+    if identifier_type in ["MAG", "PMID", "PMCID"]:
+        return py_.get(response.json(), "results[0]") | {"via": "openalex"}
     return response.json() | {"via": "openalex"}
 
 
@@ -54,8 +68,7 @@ def read_openalex(data: Optional[dict], **kwargs) -> Commonmeta:
     meta = data
     read_options = kwargs or {}
 
-    doi = meta.get("doi", None)
-    _id = normalize_doi(doi)
+    _id = meta.get("doi", None) or meta.get("id", None)
     _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:
@@ -315,7 +328,6 @@ def get_files(meta) -> Optional[list]:
 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(
@@ -364,7 +376,7 @@ def from_openalex_funding(funding_references: list) -> list:
     return py_.uniq(formatted_funding_references)
 
 
-def get_random_id_from_openalex(number: int = 1, **kwargs) -> list:
+def get_random_openalex_id(number: int = 1, **kwargs) -> list:
     """Get random ID from OpenAlex"""
     number = min(number, 20)
     url = openalex_api_sample_url(number, **kwargs)
@@ -374,7 +386,6 @@ def get_random_id_from_openalex(number: int = 1, **kwargs) -> list:
             return []
 
         items = py_.get(response.json(), "results")
-        print(items)
-        return [i.get("id") for i in items]
+        return items
     except (httpx.ReadTimeout, httpx.ConnectError):
         return []

commonmeta/readers/ris_reader.py

@@ -2,12 +2,12 @@
 
 from typing import Optional
 
-from ..utils import compact, normalize_url, wrap
-from ..base_utils import presence
 from ..author_utils import get_authors
-from ..date_utils import get_date_from_parts
-from ..doi_utils import normalize_doi, doi_from_url
+from ..base_utils import presence
 from ..constants import RIS_TO_CM_TRANSLATIONS, Commonmeta
+from ..date_utils import get_date_from_parts
+from ..doi_utils import doi_from_url, normalize_doi
+from ..utils import compact, normalize_url, wrap
 
 
 def read_ris(data: Optional[str], **kwargs) -> Commonmeta:

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/utils.py

@@ -353,37 +353,37 @@ def validate_id(id: Optional[str]) -> tuple[Optional[str], Optional[str]]:
     # Check if it's a DOI
     doi = validate_doi(id)
     if doi:
-        return normalize_doi(id), "DOI"
+        return doi, "DOI"
 
     # Check if it's an ORCID
     orcid = validate_orcid(id)
     if orcid:
-        return normalize_orcid(id), "ORCID"
+        return orcid, "ORCID"
 
     # Check if it's a ROR
     ror = validate_ror(id)
     if ror:
-        return normalize_ror(id), "ROR"
+        return ror, "ROR"
 
     # Check if it's an ISNI
     isni = validate_isni(id)
     if isni:
-        return normalize_isni(id), "ISNI"
+        return isni, "ISNI"
 
     # Check if it's an OpenAlex ID
     openalex = validate_openalex(id)
     if openalex:
-        return f"https://openalex.org/{openalex}", "OpenAlex"
+        return 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"
+        return 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"
+        return pmcid, "PMCID"
 
     # Check if it's a URL
     url_type = validate_url(id)
@@ -394,6 +394,66 @@ def validate_id(id: Optional[str]) -> tuple[Optional[str], Optional[str]]:
     return None, None
 
 
+def openalex_api_url(id: str, identifier_type: str, **kwargs) -> str:
+    """Return the OpenAlex API URL for a given ID"""
+    if identifier_type == "DOI":
+        return f"https://api.openalex.org/works/{doi_as_url(id)}"
+    if identifier_type == "OpenAlex":
+        return f"https://api.openalex.org/works/{id}"
+    if identifier_type == "PMID":
+        return f"https://api.openalex.org/works?filter=ids.pmid:{id}"
+    if identifier_type == "PMCID":
+        return f"https://api.openalex.org/works?filter=ids.pmcid:{id}"
+
+
+def openalex_api_query_url(query: dict) -> str:
+    """Return the OpenAlex API query URL"""
+    url = "https://api.openalex.org/works"
+    f = furl(url)
+    rows = min(int(query.get("rows", 20)), 1000)
+    queries = []
+    filters = []
+    _query = None
+    _filter = None
+
+    if query.get("query", None) is not None:
+        queries += [query.get("query")]
+    for key, value in query.items():
+        if key in [
+            "query.bibliographic",
+            "query.author",
+            "query.title",
+            "query.container-title",
+        ]:
+            queries += [f"{key}:{value}"]
+    if queries:
+        _query = ",".join(queries)
+
+    for key, value in query.items():
+        if key in [
+            "prefix",
+            "member",
+            "type",
+            "has-full-text",
+            "has-references",
+            "has-orcid",
+            "has-funder",
+            "has-license",
+        ]:
+            filters += [f"{key}:{value}"]
+    if filters:
+        _filter = ",".join(filters)
+
+    f.args.update(compact({"rows": rows, "query": _query, "filter": _filter}))
+
+    return f.url
+
+
+def openalex_api_sample_url(number: int = 1, **kwargs) -> str:
+    """Return the OpenAlex API URL for a sample of dois"""
+    return f"https://api.openalex.org/works?sample={number}"
+
+
 def normalize_isni(isni: Optional[str]) -> Optional[str]:
     """Normalize ISNI"""
     if isni is None or not isinstance(isni, str):
@@ -801,6 +861,20 @@ def find_from_format_by_id(pid: str) -> Optional[str]:
         is not None
     ):
         return "codemeta"
+    if re.match(r"\A(http|https):/(/)?openalex\.org/(.+)\Z", pid) is not None:
+        return "openalex"
+    if (
+        re.match(r"\A(http|https):/(/)?pubmed\.ncbi\.nlm\.nih\.gov/(.+)\Z", pid)
+        is not None
+    ):
+        return "openalex"  # pmid
+    if (
+        re.match(
+            r"\A(http|https):/(/)?www\.ncbi\.nlm\.nih\.gov/pmc/articles/(.+)\Z", pid
+        )
+        is not None
+    ):
+        return "openalex"  # pmcid
     if re.match(r"\A(http|https):/(/)?github\.com/(.+)\Z", pid) is not None:
         return "cff"
     if re.match(r"\Ahttps:/(/)?api\.rogue-scholar\.org/posts/(.+)\Z", pid) is not None:

{commonmeta_py-0.103.dist-info → commonmeta_py-0.105.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: commonmeta-py
-Version: 0.103
+Version: 0.105
 Summary: Library for conversions to/from the Commonmeta scholarly metadata format
 Project-URL: Homepage, https://python.commonmeta.org
 Project-URL: Repository, https://github.com/front-matter/commonmeta-py

{commonmeta_py-0.103.dist-info → commonmeta_py-0.105.dist-info}/RECORD

@@ -1,16 +1,16 @@
-commonmeta/__init__.py,sha256=5sJSfHhI1zKi-tT9a8UaWhlPu74UT4ilgC5MyFtWJYo,1933
+commonmeta/__init__.py,sha256=-CGF2Vsunhb1pTKiRlTsTwhtS4tU9GPGxegTdD8ASkw,1933
 commonmeta/api_utils.py,sha256=-ZHGVZZhJqnjnsLtp4-PoeHYbDqL0cQme7W70BEjo4U,2677
 commonmeta/author_utils.py,sha256=4ftyfy0tZRtP8bJ_PYdrNS8Z76FNBJ38sHj5EMhds1Y,8585
 commonmeta/base_utils.py,sha256=-HKaIts_LzTKNsdqSAw52r5zx1baGawSQawGh8l5Sio,3751
-commonmeta/cli.py,sha256=sOI9BJTePnljVcXcZ95N7TKXDT283XpjUaak7bMnbr0,6076
+commonmeta/cli.py,sha256=_sMYNzfiEgQ1qx6tZPMbOp1GZ9BBiWe0fYF3jJlamKU,6251
 commonmeta/constants.py,sha256=NuugDPtaAlYx7d-0WKPHNO-qnjt4rzcj-EbzL2vSi2Q,19259
 commonmeta/crossref_utils.py,sha256=mEXNP7LQXcJyEmCqcpWxi_VI3GU1ZD_XvarYjUMxPL0,22284
 commonmeta/date_utils.py,sha256=WW0tg0mgHdORPhAHt9nJIuVawhepZtUCouW-SdqI1OM,6317
-commonmeta/doi_utils.py,sha256=bM4D3ypyOIjeMcT5C5vx-ul-7wPGMeAOVHep9QnYAqE,9911
-commonmeta/metadata.py,sha256=8oe0GlqVq8oakjOyBTDK7BjTIxMmRoMgLuLg5fCXalU,16539
+commonmeta/doi_utils.py,sha256=uIDfE6i68bJv-AJ4STMmT6JhXEvmTu6eZwIxAr_4MD8,9570
+commonmeta/metadata.py,sha256=qgqbrvxPEbYn0pKIArhpaGjIeiHeuubc6nF37QgWp2Y,16702
 commonmeta/schema_utils.py,sha256=GFFusU6D9atmjiQ7SS-rQ5cqrOEQlwYzF3q1CnOUXRA,916
 commonmeta/translators.py,sha256=RpGJtKNLjmz41VREZDY7KyyE2eXOi8j7m-da4jHmknI,1362
-commonmeta/utils.py,sha256=7IWcP0r1oHZvLrJxyl6uadLpLy13S3muP7RWV8cGp_4,46493
+commonmeta/utils.py,sha256=APDXdeR2oWyn15vcQPJjPisRHn14hzt1q_21vPxkFCE,48589
 commonmeta/readers/__init__.py,sha256=vOf7UsOKNoh_ZCuyexxhAmPMt8wjB-pF_CfpWRaN8pk,45
 commonmeta/readers/bibtex_reader.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 commonmeta/readers/cff_reader.py,sha256=V379XNQUc0M-cDxNPwHqabu9b0NTscPUJpM9DXNgL_c,6145
@@ -19,20 +19,20 @@ commonmeta/readers/commonmeta_reader.py,sha256=46XrCr2whkUP4uiaNiFXS7ABwowcRdWcL
 commonmeta/readers/crossref_reader.py,sha256=53Up2X6ff2iVPXLoRjjhTSa5rWrjgT8FObclU50Gazc,12540
 commonmeta/readers/crossref_xml_reader.py,sha256=yZOh66_4tVS5i0TdEyOa48ckpl7_cj69hfZnaA9pjM8,18723
 commonmeta/readers/csl_reader.py,sha256=OxzC2AZKfv43BCah4XGYvlK_LUK-5mxXFcjdzB5vv_o,3216
-commonmeta/readers/datacite_reader.py,sha256=CdOtxhthrakBoQMsLTdPx6sUCmqtEWo5ICYE6ZsWDdo,12026
+commonmeta/readers/datacite_reader.py,sha256=YuYUl4tSOB6BXeY5aASek4BjFsF47Ibow1gIrsbTDOM,12027
 commonmeta/readers/datacite_xml_reader.py,sha256=nhnO92fZihr1HZlbXjyem-HJXc9_DWLgJ2zeltuPMIg,13041
 commonmeta/readers/inveniordm_reader.py,sha256=qFPXdOGArWwsb09MdPf0uCsXEkL19AgsRSgsH7KT9Pw,8437
 commonmeta/readers/json_feed_reader.py,sha256=uiFAeDmgDOpoZR7Zah2uLDsY7xrkxpkg59bo3obZ8uk,14477
 commonmeta/readers/kbase_reader.py,sha256=KH3loJvuq2bm8zAYIUG7hTsr5-2Anj3NQvoJUDiqmss,6764
-commonmeta/readers/openalex_reader.py,sha256=YbYwSbp_1aBHLnVJkITqhLEwE98yqUx2L3LJ0G8R_0k,12205
-commonmeta/readers/ris_reader.py,sha256=ttkB1ZeLZW6jry-r8nFCbEQ0gozlsNUBeRJGMJ6qKfY,3678
+commonmeta/readers/openalex_reader.py,sha256=jYBvAoawztrMQg6AdYyQf9cCVWR1M5CaraHe9CInEbU,12750
+commonmeta/readers/ris_reader.py,sha256=oQ3G7qQmNwhr4cNp-Gv5UW28J2K1oKpBlPh-tjRtnpQ,3678
 commonmeta/readers/schema_org_reader.py,sha256=oZoLG9okMxzlyCuX6oNNNFwvGCFpQ3W2Pz2TpXr3vkA,17224
 commonmeta/resources/cff_v1.2.0.json,sha256=MpfjDYgX7fN9PLiG54ISZ2uu9WItNqfh-yaRuTf6Ptg,46691
 commonmeta/resources/commonmeta_v0.12.json,sha256=HUSNReXh2JN3Q6YWSt7CE69js8dh50OlpMYGTyU98oU,16762
 commonmeta/resources/commonmeta_v0.13.json,sha256=2-WSZGijR13zVu97S_YHXr-cyeLW7hzHXYMlr6nIjdw,15787
 commonmeta/resources/commonmeta_v0.14.json,sha256=nACmkTe4IrZkygd5AeJnAv9P4EWfzCwW9oL5AhubvnE,17657
 commonmeta/resources/commonmeta_v0.15.json,sha256=kC9xmtIwrGpl7V1vcXKWthWejYvtKfqOqenBCRSjANc,17753
-commonmeta/resources/commonmeta_v0.16.json,sha256=kgeGjIGUXzVK4E2H6eKBZdI0-gnFQYthR9WIkyAZp5o,18706
+commonmeta/resources/commonmeta_v0.16.json,sha256=2TsgX69tvEUfG-k0HUUfKepCQ3z9u6lcbm2U-esOS5g,18976
 commonmeta/resources/crossref-v0.2.json,sha256=THbFem4IDSE-TFNOtP1-NOmZhED2dlLBso9RdGMbGIY,1431
 commonmeta/resources/csl-data.json,sha256=I7LAYtdSYGD0YxuwS0s7ojfkiEhCU-MnvQD6aRhhuBE,12222
 commonmeta/resources/datacite-v4.5.json,sha256=ocpQNSbORPJf5Ogidy6M6EHundgv7DSgIqRco02KgM4,18970
@@ -71,8 +71,8 @@ commonmeta/writers/datacite_writer.py,sha256=rygkSNUWdF4lvGd4BsjrlBfPHHsSLwkFp-a
 commonmeta/writers/inveniordm_writer.py,sha256=M_VmBZ_E5x_BHSgMjt2u70c34Eij2ngoaDwYWOrJzkg,11429
 commonmeta/writers/ris_writer.py,sha256=CXd9MiSHOMLReeGmr1moqteiq4x8AtLNYVS60s-aq8I,2094
 commonmeta/writers/schema_org_writer.py,sha256=J2Y-krzyhgBZ6n__S_YvdjUtwiCm-RUtpGA_esFZUwg,5742
-commonmeta_py-0.103.dist-info/METADATA,sha256=2r3bpGd72_9phuGCr0lGH6-v3rGnshQSezPU8An18GE,7444
-commonmeta_py-0.103.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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