pyobo 0.12.5__py3-none-any.whl → 0.12.6__py3-none-any.whl

pyobo/cli/database.py

@@ -6,6 +6,7 @@ from collections.abc import Iterable
 from pathlib import Path
 
 import bioregistry
+import bioversions
 import click
 from more_click import verbose_option
 from tqdm.contrib.logging import logging_redirect_tqdm
@@ -97,12 +98,17 @@ def _update_database_kwargs(kwargs: DatabaseKwargs) -> DatabaseKwargs:
 
 
 @database_annotate
+@click.option("--eager-versions", is_flag=True)
 @click.pass_context
-def build(ctx: click.Context, **kwargs: Unpack[DatabaseKwargs]) -> None:
+def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Build all databases."""
     # if no_strict and zenodo:
     #    click.secho("Must be strict before uploading", fg="red")
     #    sys.exit(1)
+
+    if eager_versions:
+        bioversions.get_rows(use_tqdm=True)
+
     with logging_redirect_tqdm():
         click.secho("Collecting metadata and building", fg="cyan", bold=True)
         # note that this is the only one that needs a force=force

pyobo/identifier_utils/api.py

@@ -287,7 +287,9 @@ def wrap_norm_prefix(f):
                 raise ValueError(f"Invalid prefix: {prefix.prefix}")
             prefix = ReferenceTuple(norm_prefix, prefix.identifier)
         else:
-            raise TypeError
+            raise TypeError(
+                f"prefix should be given as a string or reference object. Got {type(prefix)} {prefix}"
+            )
         return f(prefix, *args, **kwargs)
 
     return _wrapped

pyobo/sources/drugcentral.py

@@ -6,7 +6,6 @@ from collections.abc import Iterable
 from contextlib import closing
 
 import bioregistry
-import psycopg2
 from pydantic import ValidationError
 from tqdm.auto import tqdm
 
@@ -42,6 +41,8 @@ class DrugCentralGetter(Obo):
 
 def iter_terms() -> Iterable[Term]:
     """Iterate over DrugCentral terms."""
+    import psycopg2
+
     with closing(psycopg2.connect(**PARAMS)) as conn:
         with closing(conn.cursor()) as cur:
             cur.execute(

pyobo/sources/spdx.py

@@ -55,11 +55,15 @@ def _get_term(record: dict[str, Any]) -> Term | None:
     except ValidationError:
         tqdm.write(f"invalid: {record['licenseId']}")
         return None
-    term = Term(
-        reference=reference,
-        is_obsolete=True if record.get("isDeprecatedLicenseId") else None,
-        # type="Instance",
-    ).append_parent(ROOT)
+    term = (
+        Term(
+            reference=reference,
+            is_obsolete=True if record.get("isDeprecatedLicenseId") else None,
+            # type="Instance",
+        )
+        .append_parent(ROOT)
+        .append_synonym(record["licenseId"])
+    )
     if record.get("isOsiApproved"):
         term.annotate_boolean(IS_OSI, True)
     if record.get("isFsfLibre"):
@@ -82,4 +86,4 @@ class SPDXLicenseGetter(Obo):
 
 
 if __name__ == "__main__":
-    SPDXLicenseGetter.cli(["--obo", "--owl", "--rewrite"])
+    SPDXLicenseGetter.cli()

pyobo/struct/struct.py

@@ -8,6 +8,7 @@ import json
 import logging
 import os
 import sys
+import tempfile
 import warnings
 from collections import ChainMap, defaultdict
 from collections.abc import Callable, Collection, Iterable, Iterator, Mapping, Sequence
@@ -1021,6 +1022,15 @@ class Obo:
         ofn = get_ofn_from_obo(self)
         ofn.write_funowl(path)
 
+    def write_owl(self, path: str | Path) -> None:
+        """Write OWL, by first outputting OFN then converting with ROBOT."""
+        from bioontologies import robot
+
+        with tempfile.TemporaryDirectory() as directory:
+            ofn_path = Path(directory).joinpath("tmp.ofn")
+            self.write_ofn(ofn_path)
+            robot.convert(ofn_path, path)
+
     def write_rdf(self, path: str | Path) -> None:
         """Write as Turtle RDF."""
         from .functional.obo_to_functional import get_ofn_from_obo

pyobo/utils/misc.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import logging
-from collections.abc import Callable
+from collections.abc import Callable, Iterable
 from datetime import datetime
 
 import bioversions.utils
@@ -46,6 +46,8 @@ VERSION_PREFIXES = [
     "http://w3id.org/nfdi4ing/metadata4ing/",  # like http://w3id.org/nfdi4ing/metadata4ing/1.3.1
     "http://www.semanticweb.com/OntoRxn/",  # like http://www.semanticweb.com/OntoRxn/0.2.5
     "https://w3id.org/lehrplan/ontology/",  # like in https://w3id.org/lehrplan/ontology/1.0.0-4
+    "http://www.ebi.ac.uk/swo/version/",  # http://www.ebi.ac.uk/swo/version/6.0
+    "https://w3id.org/emi/version/",
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",
@@ -193,18 +195,23 @@ def _prioritize_version(
     return None
 
 
-def _get_version_from_artifact(prefix: str) -> str | None:
+def _get_getter_urls(prefix: str) -> Iterable[tuple[OntologyFormat, str]]:
     # assume that all possible files that can be downloaded
     # are in sync and have the same version
-    for ontology_format, func in ONTOLOGY_GETTERS:
-        url = func(prefix)
+    for ontology_format, get_url_func in ONTOLOGY_GETTERS:
+        url = get_url_func(prefix)
         if url is None:
             continue
+        yield ontology_format, url
+
+
+def _get_version_from_artifact(prefix: str) -> str | None:
+    for ontology_format, url in _get_getter_urls(prefix):
         # Try to peak into the file to get the version without fully downloading
-        version_func = VERSION_GETTERS.get(ontology_format)
-        if version_func is None:
+        get_version_func = VERSION_GETTERS.get(ontology_format)
+        if get_version_func is None:
             continue
-        version = version_func(prefix, url)
+        version = get_version_func(prefix, url)
         if version:
             return cleanup_version(version, prefix=prefix)
     return None

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.5"
+VERSION = "0.12.6"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.5.dist-info → pyobo-0.12.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.5
+Version: 0.12.6
 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
@@ -30,7 +30,6 @@ Requires-Dist: tqdm
 Requires-Dist: pyyaml
 Requires-Dist: pandas
 Requires-Dist: requests
-Requires-Dist: protmapper
 Requires-Dist: more-itertools
 Requires-Dist: more-click>=0.0.2
 Requires-Dist: humanize
@@ -43,7 +42,6 @@ Requires-Dist: bioontologies>=0.7.2
 Requires-Dist: ssslm>=0.0.13
 Requires-Dist: zenodo-client>=0.3.6
 Requires-Dist: class-resolver>=0.6.0
-Requires-Dist: psycopg2-binary
 Requires-Dist: pydantic>=2.0
 Requires-Dist: curies>=0.10.17
 Requires-Dist: curies-processing>=0.1.2
@@ -57,8 +55,11 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
+Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
+Requires-Dist: protmapper ; extra == 'pid'
+Requires-Dist: pyobo[drugcentral,pid] ; extra == 'sources'
 Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
@@ -67,8 +68,11 @@ 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
+Provides-Extra: drugcentral
 Provides-Extra: gilda
 Provides-Extra: gilda-slim
+Provides-Extra: pid
+Provides-Extra: sources
 Description-Content-Type: text/markdown
 
 <!--

{pyobo-0.12.5.dist-info → pyobo-0.12.6.dist-info}/RECORD

@@ -17,7 +17,7 @@ pyobo/api/utils.py,sha256=48232ccb8432615867f902b487dd047f55d431bc87291d5fbed791
 pyobo/api/xrefs.py,sha256=9d62cbb761b36957e780d0546ce3154a33a90ae6be23bbbedadba8c735c6aab0,5242
 pyobo/cli/__init__.py,sha256=a5388bbb38e3a62d0febdc958d0da413a9c152666e6059ea74934364b0e482f9,71
 pyobo/cli/cli.py,sha256=e5b63fed95593a81f0859b42c71f8060be726f20738d2eb9354e6fe57f43b0b0,2842
-pyobo/cli/database.py,sha256=e880ac2c78bd437d73c99cea5c44938129852571bca35e2ab0cc7de195851ce6,11963
+pyobo/cli/database.py,sha256=82b3d51b577bf3286883996f100bb7c301e404048a86d99a6f09afc78f564487,12121
 pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc7d5f7a8a05da2b7adae,5540
 pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
 pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
@@ -25,7 +25,7 @@ pyobo/constants.py,sha256=1b9132661b9c730acc9f5d4345a4d73334c76b944676d191cd8aab
 pyobo/getters.py,sha256=5f68100998658f6b070e12fbbd52cc8d280f142d5361287ac74ee3bcc406deb8,18197
 pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
 pyobo/identifier_utils/__init__.py,sha256=8921c06613b0a9666662939fa5734bb8aa2e4988fb652562697ec1179b93f2ca,793
-pyobo/identifier_utils/api.py,sha256=b65d99d4b8d223341d7d3bd4b7bc2e41ce7b52e218b0779b90bacde6a9beaa61,9247
+pyobo/identifier_utils/api.py,sha256=7e293972b20e3a1b0722e1fe89afe839078a65e5f96c1323e52ea871c59a31e6,9365
 pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
 pyobo/identifier_utils/relations/api.py,sha256=c625bca0f09379ba7ef544d05aaf4b998ee9798945a90f3b98b6d763ef9d36df,5764
 pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
@@ -77,7 +77,7 @@ pyobo/sources/dictybase_gene.py,sha256=78bbde62732e26cd92c2d287ca3e34b678e9f058f
 pyobo/sources/drugbank/__init__.py,sha256=880b2dbd9419d3525c25e0089b606727ddb7501be2f1a490e2d1158440e8540a,178
 pyobo/sources/drugbank/drugbank.py,sha256=5a216ccbfe883599207ad99b518904d6f3e983974bc2305fcf7715263228d705,10914
 pyobo/sources/drugbank/drugbank_salt.py,sha256=69b565fe280b7a698cc3850b8b7fc8b5381f09aab7bb26e3aa7b13f5187b0b59,1646
-pyobo/sources/drugcentral.py,sha256=9fb9bbcbaf0b3c494163dde2e627a6695366ca1c74cb7293efd2419871a610a1,4047
+pyobo/sources/drugcentral.py,sha256=c481bfb0f79b6d5fbf4b5bd440bcceb8ba876bf44cfb300e7d9f28aabd5aa9b7,4052
 pyobo/sources/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
 pyobo/sources/famplex.py,sha256=a82be3e9607feaeab64471d53c8686872aa47f5b9b23a5eb3bc0daf98b5af7a4,5628
 pyobo/sources/flybase.py,sha256=8144b7f4d17fa9cef6dd1d9201b85062a3e0e943a2c0ac0f5e15d0d49c02ebc4,5666
@@ -154,7 +154,7 @@ pyobo/sources/signor/__init__.py,sha256=6de6ff151aaca2a2d5317b437916405dff5783d5
 pyobo/sources/signor/download.py,sha256=ae40c954403a95dd33e221b5e2d30e70072e4658d043d48024068b75ac5a833f,1053
 pyobo/sources/signor/signor_complexes.py,sha256=04634cfe41b48eda51fa2eab0d2305e5729e0a59563b7e336762aae0532d064d,3802
 pyobo/sources/slm.py,sha256=986242c3f131a541116d6b452e8f053763607d5844befdf79bae893db85c8f62,4246
-pyobo/sources/spdx.py,sha256=3a9f32952c007c1bd1dcf661b7d0cd92caf8eccdcd340b69b1a4198e4ec50ee0,2475
+pyobo/sources/spdx.py,sha256=26354335498de8d73c6d3ff6fcea2a26978a9d9ceec0f99d504ca74e5fd80153,2530
 pyobo/sources/umls/__init__.py,sha256=10d80d5d02a1cdef73cb1b178e49fbdfe05daa6767b4be19cb5a91e36183b4ff,141
 pyobo/sources/umls/__main__.py,sha256=358e97a9eb60a5177f2cf9bde554d7d8bdeb241ffb877250b6d8270c9f5c1613,108
 pyobo/sources/umls/get_synonym_types.py,sha256=fd5266a8217b628fca6bef678e579dba3251445bc0f474d0f6f6c92c80bd7bb2,1724
@@ -188,7 +188,7 @@ pyobo/struct/obograph/export.py,sha256=7bf4b4bcd6c3c89e820fe542711dae70cb037ed45
 pyobo/struct/obograph/reader.py,sha256=dbae3255e0fc6b78c6c7d11a194655c456d243fa7043fe9c915c3d4bcc2225f3,8525
 pyobo/struct/obograph/utils.py,sha256=8ded244a40b6e0c53da56447ab5fcaf89e635a18d611263a348dd3a59aaf67f4,1516
 pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
-pyobo/struct/struct.py,sha256=772296f541bff7b35b4c420713f8c780b059d5157f8897f1458c7371ffcb4263,92916
+pyobo/struct/struct.py,sha256=e833c86ec9e302808afc3750a0d9b1cfc4237251fc10450e48bda8b181761a00,93297
 pyobo/struct/struct_utils.py,sha256=be63a06ade7ba29cf3c02410a245e715103884c5e886d4b23e49050bb8f7dd5a,39930
 pyobo/struct/typedef.py,sha256=eed11961bc01efa4f2fec3c7ae9ba8eff5dd6776d70bf0d4a9cc13b72c042e3f,13031
 pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
@@ -197,12 +197,12 @@ pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568
 pyobo/utils/cache.py,sha256=c7b0e7c3cbc762ca2c9575a257d2fd65d4eee59b9e211d648b935c7696fb1f5d,3136
 pyobo/utils/io.py,sha256=413bc68cd0e46887fbf1371adb7079456fda57078a892b319a0c1229770c48da,3921
 pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d26c4591fe736,1524
-pyobo/utils/misc.py,sha256=1dc1bc786ae2ae479facaa6341aa8ea565f167fab285ddb0df387aa7ee5ab9ef,7666
+pyobo/utils/misc.py,sha256=e3df697a77320ea5bdff19b41f40aad0584ec34328368abef485504ca87e79a1,7992
 pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
 pyobo/utils/path.py,sha256=129f254d15a0154f7f5c5e6fa895790771b83dc501825222b4c91a50dc63cefa,4091
-pyobo/version.py,sha256=6ff6d2700b14e326e314f95afbb5b5fafe7b58e959aace2bb1029526a8a9ee2d,926
-pyobo-0.12.5.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-pyobo-0.12.5.dist-info/WHEEL,sha256=ec89e25a684ec3ad8fb2a9be806e47666a27f7dcdcf9b55bff3f1d3ed5e60e0a,78
-pyobo-0.12.5.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
-pyobo-0.12.5.dist-info/METADATA,sha256=c48d14635954af46f3f382e4f867fe7ca84ec0d0ac3756c8de05cd8e4cc9a344,21661
-pyobo-0.12.5.dist-info/RECORD,,
+pyobo/version.py,sha256=a0f95e1dc5c6ae4d27ebf8475452242e445573a9b03e3602e3b3fd402309fd94,926
+pyobo-0.12.6.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+pyobo-0.12.6.dist-info/WHEEL,sha256=ec89e25a684ec3ad8fb2a9be806e47666a27f7dcdcf9b55bff3f1d3ed5e60e0a,78
+pyobo-0.12.6.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
+pyobo-0.12.6.dist-info/METADATA,sha256=9725b7bbe5fa4b43a5d11e33fc551f38bfec3c5e2a6066f44cf0ea94f6cc9686,21834
+pyobo-0.12.6.dist-info/RECORD,,