pyobo 0.12.14__py3-none-any.whl → 0.12.16__py3-none-any.whl

pyobo/api/xrefs.py

@@ -124,7 +124,11 @@ def get_semantic_mappings(
     )
     if converter is None:
         converter = get_converter()
-    return [row_to_semantic_mapping(row, converter=converter) for _, row in df.iterrows()]
+    return [
+        # TODO upstream this into sssom-pydantic?
+        row_to_semantic_mapping({k: v for k, v in row.items() if pd.notna(v)}, converter=converter)
+        for _, row in df.iterrows()
+    ]
 
 
 def get_mappings_df(

pyobo/cli/cli.py

@@ -10,6 +10,7 @@ import click
 
 from .database import main as database_main
 from .lookup import lookup
+from .obo_lexical_review import obo_lexical_review
 from ..constants import GLOBAL_SKIP, RAW_DIRECTORY
 from ..plugins import has_nomenclature_plugin
 
@@ -101,6 +102,7 @@ def _no_download() -> set[str]:
 
 main.add_command(lookup)
 main.add_command(database_main)
+main.add_command(obo_lexical_review)
 
 if __name__ == "__main__":
     main()

pyobo/cli/lookup.py

@@ -1,8 +1,12 @@
 """CLI for PyOBO lookups."""
 
+from __future__ import annotations
+
+import inspect
 import json
 import sys
-from collections.abc import Mapping
+from collections.abc import Iterable, Mapping
+from typing import TYPE_CHECKING
 
 import click
 from more_click import verbose_option
@@ -17,7 +21,10 @@ from .utils import (
     strict_option,
     version_option,
 )
-from ..constants import LookupKwargs
+from ..constants import GetOntologyKwargs, LookupKwargs
+
+if TYPE_CHECKING:
+    from curies import Reference
 
 __all__ = [
     "lookup",
@@ -31,9 +38,12 @@ def lookup():
 
 def lookup_annotate(f: Clickable) -> Clickable:
     """Add appropriate decorators to lookup CLI functions."""
+    signature = inspect.signature(f)
+    param = signature.parameters["kwargs"]
+    if param.kind is not inspect.Parameter.VAR_KEYWORD:
+        raise ValueError("programmer error")
     for decorator in [
         lookup.command(),
-        prefix_argument,
         verbose_option,
         force_option,
         force_process_option,
@@ -41,6 +51,15 @@ def lookup_annotate(f: Clickable) -> Clickable:
         version_option,
     ]:
         f = decorator(f)
+
+    if param.annotation is None:
+        pass
+    if param.annotation in {"Unpack[LookupKwargs]", Unpack[LookupKwargs]}:
+        f = prefix_argument(f)
+    elif param.annotation in {"Unpack[GetOntologyKwargs]", Unpack[GetOntologyKwargs]}:
+        pass
+    else:
+        raise ValueError(f"unknown parameter type for {f}: {param.annotation}")
     return f
 
 
@@ -249,33 +268,35 @@ def hierarchy(
 
 
 @lookup_annotate
-@click.argument("identifier")
-def ancestors(
-    identifier: str,
-    **kwargs: Unpack[LookupKwargs],
-) -> None:
+@click.argument("curie")
+def ancestors(curie: str, **kwargs: Unpack[GetOntologyKwargs]) -> None:
     """Look up ancestors."""
-    from ..api import get_ancestors, get_name
+    from ..api import get_ancestors
 
-    # note, prefix is passed via kwargs
-    ancestors = get_ancestors(identifier=identifier, **kwargs)
-    for ancestor in sorted(ancestors or []):
-        click.echo(f"{ancestor.curie}\t{get_name(ancestor, version=kwargs['version'])}")
+    ancestors = get_ancestors(curie, **kwargs)
+    _list_curies(ancestors, **kwargs)
 
 
 @lookup_annotate
-@click.argument("identifier")
-def descendants(
-    identifier: str,
-    **kwargs: Unpack[LookupKwargs],
-) -> None:
+@click.argument("curie")
+def descendants(curie: str, **kwargs: Unpack[GetOntologyKwargs]) -> None:
     """Look up descendants."""
-    from ..api import get_descendants, get_name
+    from ..api import get_descendants
+
+    descendants = get_descendants(curie, **kwargs)
+    _list_curies(descendants, **kwargs)
+
+
+def _list_curies(
+    references: Iterable[Reference] | None, **kwargs: Unpack[GetOntologyKwargs]
+) -> None:
+    if not references:
+        return
+
+    from ..api import get_name
 
-    # note, prefix is passed via kwargs
-    descendants = get_descendants(identifier=identifier, **kwargs)
-    for descendant in sorted(descendants or []):
-        click.echo(f"{descendant.curie}\t{get_name(descendant, version=kwargs['version'])}")
+    for reference in sorted(references or []):
+        click.echo(f"{reference.curie}\t{get_name(reference, version=kwargs['version'])}")
 
 
 @lookup_annotate

pyobo/cli/obo_lexical_review.py

@@ -0,0 +1,207 @@
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "click>=8.3.1",
+#     "obographs>=0.0.8",
+#     "pyperclip>=1.11.0",
+#     "robot-obo-tool>=0.0.1",
+#     "ssslm[gilda-slim]>=0.1.3",
+#     "tabulate>=0.9.0",
+#     "tqdm>=4.67.3",
+# ]
+# ///
+
+"""Implement lexical review for an ontology."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import click
+
+if TYPE_CHECKING:
+    import obographs
+    import ssslm
+
+INDEX_URL = "https://github.com/biopragmatics/biolexica/raw/main/lexica/obo/obo.ssslm.tsv.gz"
+UPPER = {"ncit"}
+
+
+@click.command()
+@click.argument("prefix")
+@click.option(
+    "--location",
+    help="Local path or URL to an OBO Graph JSON file or OWL file. If not given, will try and look up through the OBO PURL system",
+)
+@click.option(
+    "--uri-prefix",
+    help="Local path to an OBO Graph JSON file. If not given, will try and look up through the OBO PURL system",
+)
+@click.option("--index-url", default=INDEX_URL, show_default=True)
+@click.option("--show-passed", is_flag=True)
+@click.option("--skip-upper", is_flag=True, help=f"if true, skip upper level ontologies {UPPER}")
+@click.option("--index-force", is_flag=True, help="if true, force re-downloading the lexical index")
+def obo_lexical_review(
+    prefix: str,
+    location: str | None,
+    uri_prefix: str | None,
+    index_url: str,
+    show_passed: bool,
+    skip_upper: bool,
+    index_force: bool,
+) -> None:
+    """Make a lexical review of an ontology."""
+    import sys
+    import time
+
+    import pyperclip
+    import pystow
+    import ssslm
+    from tabulate import tabulate
+
+    module = pystow.module("pyobo", "obo-lexical-review")
+
+    args = " ".join(sys.argv[1:])
+    output = f"Analysis of {prefix} run on {time.asctime()} with the following command:\n\n```console\n$ uvx pyobo obo-lexical-review {args}\n```\n\n"
+
+    graph_document, uri_prefix = _get_graph_document(
+        prefix=prefix,
+        uri_prefix=uri_prefix,
+        ontology_path=location,
+    )
+
+    click.echo(f"Loading lexical index from {index_url} using SSSLM")
+    path = module.ensure(url=index_url, force=index_force)
+    grounder = ssslm.make_grounder(path)
+    click.echo("Done loading lexical index")
+
+    passed, failed = _get_calls(
+        graph_document=graph_document,
+        matcher=grounder,
+        uri_prefix=uri_prefix,
+        skip_upper=skip_upper,
+    )
+
+    total = len(passed) + len(failed)
+
+    if passed and show_passed:
+        passed_table = tabulate(passed, headers=["LUID", "Name"], tablefmt="github")
+        passed_msg = f"## Passed Nodes ({len(passed):,}/{total:,}; {len(passed) / total:.1%})\n\n{passed_table}\n\n"
+        output += passed_msg
+
+    if failed:
+        rows = []
+        for luid, name, matches in failed:
+            rows.append((luid, name, *_parts(matches[0])))
+            for match in matches[1:]:
+                rows.append(("", "", *_parts(match)))
+        failed_table = tabulate(
+            rows, headers=[prefix, "name", "obo-curie", "obo-name", "obo-score"], tablefmt="github"
+        )
+        failed_message = f"## Failed Nodes ({len(failed):,}/{total:,}; {len(failed) / total:.1%})\n\n{failed_table}\n\n"
+        output += failed_message
+
+    click.echo(output)
+    click.echo("Finished! automatically copied to the clipboard, e.g., for pasting into GitHub)")
+    pyperclip.copy(output)
+
+
+def _parts(match: ssslm.Match) -> tuple[str, str, float]:
+    return (
+        f"[`{match.curie}`](https://semantic.farm/{match.curie})",
+        match.name or "",
+        round(match.score, 3),
+    )
+
+
+def _get_graph_document(
+    prefix: str, uri_prefix: str | None = None, ontology_path: str | None = None
+) -> tuple[obographs.GraphDocument, str]:
+    from pathlib import Path
+
+    import obographs
+    import robot_obo_tool
+
+    if uri_prefix is None:
+        uri_prefix = f"http://purl.obolibrary.org/obo/{prefix}_"
+        click.echo(f"Inferred URI prefix from given OBO CURIE prefix: {uri_prefix}")
+    if ontology_path is None:
+        ontology_path = f"https://purl.obolibrary.org/obo/{prefix.lower()}.json"
+        click.echo(f"No ontology path given, guessing it's available at {ontology_path}")
+    if ontology_path.endswith(".json"):
+        click.echo(f"reading OBO Graph JSON from {ontology_path}")
+        graph_documents = obographs.read(ontology_path, squeeze=False, timeout=60)
+    else:
+        import tempfile
+
+        with tempfile.TemporaryDirectory() as tmpdir:
+            tmppath = Path(tmpdir).joinpath("temp.json")
+            click.echo(
+                "given ontology path does not end with JSON. implicitly converting to OBO Graph JSON using ROBOT"
+            )
+            robot_obo_tool.convert(
+                input_path=ontology_path,
+                output_path=tmppath,
+                check=False,
+                merge=False,
+                reason=False,
+            )
+            click.echo("reading converted OBO Graph JSON")
+            graph_documents = obographs.read(tmppath, squeeze=False)
+
+    return graph_documents, uri_prefix
+
+
+def _get_calls(
+    *,
+    graph_document: obographs.GraphDocument,
+    matcher: ssslm.Matcher,
+    uri_prefix: str,
+    skip_upper: bool = False,
+) -> tuple[list[tuple[str, str]], list[tuple[str, str, list[ssslm.Match]]]]:
+    """Get matches."""
+    from tqdm import tqdm
+
+    passed = []
+    failed = []
+    total = 0
+    skipped = 0
+    for graph in tqdm(graph_document.graphs, unit="graph"):
+        for node in tqdm(sorted(graph.nodes, key=lambda n: n.id), unit="node", leave=False):
+            if node.id is None:
+                continue
+
+            total += 1
+            if not node.id.startswith(uri_prefix):
+                skipped += 1
+                continue
+
+            if not node.lbl:
+                continue
+
+            local_unique_identifier = node.id[len(uri_prefix) :]
+
+            matches: list[ssslm.Match] = []
+            matches.extend(matcher.get_matches(node.lbl))
+            if node.meta is not None and node.meta.synonyms is not None:
+                matches.extend(
+                    match
+                    for synonym in node.meta.synonyms
+                    for match in matcher.get_matches(synonym.val)
+                )
+
+            # there are a lot of NCIT matches, which aren't that informative
+            # since OBO doesn't mind duplicating these terms
+            if skip_upper:
+                matches = [m for m in matches if m.prefix not in UPPER]
+
+            if not matches:
+                passed.append((local_unique_identifier, node.lbl))
+            else:
+                failed.append((local_unique_identifier, node.lbl, matches))
+
+    return passed, failed
+
+
+if __name__ == "__main__":
+    obo_lexical_review()

pyobo/getters.py

@@ -17,7 +17,6 @@ from pathlib import Path
 from textwrap import indent
 from typing import Any, TypeVar
 
-import bioontologies.robot
 import bioregistry
 import click
 import pystow.utils
@@ -80,10 +79,10 @@ REQUIRES_NO_ROBOT_CHECK = {
 
 
 def _convert_to_obo(path: Path) -> Path:
-    import bioontologies.robot
+    import robot_obo_tool
 
     _converted_obo_path = path.with_suffix(".obo")
-    bioontologies.robot.convert(path, _converted_obo_path, check=False)
+    robot_obo_tool.convert(path, _converted_obo_path, check=False)
     return _converted_obo_path
 
 
@@ -338,6 +337,8 @@ def iter_helper_helper(
 
     :yields: A prefix and the result of the callable ``f``
     """
+    from robot_obo_tool import ROBOTError
+
     strict = kwargs.get("strict", True)
     prefixes = list(
         _prefixes(
@@ -382,7 +383,7 @@ def iter_helper_helper(
             if "DrugBank" not in str(e):
                 raise
             logger.warning("[drugbank] invalid credentials")
-        except (subprocess.CalledProcessError, bioontologies.robot.ROBOTError):
+        except (subprocess.CalledProcessError, ROBOTError):
             logger.warning("[%s] ROBOT was unable to convert OWL to OBO", prefix)
         except ValueError as e:
             if _is_xml(e):

pyobo/sources/ror.py

@@ -2,18 +2,14 @@
 
 from __future__ import annotations
 
-import datetime
-import json
 import logging
-import zipfile
 from collections.abc import Iterable
-from functools import lru_cache
-from pathlib import Path
-from typing import Any, Literal, NamedTuple, TypeAlias
+from typing import Any
 
 import bioregistry
-import zenodo_client
-from pydantic import BaseModel, ValidationError
+import ror_downloader
+from pydantic import ValidationError
+from ror_downloader import OrganizationType
 from tqdm.auto import tqdm
 
 from pyobo.struct import Obo, Reference, Term
@@ -29,16 +25,12 @@ from pyobo.struct.typedef import (
 )
 
 __all__ = [
-    "OrganizationType",
-    "RORStatus",
-    "get_ror_records",
-    "get_ror_status",
+    "RORGetter",
     "get_ror_to_country_geonames",
 ]
 
 logger = logging.getLogger(__name__)
 PREFIX = "ror"
-ROR_ZENODO_RECORD_ID = "17953395"
 
 # Constants
 ORG_CLASS = Reference(prefix="OBI", identifier="0000245", name="organization")
@@ -70,7 +62,7 @@ class RORGetter(Obo):
     root_terms = [CITY_CLASS, ORG_CLASS]
 
     def __post_init__(self):
-        self.data_version, _url, _path = get_ror_status()
+        self.data_version = ror_downloader.get_version_info(download=False).version
         super().__post_init__()
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
@@ -83,18 +75,6 @@ class RORGetter(Obo):
         yield from iterate_ror_terms(force=force)
 
 
-OrganizationType: TypeAlias = Literal[
-    "education",
-    "facility",
-    "funder",
-    "company",
-    "government",
-    "healthcare",
-    "archive",
-    "nonprofit",
-    "other",
-]
-
 ROR_ORGANIZATION_TYPE_TO_OBI: dict[OrganizationType, Term] = {
     "education": Term.default(PREFIX, "education", "educational organization"),
     "facility": Term.default(PREFIX, "facility", "facility"),
@@ -115,127 +95,9 @@ for _k, v in ROR_ORGANIZATION_TYPE_TO_OBI.items():
 _MISSED_ORG_TYPES: set[str] = set()
 
 
-class LocationDetails(BaseModel):
-    """The location details slot in the ROR schema."""
-
-    continent_code: str
-    continent_name: str
-    country_code: str
-    country_name: str
-    country_subdivision_code: str | None = None
-    country_subdivision_name: str | None = None
-    lat: float
-    lng: float
-    name: str
-
-
-class Location(BaseModel):
-    """The lcoation slot in the ROR schema."""
-
-    geonames_id: int
-    geonames_details: LocationDetails
-
-
-class ExternalID(BaseModel):
-    """The external ID slot in the ROR schema."""
-
-    type: str
-    all: list[str]
-    preferred: str | None = None
-
-
-class Link(BaseModel):
-    """The link slot in the ROR schema."""
-
-    type: str
-    value: str
-
-
-class Name(BaseModel):
-    """The name slot in the ROR schema."""
-
-    value: str
-    types: list[str]
-    lang: str | None = None
-
-
-class Relationship(BaseModel):
-    """The relationship slot in the ROR schema."""
-
-    type: str
-    label: str
-    id: str
-
-
-class DateAnnotated(BaseModel):
-    """The annotated date slot in the ROR schema."""
-
-    date: datetime.date
-    schema_version: str
-
-
-class Admin(BaseModel):
-    """The admin slot in the ROR schema."""
-
-    created: DateAnnotated
-    last_modified: DateAnnotated
-
-
-Status: TypeAlias = Literal["active", "inactive", "withdrawn"]
-
-
-class Record(BaseModel):
-    """A ROR record."""
-
-    locations: list[Location]
-    established: int | None = None
-    external_ids: list[ExternalID]
-    id: str
-    domains: list[str]
-    links: list[Link]
-    names: list[Name]
-    relationships: list[Relationship]
-    status: Status
-    types: list[OrganizationType]
-    admin: Admin
-
-    def get_preferred_label(self) -> str | None:
-        """Get the preferred label."""
-        primary_name: str | None = None
-        for name in self.names:
-            if "ror_display" in name.types:
-                primary_name = name.value
-        if primary_name is None:
-            return None
-        primary_name = NAME_REMAPPING.get(primary_name, primary_name)
-        return primary_name
-
-
-_description_prefix = {
-    "education": "an educational organization",
-    "facility": "a facility",
-    "funder": "a funder",
-    "company": "a company",
-    "government": "a governmental organization",
-    "healthcare": "a healthcare organization",
-    "archive": "an archive",
-    "nonprofit": "a nonprofit organization",
-    "other": "an organization",
-}
-
-
-def _get_description(record: Record) -> str | None:
-    description = (
-        f"{_description_prefix[record.types[0]]} in {record.locations[0].geonames_details.name}"
-    )
-    if record.established:
-        description += f" established in {record.established}"
-    return description
-
-
 def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
     """Iterate over terms in ROR."""
-    status, records = get_ror_records(force=force)
+    status, records = ror_downloader.get_organizations(force=force)
     unhandled_xref_prefixes: set[str] = set()
 
     seen_geonames_references = set()
@@ -249,7 +111,7 @@ def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
         term = Term(
             reference=Reference(prefix=PREFIX, identifier=identifier, name=primary_name),
             type="Instance",
-            definition=_get_description(record),
+            definition=record.get_description(),
         )
         for organization_type in record.types:
             if organization_type in ROR_ORGANIZATION_TYPE_TO_OBI:
@@ -339,63 +201,6 @@ def iterate_ror_terms(*, force: bool = False) -> Iterable[Term]:
         yield geonames_term
 
 
-class RORStatus(NamedTuple):
-    """A version information tuple."""
-
-    version: str
-    url: str
-    path: Path
-
-
-def get_ror_status(*, force: bool = False, authenticate_zenodo: bool = True) -> RORStatus:
-    """Ensure the latest ROR record, metadata, and filepath.
-
-    :param force: Should the record be downloaded again? This almost
-        never needs to be true, since the data doesn't change for
-        a given version
-    :param authenticate_zenodo: Should Zenodo be authenticated?
-        This isn't required, but can help avoid rate limits
-    :return: A version information tuple
-
-    .. note::
-
-        this goes into the ``~/.data/zenodo/6347574`` folder,
-        because 6347574 is the super-record ID, which groups all
-        versions together. this is different from the value
-        for :data:`ROR_ZENODO_RECORD_ID`
-    """
-    client = zenodo_client.Zenodo()
-    latest_record_id = client.get_latest_record(
-        ROR_ZENODO_RECORD_ID, authenticate=authenticate_zenodo
-    )
-    response = client.get_record(latest_record_id, authenticate=authenticate_zenodo)
-    response_json = response.json()
-    version = response_json["metadata"]["version"].lstrip("v")
-    file_record = response_json["files"][0]
-    name = file_record["key"]
-    url = file_record["links"]["self"]
-    path = client.download(latest_record_id, name=name, force=force)
-    return RORStatus(version=version, url=url, path=path)
-
-
-@lru_cache
-def get_ror_records(
-    *, force: bool = False, authenticate_zenodo: bool = True
-) -> tuple[RORStatus, list[Record]]:
-    """Get the latest ROR metadata and records."""
-    status = get_ror_status(force=force, authenticate_zenodo=authenticate_zenodo)
-    with zipfile.ZipFile(status.path) as zf:
-        for zip_info in zf.filelist:
-            if zip_info.filename.endswith(".json"):
-                with zf.open(zip_info) as file:
-                    records = [
-                        Record.model_validate(record)
-                        for record in tqdm(json.load(file), unit_scale=True)
-                    ]
-                    return status, records
-    raise FileNotFoundError
-
-
 def get_ror_to_country_geonames(**kwargs: Any) -> dict[str, str]:
     """Get a mapping of ROR ids to GeoNames IDs for countries."""
     from pyobo.sources.geonames.geonames import get_city_to_country

pyobo/struct/functional/ontology.py

@@ -250,7 +250,7 @@ class Import(Box):
 
 def get_rdf_graph_oracle(boxes: list[Box], *, prefix_map: dict[str, str]) -> Graph:
     """Serialize to turtle via OFN and conversion with ROBOT."""
-    import bioontologies.robot
+    import robot_obo_tool
 
     ontology = Ontology(
         iri=EXAMPLE_ONTOLOGY_IRI,
@@ -265,7 +265,7 @@ def get_rdf_graph_oracle(boxes: list[Box], *, prefix_map: dict[str, str]) -> Gra
         ofn_path.write_text(text)
         ttl_path = stub.with_suffix(".ttl")
         try:
-            bioontologies.robot.convert(ofn_path, ttl_path)
+            robot_obo_tool.convert(ofn_path, ttl_path)
         except subprocess.CalledProcessError:
             raise RuntimeError(f"failed to convert axioms from:\n\n{text}") from None
         graph.parse(ttl_path)

pyobo/struct/obograph/export.py

@@ -33,7 +33,7 @@ def to_parsed_obograph_oracle(
     obo: Obo, *, converter: Converter | None = None
 ) -> og.StandardizedGraphDocument:
     """Serialize to OBO, convert to OBO Graph JSON with ROBOT, load, then parse."""
-    import bioontologies.robot
+    import robot_obo_tool
 
     if converter is None:
         converter = get_converter()
@@ -43,7 +43,7 @@ def to_parsed_obograph_oracle(
         obo_path = stub.with_suffix(".obo")
         obograph_path = stub.with_suffix(".json")
         obo.write_obo(obo_path)
-        bioontologies.robot.convert(input_path=obo_path, output_path=obograph_path)
+        robot_obo_tool.convert(input_path=obo_path, output_path=obograph_path)
         raw = og.read(obograph_path, squeeze=False)
     rv = raw.standardize(converter)
     for graph in rv.graphs:

pyobo/struct/struct.py

@@ -1067,12 +1067,12 @@ class Obo:
 
     def write_owl(self, path: str | Path) -> None:
         """Write OWL, by first outputting OFN then converting with ROBOT."""
-        from bioontologies import robot
+        import robot_obo_tool
 
         with tempfile.TemporaryDirectory() as directory:
             ofn_path = Path(directory).joinpath("tmp.ofn")
             self.write_ofn(ofn_path)
-            robot.convert(ofn_path, path)
+            robot_obo_tool.convert(ofn_path, path)
 
     def write_rdf(self, path: str | Path) -> None:
         """Write as Turtle RDF."""
@@ -1312,19 +1312,19 @@ class Obo:
                 tqdm.write(f"[{self._prefix_version}] writing OBO Graph to {self._obograph_path}")
                 self.write_obograph(self._obograph_path)
             else:
-                import bioontologies.robot
+                import robot_obo_tool
 
                 tqdm.write(
                     f"[{self.ontology}] converting OFN to OBO Graph at {self._obograph_path}"
                 )
-                bioontologies.robot.convert(
+                robot_obo_tool.convert(
                     self._ofn_path, self._obograph_path, debug=True, merge=False, reason=False
                 )
         if write_owl and (not self._owl_path.is_file() or force):
             tqdm.write(f"[{self._prefix_version}] writing OWL to {self._owl_path}")
-            import bioontologies.robot
+            import robot_obo_tool
 
-            bioontologies.robot.convert(
+            robot_obo_tool.convert(
                 self._ofn_path, self._owl_path, debug=True, merge=False, reason=False
             )
         if write_ttl and (not self._ttl_path.is_file() or force):

pyobo/utils/path.py

@@ -107,7 +107,6 @@ def ensure_json(
     version: VersionHint = None,
     name: str | None = None,
     force: bool = False,
-    dtype=str,
     verify: bool = True,
     backend: Literal["requests", "urllib"] | None = None,
     **kwargs: Any,

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.14"
+VERSION = "0.12.16"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.14.dist-info → pyobo-0.12.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.14
+Version: 0.12.16
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt
@@ -36,11 +36,10 @@ Requires-Dist: humanize
 Requires-Dist: tabulate
 Requires-Dist: cachier
 Requires-Dist: pystow>=0.7.5
-Requires-Dist: bioversions>=0.8.101
+Requires-Dist: bioversions>=0.8.243
 Requires-Dist: bioregistry>=0.12.30
-Requires-Dist: bioontologies>=0.7.2
 Requires-Dist: ssslm>=0.0.13
-Requires-Dist: zenodo-client>=0.4.0
+Requires-Dist: zenodo-client>=0.4.1
 Requires-Dist: class-resolver>=0.6.0
 Requires-Dist: pydantic>=2.0
 Requires-Dist: curies>=0.10.17
@@ -52,10 +51,14 @@ Requires-Dist: chembl-downloader
 Requires-Dist: umls-downloader>=0.1.3
 Requires-Dist: clinicaltrials-downloader>=0.0.2
 Requires-Dist: nih-reporter-downloader>=0.0.1
+Requires-Dist: ror-downloader>=0.0.4
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
-Requires-Dist: sssom-pydantic>=0.1.1
+Requires-Dist: sssom-pydantic>=0.2.0
+Requires-Dist: pytz
+Requires-Dist: robot-obo-tool
+Requires-Dist: pyperclip
 Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
@@ -72,10 +75,10 @@ Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
 Project-URL: Bug Tracker, https://github.com/biopragmatics/pyobo/issues
-Project-URL: Documentation, https://pyobo.readthedocs.io
-Project-URL: Funding, https://github.com/sponsors/cthoyt
 Project-URL: Homepage, https://github.com/biopragmatics/pyobo
 Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
+Project-URL: Documentation, https://pyobo.readthedocs.io
+Project-URL: Funding, https://github.com/sponsors/cthoyt
 Provides-Extra: drugcentral
 Provides-Extra: gilda
 Provides-Extra: gilda-slim

{pyobo-0.12.14.dist-info → pyobo-0.12.16.dist-info}/RECORD

@@ -14,15 +14,16 @@ pyobo/api/relations.py,sha256=Kebguj5khScU2c0Pm8dJrewu8je9DnKlNenRtmYWGKI,5875
 pyobo/api/species.py,sha256=YxzJeClfuKI-pjYLpu5797jdDeyTkXpjQDgdmc9MKwo,2376
 pyobo/api/typedefs.py,sha256=HTui0kl_VELxgji0vfBr-NBG3zrrpCU8tmuQOSWK6fw,1262
 pyobo/api/utils.py,sha256=SCMsy4QyYVhn-QK0h90Ef1XUMbyHKR1fvteRESzs-bk,5192
-pyobo/api/xrefs.py,sha256=szsPOMwkKmfDRb7CNgyEoe7hRQK8aX1Vm6Vcz0FYN2w,5956
+pyobo/api/xrefs.py,sha256=xrs-c56GThSzIE5Rj0dmrbztxNTr22Y7NykQHeIBPk4,6070
 pyobo/cli/__init__.py,sha256=pTiLuzjjpi0P69yVjQ2kE6nBUmZuYFnqdJNDZLDkgvk,71
-pyobo/cli/cli.py,sha256=lyN_Hi5Hf2jyCUXjD87pG7RU3g7TnbBiOd8o-PMqIEw,2904
+pyobo/cli/cli.py,sha256=nEU70l12ChHKSYWwWNzwgo-0ldOEa0FCkvH7745u5qA,2992
 pyobo/cli/database.py,sha256=iq4-eJ_8Kgim0MMnSqf1wu2hvHDZk9BWNMVuwykz2Ko,13407
 pyobo/cli/database_utils.py,sha256=jQ7qSg-oZk-Q-RC121NkUbqXeNg0K8fV96igXaK3ra4,5540
-pyobo/cli/lookup.py,sha256=-Tz6E3OP6HBPipVqSrMn7LyzrezbT0pngeDExF5uyn4,9467
+pyobo/cli/lookup.py,sha256=1VexVdPXM2_tTL2eFyDnepcH-_fsdEDxaQId-LblAXI,10089
+pyobo/cli/obo_lexical_review.py,sha256=x6AJdNPH4WLC419KNV9_dHInVfas97MWMzQhSJRqrho,6709
 pyobo/cli/utils.py,sha256=SfW9JC8olzp4AcAsDodMPdgHfteeXq0Ngd8yQ2kzOMA,1812
 pyobo/constants.py,sha256=_Y4IACPsRu5jHntoc8nEHKLGDl1Bl7YrdS0gG4qxmqw,7582
-pyobo/getters.py,sha256=exZNjlseRoWhshQYArWwN2KLvkk4NmCQnHM88YUYf-w,18340
+pyobo/getters.py,sha256=nZjynOIXzkeytqgu1UE-WleoStQtdQ3fJeWt8_r_Qxc,18326
 pyobo/gilda_utils.py,sha256=uThAArALSNzJi-hrR9lUvtQci5VIw4Cqq2L6mtkp0Ko,1990
 pyobo/identifier_utils/__init__.py,sha256=iSHAZhOwqWZmYpOfpXNLuKouSYj7ZSViaX7BF5uT8so,793
 pyobo/identifier_utils/api.py,sha256=fik5crIOOhsHIuH-ia_oOQeKZeX5bBMj5S6occWaMeY,9365
@@ -146,7 +147,7 @@ pyobo/sources/pubchem.py,sha256=lTsc0dgrSJ5kxlcaUcUXJydi-xsMf2fI2EcWsbW8xTU,5153
 pyobo/sources/reactome.py,sha256=yzeCCy19Hxr7KFUrg1tePjN40eZLN9G4dm4q0A7izbI,5842
 pyobo/sources/rgd.py,sha256=I6HC7_GZqFPXlRIuuroOgZM7wG85jcE3Po-sry8a1XU,5194
 pyobo/sources/rhea.py,sha256=dbhyVJ1yoAQoxoWp47OKegLAmMh6qoe-7_DafJDeWrk,8164
-pyobo/sources/ror.py,sha256=pFKV5qzTSU2XxvZhMOB-WyMLQ6u2dsAqadACswCqyNk,13387
+pyobo/sources/ror.py,sha256=osvjhinGU2XJulbne2i2zaZuD_ZuDK4mwkxL3wERNQc,8226
 pyobo/sources/selventa/__init__.py,sha256=cIIDlWL9znL2r0aZIJ2r1FN3NM9io74w-He2egzJwX8,254
 pyobo/sources/selventa/schem.py,sha256=vqN_a_NLeshj-2dRuZelfOLJQ5dyU3ZghfSRIq9EFVA,1162
 pyobo/sources/selventa/scomp.py,sha256=nshskLQeXuzf5t79STJsVKJg3R80CX3DuJBUrEhwSbc,1531
@@ -181,17 +182,17 @@ pyobo/struct/functional/__init__.py,sha256=1Tbtt_6GoarRlgffPepitJ3QtLsrMPMbhDGoQ
 pyobo/struct/functional/dsl.py,sha256=odDX33lzSkKcRjcrsteraFSc00wIOPBHJtxXe9c9RHE,101591
 pyobo/struct/functional/macros.py,sha256=yYHGmAEMpin47U7U3S7aCC3o02khWyoON4Xgpv-gHN4,13811
 pyobo/struct/functional/obo_to_functional.py,sha256=65OmttFto-tm6-7T0RQlgIKo34swVqTpz2B9ykPLNuw,13727
-pyobo/struct/functional/ontology.py,sha256=-a8jx-61NsI3dgCBEYNP-VeswAy8wWxLBlAEFMJucyI,9342
+pyobo/struct/functional/ontology.py,sha256=1CjtKUtpjCv8MivMfENA2t0LmWx9ZDPlt1nc-0SLrZI,9332
 pyobo/struct/functional/utils.py,sha256=c-XG2SJ7ChYtz7KU3K0F-T6ocMjYevei0WxlkfkkmtE,3487
 pyobo/struct/obo/__init__.py,sha256=xJAFJ4yueWBQv3BrtTuHHJ7AzOqCgOuHgKY4RQocsW0,157
 pyobo/struct/obo/reader.py,sha256=HJ4u1c2ScA-2qxKhyKIZZo8RI2QOUSXwushK9FZGdrQ,50664
 pyobo/struct/obo/reader_utils.py,sha256=UyQVTQhXbhZ9fCizZg26o5TmeHis9-qZMKvQFwIBRgo,4423
 pyobo/struct/obograph/__init__.py,sha256=B4rNP9OCTnMXm8YpQ0rar1swn4GIw9b4gQD-IVuqHyw,452
-pyobo/struct/obograph/export.py,sha256=yk3MHulDM_SMohfwiFdeB62-XGJ2ZNgRUZGjGjiyonY,9945
+pyobo/struct/obograph/export.py,sha256=Z2IAYK9fRvD5QtR24oxuTFN8oPFS-eKqlvv4i9-CmXk,9935
 pyobo/struct/obograph/reader.py,sha256=264yVeD8a3jGx9EaGUZVxFbSQ_pwQ_6ckVw9S8wiJfM,8525
 pyobo/struct/obograph/utils.py,sha256=je0kSkC24MU9pWRHq1_K-J5jWhjWESY6NI3TpZqvZ_Q,1516
 pyobo/struct/reference.py,sha256=qgwTa-0VIoDklQ7LjlYH-mf2WG0_uO7KlHt0PSBail4,11744
-pyobo/struct/struct.py,sha256=FaNyYUSFgM700xE74i8zSVQQiR4g91jbmAMOqPyJ9NQ,96669
+pyobo/struct/struct.py,sha256=cxVTrRRlV8KnLaVQBK-3dLVDfpuryBKLuA59lMN2XBk,96648
 pyobo/struct/struct_utils.py,sha256=VFC82fgphTs7sBSNGn53sv2WMl7Ho9srALFq92bRFQQ,41021
 pyobo/struct/typedef.py,sha256=jvETRmNc4g09X7waSjcvEkw7g0kNteLaDOt3mjKbmDc,14871
 pyobo/struct/utils.py,sha256=zkpOE42JQIfkN0rc5qNENK03VIKmkf_57tHojMJK71Y,906
@@ -202,10 +203,10 @@ pyobo/utils/io.py,sha256=QTvGjNDkaIf78Tca23B5RW_aVweKiSsxmgwSKXcMSNo,3921
 pyobo/utils/iter.py,sha256=rYRbbaFJHxMaE0yU-rQZoCagYIrtev09uY0mxFkf5zY,1524
 pyobo/utils/misc.py,sha256=DVLxPynunSubp2xSVKFF_E57BPS3p5wU4Z4A38PI17M,8717
 pyobo/utils/ndex_utils.py,sha256=EokCWS00Wrk_4y8ldeQuUyaaC6yNzBg3DagUl-J2czY,2326
-pyobo/utils/path.py,sha256=snV58UHxHO6GI2QPPE46ssR4RWozaw83V59sS_I9BY8,4109
-pyobo/version.py,sha256=-RjPuUzkByyIQ26Vfaw4q_Cb--M-vMCnMRNP78aBv58,927
-pyobo-0.12.14.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.12.14.dist-info/WHEEL,sha256=eycQt0QpYmJMLKpE3X9iDk8R04v2ZF0x82ogq-zP6bQ,79
-pyobo-0.12.14.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
-pyobo-0.12.14.dist-info/METADATA,sha256=3bCbmYuRjLGPhWqwRm337UrFL0Nb7iU1--Ici26iZnc,22783
-pyobo-0.12.14.dist-info/RECORD,,
+pyobo/utils/path.py,sha256=oHfYbsfI4UaQ8_rAHqoOTCcCceXhY82_0kLUuxs5BY0,4094
+pyobo/version.py,sha256=nW8tGi5FCn_intTOMB6X02kfn9x4iYN7s9z5HXWvmko,927
+pyobo-0.12.16.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.12.16.dist-info/WHEEL,sha256=fAguSjoiATBe7TNBkJwOjyL1Tt4wwiaQGtNtjRPNMQA,80
+pyobo-0.12.16.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
+pyobo-0.12.16.dist-info/METADATA,sha256=y5tMlvDbm9jqjJTseIveUFKs-Sb2uBhXIVs75RFKDvg,22859
+pyobo-0.12.16.dist-info/RECORD,,

{pyobo-0.12.14.dist-info → pyobo-0.12.16.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.9.24
+Generator: uv 0.9.28
 Root-Is-Purelib: true
-Tag: py3-none-any
+Tag: py3-none-any