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

commonmeta/metadata.py

@@ -8,8 +8,7 @@ import yaml
 from pydash import py_
 
 from .base_utils import parse_xml, wrap
-from .constants import CM_TO_CR_TRANSLATIONS
-from .doi_utils import doi_from_url
+from .file_utils import write_output
 from .readers.cff_reader import get_cff, read_cff
 from .readers.codemeta_reader import (
     get_codemeta,
@@ -34,7 +33,7 @@ from .readers.inveniordm_reader import (
     get_inveniordm,
     read_inveniordm,
 )
-from .readers.json_feed_reader import get_json_feed_item, read_json_feed_item
+from .readers.jsonfeed_reader import get_jsonfeed, read_jsonfeed
 from .readers.kbase_reader import read_kbase
 from .readers.openalex_reader import (
     get_openalex,
@@ -45,17 +44,25 @@ from .readers.schema_org_reader import (
     get_schema_org,
     read_schema_org,
 )
-from .schema_utils import json_schema_errors
+from .schema_utils import json_schema_errors, xml_schema_errors
 from .utils import find_from_format, normalize_id
 from .writers.bibtex_writer import write_bibtex, write_bibtex_list
 from .writers.citation_writer import write_citation, write_citation_list
 from .writers.commonmeta_writer import write_commonmeta, write_commonmeta_list
-from .writers.crossref_xml_writer import write_crossref_xml, write_crossref_xml_list
+from .writers.crossref_xml_writer import (
+    push_crossref_xml_list,
+    write_crossref_xml,
+    write_crossref_xml_list,
+)
 from .writers.csl_writer import write_csl, write_csl_list
-from .writers.datacite_writer import write_datacite
-from .writers.inveniordm_writer import write_inveniordm
+from .writers.datacite_writer import write_datacite, write_datacite_list
+from .writers.inveniordm_writer import (
+    push_inveniordm_list,
+    write_inveniordm,
+    write_inveniordm_list,
+)
 from .writers.ris_writer import write_ris, write_ris_list
-from .writers.schema_org_writer import write_schema_org
+from .writers.schema_org_writer import write_schema_org, write_schema_org_list
 
 
 # pylint: disable=R0902
@@ -154,8 +161,8 @@ class Metadata:
             return get_codemeta(pid)
         elif via == "cff":
             return get_cff(pid)
-        elif via == "json_feed_item":
-            return get_json_feed_item(pid)
+        elif via == "jsonfeed":
+            return get_jsonfeed(pid)
         elif via == "inveniordm":
             return get_inveniordm(pid)
         elif via == "openalex":
@@ -195,7 +202,7 @@ class Metadata:
                 "datacite",
                 "schema_org",
                 "csl",
-                "json_feed_item",
+                "jsonfeed",
                 "codemeta",
                 "kbase",
                 "inveniordm",
@@ -231,8 +238,8 @@ class Metadata:
             return dict(read_codemeta(data))
         elif via == "cff":
             return dict(read_cff(data))
-        elif via == "json_feed_item":
-            return dict(read_json_feed_item(data, **kwargs))
+        elif via == "jsonfeed":
+            return dict(read_jsonfeed(data, **kwargs))
         elif via == "inveniordm":
             return dict(read_inveniordm(data))
         elif via == "kbase":
@@ -270,13 +277,13 @@ class Metadata:
     def _write_json_format(self, to: str) -> str:
         """Handle JSON-based output formats."""
         if to == "commonmeta":
-            result = write_commonmeta(self)
+            result = json.dumps(write_commonmeta(self))
         elif to == "datacite":
-            result = write_datacite(self)
+            result = json.dumps(write_datacite(self))
         elif to == "inveniordm":
-            result = write_inveniordm(self)
+            result = json.dumps(write_inveniordm(self))
         elif to == "schema_org":
-            result = write_schema_org(self)
+            result = json.dumps(write_schema_org(self))
         else:
             return "{}"
 
@@ -340,16 +347,19 @@ class Metadata:
 
     def _write_crossref_xml(self, **kwargs) -> str:
         """Write in Crossref XML format with error checking."""
-        doi = doi_from_url(self.id)
-        _type = CM_TO_CR_TRANSLATIONS.get(str(self.type or ""), None)
-        url = self.url
-        instance = {"doi": doi, "type": _type, "url": url}
+        # doi = doi_from_url(self.id)
+        # _type = CM_TO_CR_TRANSLATIONS.get(str(self.type or ""), 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")
-        result = write_crossref_xml(self)
-        return result if result is not None else ""
+        output = write_crossref_xml(self)
+        self.write_errors = xml_schema_errors(output, schema="crossref_xml")
+        if self.write_errors is not None:
+            self.is_valid = False
+            return ""
+        return output if output is not None else ""
 
 
 class MetadataList:
@@ -378,6 +388,12 @@ class MetadataList:
         self.depositor = kwargs.get("depositor", None)
         self.email = kwargs.get("email", None)
         self.registrant = kwargs.get("registrant", None)
+        self.login_id = kwargs.get("login_id", None)
+        self.login_passwd = kwargs.get("login_passwd", None)
+
+        # options needed for InvenioRDM registration
+        self.host = kwargs.get("host", None)
+        self.token = kwargs.get("token", 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]
@@ -387,8 +403,7 @@ class MetadataList:
         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)
+        self.file = kwargs.get("file", None)
 
     def get_metadata_list(self, string) -> list:
         if string is None or not isinstance(string, (str, bytes)):
@@ -396,11 +411,12 @@ class MetadataList:
         if self.via in [
             "commonmeta",
             "crossref",
+            "csl",
             "datacite",
-            "schema_org",
+            "inveniordm",
+            "jsonfeed",
             "openalex",
-            "csl",
-            "json_feed_item",
+            "schema_org",
         ]:
             return json.loads(string)
         else:
@@ -413,23 +429,67 @@ class MetadataList:
 
     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)
+        if to == "bibtex":
+            output = write_bibtex_list(self)
+            if self.file:
+                return write_output(self.file, output, [".bib"])
+            else:
+                return output
         elif to == "citation":
             return write_citation_list(self, **kwargs)
+        elif to == "commonmeta":
+            output = json.dumps(write_commonmeta_list(self))
+            if self.file:
+                return write_output(self.file, output, [".json", ".jsonl"])
+            else:
+                return output
+        elif to == "crossref_xml":
+            output = write_crossref_xml_list(self)
+            if self.file:
+                return write_output(self.file, output, [".xml"])
+            else:
+                return output
+        elif to == "csl":
+            output = json.dumps(write_csl_list(self))
+            if self.file:
+                return write_output(self.file, output, [".json"])
+            else:
+                return output
+        elif to == "datacite":
+            output = json.dumps(write_datacite_list(self))
+            if self.file:
+                return write_output(self.file, output, [".json"])
+            else:
+                return output
+        elif to == "inveniordm":
+            output = json.dumps(write_inveniordm_list(self))
+            if self.file:
+                return write_output(self.file, output, [".json"])
+            else:
+                return output
         elif to == "ris":
             return write_ris_list(self)
         elif to == "schema_org":
-            raise ValueError("Schema.org not supported for metadata lists")
+            output = json.dumps(write_schema_org_list(self))
+            if self.file:
+                return write_output(self.file, output, [".json"])
+            else:
+                return output
+        else:
+            raise ValueError("No valid output format found")
+
+    def push(self, to: str = "commonmeta", **kwargs) -> str:
+        """push metadata list to external APIs"""
+
+        if to == "crossref_xml":
+            response = push_crossref_xml_list(
+                self, login_id=self.login_id, login_passwd=self.login_passwd
+            )
+            return response
         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)
+            raise ValueError("Datacite not yet supported for metadata lists")
+        elif to == "inveniordm":
+            response = push_inveniordm_list(self, host=self.host, token=self.token)
+            return response
         else:
-            raise ValueError("No output format found")
+            raise ValueError("No valid output format found")

commonmeta/readers/codemeta_reader.py

@@ -75,7 +75,7 @@ def read_codemeta(data: Optional[dict], **kwargs) -> Commonmeta:
         descriptions = [
             {
                 "description": sanitize(str(meta.get("description"))),
-                "descriptionType": "Abstract",
+                "type": "Abstract",
             }
         ]
     else:

commonmeta/readers/crossref_reader.py

@@ -1,13 +1,14 @@
 """crossref reader for commonmeta-py"""
 
 from typing import Optional
+from xml.parsers.expat import ExpatError
 
 import requests
 from pydash import py_
 from requests.exceptions import ConnectionError, ReadTimeout
 
 from ..author_utils import get_authors
-from ..base_utils import compact, parse_attributes, presence, sanitize, wrap
+from ..base_utils import compact, parse_attributes, parse_xml, presence, sanitize, wrap
 from ..constants import (
     CR_TO_CM_CONTAINER_TRANSLATIONS,
     CR_TO_CM_TRANSLATIONS,
@@ -66,6 +67,7 @@ def read_crossref(data: Optional[dict], **kwargs) -> Commonmeta:
     doi = meta.get("DOI", None)
     _id = doi_as_url(doi)
     _type = CR_TO_CM_TRANSLATIONS.get(meta.get("type", None)) or "Other"
+    additional_type = meta.get("subtype", None)
 
     archive_locations = wrap(meta.get("archive", None))
 
@@ -120,13 +122,7 @@ def read_crossref(data: Optional[dict], **kwargs) -> Commonmeta:
         relations = py_.uniq(relations)
     references = py_.uniq([get_reference(i) for i in wrap(meta.get("reference", None))])
     funding_references = from_crossref_funding(wrap(meta.get("funder", None)))
-
-    description = meta.get("abstract", None)
-    if description is not None:
-        descriptions = [{"description": sanitize(description), "type": "Abstract"}]
-    else:
-        descriptions = None
-
+    descriptions = get_abstract(meta)
     subjects = py_.uniq(
         [
             {"subject": i}
@@ -146,7 +142,7 @@ def read_crossref(data: Optional[dict], **kwargs) -> Commonmeta:
         "id": _id,
         "type": _type,
         # recommended and optional properties
-        "additionalType": None,
+        "additionalType": additional_type,
         "archiveLocations": presence(archive_locations),
         "container": presence(container),
         "contributors": presence(contributors),
@@ -201,6 +197,23 @@ def get_titles(meta):
     )
 
 
+def get_abstract(meta: dict) -> Optional[str]:
+    """Get abstract from Crossref metadata."""
+    abstract = meta.get("abstract", None)
+    if abstract is None:
+        return None
+
+    try:
+        # Parse the abstract XML if it is JATS formatted
+        description_dct = parse_xml(abstract, xml_attribs=True)
+        description = py_.get(description_dct, "jats:p")
+        if description is None:
+            description = abstract
+        return [{"description": sanitize(description), "type": "Abstract"}]
+    except (TypeError, ExpatError):
+        return [{"description": sanitize(abstract), "type": "Abstract"}]
+
+
 def get_reference(reference: Optional[dict]) -> Optional[dict]:
     """Get reference from Crossref reference"""
     if reference is None or not isinstance(reference, dict):
@@ -341,7 +354,7 @@ def get_container(meta: dict, issn: str) -> dict:
     )
     isbn = isbn["value"] if isbn else None
     container_title = parse_attributes(meta.get("container-title", None), first=True)
-    if not container_title and container_type in ["Periodical"]:
+    if not container_title:
         container_title = py_.get(meta, "institution.0.name")
     volume = meta.get("volume", None)
     issue = py_.get(meta, "journal-issue.issue")

commonmeta/readers/crossref_xml_reader.py

@@ -332,7 +332,7 @@ def crossref_description(bibmeta):
         )
         return compact(
             {
-                "descriptionType": description_type,
+                "type": description_type,
                 "description": sanitize(
                     parse_attributes(element, content="p", first=True)
                 ),

commonmeta/readers/datacite_reader.py

@@ -267,13 +267,15 @@ def get_descriptions(descriptions: list) -> list:
 
     def map_description(description):
         """map_description"""
+        type = description.get("descriptionType", None)
+        if type is None:
+            type = "Abstract"
+        elif type not in ["Abstract", "Methods", "TechnicalInfo", "Other"]:
+            type = "Other"
         return compact(
             {
                 "description": description.get("description", None),
-                "type": description.get("descriptionType")
-                if description.get("descriptionType", None)
-                in ["Abstract", "Methods", "TechnicalInfo", "Other"]
-                else "Other",
+                "type": type,
                 "language": description.get("lang", None),
             }
         )

commonmeta/readers/{json_feed_reader.py → jsonfeed_reader.py}

@@ -21,7 +21,7 @@ from ..doi_utils import (
 from ..utils import (
     compact,
     dict_to_spdx,
-    from_json_feed,
+    from_jsonfeed,
     issn_as_url,
     name_to_fos,
     normalize_url,
@@ -31,19 +31,19 @@ from ..utils import (
 )
 
 
-def get_json_feed_item(pid: str, **kwargs) -> dict:
-    """get_json_feed_item"""
+def get_jsonfeed(pid: str, **kwargs) -> dict:
+    """get_jsonfeed"""
     if pid is None:
         return {"state": "not_found"}
     url = normalize_url(pid)
     response = requests.get(url, timeout=10, allow_redirects=True, **kwargs)
     if response.status_code != 200:
         return {"state": "not_found"}
-    return response.json() | {"via": "json_feed_item"}
+    return response.json() | {"via": "jsonfeed"}
 
 
-def read_json_feed_item(data: Optional[dict], **kwargs) -> Commonmeta:
-    """read_json_feed_item"""
+def read_jsonfeed(data: Optional[dict], **kwargs) -> Commonmeta:
+    """read_jsonfeed"""
     if data is None:
         return {"state": "not_found"}
     meta = data
@@ -64,7 +64,7 @@ def read_json_feed_item(data: Optional[dict], **kwargs) -> Commonmeta:
         _id = encode_doi(prefix)
 
     if meta.get("authors", None):
-        contributors = get_authors(from_json_feed(wrap(meta.get("authors"))))
+        contributors = get_authors(from_jsonfeed(wrap(meta.get("authors"))))
     else:
         contributors = None
 
@@ -176,7 +176,7 @@ def read_json_feed_item(data: Optional[dict], **kwargs) -> Commonmeta:
 
 
 def get_references(references: list) -> list:
-    """get json feed references."""
+    """get jsonfeed references."""
 
     def get_reference(reference: dict) -> Optional[dict]:
         if reference is None or not isinstance(reference, dict):
@@ -396,8 +396,8 @@ def get_files(pid: str) -> Optional[list]:
     ]
 
 
-def get_json_feed_item_uuid(id: str):
-    """get JSON Feed item by uuid"""
+def get_jsonfeed_uuid(id: str):
+    """get jsonfeed by uuid"""
     if id is None:
         return None
     url = f"https://api.rogue-scholar.org/posts/{id}"
@@ -424,8 +424,8 @@ def get_json_feed_item_uuid(id: str):
     )
 
 
-def get_json_feed_blog_slug(id: str):
-    """get JSON Feed item by id and return blog slug"""
+def get_jsonfeed_blog_slug(id: str):
+    """get jsonfeed by id and return blog slug"""
     if id is None:
         return None
     url = f"https://api.rogue-scholar.org/posts/{id}"