From 05c7767a95ad33f31f18573d15bb4e635d5b15d6 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Tue, 15 Oct 2024 16:48:58 +0100 Subject: [PATCH 1/8] feat: update all ontologies and configs to new versions --- kazu/conf/SynonymGeneration/default.yaml | 224 +++++++++--------- kazu/conf/ontologies/cellosaurus.yaml | 2 +- kazu/conf/ontologies/cl.yaml | 2 +- kazu/conf/ontologies/go_bp.yaml | 2 +- kazu/conf/ontologies/go_cc.yaml | 2 +- kazu/conf/ontologies/go_mf.yaml | 2 +- kazu/conf/ontologies/mondo.yaml | 2 +- kazu/conf/ontologies/ot_bio_proc.yaml | 4 +- kazu/conf/ontologies/ot_disease.yaml | 46 ++-- kazu/conf/ontologies/ot_medical_proc.yaml | 4 +- kazu/conf/ontologies/ot_molecule.yaml | 2 +- kazu/conf/ontologies/ot_phenotype.yaml | 4 +- kazu/conf/ontologies/ot_target.yaml | 2 +- kazu/conf/ontologies/stato.yaml | 2 +- kazu/conf/ontologies/uberon.yaml | 2 +- .../BP_GENE_ONTOLOGY_curations.jsonl/0.jsonl | 2 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/0.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/1.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/2.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/3.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/4.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/5.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/6.jsonl | 4 +- .../BP_GENE_ONTOLOGY_defaults.jsonl/7.jsonl | 4 +- .../CC_GENE_ONTOLOGY_curations.jsonl/0.jsonl | 2 +- .../CC_GENE_ONTOLOGY_defaults.jsonl/0.jsonl | 4 +- .../CELLOSAURUS_curations.jsonl/0.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/0.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/1.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/10.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/11.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/12.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/13.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/14.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/15.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/2.jsonl | 4 +- .../CELLOSAURUS_defaults.jsonl/3.jsonl | 4 +- 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a/kazu/conf/SynonymGeneration/default.yaml b/kazu/conf/SynonymGeneration/default.yaml index d2a6cd105..0f2b88787 100644 --- a/kazu/conf/SynonymGeneration/default.yaml +++ b/kazu/conf/SynonymGeneration/default.yaml @@ -58,37 +58,37 @@ meddra: include_greek: true - _target_: kazu.ontology_preprocessing.synonym_generation.TokenListReplacementGenerator token_lists_to_consider: - - - anomalous - - unusual - - atypical - - deviant - - aberrant - - peculiar - - eccentric - - strange - - bizarre - - odd - - weird - - uncommon - - freakish - - irregular - - outlandish - - exceptional - - unnatural - - unhealthy - - abnormal - - - typical - - ordinary - - standard - - regular - - usual - - natural - - routine - - average - - expected - - balanced - - stable - - healthy + - - anomalous + - unusual + - atypical + - deviant + - aberrant + - peculiar + - eccentric + - strange + - bizarre + - odd + - weird + - uncommon + - freakish + - irregular + - outlandish + - exceptional + - unnatural + - unhealthy + - abnormal + - - typical + - ordinary + - standard + - regular + - usual + - natural + - routine + - average + - expected + - balanced + - stable + - healthy - _target_: kazu.ontology_preprocessing.synonym_generation.VerbPhraseVariantGenerator spacy_model_path: ${SciSpacyPipeline.path} @@ -107,112 +107,112 @@ meddra: - "{NOUN} {TARGET}" lemmas_to_consider: increase: - - increasing - - increased - - increases + - increasing + - increased + - increases expand: - - expanding - - expands - - expanded + - expanding + - expands + - expanded enhance: - - enhancing - - enhances - - enhanced + - enhancing + - enhances + - enhanced raise: - - raising - - raises - - raised + - raising + - raises + - raised boost: - - boosting - - boosts - - boosted + - boosting + - boosts + - boosted escalate: - - escalating - - escalates - - escalated + - escalating + - escalates + - escalated augment: - - augmenting - - augments - - augmented + - augmenting + - augments + - augmented intensify: - - intensifying - - intensifies - - intensifed + - intensifying + - intensifies + - intensifed amplify: - - amplifing - - amplifies - - amplified + - amplifing + - amplifies + - amplified strengthen: - - strengthening - - strengthens - - strengthened + - strengthening + - strengthens + - strengthened heighten: - - heightening - - heightens - - heightened + - heightening + - heightens + - heightened decrease: - - decreasing - - decreases - - decreased + - decreasing + - decreases + - decreased reduce: - - reducing - - reduces - - reduced + - reducing + - reduces + - reduced diminish: - - diminishing - - diminishes - - diminished + - diminishing + - diminishes + - diminished lower: - - lowering - - lowers - - lowered + - lowering + - lowers + - lowered minimize: - - minimizing - - minimizes - - minimized + - minimizing + - minimizes + - minimized minimise: - - minimising - - minimises - - minimised + - minimising + - minimises + - minimised curtail: - - curtailing - - curtails - - curtailed + - curtailing + - curtails + - curtailed shrink: - - shrinking - - shrinks - - shrinked + - shrinking + - shrinks + - shrinked contract: - - contracting - - contracts - - contracted + - contracting + - contracts + - contracted narrow: - - narrowing - - narrows - - narrowed + - narrowing + - narrows + - narrowed taper: - - tapering - - tapers - - tapered + - tapering + - tapers + - tapered constrict: - - constricting - - constricts - - constricted + - constricting + - constricts + - constricted dwindle: - - dwindling - - dwindles - - dwindled + - dwindling + - dwindles + - dwindled subside: - - subsiding - - subsides - - subsided + - subsiding + - subsides + - subsided weaken: - - weakening - - weakens - - weakened + - weakening + - weakens + - weakened decrement: - - decrementing - - decrements - - decremented + - decrementing + - decrements + - decremented diff --git a/kazu/conf/ontologies/cellosaurus.yaml b/kazu/conf/ontologies/cellosaurus.yaml index 3c6291603..9035ffa68 100644 --- a/kazu/conf/ontologies/cellosaurus.yaml +++ b/kazu/conf/ontologies/cellosaurus.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.CellosaurusOntologyParser name: CELLOSAURUS in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/cellosaurus.obo - data_origin: '49.0' + data_origin: "50.0" string_scorer: ${SapbertStringSimilarityScorer} entity_class: cell_line curations_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/${.name}_curations.jsonl diff --git a/kazu/conf/ontologies/cl.yaml b/kazu/conf/ontologies/cl.yaml index d0b77609d..089b0d97c 100644 --- a/kazu/conf/ontologies/cl.yaml +++ b/kazu/conf/ontologies/cl.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.CLOntologyParser name: CL in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/cl.owl - data_origin: '2024-05-15' + data_origin: "2024-09-26" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: cell_type diff --git a/kazu/conf/ontologies/go_bp.yaml b/kazu/conf/ontologies/go_bp.yaml index 3cf143a78..56fc61ea4 100644 --- a/kazu/conf/ontologies/go_bp.yaml +++ b/kazu/conf/ontologies/go_bp.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.BiologicalProcessGeneOntologyParser name: BP_GENE_ONTOLOGY in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/go.owl - data_origin: '2024-06-17' + data_origin: "2024-09-08" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: biological_process diff --git a/kazu/conf/ontologies/go_cc.yaml b/kazu/conf/ontologies/go_cc.yaml index b703e21f1..50384845f 100644 --- a/kazu/conf/ontologies/go_cc.yaml +++ b/kazu/conf/ontologies/go_cc.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.CellularComponentGeneOntologyParser name: CC_GENE_ONTOLOGY in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/go.owl - data_origin: '2024-06-17' + data_origin: "2024-09-08" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: cellular_component diff --git a/kazu/conf/ontologies/go_mf.yaml b/kazu/conf/ontologies/go_mf.yaml index 0344e0583..85a19e0f2 100644 --- a/kazu/conf/ontologies/go_mf.yaml +++ b/kazu/conf/ontologies/go_mf.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.MolecularFunctionGeneOntologyParser name: MF_GENE_ONTOLOGY in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/go.owl - data_origin: '2024-06-17' + data_origin: "2024-09-08" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: molecular_function diff --git a/kazu/conf/ontologies/mondo.yaml b/kazu/conf/ontologies/mondo.yaml index d9075b62d..f79cb2a27 100644 --- a/kazu/conf/ontologies/mondo.yaml +++ b/kazu/conf/ontologies/mondo.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.MondoOntologyParser name: MONDO in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/mondo.json - data_origin: '2024-06-04' + data_origin: "2024-10-15T13:28:52.008470" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: disease diff --git a/kazu/conf/ontologies/ot_bio_proc.yaml b/kazu/conf/ontologies/ot_bio_proc.yaml index 781e8c8fc..472e06e99 100644 --- a/kazu/conf/ontologies/ot_bio_proc.yaml +++ b/kazu/conf/ontologies/ot_bio_proc.yaml @@ -8,14 +8,14 @@ parsers: name: OPENTARGETS_BIOLOGICAL_PROC _target_: kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/diseases - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: biological_process curations_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/${.name}_curations.jsonl global_actions: ${global_actions} allowed_therapeutic_areas: - - 'GO_0008150' + - "GO_0008150" autocurator: ${autocurator.basic} ontology_downloader: _target_: kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader diff --git a/kazu/conf/ontologies/ot_disease.yaml b/kazu/conf/ontologies/ot_disease.yaml index 828049bbb..085b16c00 100644 --- a/kazu/conf/ontologies/ot_disease.yaml +++ b/kazu/conf/ontologies/ot_disease.yaml @@ -8,35 +8,35 @@ parsers: name: OPENTARGETS_DISEASE _target_: kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/diseases - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: disease curations_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/${.name}_curations.jsonl global_actions: ${global_actions} allowed_therapeutic_areas: - - 'MONDO_0024458' - - 'OTAR_0000006' - - 'MONDO_0002025' - - 'EFO_0001379' - - 'EFO_0009690' - - 'EFO_0000540' - - 'EFO_0005741' - - 'EFO_0000319' - - 'EFO_0009605' - - 'MONDO_0045024' - - 'OTAR_0000018' - - 'OTAR_0000020' - - 'EFO_0010285' - - 'OTAR_0000010' - - 'EFO_0005803' - - 'EFO_0005932' - - 'OTAR_0000009' - - 'MONDO_0021205' - - 'OTAR_0000017' - - 'EFO_0010282' - - 'OTAR_0000014' - - 'EFO_0000618' + - "MONDO_0024458" + - "OTAR_0000006" + - "MONDO_0002025" + - "EFO_0001379" + - "EFO_0009690" + - "EFO_0000540" + - "EFO_0005741" + - "EFO_0000319" + - "EFO_0009605" + - "MONDO_0045024" + - "OTAR_0000018" + - "OTAR_0000020" + - "EFO_0010285" + - "OTAR_0000010" + - "EFO_0005803" + - "EFO_0005932" + - "OTAR_0000009" + - "MONDO_0021205" + - "OTAR_0000017" + - "EFO_0010282" + - "OTAR_0000014" + - "EFO_0000618" autocurator: ${autocurator.basic} ontology_downloader: _target_: kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader diff --git a/kazu/conf/ontologies/ot_medical_proc.yaml b/kazu/conf/ontologies/ot_medical_proc.yaml index 20668b4ff..ddaddb273 100644 --- a/kazu/conf/ontologies/ot_medical_proc.yaml +++ b/kazu/conf/ontologies/ot_medical_proc.yaml @@ -8,14 +8,14 @@ parsers: name: OPENTARGETS_MEDICAL_PROC _target_: kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/diseases - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: medical_procedure curations_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/${.name}_curations.jsonl global_actions: ${global_actions} allowed_therapeutic_areas: - - 'EFO_0002571' + - "EFO_0002571" autocurator: ${autocurator.basic} ontology_downloader: _target_: kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader diff --git a/kazu/conf/ontologies/ot_molecule.yaml b/kazu/conf/ontologies/ot_molecule.yaml index 1f0d52a7c..d1a986e9c 100644 --- a/kazu/conf/ontologies/ot_molecule.yaml +++ b/kazu/conf/ontologies/ot_molecule.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.OpenTargetsMoleculeOntologyParser name: OPENTARGETS_MOLECULE in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/molecule - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.chemical} entity_class: drug diff --git a/kazu/conf/ontologies/ot_phenotype.yaml b/kazu/conf/ontologies/ot_phenotype.yaml index a65856115..9e2dfec38 100644 --- a/kazu/conf/ontologies/ot_phenotype.yaml +++ b/kazu/conf/ontologies/ot_phenotype.yaml @@ -8,14 +8,14 @@ parsers: name: OPENTARGETS_PHENOTYPE _target_: kazu.ontology_preprocessing.parsers.OpenTargetsDiseaseOntologyParser in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/diseases - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: disease curations_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/${.name}_curations.jsonl global_actions: ${global_actions} allowed_therapeutic_areas: - - 'EFO_0000651' + - "EFO_0000651" autocurator: ${autocurator.basic} ontology_downloader: _target_: kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader diff --git a/kazu/conf/ontologies/ot_target.yaml b/kazu/conf/ontologies/ot_target.yaml index fd5ceb5bc..0d0e21015 100644 --- a/kazu/conf/ontologies/ot_target.yaml +++ b/kazu/conf/ontologies/ot_target.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.OpenTargetsTargetOntologyParser name: OPENTARGETS_TARGET in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/opentargets/targets - data_origin: '24.06' + data_origin: "24.09" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.gene} entity_class: gene diff --git a/kazu/conf/ontologies/stato.yaml b/kazu/conf/ontologies/stato.yaml index eb87989a3..c60de194d 100644 --- a/kazu/conf/ontologies/stato.yaml +++ b/kazu/conf/ontologies/stato.yaml @@ -9,7 +9,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.StatoParser name: STATO in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/stato.owl - data_origin: 'RC1.4' + data_origin: "2024-07-07" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: measurement diff --git a/kazu/conf/ontologies/uberon.yaml b/kazu/conf/ontologies/uberon.yaml index 73fc9865e..ae26d39f4 100644 --- a/kazu/conf/ontologies/uberon.yaml +++ b/kazu/conf/ontologies/uberon.yaml @@ -8,7 +8,7 @@ parsers: _target_: kazu.ontology_preprocessing.parsers.UberonOntologyParser name: UBERON in_path: ${oc.env:KAZU_MODEL_PACK}/ontologies/uberon.owl - data_origin: 'http://purl.obolibrary.org/obo/uberon/releases/2024-05-13/uberon.owl' + data_origin: "http://purl.obolibrary.org/obo/uberon/releases/2024-09-03/uberon.owl" string_scorer: ${SapbertStringSimilarityScorer} synonym_generator: ${SynonymGeneration.default} entity_class: anatomy diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_curations.jsonl/0.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_curations.jsonl/0.jsonl index 456de2008..f9fa76d2a 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_curations.jsonl/0.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_curations.jsonl/0.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d257fed9f073ee37500136e042dc909656bb2b091e0577fbb07155ae0b3a62b7 +oid sha256:53d7c2c806c4cab8614c7041aada0354800e38dea9423e36370693dcda8d76e0 size 451130 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/0.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/0.jsonl index ecae2e409..22f2d014a 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/0.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/0.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:400e1712c9ab453a8f1f48c7cfaa2832e7f276108f123bf4db6118155a80af7d -size 10651707 +oid sha256:e2eb15918a19196242cd1b77af4f01de98c23627a9520ce87b3928244b872a87 +size 10645978 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/1.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/1.jsonl index 0f73348d9..fdac20fe4 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/1.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/1.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:04f9e0ef376eff61d5f65786af3e2950b05a7740508d01695a21edd3b55fb33c -size 7514512 +oid sha256:f4c1440bfc52367321bff4badc3f0669c6955f2119e210d2306b0767849e125d +size 7454884 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/2.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/2.jsonl index 78a2fe834..e01f64611 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/2.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/2.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:59fcdfb287a58279d91d60605d75819360bee8d1599ccaf976ec89196c30913d -size 5398926 +oid sha256:3267289d3a6de6866ef6b26c0fa1b3423794b38fab83029824b5909d233c22d2 +size 5350741 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/3.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/3.jsonl index 37d1363fc..bfa3670d3 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/3.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/3.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:39a8d56d53634e1a4548d7242a4df1a5700a26d39077cfe689f821a00f0eee76 -size 5206324 +oid sha256:09138013a0f870033d9c261aa278bda60c2b1c0224b3228ca53aa67077082c44 +size 5175794 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/4.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/4.jsonl index 59cbb9318..0ff3307ee 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/4.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/4.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:63a048eb5e7ef5ddd38f0e478042a3fa5b56dda762748924aaac8283004cc230 -size 5850347 +oid sha256:29cb20f246268ef40b562490d58cc764fcaa476d635bc637f42ced61913c0e89 +size 5928270 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/5.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/5.jsonl index 097b65590..982c77ecb 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/5.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/5.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:6ee8d1989e89ba075d553344462706f9cd52a1cd7bd39f9ba494de6a68eec554 -size 6917271 +oid sha256:250913d8b5ce1790e48df3500d88f1198cc624baf38bff85b5cda56ab22b7ab1 +size 6779654 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/6.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/6.jsonl index cf61d96a1..eb9136b1b 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/6.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/6.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:f946d3a5fb605c484a053a4a57e514f3c3b8f378b205ea06367cfbb6cf362bbf -size 8212659 +oid sha256:2de2ae990a904bc17ac72d07858fbb922e6bbb228646b56f1a9a797fb89e46b0 +size 8506401 diff --git a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/7.jsonl b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/7.jsonl index 2422e5656..f80dd11ea 100644 --- a/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/7.jsonl +++ b/resources/kazu_model_pack_public/ontologies/BP_GENE_ONTOLOGY_defaults.jsonl/7.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:106d0eace504da496a831f01ffa442e054442d4941098e0f7af5589a9cb309d6 -size 5427190 +oid sha256:97f7c2634b0c3af993b5b1214103565e2d5605ebaca41f44ec7c251c49f0ffcb +size 3384422 diff --git a/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_curations.jsonl/0.jsonl b/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_curations.jsonl/0.jsonl index 34434b767..2f26c1ba2 100644 --- a/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_curations.jsonl/0.jsonl +++ b/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_curations.jsonl/0.jsonl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:72072ad8f4a457c4a5206520c9d3ea42c5bd87b82b63d4894eedeb3265b97e1b +oid sha256:8b496ef52a445b17bbb4e5503a04624922458d11854309d3812434f27bebbaea size 242040 diff --git a/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_defaults.jsonl/0.jsonl b/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_defaults.jsonl/0.jsonl index 719b26262..eedf78151 100644 --- a/resources/kazu_model_pack_public/ontologies/CC_GENE_ONTOLOGY_defaults.jsonl/0.jsonl +++ 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a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-26ac193e-466c-46bd-a767-62948a3b9737-c000.json b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-26ac193e-466c-46bd-a767-62948a3b9737-c000.json deleted file mode 100644 index 94a4722d8..000000000 --- a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-26ac193e-466c-46bd-a767-62948a3b9737-c000.json +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d2d0220884273d3e36a73134ddc5647126e4a2326284850131106a26b47c1410 -size 4412685 diff --git a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json new file mode 100644 index 000000000..6c2c8bc83 --- /dev/null +++ b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00198-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4e2693d31c3e6a5ae8c398138f91ec44d2db550f7e6ab9f87820ff5a8e75597d +size 4420515 diff --git a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-26ac193e-466c-46bd-a767-62948a3b9737-c000.json b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-26ac193e-466c-46bd-a767-62948a3b9737-c000.json deleted file mode 100644 index 811f5a65e..000000000 --- a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-26ac193e-466c-46bd-a767-62948a3b9737-c000.json +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:9aa43c3cb717e8798133e841d3cfd7a0448213dab1d55281b5f7be3cbf99b25d -size 4947863 diff --git a/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json new file mode 100644 index 000000000..f9b2b3a4c --- /dev/null +++ b/resources/kazu_model_pack_public/ontologies/opentargets/targets/part-00199-69c5ec3c-99f2-4d62-a552-4ce30eb14bdb-c000.json @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fef4a9134f59890f24d1b89a540323181bcc44b8c2b62227b8235c9a86ca5989 +size 4959391 diff --git a/resources/kazu_model_pack_public/ontologies/stato.owl b/resources/kazu_model_pack_public/ontologies/stato.owl index 8cc6c9802..6822a7cd1 100644 --- a/resources/kazu_model_pack_public/ontologies/stato.owl +++ b/resources/kazu_model_pack_public/ontologies/stato.owl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e0a1c7850da428f714f799b37b3a1c79634e97fcec785f222d8475bbe17c5cac -size 1967804 +oid sha256:1339d0e06e2234fbfc4f2c7176d909fb3fe40d132c42fe8d6e0d55964a9a6578 +size 2038542 diff --git a/resources/kazu_model_pack_public/ontologies/uberon.owl b/resources/kazu_model_pack_public/ontologies/uberon.owl index 82b9569dc..040d5f1d8 100644 --- a/resources/kazu_model_pack_public/ontologies/uberon.owl +++ b/resources/kazu_model_pack_public/ontologies/uberon.owl @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:797a8c68505e48d9a7381fb8da50d514adb43f0b77fffda7993485f3a70b0258 -size 91004643 +oid sha256:d1b34f440ff8300ea36967eeba4c275cd0a0fe6809d982aa7a23c0a6effbbb0a +size 92371275 From a17a907319464285430dea1587f19816468a74b0 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 14:06:39 +0100 Subject: [PATCH 2/8] fox: remove cache which doesn't recognise different func arguments --- kazu/ontology_preprocessing/downloads.py | 1 - 1 file changed, 1 deletion(-) diff --git a/kazu/ontology_preprocessing/downloads.py b/kazu/ontology_preprocessing/downloads.py index 88991d47d..12bf578bf 100644 --- a/kazu/ontology_preprocessing/downloads.py +++ b/kazu/ontology_preprocessing/downloads.py @@ -224,7 +224,6 @@ def __init__(self, open_targets_version: str, open_targets_dataset_name: str): self.open_targets_version = open_targets_version @staticmethod - @functools.cache def _cached_wget(full_url: str, cwd: Path) -> None: args = _get_proxy_args_for_wget() args.extend( From bb586990e803b3699a928e3a70a9bde70b7442b2 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 14:09:18 +0100 Subject: [PATCH 3/8] fix: remove button reserved for other pages --- krt/pages/1_update_ontology_version.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/krt/pages/1_update_ontology_version.py b/krt/pages/1_update_ontology_version.py index 0945bc510..c6ecd963c 100644 --- a/krt/pages/1_update_ontology_version.py +++ b/krt/pages/1_update_ontology_version.py @@ -1,13 +1,7 @@ import streamlit as st -from kazu.krt.components import show_save_button, show_reset_button -from kazu.krt.string_editor.components import ( - reset, -) from kazu.krt.ontology_update_editor.components import OntologyUpdateForm st.markdown("# Update Ontology Version") -show_save_button() -show_reset_button(reset) st.write("""This page allows you to update various public ontologies to their latest version. """) st.write("choose a parser to update") From b04ee19ffa9adc07eb87e033e08e65506efef24f Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 14:34:04 +0100 Subject: [PATCH 4/8] refactor: decouple different tests for extensibility Need to add a new test with more than one original synonym --- kazu/tests/test_synonym_generators.py | 83 +++++++++++++-------------- 1 file changed, 40 insertions(+), 43 deletions(-) diff --git a/kazu/tests/test_synonym_generators.py b/kazu/tests/test_synonym_generators.py index c0dceed64..148f9278c 100644 --- a/kazu/tests/test_synonym_generators.py +++ b/kazu/tests/test_synonym_generators.py @@ -1,6 +1,5 @@ import unicodedata from sys import maxunicode -from typing import Union import pytest from kazu.data import ( @@ -26,28 +25,9 @@ def check_generator_result( input_str: str, expected_syns: set[str], - generator: Union[CombinatorialSynonymGenerator, SynonymGenerator], + generator: SynonymGenerator, ): - if isinstance(generator, CombinatorialSynonymGenerator): - resource = OntologyStringResource( - original_synonyms=frozenset( - [ - Synonym( - text=input_str, - mention_confidence=MentionConfidence.PROBABLE, - case_sensitive=False, - ) - ] - ), - behaviour=OntologyStringBehaviour.ADD_FOR_NER_AND_LINKING, - ) - generated_resources = generator({resource}) - new_syns = { - s.text for resource in generated_resources for s in resource.alternative_synonyms - } - - else: - new_syns = generator(input_str) + new_syns = generator(input_str) assert new_syns == expected_syns @@ -238,24 +218,41 @@ def test_greek_substitution_dict_uncode_variants(): pass -def test_CombinatorialSynonymGenerator(): - generator = CombinatorialSynonymGenerator( - [ - StringReplacement(include_greek=True), - StringReplacement(replacement_dict={"-": [" ", "_"]}, include_greek=False), - ] - ) - check_generator_result( - input_str="alpha-thalassaemia", - expected_syns={ - "alpha thalassaemia", - "alpha_thalassaemia", - "α-thalassaemia", - "α thalassaemia", - "α_thalassaemia", - "Α-thalassaemia", - "Α thalassaemia", - "Α_thalassaemia", - }, - generator=generator, - ) +@pytest.mark.parametrize( + argnames=("resource", "expected_syns", "generators"), + argvalues=( + ( + OntologyStringResource( + original_synonyms=frozenset( + [ + Synonym( + text="alpha-thalassaemia", + mention_confidence=MentionConfidence.PROBABLE, + case_sensitive=False, + ) + ] + ), + behaviour=OntologyStringBehaviour.ADD_FOR_NER_AND_LINKING, + ), + { + "alpha thalassaemia", + "alpha_thalassaemia", + "α-thalassaemia", + "α thalassaemia", + "α_thalassaemia", + "Α-thalassaemia", + "Α thalassaemia", + "Α_thalassaemia", + }, + [ + StringReplacement(include_greek=True), + StringReplacement(replacement_dict={"-": [" ", "_"]}, include_greek=False), + ], + ), + ), +) +def test_CombinatorialSynonymGenerator(resource, expected_syns, generators): + generator = CombinatorialSynonymGenerator(generators) + generated_resources = generator({resource}) + new_syns = {s.text for resource in generated_resources for s in resource.alternative_synonyms} + assert new_syns == expected_syns From 989f7722b64a20eaf224d13799dfc5506e839260 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 15:27:56 +0100 Subject: [PATCH 5/8] fix: CombinatorialSynonmyGenerator should only check for original strings --- .../synonym_generation.py | 6 +-- kazu/tests/test_synonym_generators.py | 51 +++++++++++++++++++ 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/kazu/ontology_preprocessing/synonym_generation.py b/kazu/ontology_preprocessing/synonym_generation.py index 1f56dd1f7..b6f52d315 100644 --- a/kazu/ontology_preprocessing/synonym_generation.py +++ b/kazu/ontology_preprocessing/synonym_generation.py @@ -63,7 +63,7 @@ def __call__( ) final_results: defaultdict[OntologyStringResource, set[Synonym]] = defaultdict(set) original_strings = { - syn.text for resource in ontology_resources for syn in resource.active_ner_synonyms() + syn.text for resource in ontology_resources for syn in resource.original_synonyms } for i, permutation_list in enumerate(synonym_gen_permutations): logger.info( @@ -80,9 +80,7 @@ def __call__( desc=f"generating synonyms for {generator.__class__.__name__}", ): - for syn in list( - generated_results.get(resource, resource.active_ner_synonyms()) - ): + for syn in list(generated_results.get(resource, resource.original_synonyms)): new_strings = generator(syn.text) for new_syn_text in new_strings: if new_syn_text in original_strings: diff --git a/kazu/tests/test_synonym_generators.py b/kazu/tests/test_synonym_generators.py index 148f9278c..37a653f70 100644 --- a/kazu/tests/test_synonym_generators.py +++ b/kazu/tests/test_synonym_generators.py @@ -249,6 +249,57 @@ def test_greek_substitution_dict_uncode_variants(): StringReplacement(replacement_dict={"-": [" ", "_"]}, include_greek=False), ], ), + ( + OntologyStringResource( + original_synonyms=frozenset( + [ + Synonym( + text="estimate", + mention_confidence=MentionConfidence.PROBABLE, + case_sensitive=False, + ), + Synonym( + text="estimate of", + mention_confidence=MentionConfidence.PROBABLE, + case_sensitive=False, + ), + ] + ), + behaviour=OntologyStringBehaviour.ADD_FOR_NER_AND_LINKING, + ), + set(), + [ + StopWordRemover(), # normally stopword remover would remove 'of' but since "estimate" is an original synonym + # CombinatorialSynonymGenerator will skip the alternative synonym generation + ], + ), + ( + OntologyStringResource( + original_synonyms=frozenset( + [ + Synonym( + text="estimate of", + mention_confidence=MentionConfidence.PROBABLE, + case_sensitive=False, + ), + ] + ), + behaviour=OntologyStringBehaviour.ADD_FOR_NER_AND_LINKING, + alternative_synonyms=frozenset( + [ + Synonym( + text="estimate", + mention_confidence=MentionConfidence.PROBABLE, + case_sensitive=False, + ) + ] + ), + ), + {"estimate"}, + [ + StopWordRemover(), + ], + ), ), ) def test_CombinatorialSynonymGenerator(resource, expected_syns, generators): From 63392323868d8a418c0a243ec303b99f6f2364f3 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 16:13:07 +0100 Subject: [PATCH 6/8] refactor: add typing annotations in test file --- kazu/tests/test_synonym_generators.py | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/kazu/tests/test_synonym_generators.py b/kazu/tests/test_synonym_generators.py index 37a653f70..3c672223c 100644 --- a/kazu/tests/test_synonym_generators.py +++ b/kazu/tests/test_synonym_generators.py @@ -1,6 +1,7 @@ import unicodedata from sys import maxunicode +from omegaconf import DictConfig import pytest from kazu.data import ( OntologyStringResource, @@ -26,7 +27,7 @@ def check_generator_result( input_str: str, expected_syns: set[str], generator: SynonymGenerator, -): +) -> None: new_syns = generator(input_str) assert new_syns == expected_syns @@ -58,11 +59,11 @@ def check_generator_result( ), ), ) -def test_SeparatorExpansion(input_str, expected_syns): +def test_SeparatorExpansion(input_str: str, expected_syns: set[str]) -> None: check_generator_result(input_str, expected_syns, SeparatorExpansion()) -def test_StopWordRemover(): +def test_StopWordRemover() -> None: generator = StopWordRemover() check_generator_result( input_str="The cat sat in the mat", @@ -71,7 +72,7 @@ def test_StopWordRemover(): ) -def test_StringReplacement(): +def test_StringReplacement() -> None: generator = StringReplacement(replacement_dict={"cat": ["dog", "chicken"]}) check_generator_result( input_str="The cat sat on the mat", @@ -131,11 +132,13 @@ def greek_symbol_generator() -> StringReplacement: ), ), ) -def test_GreekSymbolSubstitution(input_str, expected_syns, greek_symbol_generator): +def test_GreekSymbolSubstitution( + input_str: str, expected_syns: set[str], greek_symbol_generator: StringReplacement +) -> None: check_generator_result(input_str, expected_syns, greek_symbol_generator) -def test_TokenListReplacementGenerator(): +def test_TokenListReplacementGenerator() -> None: generator = TokenListReplacementGenerator( token_lists_to_consider=[["typical", "ordinary"], ["abnormal", "incorrect"]], ) @@ -148,7 +151,7 @@ def test_TokenListReplacementGenerator(): @requires_model_pack -def test_VerbPhraseVariantGenerator(kazu_test_config): +def test_VerbPhraseVariantGenerator(kazu_test_config: DictConfig) -> None: generator = VerbPhraseVariantGenerator( tense_templates=["{NOUN} {TARGET}", "{TARGET} in {NOUN}"], spacy_model_path=kazu_test_config.SciSpacyPipeline.path, @@ -182,7 +185,7 @@ def test_VerbPhraseVariantGenerator(kazu_test_config): check_generator_result(input_str, expected_syns, generator) -def test_greek_substitution_is_stripped(): +def test_greek_substitution_is_stripped() -> None: for k, val_set in GreekSymbolSubstitution.ALL_SUBS.items(): assert k.strip() == k assert all(val.strip() == val for val in val_set) @@ -191,7 +194,7 @@ def test_greek_substitution_is_stripped(): @pytest.mark.xfail( reason="awkward casing behaviour where there are e.g. multiple uppercase theta's in unicode." ) -def test_greek_substitution_dict_casing(): +def test_greek_substitution_dict_casing() -> None: for k, val_set in GreekSymbolSubstitution.ALL_SUBS.items(): for v in val_set: # if we substitute to a greek letter, we should sub @@ -206,7 +209,7 @@ def test_greek_substitution_dict_casing(): @pytest.mark.xfail(reason="haven't covered (or marked as exceptions) all unicode greek chars yet") -def test_greek_substitution_dict_uncode_variants(): +def test_greek_substitution_dict_uncode_variants() -> None: for i in range(maxunicode): char = chr(i) try: @@ -302,7 +305,9 @@ def test_greek_substitution_dict_uncode_variants(): ), ), ) -def test_CombinatorialSynonymGenerator(resource, expected_syns, generators): +def test_CombinatorialSynonymGenerator( + resource: OntologyStringResource, expected_syns: set[str], generators: list[SynonymGenerator] +) -> None: generator = CombinatorialSynonymGenerator(generators) generated_resources = generator({resource}) new_syns = {s.text for resource in generated_resources for s in resource.alternative_synonyms} From 15741cc0d7862891808fbbea804f209ebf455d78 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Wed, 16 Oct 2024 16:24:15 +0100 Subject: [PATCH 7/8] feat: update changelog --- docs/_changelog.d/combinatorial_synonym_generator.bugfix.rst | 1 + docs/_changelog.d/krt.bugfix.rst | 1 + docs/_changelog.d/ontology_updates.feature.rst | 1 + 3 files changed, 3 insertions(+) create mode 100644 docs/_changelog.d/combinatorial_synonym_generator.bugfix.rst create mode 100644 docs/_changelog.d/krt.bugfix.rst create mode 100644 docs/_changelog.d/ontology_updates.feature.rst diff --git a/docs/_changelog.d/combinatorial_synonym_generator.bugfix.rst b/docs/_changelog.d/combinatorial_synonym_generator.bugfix.rst new file mode 100644 index 000000000..2655675d0 --- /dev/null +++ b/docs/_changelog.d/combinatorial_synonym_generator.bugfix.rst @@ -0,0 +1 @@ +Fix synonym generator to only check if strings exist in original synonyms. Update tests diff --git a/docs/_changelog.d/krt.bugfix.rst b/docs/_changelog.d/krt.bugfix.rst new file mode 100644 index 000000000..db9e33750 --- /dev/null +++ b/docs/_changelog.d/krt.bugfix.rst @@ -0,0 +1 @@ +Remove save/reset button not belonging on page 1 diff --git a/docs/_changelog.d/ontology_updates.feature.rst b/docs/_changelog.d/ontology_updates.feature.rst new file mode 100644 index 000000000..df8c38e36 --- /dev/null +++ b/docs/_changelog.d/ontology_updates.feature.rst @@ -0,0 +1 @@ +Update ontologies to later versions From 6cf4178b2acb2d4bcb9cf1c1f7bcc221a3bcb911 Mon Sep 17 00:00:00 2001 From: Szymon Palucha Date: Thu, 17 Oct 2024 13:04:11 +0100 Subject: [PATCH 8/8] refactor: update confusing function name --- kazu/ontology_preprocessing/downloads.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/kazu/ontology_preprocessing/downloads.py b/kazu/ontology_preprocessing/downloads.py index 12bf578bf..11c4fb402 100644 --- a/kazu/ontology_preprocessing/downloads.py +++ b/kazu/ontology_preprocessing/downloads.py @@ -224,7 +224,7 @@ def __init__(self, open_targets_version: str, open_targets_dataset_name: str): self.open_targets_version = open_targets_version @staticmethod - def _cached_wget(full_url: str, cwd: Path) -> None: + def _wget(full_url: str, cwd: Path) -> None: args = _get_proxy_args_for_wget() args.extend( [ @@ -241,7 +241,7 @@ def _cached_wget(full_url: str, cwd: Path) -> None: def download(self, local_path: Path, skip_download: bool = False) -> Path: if not skip_download: full_url = f"{self.OT_PREFIX}{self.open_targets_version}/output/etl/json/{self.open_targets_dataset_name}" - OpenTargetsOntologyDownloader._cached_wget(full_url, local_path.parent) + OpenTargetsOntologyDownloader._wget(full_url, local_path.parent) return local_path def version(self, local_path: Optional[Path] = None) -> str: