From fd5a294d089a5fdd92de5b9bdfc57c423c4dc7e0 Mon Sep 17 00:00:00 2001 From: cmungall Date: Sat, 17 Dec 2022 12:35:11 -0800 Subject: [PATCH 1/2] node identifiers --- Makefile | 28 +- ontologies.Makefile | 48 +- src/semsql/builder/build.Makefile | 2 +- src/semsql/builder/prefixes/obo_prefixes.csv | 762 +++++++++++++++++ src/semsql/builder/prefixes/obo_prefixes.db | Bin 110592 -> 204800 bytes src/semsql/builder/prefixes/prefixes.csv | 767 ++++++++++++++++++ .../builder/prefixes/prefixes_local.csv | 5 + src/semsql/builder/registry/ontologies.yaml | 21 + src/semsql/builder/sql_schema/rdf.sql | 17 + src/semsql/builder/sql_schema/semsql.sql | 17 + src/semsql/linkml/rdf.yaml | 21 + src/semsql/linkml/semsql.yaml | 2 +- src/semsql/sqla/omo.py | 96 ++- src/semsql/sqla/owl.py | 13 + src/semsql/sqla/rdf.py | 13 + src/semsql/sqla/semsql.py | 68 ++ tests/inputs/go-nucleus.db | Bin 1847296 -> 1847296 bytes tests/test_orm/test_basic_sqla.py | 14 +- 18 files changed, 1861 insertions(+), 33 deletions(-) diff --git a/Makefile b/Makefile index b47c99d..2062528 100644 --- a/Makefile +++ b/Makefile @@ -22,8 +22,11 @@ STAGED_ONTOLOGIES = $(patsubst %, stage/%.db.gz, $(ALL_ONTS)) TEST_ONTOLOGIES = go-nucleus robot-example +include ontologies.Makefile + all: build_all stage_all -build_all: $(patsubst %,all-%,$(ALL_ONTS)) +build_all: $(patsubst %, all-%, $(ALL_ONTS)) + echo building $(ALL_ONTS) stage_all: $(STAGED_ONTOLOGIES) echo done $(STAGED_ONTOLOGIES) @@ -79,17 +82,17 @@ realclean-%: build_prefixes: $(PREFIX_DIR)/prefixes.csv -$(PREFIX_DIR)/obo_prefixes.owl: - robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ +#$(PREFIX_DIR)/obo_prefixes.owl: +# robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ -$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl - sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $< +#$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl +# sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $< -$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db - sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ +#$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db +# sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ -$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv - cat $^ > $@ +#$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv# +# cat $^ > $@ # --- @@ -133,13 +136,6 @@ reports/%.problems.tsv: db/%.db target/%.views STAMP: touch $@ -db/reactome-Homo-sapiens.owl: download/reactome-biopax.zip db/biopax.owl - unzip -p $< Homo_sapiens.owl > $@.tmp &&\ - robot merge -i $@.tmp -i db/biopax.owl -o $@ - -download/reactome-biopax.zip: - curl -L -s https://reactome.org/download/current/biopax.zip > $@ - ## Additional ontologies src/semsql/builder/registry/registry_schema.py: src/semsql/builder/registry/registry_schema.yaml diff --git a/ontologies.Makefile b/ontologies.Makefile index ff655a3..a0c1c0c 100644 --- a/ontologies.Makefile +++ b/ontologies.Makefile @@ -28,7 +28,7 @@ download/maxo.owl: STAMP .PRECIOUS: download/maxo.owl db/maxo.owl: download/maxo.owl - robot relax -i $< merge -o $@ + robot relax -i $< merge reason -r structural -o $@ download/foodon.owl: STAMP @@ -372,6 +372,50 @@ db/uniprot.owl: download/uniprot.owl cp $< $@ +download/rhea.owl: STAMP + curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/rhea/122/rhea.owl.gz | gzip -dc > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/rhea.owl + +db/rhea.owl: download/rhea.owl + cp $< $@ + + +download/drugbank.owl: STAMP + curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz | gzip -dc > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/drugbank.owl + +db/drugbank.owl: download/drugbank.owl + cp $< $@ + + +download/drugcentral.owl: STAMP + curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz | gzip -dc > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/drugcentral.owl + +db/drugcentral.owl: download/drugcentral.owl + cp $< $@ + + +download/complexportal.owl: STAMP + curl -L -s https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz | gzip -dc > $@.tmp + sha256sum -b $@.tmp > $@.sha256 + mv $@.tmp $@ + +.PRECIOUS: download/complexportal.owl + +db/complexportal.owl: download/complexportal.owl + cp $< $@ + + download/%.owl: STAMP curl -L -s http://purl.obolibrary.org/obo/$*.owl > $@.tmp sha256sum -b $@.tmp > $@.sha256 @@ -382,4 +426,4 @@ download/%.owl: STAMP db/%.owl: download/%.owl robot merge -i $< -o $@ -EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot +EXTRA_ONTOLOGIES = chiro ncit maxo foodon chebiplus msio phenio comploinc bero aio reacto go go-lego bao orcid cpont biolink biopax enanomapper mlo ito reactome-Homo-sapiens efo edam sweetAll lov schema-dot-org cosmo co_324 hgnc.genegroup hgnc dictybase eccode uniprot rhea drugbank drugcentral complexportal diff --git a/src/semsql/builder/build.Makefile b/src/semsql/builder/build.Makefile index 0d5078f..0af149e 100644 --- a/src/semsql/builder/build.Makefile +++ b/src/semsql/builder/build.Makefile @@ -95,7 +95,7 @@ $(PREFIX_DIR)/obo_prefixes.owl: robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@ $(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl - sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $< + sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && rdftab $@ < $< $(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='' AND ns.predicate=''" > $@ diff --git a/src/semsql/builder/prefixes/obo_prefixes.csv b/src/semsql/builder/prefixes/obo_prefixes.csv index 46b0639..e71567d 100644 --- a/src/semsql/builder/prefixes/obo_prefixes.csv +++ b/src/semsql/builder/prefixes/obo_prefixes.csv @@ -1,254 +1,1016 @@ RBO,http://purl.obolibrary.org/obo/RBO_ +RBO,http://purl.obolibrary.org/obo/RBO_ +CLYH,http://purl.obolibrary.org/obo/CLYH_ +CLYH,http://purl.obolibrary.org/obo/CLYH_ +RO,http://purl.obolibrary.org/obo/RO_ +RO,http://purl.obolibrary.org/obo/RO_ +CMO,http://purl.obolibrary.org/obo/CMO_ +CMO,http://purl.obolibrary.org/obo/CMO_ +RS,http://purl.obolibrary.org/obo/RS_ +RS,http://purl.obolibrary.org/obo/RS_ +COB,http://purl.obolibrary.org/obo/COB_ +COB,http://purl.obolibrary.org/obo/COB_ +RXNO,http://purl.obolibrary.org/obo/RXNO_ +RXNO,http://purl.obolibrary.org/obo/RXNO_ +COLAO,http://purl.obolibrary.org/obo/COLAO_ +COLAO,http://purl.obolibrary.org/obo/COLAO_ +PSDO,http://purl.obolibrary.org/obo/PSDO_ +PSDO,http://purl.obolibrary.org/obo/PSDO_ +PSO,http://purl.obolibrary.org/obo/PSO_ +PSO,http://purl.obolibrary.org/obo/PSO_ +CLAO,http://purl.obolibrary.org/obo/CLAO_ +CLAO,http://purl.obolibrary.org/obo/CLAO_ +PW,http://purl.obolibrary.org/obo/PW_ +PW,http://purl.obolibrary.org/obo/PW_ +CLO,http://purl.obolibrary.org/obo/CLO_ +CLO,http://purl.obolibrary.org/obo/CLO_ +SEPIO,http://purl.obolibrary.org/obo/SEPIO_ +SEPIO,http://purl.obolibrary.org/obo/SEPIO_ +CRO,http://purl.obolibrary.org/obo/CRO_ +CRO,http://purl.obolibrary.org/obo/CRO_ +SO,http://purl.obolibrary.org/obo/SO_ +SO,http://purl.obolibrary.org/obo/SO_ +CTENO,http://purl.obolibrary.org/obo/CTENO_ +CTENO,http://purl.obolibrary.org/obo/CTENO_ +SPD,http://purl.obolibrary.org/obo/SPD_ +SPD,http://purl.obolibrary.org/obo/SPD_ +CTO,http://purl.obolibrary.org/obo/CTO_ +CTO,http://purl.obolibrary.org/obo/CTO_ +CVDO,http://purl.obolibrary.org/obo/CVDO_ +CVDO,http://purl.obolibrary.org/obo/CVDO_ +DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_ +DISDRIV,http://purl.obolibrary.org/obo/DISDRIV_ +DOID,http://purl.obolibrary.org/obo/DOID_ +DOID,http://purl.obolibrary.org/obo/DOID_ +FBcv,http://purl.obolibrary.org/obo/FBcv_ +FBcv,http://purl.obolibrary.org/obo/FBcv_ +DRON,http://purl.obolibrary.org/obo/DRON_ +DRON,http://purl.obolibrary.org/obo/DRON_ +DDANAT,http://purl.obolibrary.org/obo/DDANAT_ +DDANAT,http://purl.obolibrary.org/obo/DDANAT_ +DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_ +DDPHENO,http://purl.obolibrary.org/obo/DDPHENO_ +DIDEO,http://purl.obolibrary.org/obo/DIDEO_ +DIDEO,http://purl.obolibrary.org/obo/DIDEO_ +DUO,http://purl.obolibrary.org/obo/DUO_ +DUO,http://purl.obolibrary.org/obo/DUO_ +ECAO,http://purl.obolibrary.org/obo/ECAO_ +ECAO,http://purl.obolibrary.org/obo/ECAO_ +ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_ +ECOCORE,http://purl.obolibrary.org/obo/ECOCORE_ +EUPATH,http://purl.obolibrary.org/obo/EUPATH_ +EUPATH,http://purl.obolibrary.org/obo/EUPATH_ +ExO,http://purl.obolibrary.org/obo/ExO_ +ExO,http://purl.obolibrary.org/obo/ExO_ +FAO,http://purl.obolibrary.org/obo/FAO_ +FAO,http://purl.obolibrary.org/obo/FAO_ +FBbi,http://purl.obolibrary.org/obo/FBbi_ +FBbi,http://purl.obolibrary.org/obo/FBbi_ +ECTO,http://purl.obolibrary.org/obo/ECTO_ +ECTO,http://purl.obolibrary.org/obo/ECTO_ +EMAPA,http://purl.obolibrary.org/obo/EMAPA_ +EMAPA,http://purl.obolibrary.org/obo/EMAPA_ +ENVO,http://purl.obolibrary.org/obo/ENVO_ +ENVO,http://purl.obolibrary.org/obo/ENVO_ 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PGDSO,http://purl.obolibrary.org/obo/PGDSO_ +PGDSO,http://purl.obolibrary.org/obo/PGDSO_ +ONS,http://purl.obolibrary.org/obo/ONS_ ONS,http://purl.obolibrary.org/obo/ONS_ ONTOAVIDA,http://purl.obolibrary.org/obo/ONTOAVIDA_ +ONTOAVIDA,http://purl.obolibrary.org/obo/ONTOAVIDA_ +ADO,http://purl.obolibrary.org/obo/ADO_ ADO,http://purl.obolibrary.org/obo/ADO_ OGI,http://purl.obolibrary.org/obo/OGI_ +OGI,http://purl.obolibrary.org/obo/OGI_ +OMO,http://purl.obolibrary.org/obo/OMO_ OMO,http://purl.obolibrary.org/obo/OMO_ OMIABIS,http://purl.obolibrary.org/obo/OMIABIS_ +OMIABIS,http://purl.obolibrary.org/obo/OMIABIS_ +OMP,http://purl.obolibrary.org/obo/OMP_ OMP,http://purl.obolibrary.org/obo/OMP_ PAO,http://purl.obolibrary.org/obo/PAO_ +PAO,http://purl.obolibrary.org/obo/PAO_ +OMRSE,http://purl.obolibrary.org/obo/OMRSE_ OMRSE,http://purl.obolibrary.org/obo/OMRSE_ PD_ST,http://purl.obolibrary.org/obo/PD_ST_ +PD_ST,http://purl.obolibrary.org/obo/PD_ST_ +ONE,http://purl.obolibrary.org/obo/ONE_ ONE,http://purl.obolibrary.org/obo/ONE_ RESID,http://purl.obolibrary.org/obo/RESID_ +RESID,http://purl.obolibrary.org/obo/RESID_ +OOSTT,http://purl.obolibrary.org/obo/OOSTT_ OOSTT,http://purl.obolibrary.org/obo/OOSTT_ AGRO,http://purl.obolibrary.org/obo/AGRO_ +AGRO,http://purl.obolibrary.org/obo/AGRO_ +SAO,http://purl.obolibrary.org/obo/SAO_ SAO,http://purl.obolibrary.org/obo/SAO_ OPL,http://purl.obolibrary.org/obo/OPL_ +OPL,http://purl.obolibrary.org/obo/OPL_ +AISM,http://purl.obolibrary.org/obo/AISM_ AISM,http://purl.obolibrary.org/obo/AISM_ SEP,http://purl.obolibrary.org/obo/SEP_ +SEP,http://purl.obolibrary.org/obo/SEP_ +OPMI,http://purl.obolibrary.org/obo/OPMI_ OPMI,http://purl.obolibrary.org/obo/OPMI_ AMPHX,http://purl.obolibrary.org/obo/AMPHX_ +AMPHX,http://purl.obolibrary.org/obo/AMPHX_ +SOPHARM,http://purl.obolibrary.org/obo/SOPHARM_ SOPHARM,http://purl.obolibrary.org/obo/SOPHARM_ ORNASEQ,http://purl.obolibrary.org/obo/ORNASEQ_ +ORNASEQ,http://purl.obolibrary.org/obo/ORNASEQ_ +APO,http://purl.obolibrary.org/obo/APO_ APO,http://purl.obolibrary.org/obo/APO_ PLO,http://purl.obolibrary.org/obo/PLO_ +PLO,http://purl.obolibrary.org/obo/PLO_ +PROPREO,http://purl.obolibrary.org/obo/PROPREO_ PROPREO,http://purl.obolibrary.org/obo/PROPREO_ ONTONEO,http://purl.obolibrary.org/obo/ONTONEO_ +ONTONEO,http://purl.obolibrary.org/obo/ONTONEO_ +PDRO,http://purl.obolibrary.org/obo/PDRO_ PDRO,http://purl.obolibrary.org/obo/PDRO_ BSPO,http://purl.obolibrary.org/obo/BSPO_ +BSPO,http://purl.obolibrary.org/obo/BSPO_ +BTO,http://purl.obolibrary.org/obo/BTO_ BTO,http://purl.obolibrary.org/obo/BTO_ TAHE,http://purl.obolibrary.org/obo/TAHE_ +TAHE,http://purl.obolibrary.org/obo/TAHE_ +OVAE,http://purl.obolibrary.org/obo/OVAE_ OVAE,http://purl.obolibrary.org/obo/OVAE_ APOLLO_SV,http://purl.obolibrary.org/obo/APOLLO_SV_ +APOLLO_SV,http://purl.obolibrary.org/obo/APOLLO_SV_ +TAHH,http://purl.obolibrary.org/obo/TAHH_ TAHH,http://purl.obolibrary.org/obo/TAHH_ PATO,http://purl.obolibrary.org/obo/PATO_ +PATO,http://purl.obolibrary.org/obo/PATO_ +ARO,http://purl.obolibrary.org/obo/ARO_ ARO,http://purl.obolibrary.org/obo/ARO_ TAO,http://purl.obolibrary.org/obo/TAO_ +TAO,http://purl.obolibrary.org/obo/TAO_ +PCL,http://purl.obolibrary.org/obo/PCL_ PCL,http://purl.obolibrary.org/obo/PCL_ BCO,http://purl.obolibrary.org/obo/BCO_ +BCO,http://purl.obolibrary.org/obo/BCO_ +VHOG,http://purl.obolibrary.org/obo/VHOG_ VHOG,http://purl.obolibrary.org/obo/VHOG_ PCO,http://purl.obolibrary.org/obo/PCO_ +PCO,http://purl.obolibrary.org/obo/PCO_ +BFO,http://purl.obolibrary.org/obo/BFO_ BFO,http://purl.obolibrary.org/obo/BFO_ PHIPO,http://purl.obolibrary.org/obo/PHIPO_ +PHIPO,http://purl.obolibrary.org/obo/PHIPO_ +CDAO,http://purl.obolibrary.org/obo/CDAO_ CDAO,http://purl.obolibrary.org/obo/CDAO_ PLANA,http://purl.obolibrary.org/obo/PLANA_ +PLANA,http://purl.obolibrary.org/obo/PLANA_ +CDNO,http://purl.obolibrary.org/obo/CDNO_ CDNO,http://purl.obolibrary.org/obo/CDNO_ PLANP,http://purl.obolibrary.org/obo/PLANP_ +PLANP,http://purl.obolibrary.org/obo/PLANP_ +CHEBI,http://purl.obolibrary.org/obo/CHEBI_ CHEBI,http://purl.obolibrary.org/obo/CHEBI_ PO,http://purl.obolibrary.org/obo/PO_ +PO,http://purl.obolibrary.org/obo/PO_ +CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_ CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_ PdumDv,http://purl.obolibrary.org/obo/PdumDv_ +PdumDv,http://purl.obolibrary.org/obo/PdumDv_ +PECO,http://purl.obolibrary.org/obo/PECO_ PECO,http://purl.obolibrary.org/obo/PECO_ CARO,http://purl.obolibrary.org/obo/CARO_ +CARO,http://purl.obolibrary.org/obo/CARO_ +CL,http://purl.obolibrary.org/obo/CL_ CL,http://purl.obolibrary.org/obo/CL_ PORO,http://purl.obolibrary.org/obo/PORO_ +PORO,http://purl.obolibrary.org/obo/PORO_ +CHIRO,http://purl.obolibrary.org/obo/CHIRO_ CHIRO,http://purl.obolibrary.org/obo/CHIRO_ PPO,http://purl.obolibrary.org/obo/PPO_ +PPO,http://purl.obolibrary.org/obo/PPO_ +CHMO,http://purl.obolibrary.org/obo/CHMO_ CHMO,http://purl.obolibrary.org/obo/CHMO_ PR,http://purl.obolibrary.org/obo/PR_ +PR,http://purl.obolibrary.org/obo/PR_ +CIDO,http://purl.obolibrary.org/obo/CIDO_ CIDO,http://purl.obolibrary.org/obo/CIDO_ PROCO,http://purl.obolibrary.org/obo/PROCO_ +PROCO,http://purl.obolibrary.org/obo/PROCO_ +CIO,http://purl.obolibrary.org/obo/CIO_ CIO,http://purl.obolibrary.org/obo/CIO_ diff --git a/src/semsql/builder/prefixes/obo_prefixes.db b/src/semsql/builder/prefixes/obo_prefixes.db index 38c84d89639eb56cb568c5e1e7d036af6eb27612..814f77040880e6dcc6bf4bca4c6389879d62a9dd 100644 GIT binary patch delta 12536 zcmZX5d3+Ps)wbtK8cCKcnGlk&*v72hH*72c3CO#!yqn$Nh0WN)n0;T=1dV2f5X>~0 z03krzB)pKav}9{YLYwv_eVcu2NScMF&C)Cl+1t?YKKESl{dj-hKZ7;%+;h)4_c_bG zGwgUz-f_;oXSmIhkdRO`FmfvX$eT6&^rFN0j$F?-xS3F7xC?Ufyc@l%z018zy`A29 z-WlEoZ_r!rz1dspE%au4$9mJeL%oB&NnX2G^8DcW=GTLg_jKie>K%a$czFvZB zo<11YTx}(;Ia&j**;+2HS(*#iOm!Kq8EQ4IZK9!X|(W&;6 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+BSPO,http://purl.obolibrary.org/obo/BSPO_ +BTO,http://purl.obolibrary.org/obo/BTO_ BTO,http://purl.obolibrary.org/obo/BTO_ TAHE,http://purl.obolibrary.org/obo/TAHE_ +TAHE,http://purl.obolibrary.org/obo/TAHE_ +OVAE,http://purl.obolibrary.org/obo/OVAE_ OVAE,http://purl.obolibrary.org/obo/OVAE_ APOLLO_SV,http://purl.obolibrary.org/obo/APOLLO_SV_ +APOLLO_SV,http://purl.obolibrary.org/obo/APOLLO_SV_ +TAHH,http://purl.obolibrary.org/obo/TAHH_ TAHH,http://purl.obolibrary.org/obo/TAHH_ PATO,http://purl.obolibrary.org/obo/PATO_ +PATO,http://purl.obolibrary.org/obo/PATO_ +ARO,http://purl.obolibrary.org/obo/ARO_ ARO,http://purl.obolibrary.org/obo/ARO_ TAO,http://purl.obolibrary.org/obo/TAO_ +TAO,http://purl.obolibrary.org/obo/TAO_ +PCL,http://purl.obolibrary.org/obo/PCL_ PCL,http://purl.obolibrary.org/obo/PCL_ BCO,http://purl.obolibrary.org/obo/BCO_ +BCO,http://purl.obolibrary.org/obo/BCO_ +VHOG,http://purl.obolibrary.org/obo/VHOG_ VHOG,http://purl.obolibrary.org/obo/VHOG_ PCO,http://purl.obolibrary.org/obo/PCO_ +PCO,http://purl.obolibrary.org/obo/PCO_ +BFO,http://purl.obolibrary.org/obo/BFO_ BFO,http://purl.obolibrary.org/obo/BFO_ PHIPO,http://purl.obolibrary.org/obo/PHIPO_ +PHIPO,http://purl.obolibrary.org/obo/PHIPO_ +CDAO,http://purl.obolibrary.org/obo/CDAO_ CDAO,http://purl.obolibrary.org/obo/CDAO_ PLANA,http://purl.obolibrary.org/obo/PLANA_ +PLANA,http://purl.obolibrary.org/obo/PLANA_ +CDNO,http://purl.obolibrary.org/obo/CDNO_ CDNO,http://purl.obolibrary.org/obo/CDNO_ PLANP,http://purl.obolibrary.org/obo/PLANP_ +PLANP,http://purl.obolibrary.org/obo/PLANP_ +CHEBI,http://purl.obolibrary.org/obo/CHEBI_ CHEBI,http://purl.obolibrary.org/obo/CHEBI_ PO,http://purl.obolibrary.org/obo/PO_ +PO,http://purl.obolibrary.org/obo/PO_ +CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_ CHEMINF,http://purl.obolibrary.org/obo/CHEMINF_ PdumDv,http://purl.obolibrary.org/obo/PdumDv_ +PdumDv,http://purl.obolibrary.org/obo/PdumDv_ +PECO,http://purl.obolibrary.org/obo/PECO_ PECO,http://purl.obolibrary.org/obo/PECO_ CARO,http://purl.obolibrary.org/obo/CARO_ +CARO,http://purl.obolibrary.org/obo/CARO_ +CL,http://purl.obolibrary.org/obo/CL_ CL,http://purl.obolibrary.org/obo/CL_ PORO,http://purl.obolibrary.org/obo/PORO_ +PORO,http://purl.obolibrary.org/obo/PORO_ +CHIRO,http://purl.obolibrary.org/obo/CHIRO_ CHIRO,http://purl.obolibrary.org/obo/CHIRO_ PPO,http://purl.obolibrary.org/obo/PPO_ +PPO,http://purl.obolibrary.org/obo/PPO_ +CHMO,http://purl.obolibrary.org/obo/CHMO_ CHMO,http://purl.obolibrary.org/obo/CHMO_ PR,http://purl.obolibrary.org/obo/PR_ +PR,http://purl.obolibrary.org/obo/PR_ +CIDO,http://purl.obolibrary.org/obo/CIDO_ CIDO,http://purl.obolibrary.org/obo/CIDO_ PROCO,http://purl.obolibrary.org/obo/PROCO_ +PROCO,http://purl.obolibrary.org/obo/PROCO_ +CIO,http://purl.obolibrary.org/obo/CIO_ CIO,http://purl.obolibrary.org/obo/CIO_ diff --git a/src/semsql/builder/prefixes/prefixes_local.csv b/src/semsql/builder/prefixes/prefixes_local.csv index df21910..8038244 100644 --- a/src/semsql/builder/prefixes/prefixes_local.csv +++ b/src/semsql/builder/prefixes/prefixes_local.csv @@ -13,3 +13,8 @@ hgnc.genegroup,http://purl.obolibrary.org/obo/dictybase_ EC,http://purl.obolibrary.org/obo/eccode_ uniprot.obo,http://purl.obolibrary.org/obo/uniprot_ uniprot.obo,http://purl.obolibrary.org/obo/uniprot_ +rhea,http://purl.obolibrary.org/obo/rhea_ +uniprot.obo,http://purl.obolibrary.org/obo/uniprot_ +drugbank,http://purl.obolibrary.org/obo/drugbank_ +drugbank,http://purl.obolibrary.org/obo/drugcentral_ +complexportal,http://purl.obolibrary.org/obo/complexportal_ diff --git a/src/semsql/builder/registry/ontologies.yaml b/src/semsql/builder/registry/ontologies.yaml index 5f98321..c4dde36 100644 --- a/src/semsql/builder/registry/ontologies.yaml +++ b/src/semsql/builder/registry/ontologies.yaml @@ -143,3 +143,24 @@ ontologies: compression: gzip prefixmap: uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ + rhea: + url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/rhea/122/rhea.owl.gz + compression: gzip + prefixmap: + rhea: http://purl.obolibrary.org/obo/rhea_ + uniprot.obo: http://purl.obolibrary.org/obo/uniprot_ + drugbank: + url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugbank/5.1.9/drugbank.owl.gz + compression: gzip + prefixmap: + drugbank: http://purl.obolibrary.org/obo/drugbank_ + drugcentral: + url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/drugcentral.owl.gz + compression: gzip + prefixmap: + drugbank: http://purl.obolibrary.org/obo/drugcentral_ + complexportal: + url: https://github.com/biopragmatics/obo-db-ingest/raw/main/export/complexportal/2022-02-03/complexportal.owl.gz + compression: gzip + prefixmap: + complexportal: http://purl.obolibrary.org/obo/complexportal_ diff --git a/src/semsql/builder/sql_schema/rdf.sql b/src/semsql/builder/sql_schema/rdf.sql index 19af11f..263cb94 100644 --- a/src/semsql/builder/sql_schema/rdf.sql +++ b/src/semsql/builder/sql_schema/rdf.sql @@ -123,6 +123,10 @@ -- * Slot: language Description: the human language in which the value is encoded, e.g. en -- # Class: "node" Description: "The basic unit of representation in an RDF or OWL graph" -- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases +-- # Class: "node_identifier" Description: "" +-- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases +-- * Slot: prefix Description: A standardized prefix such as 'GO' or 'rdf' or 'FlyBase' +-- * Slot: local_identifier Description: The part of a CURIE after the colon -- # Class: "blank_node" Description: "A node with an ID that is not preserved between databases" -- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases -- # Class: "rdf_list_node" Description: "A node representing an RDF list. Note that you will not likely need to use this directly." @@ -296,6 +300,12 @@ CREATE TABLE node ( id TEXT, PRIMARY KEY (id) ); +CREATE TABLE node_identifier ( + id TEXT, + prefix TEXT, + local_identifier TEXT, + PRIMARY KEY (id) +); CREATE TABLE blank_node ( id TEXT, PRIMARY KEY (id) @@ -398,6 +408,13 @@ CREATE VIEW rdf_list_member_statement AS SELECT DROP TABLE node; CREATE VIEW node AS SELECT distinct(subject) AS id FROM statements UNION SELECT distinct(object) AS id FROM statements WHERE datatype IS NOT NULL; +DROP TABLE node_identifier; +CREATE VIEW node_identifier AS SELECT + id AS id, + substr(id,0, instr(id,':')) AS prefix, + substr(id,instr(id,':')+1) AS local_identifier + FROM node; + DROP TABLE blank_node; CREATE VIEW blank_node AS SELECT * FROM node WHERE id LIKE '_:%'; diff --git a/src/semsql/builder/sql_schema/semsql.sql b/src/semsql/builder/sql_schema/semsql.sql index cb1d788..aaf8d4d 100644 --- a/src/semsql/builder/sql_schema/semsql.sql +++ b/src/semsql/builder/sql_schema/semsql.sql @@ -416,6 +416,10 @@ -- * Slot: language Description: the human language in which the value is encoded, e.g. en -- # Class: "node" Description: "The basic unit of representation in an RDF or OWL graph" -- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases +-- # Class: "node_identifier" Description: "" +-- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases +-- * Slot: prefix Description: A standardized prefix such as 'GO' or 'rdf' or 'FlyBase' +-- * Slot: local_identifier Description: The part of a CURIE after the colon -- # Class: "blank_node" Description: "A node with an ID that is not preserved between databases" -- * Slot: id Description: An identifier for an element. Note blank node ids are not unique across databases -- # Class: "rdf_list_node" Description: "A node representing an RDF list. Note that you will not likely need to use this directly." @@ -1060,6 +1064,12 @@ CREATE TABLE node ( id TEXT, PRIMARY KEY (id) ); +CREATE TABLE node_identifier ( + id TEXT, + prefix TEXT, + local_identifier TEXT, + PRIMARY KEY (id) +); CREATE TABLE blank_node ( id TEXT, PRIMARY KEY (id) @@ -1496,6 +1506,13 @@ CREATE VIEW rdf_list_member_statement AS SELECT DROP TABLE node; CREATE VIEW node AS SELECT distinct(subject) AS id FROM statements UNION SELECT distinct(object) AS id FROM statements WHERE datatype IS NOT NULL; +DROP TABLE node_identifier; +CREATE VIEW node_identifier AS SELECT + id AS id, + substr(id,0, instr(id,':')) AS prefix, + substr(id,instr(id,':')+1) AS local_identifier + FROM node; + DROP TABLE blank_node; CREATE VIEW blank_node AS SELECT * FROM node WHERE id LIKE '_:%'; diff --git a/src/semsql/linkml/rdf.yaml b/src/semsql/linkml/rdf.yaml index 2a964b8..8073cba 100644 --- a/src/semsql/linkml/rdf.yaml +++ b/src/semsql/linkml/rdf.yaml @@ -99,6 +99,14 @@ slots: description: The base URI a prefix will expand to slot_uri: sh:namespace range: uri + local_identifier: + description: The part of a CURIE after the colon + comments: + - for OBOs this is frequently a string of zero-padded digits, but this is not always the case + aliases: + - code + - accession + range: string description: slot_uri: dcterms:description classes: @@ -257,6 +265,19 @@ classes: AS id FROM statements WHERE datatype IS NOT NULL slots: - id + node_identifier: + comments: + - |- + sqlview>> + SELECT + id AS id, + substr(id,0, instr(id,':')) AS prefix, + substr(id,instr(id,':')+1) AS local_identifier + FROM node + slots: + - id + - prefix + - local_identifier blank_node: description: A node with an ID that is not preserved between databases comments: diff --git a/src/semsql/linkml/semsql.yaml b/src/semsql/linkml/semsql.yaml index 616f7c9..6eafad8 100644 --- a/src/semsql/linkml/semsql.yaml +++ b/src/semsql/linkml/semsql.yaml @@ -47,4 +47,4 @@ imports: - obo - omo - relation_graph - - term_associations \ No newline at end of file + - term_associations diff --git a/src/semsql/sqla/omo.py b/src/semsql/sqla/omo.py index 5373f13..c1b1eb8 100644 --- a/src/semsql/sqla/omo.py +++ b/src/semsql/sqla/omo.py @@ -68,6 +68,19 @@ def __repr__(self): return f"node(id={self.id},)" +class NodeIdentifier(Base): + """ """ + + __tablename__ = "node_identifier" + + id = Column(Text(), primary_key=True) + prefix = Column(Text(), primary_key=True) + local_identifier = Column(Text(), primary_key=True) + + def __repr__(self): + return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)" + + class RdfLevelSummaryStatistic(Base): """ Abstract grouping for views/classes that provide some kind of count summary about an individual element @@ -82,6 +95,21 @@ def __repr__(self): return f"rdf_level_summary_statistic(element={self.element},count_value={self.count_value},)" +class Orcid(Node): + """ """ + + __tablename__ = "orcid" + + label = Column(Text(), primary_key=True) + id = Column(Text(), primary_key=True) + + def __repr__(self): + return f"orcid(label={self.label},id={self.id},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + class OntologyNode(Node): """ A node representing an ontology @@ -161,11 +189,13 @@ class OwlAxiomAnnotation(Statements): __tablename__ = "owl_axiom_annotation" - axiom_predicate = Column(Text(), primary_key=True) - axiom_object = Column(Text(), primary_key=True) - axiom_value = Column(Text(), primary_key=True) - axiom_language = Column(Text(), primary_key=True) - axiom_datatype = Column(Text(), primary_key=True) + annotation_subject = Column(Text(), primary_key=True) + annotation_predicate = Column(Text(), primary_key=True) + annotation_object = Column(Text(), primary_key=True) + annotation_value = Column(Text(), primary_key=True) + annotation_language = Column(Text(), primary_key=True) + annotation_datatype = Column(Text(), primary_key=True) + id = Column(Text(), primary_key=True) stanza = Column(Text(), primary_key=True) subject = Column(Text(), primary_key=True) predicate = Column(Text(), primary_key=True) @@ -175,7 +205,7 @@ class OwlAxiomAnnotation(Statements): language = Column(Text(), primary_key=True) def __repr__(self): - return f"owl_axiom_annotation(axiom_predicate={self.axiom_predicate},axiom_object={self.axiom_object},axiom_value={self.axiom_value},axiom_language={self.axiom_language},axiom_datatype={self.axiom_datatype},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + return f"owl_axiom_annotation(annotation_subject={self.annotation_subject},annotation_predicate={self.annotation_predicate},annotation_object={self.annotation_object},annotation_value={self.annotation_value},annotation_language={self.annotation_language},annotation_datatype={self.annotation_datatype},id={self.id},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html __mapper_args__ = {"concrete": True} @@ -512,16 +542,58 @@ def __repr__(self): __mapper_args__ = {"concrete": True} +class Contributor(NodeToNodeStatement): + """ """ + + __tablename__ = "contributor" + + stanza = Column(Text(), primary_key=True) + subject = Column(Text(), primary_key=True) + predicate = Column(Text(), primary_key=True) + object = Column(Text(), primary_key=True) + value = Column(Text(), primary_key=True) + datatype = Column(Text(), primary_key=True) + language = Column(Text(), primary_key=True) + + def __repr__(self): + return f"contributor(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + +class Creator(NodeToNodeStatement): + """ """ + + __tablename__ = "creator" + + stanza = Column(Text(), primary_key=True) + subject = Column(Text(), primary_key=True) + predicate = Column(Text(), primary_key=True) + object = Column(Text(), primary_key=True) + value = Column(Text(), primary_key=True) + datatype = Column(Text(), primary_key=True) + language = Column(Text(), primary_key=True) + + def __repr__(self): + return f"creator(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + class AxiomDbxrefAnnotation(OwlAxiomAnnotation): """ """ __tablename__ = "axiom_dbxref_annotation" - axiom_predicate = Column(Text(), primary_key=True) - axiom_object = Column(Text(), primary_key=True) - axiom_value = Column(Text(), primary_key=True) - axiom_language = Column(Text(), primary_key=True) - axiom_datatype = Column(Text(), primary_key=True) + annotation_subject = Column(Text(), primary_key=True) + annotation_predicate = Column(Text(), primary_key=True) + annotation_object = Column(Text(), primary_key=True) + annotation_value = Column(Text(), primary_key=True) + annotation_language = Column(Text(), primary_key=True) + annotation_datatype = Column(Text(), primary_key=True) + id = Column(Text(), primary_key=True) stanza = Column(Text(), primary_key=True) subject = Column(Text(), primary_key=True) predicate = Column(Text(), primary_key=True) @@ -531,7 +603,7 @@ class AxiomDbxrefAnnotation(OwlAxiomAnnotation): language = Column(Text(), primary_key=True) def __repr__(self): - return f"axiom_dbxref_annotation(axiom_predicate={self.axiom_predicate},axiom_object={self.axiom_object},axiom_value={self.axiom_value},axiom_language={self.axiom_language},axiom_datatype={self.axiom_datatype},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + return f"axiom_dbxref_annotation(annotation_subject={self.annotation_subject},annotation_predicate={self.annotation_predicate},annotation_object={self.annotation_object},annotation_value={self.annotation_value},annotation_language={self.annotation_language},annotation_datatype={self.annotation_datatype},id={self.id},stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html __mapper_args__ = {"concrete": True} diff --git a/src/semsql/sqla/owl.py b/src/semsql/sqla/owl.py index ef4fce7..fff6927 100644 --- a/src/semsql/sqla/owl.py +++ b/src/semsql/sqla/owl.py @@ -68,6 +68,19 @@ def __repr__(self): return f"node(id={self.id},)" +class NodeIdentifier(Base): + """ """ + + __tablename__ = "node_identifier" + + id = Column(Text(), primary_key=True) + prefix = Column(Text(), primary_key=True) + local_identifier = Column(Text(), primary_key=True) + + def __repr__(self): + return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)" + + class RdfLevelSummaryStatistic(Base): """ Abstract grouping for views/classes that provide some kind of count summary about an individual element diff --git a/src/semsql/sqla/rdf.py b/src/semsql/sqla/rdf.py index d0e8abe..2e9d0e8 100644 --- a/src/semsql/sqla/rdf.py +++ b/src/semsql/sqla/rdf.py @@ -53,6 +53,19 @@ def __repr__(self): return f"node(id={self.id},)" +class NodeIdentifier(Base): + """ """ + + __tablename__ = "node_identifier" + + id = Column(Text(), primary_key=True) + prefix = Column(Text(), primary_key=True) + local_identifier = Column(Text(), primary_key=True) + + def __repr__(self): + return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)" + + class RdfLevelSummaryStatistic(Base): """ Abstract grouping for views/classes that provide some kind of count summary about an individual element diff --git a/src/semsql/sqla/semsql.py b/src/semsql/sqla/semsql.py index 07a4a06..589f0ec 100644 --- a/src/semsql/sqla/semsql.py +++ b/src/semsql/sqla/semsql.py @@ -87,6 +87,19 @@ def __repr__(self): return f"node(id={self.id},)" +class NodeIdentifier(Base): + """ """ + + __tablename__ = "node_identifier" + + id = Column(Text(), primary_key=True) + prefix = Column(Text(), primary_key=True) + local_identifier = Column(Text(), primary_key=True) + + def __repr__(self): + return f"node_identifier(id={self.id},prefix={self.prefix},local_identifier={self.local_identifier},)" + + class RdfLevelSummaryStatistic(Base): """ Abstract grouping for views/classes that provide some kind of count summary about an individual element @@ -145,6 +158,21 @@ def __repr__(self): return f"problem(subject={self.subject},predicate={self.predicate},value={self.value},)" +class Orcid(Node): + """ """ + + __tablename__ = "orcid" + + label = Column(Text(), primary_key=True) + id = Column(Text(), primary_key=True) + + def __repr__(self): + return f"orcid(label={self.label},id={self.id},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + class OntologyNode(Node): """ A node representing an ontology @@ -756,6 +784,46 @@ def __repr__(self): __mapper_args__ = {"concrete": True} +class Contributor(NodeToNodeStatement): + """ """ + + __tablename__ = "contributor" + + stanza = Column(Text(), primary_key=True) + subject = Column(Text(), primary_key=True) + predicate = Column(Text(), primary_key=True) + object = Column(Text(), primary_key=True) + value = Column(Text(), primary_key=True) + datatype = Column(Text(), primary_key=True) + language = Column(Text(), primary_key=True) + + def __repr__(self): + return f"contributor(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + +class Creator(NodeToNodeStatement): + """ """ + + __tablename__ = "creator" + + stanza = Column(Text(), primary_key=True) + subject = Column(Text(), primary_key=True) + predicate = Column(Text(), primary_key=True) + object = Column(Text(), primary_key=True) + value = Column(Text(), primary_key=True) + datatype = Column(Text(), primary_key=True) + language = Column(Text(), primary_key=True) + + def __repr__(self): + return f"creator(stanza={self.stanza},subject={self.subject},predicate={self.predicate},object={self.object},value={self.value},datatype={self.datatype},language={self.language},)" + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = {"concrete": True} + + class AxiomDbxrefAnnotation(OwlAxiomAnnotation): """ """ diff --git a/tests/inputs/go-nucleus.db b/tests/inputs/go-nucleus.db index f406bd1a3cbeb0c616ca8aea963f333b863ac031..836a24f8b26dc45fe567534c183379cca46f1665 100644 GIT binary patch delta 515 zcmZp8P|)z8V1l&Ze+CA|!wd-UXQGZV>wgBlaF2~C4gBJEKpEpk86YXr$O|M{fY_u_ zr};O3`)__mAZFVBo1d9efmwhdU^=@2v*&b$FDyOncMO=f-!WiO+s~%JAjA;HFrDiI zivk;qFOXR^Inh94dcjS$Z`*x7vRq-BzD}QCcY4|_w%6?zUs<+Wd}Td(i=DH8L4d)C zVLHzRHaRwK2Tlea#qBy5*jzY)_A_4CEa-5CF|jeN(T`nJTbrYqy(}}eJTE^bH9j*X zHLoNyEi<(Ujq4ob>KNjx5a#I`u7D<`kXWn`?CRs{9Kxl51Ts^mJD4+z)EAc~6_*rg zWTxmC=qP07LD}k7>YADgj=>5AMX70-6*?$d5n52xYa4=fpuoP6NQZ_4gBIZKpEpk86YXr$O|M{fY_u_ zyZJYN`)__mAZFVBo1d9eftjD-&UAJIW=|IG`HUMTCmM9L-!Wj`e#d}CZ9m5v20=z2 z1{Q_s93NN|SQwfas(=doxj2DlfdJct$$}0?xBGl#xxzF(z<{|2WJwR$42!QU+bzDb zp1j4)9mpWaV8pnZP&UZ HeJvOONljz7 diff --git a/tests/test_orm/test_basic_sqla.py b/tests/test_orm/test_basic_sqla.py index 10c038b..e305013 100644 --- a/tests/test_orm/test_basic_sqla.py +++ b/tests/test_orm/test_basic_sqla.py @@ -6,7 +6,7 @@ from sqlalchemy.orm import aliased, sessionmaker from semsql.sqla.semsql import (OwlAxiomAnnotation, OwlSomeValuesFrom, - RdfsLabelStatement, RdfsSubclassOfStatement) + RdfsLabelStatement, RdfsSubclassOfStatement, NodeIdentifier) cwd = os.path.abspath(os.path.dirname(__file__)) DB_DIR = os.path.join(cwd, "../inputs") @@ -115,3 +115,15 @@ def test_axiom_annotation(self): ): ok1 = True assert ok1 + + def test_node_prefixes(self): + session = self.session + n = 0 + for row in session.query(NodeIdentifier).filter( + NodeIdentifier.prefix == "RO" + ): + logging.info(row) + n += 1 + assert row.id.startswith("RO:") + self.assertEqual(row.id, row.prefix + ":" + row.local_identifier) + From 3132bcec0bfc5e6e319c1229ab828ec0a7d9ef52 Mon Sep 17 00:00:00 2001 From: cmungall Date: Sat, 17 Dec 2022 12:36:13 -0800 Subject: [PATCH 2/2] lint --- tests/test_orm/test_basic_sqla.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/tests/test_orm/test_basic_sqla.py b/tests/test_orm/test_basic_sqla.py index e305013..80808a1 100644 --- a/tests/test_orm/test_basic_sqla.py +++ b/tests/test_orm/test_basic_sqla.py @@ -5,8 +5,9 @@ from sqlalchemy import create_engine from sqlalchemy.orm import aliased, sessionmaker -from semsql.sqla.semsql import (OwlAxiomAnnotation, OwlSomeValuesFrom, - RdfsLabelStatement, RdfsSubclassOfStatement, NodeIdentifier) +from semsql.sqla.semsql import (NodeIdentifier, OwlAxiomAnnotation, + OwlSomeValuesFrom, RdfsLabelStatement, + RdfsSubclassOfStatement) cwd = os.path.abspath(os.path.dirname(__file__)) DB_DIR = os.path.join(cwd, "../inputs") @@ -119,11 +120,8 @@ def test_axiom_annotation(self): def test_node_prefixes(self): session = self.session n = 0 - for row in session.query(NodeIdentifier).filter( - NodeIdentifier.prefix == "RO" - ): + for row in session.query(NodeIdentifier).filter(NodeIdentifier.prefix == "RO"): logging.info(row) n += 1 assert row.id.startswith("RO:") self.assertEqual(row.id, row.prefix + ":" + row.local_identifier) -