pyobo 0.12.2__py3-none-any.whl → 0.12.4__py3-none-any.whl

{pyobo-0.12.2.dist-info → pyobo-0.12.4.dist-info}/RECORD

@@ -1,5 +1,5 @@
 pyobo/.DS_Store,sha256=00b8c741cd5b001c03c1a582f55bfbcda0ad16f0e55019d64f93241b74991980,8196
-pyobo/__init__.py,sha256=0d90185e6e3aa041ccc27c68226c45e456e39369328e3db17706d65b52015819,3439
+pyobo/__init__.py,sha256=ae0b55a37ac88a8423fd32252683d3447102bcce078fe4c2a418f78196e9d648,3434
 pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
 pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
 pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
@@ -7,7 +7,7 @@ pyobo/api/combine.py,sha256=ed3f108fc5b5c164352a0289b0ed641511d9c6441cadf28cd610
 pyobo/api/edges.py,sha256=4849b6809c7a2e83a48571a3d75578dae2e0e0589d15af6326a5bd1f39e57f09,1974
 pyobo/api/hierarchy.py,sha256=37f27381f08a3c859adb4a1d46132fa60889a5ccce8867620db2e4353aa5a69f,10314
 pyobo/api/metadata.py,sha256=b2d25a897fe5ef1d11d55efb4cdc07bcfb6892e67e128a9bf473112fbd0d896b,1029
-pyobo/api/names.py,sha256=2f620187285c1fccbeac23708d624bc374ec1e9d6abce65ebf5eb4f9c63070b8,10673
+pyobo/api/names.py,sha256=674d2fb91794ec218a2f7f4466f300310bb75462ca625245ccc0474f8915e310,10935
 pyobo/api/properties.py,sha256=6d85af1ebd5b7f4c5d232323faab9d8f8a11a419eab0a86eca36052b22b2f778,6914
 pyobo/api/relations.py,sha256=6dfda59d8ae2c3addb816d7dad2b97856916c6f2e6114f7a774bfcaff1c25747,5859
 pyobo/api/species.py,sha256=631cc978295fb8a23ea6360ba6ee7bf7b8dd0dec93917a6340381d99cf4c2b0a,2376
@@ -21,10 +21,10 @@ pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc
 pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
 pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
 pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
-pyobo/getters.py,sha256=0d9a129a46213f3657cb80d7a70a73aa24567644a1d9090c57f09c67cb86921a,17375
+pyobo/getters.py,sha256=0bbd39aeba8b4511230ebadd209b2c9c64b117f81d80e1a1327230a068a13eeb,17618
 pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
-pyobo/identifier_utils/__init__.py,sha256=ef7bbb0ffb088daa04ee79446bafc8a5ee1d404e347e637361b835879755dea2,753
-pyobo/identifier_utils/api.py,sha256=c308dc9f48753d14084d19362f08003f822c2e495fe0badd9b9d3bc176fbaba1,9215
+pyobo/identifier_utils/__init__.py,sha256=8921c06613b0a9666662939fa5734bb8aa2e4988fb652562697ec1179b93f2ca,793
+pyobo/identifier_utils/api.py,sha256=b65d99d4b8d223341d7d3bd4b7bc2e41ce7b52e218b0779b90bacde6a9beaa61,9247
 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
@@ -35,11 +35,8 @@ pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15
 pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
 pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
 pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
-pyobo/obographs.py,sha256=8b4258792727430b6c4f15833116313905abb83511f1fee565091c400323f49d,4345
 pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
 pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
-pyobo/reader.py,sha256=6fc2522a89772b718eaa6278e2abc7d5ca536378b537992b34bfe12bcfd10d72,52246
-pyobo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
 pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
 pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
 pyobo/resources/ncbitaxon.py,sha256=92484774b0f45247cb4090b34e3851a5c175dde2da03e472d891c9953968116b,1979
@@ -49,7 +46,7 @@ pyobo/resources/ro.tsv,sha256=62f9412cf00acb6c38221798ccef68c75620e9690774c57331
 pyobo/resources/so.py,sha256=4bebe643b2fc009134f057c6543209a8d40d68b3d49ae27a1c2e45e2158732b0,1466
 pyobo/resources/so.tsv,sha256=50964a153100bff5eccd861bba7e167fa6f88e8bc38d229cd51591411713cc3c,82068
 pyobo/sources/README.md,sha256=0296f0a48da16d8422c3837a284fd5000a5f3a64d01e47936eb34413121b5f82,901
-pyobo/sources/__init__.py,sha256=94db6754ef36ea969a347c2ae38ff9eddb44dbe177ce06d9f93e5432592bc404,4630
+pyobo/sources/__init__.py,sha256=fb9f5ba3c87a3ea2f2d28144659897c99de0ad824e4ed2382035a8814184313c,4683
 pyobo/sources/agrovoc.py,sha256=489b1b27b2adc5d2541bd4629a66f609f2dfce92bd78eccfd30c79f608feeace,787
 pyobo/sources/antibodyregistry.py,sha256=3726d4ccf1286e7e73aebd6252f0bc67d72ea83103335bb4eec8d5d540037664,3353
 pyobo/sources/bigg/__init__.py,sha256=e292beef5071d08bfddcfaa665e714297f4b71aa5b5bdc26ef304df6f85ba582,349
@@ -74,7 +71,7 @@ pyobo/sources/cvx.py,sha256=97d0acbae76bf54ca8d0f35c8c94db346eb610e51cac05688a3d
 pyobo/sources/depmap.py,sha256=7f05bfd54901e49b6c797c137dbd017e32ef626fb17feb17c1feb368f2a4960f,3585
 pyobo/sources/dictybase_gene.py,sha256=78bbde62732e26cd92c2d287ca3e34b678e9f058f2d72157a0f0e8b9bd5d6164,2672
 pyobo/sources/drugbank/__init__.py,sha256=880b2dbd9419d3525c25e0089b606727ddb7501be2f1a490e2d1158440e8540a,178
-pyobo/sources/drugbank/drugbank.py,sha256=eb2fc65b2d43ac54c0c81fefb0701b1326411027cf3cfb5eac7534df925cb33c,10899
+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/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
@@ -90,7 +87,7 @@ pyobo/sources/go.py,sha256=cd72c37dca9b894eb43371540adab37cfcd8a07952be4533000f1
 pyobo/sources/gtdb.py,sha256=ab420486568c8ad1d6a39200cb6979f2e5cc2d67a40addeb2303a60ecb031138,5221
 pyobo/sources/gwascentral/__init__.py,sha256=55d1c8801551fb7e81ee02ee851e175795179ff120359d3e8b583d36384e8d8d,231
 pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=4af302177b18a9cdc5e6735709fefa033221353ebdf191c79d3a4ed0819fb7ca,1788
-pyobo/sources/gwascentral/gwascentral_study.py,sha256=bddb3b20e2374cc3ff14601aba36c17466897d46f1d086bf75ecf62992263bd9,2657
+pyobo/sources/gwascentral/gwascentral_study.py,sha256=7f30e246e594f38d3ce60725cee58d2dbc4312c21d572b2a5d270c53405d5e73,2672
 pyobo/sources/hgnc/__init__.py,sha256=d5084cec674febf03108ccda073da4dd244b9034ce912da15213cc2c44d21963,157
 pyobo/sources/hgnc/hgnc.py,sha256=f05121570f4e4b06f4d70bbf6950363349a726de22c6f2ed5e3e43411591bf95,16377
 pyobo/sources/hgnc/hgncgenefamily.py,sha256=e3e8d0b750d59a7da3d0ac2b100e248e8dad51af54c045405a12704e36db20cd,3710
@@ -98,6 +95,7 @@ pyobo/sources/icd/__init__.py,sha256=0eb65597be8ff1eb2c278b6564f71ab8556b5d59082
 pyobo/sources/icd/icd10.py,sha256=61ab55ce0af6dbd27f59e25c6b8150007a96af1edcecde1f1db85bd5c4354de5,2587
 pyobo/sources/icd/icd11.py,sha256=5b6e59f8028cfbd41f860151d1164514be2653a50078c0fc8748c20b815ee11b,4867
 pyobo/sources/icd/icd_utils.py,sha256=8fbc63228bd61b4f86c47eee5d6ad76433b52d7132a3fe0275680f4874c85c96,4525
+pyobo/sources/intact.py,sha256=7e78d9e164acadf67b6df963a4c58116d4861a4e959aef0fb1d7d1f6c6f15cfe,2497
 pyobo/sources/interpro.py,sha256=d6d99771293946b8228fbd35183aa845b77f7c46af1e5f3f03a6887f92ba10b1,4809
 pyobo/sources/itis.py,sha256=6b1d54c40ece2a97176c497aaa3113fbf78ea32845e918fc76de4a1bf254dbbf,2876
 pyobo/sources/kegg/__init__.py,sha256=8553f4b6ec15a6234c8a416ffdb34faf3b98bfe1c0d7f6cf742bcdc7e7e6e458,219
@@ -169,19 +167,26 @@ pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5fe
 pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
 pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
 pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
-pyobo/struct/__init__.py,sha256=fb813dfa7de27f195c07cd5311de78403b03dfbf0a183995c8fb448033ace311,1444
+pyobo/struct/__init__.py,sha256=653697fa0c263df189df3550d1e79772c8c4f20e6886a8fffaccc676fbbb94d2,1474
 pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
 pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
 pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
 pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
-pyobo/struct/functional/ontology.py,sha256=bc610a206c5f502cc658cbf7dcaa9caeb112a596ab1cb07fcbd571c8a6da2894,9331
+pyobo/struct/functional/ontology.py,sha256=c261c91ed950d3a6564ffcbda379fb228ffd28f0d873cb5f9c1a237a4e744328,9338
 pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
+pyobo/struct/obo/__init__.py,sha256=c49005278cae796050bf706bb53b871c9ec0ccea8280eb8780a638450a1cb16d,157
+pyobo/struct/obo/reader.py,sha256=6dd8c153e8210c8da1cceed08a4c4bf4addaa3355529b2d34d03960d7c446916,52261
+pyobo/struct/obo/reader_utils.py,sha256=5324154d08576e167d7c28b3660dbaa394e67878acf7ea9930abd0170201460a,4423
+pyobo/struct/obograph/__init__.py,sha256=078acd3fd3824e73179bc629434adaaf5b309f8188c3d6f88100fe215baa1f2c,452
+pyobo/struct/obograph/export.py,sha256=a4630989db4171855683d76a169ef6a554dad3c3944401fdb0b4ea37cdef93da,9747
+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=29b77204d903a948aff74f93aa043e5421cc932c22a893e70dbfd3f27b911fb7,89480
-pyobo/struct/struct_utils.py,sha256=7b8bfd7a322f34cf1436b83c8eab983944651ba467923045bf61ecc245800d2c,39164
-pyobo/struct/typedef.py,sha256=fd94429e28efcdf7bbeba4b1729fa66af5f64c34e49437d82e4b3e5a457d064d,12099
+pyobo/struct/struct.py,sha256=fd60053e55c16c3ca2222852ad0f8bd6de20ac8151e096340d271086d6fa9099,89172
+pyobo/struct/struct_utils.py,sha256=a4fa0ee672bc626095fbc0df66f0b948ad35ff39b55971b0145cd6bd80e640fb,39511
+pyobo/struct/typedef.py,sha256=8817a49f6426a9adc9ed8462d5db3d3324780b2ad3874d8781a1648e64fe9ce5,12429
 pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
-pyobo/struct/vocabulary.py,sha256=56e0f6770cf7da2d6f1221e3fc8261f1c07dc8358a1f3dfb487894a25b1ed133,4335
+pyobo/struct/vocabulary.py,sha256=1d853a86c2d0e34dd6bd64e68d1323b8ac51d3a4b2932a6bde4fc8c4b52104e9,4645
 pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
 pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
 pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
@@ -189,9 +194,9 @@ pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d2
 pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
 pyobo/utils/ndex_utils.py,sha256=128902592d345ab93fe32f2575e42e53269a0bac8dcc18370da81497e2767336,2326
 pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
-pyobo/version.py,sha256=d76710b61a3b9c38c2f582b5788dc0c462786829754363c869633e386dccebd6,926
-pyobo-0.12.2.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
-pyobo-0.12.2.dist-info/WHEEL,sha256=ec89e25a684ec3ad8fb2a9be806e47666a27f7dcdcf9b55bff3f1d3ed5e60e0a,78
-pyobo-0.12.2.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
-pyobo-0.12.2.dist-info/METADATA,sha256=37f00c716dd218308afda6c1d5543267fae9c0dab78c5e17879388a6491b9a36,21626
-pyobo-0.12.2.dist-info/RECORD,,
+pyobo/version.py,sha256=a57d58ec84e8181d4fa5ab4ce8c6fbd23ae0a3be23927e993efd3b67d3cc6966,926
+pyobo-0.12.4.dist-info/licenses/LICENSE,sha256=41c80964a1b1956e41c013670812fc5592d5b51bd7b3cd4287d949450488a498,1076
+pyobo-0.12.4.dist-info/WHEEL,sha256=ec89e25a684ec3ad8fb2a9be806e47666a27f7dcdcf9b55bff3f1d3ed5e60e0a,78
+pyobo-0.12.4.dist-info/entry_points.txt,sha256=00d833beec05ffdff58a90a8c49b5b04ce80e22d8c92ddfd80c3f340eea1bc6b,42
+pyobo-0.12.4.dist-info/METADATA,sha256=6a63fea373d80648846c0e7a0885c887f9597e27d5c2c84302cd49427bf90d09,21658
+pyobo-0.12.4.dist-info/RECORD,,

pyobo/obographs.py

@@ -1,152 +0,0 @@
-"""Convert PyOBO into OBO Graph."""
-
-from __future__ import annotations
-
-import logging
-from collections.abc import Iterable
-from typing import TYPE_CHECKING
-
-import bioregistry
-from bioontologies.obograph import (
-    Definition,
-    Edge,
-    Graph,
-    GraphDocument,
-    Meta,
-    Node,
-    Synonym,
-    Xref,
-)
-from tqdm import tqdm
-
-from pyobo.struct import Obo, OBOLiteral, Reference, Term
-from pyobo.struct.typedef import definition_source, is_a
-
-if TYPE_CHECKING:
-    from bioontologies.robot import ParseResults
-
-__all__ = [
-    "graph_from_obo",
-    "parse_results_from_obo",
-]
-
-logger = logging.getLogger(__name__)
-
-
-def parse_results_from_obo(obo: Obo) -> ParseResults:
-    """Get parse results from an OBO graph."""
-    graph = graph_from_obo(obo)
-    from bioontologies.robot import ParseResults
-
-    return ParseResults(graph_document=GraphDocument(graphs=[graph]))
-
-
-def graph_from_obo(obo: Obo, use_tqdm: bool = True) -> Graph:
-    """Get an OBO Graph object from a PyOBO object."""
-    nodes: list[Node] = []
-    edges: list[Edge] = []
-    for term in tqdm(
-        obo,
-        disable=not use_tqdm,
-        unit="term",
-        unit_scale=True,
-        desc=f"[{obo._prefix_version}] to OBO Graph JSON",
-    ):
-        nodes.append(_get_class_node(term))
-        edges.extend(_iter_edges(term))
-    return Graph(
-        id=bioregistry.get_bioregistry_iri("bioregistry", obo.ontology),
-        prefix=obo.ontology,
-        meta=_get_meta(obo),
-        nodes=nodes,
-        edges=edges,
-        standardized=True,  # from construction :)
-    )
-
-
-def _get_meta(obo: Obo) -> Meta:
-    return Meta(
-        version=obo.data_version,
-    )
-
-
-def _get_class_node(term: Term) -> Node:
-    if term.provenance or term.definition:
-        definition = Definition.from_parsed(
-            value=term.definition, references=_prep_prov(term.provenance)
-        )
-    else:
-        definition = None
-    xrefs = [
-        Xref.from_parsed(
-            predicate=Reference.from_reference(mapping_predicate),
-            value=Reference.from_reference(mapping_object),
-        )
-        for mapping_predicate, mapping_object in term.get_mappings(
-            include_xrefs=True, add_context=False
-        )
-    ]
-    synonyms = [
-        Synonym.from_parsed(
-            name=synonym.name,
-            predicate=Reference.from_reference(synonym.predicate),
-            synonym_type=Reference.from_reference(synonym.type) if synonym.type else None,
-            references=_prep_prov(synonym.provenance),
-        )
-        for synonym in term.synonyms
-    ]
-
-    meta = Meta(
-        definition=definition,
-        xrefs=xrefs,
-        synonyms=synonyms,
-        basicPropertyValues=None,  # TODO properties
-        deprecated=term.is_obsolete or False,
-    )
-    return Node(
-        # FIXME do expansion same as for OFN
-        id=f"https://bioregistry.io/{term.curie}",
-        lbl=term.name,
-        meta=meta,
-        type="CLASS",
-        reference=Reference.from_reference(term.reference),
-        standardized=True,
-    )
-
-
-def _prep_prov(provenance):
-    rv = []
-    for x in provenance:
-        match x:
-            case Reference():
-                rv.append(Reference.from_reference(x))
-            case OBOLiteral():
-                logger.debug("not implemented to convert literal provenance")
-                continue
-    return rv
-
-
-def _iter_edges(term: Term) -> Iterable[Edge]:
-    for parent in term.parents:
-        yield Edge.from_parsed(
-            Reference.from_reference(term.reference),
-            Reference.from_reference(is_a.reference),
-            Reference.from_reference(parent),
-        )
-
-    for typedef, targets in term.relationships.items():
-        for target in targets:
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(typedef),
-                Reference.from_reference(target),
-            )
-
-    for provenance_reference in term.provenance:
-        if isinstance(provenance_reference, Reference):
-            yield Edge.from_parsed(
-                Reference.from_reference(term.reference),
-                Reference.from_reference(definition_source.reference),
-                Reference.from_reference(provenance_reference),
-            )
-    # TODO also look through xrefs and seealso to get provenance xrefs?