From 75bf89fd0e6bf4a82d11eb56bcff32d25d885199 Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Fri, 17 Mar 2017 12:22:35 +0000 Subject: [PATCH] Issue #57 changed uses of 'data' to 'individualAssociations' in context of the Ontology/OntologySourceData/OwlKnowledgebase in order to be more specific. --- .../org/monarchinitiative/owlsim/io/Ontology.java | 20 ++++---- .../owlsim/io/OntologySourceData.java | 55 +++++++++++----------- .../owlsim/io/OwlKnowledgeBase.java | 16 +++---- .../compute/matcher/perf/HomologyPhenoPerfIT.java | 2 +- .../owlsim/io/OntologySourceDataTest.java | 10 ++-- .../monarchinitiative/owlsim/io/OntologyTest.java | 8 ++-- .../owlsim/io/OwlKnowledgeBaseTest.java | 13 ++--- .../services/modules/KnowledgeBaseModule.java | 4 +- 8 files changed, 64 insertions(+), 64 deletions(-) diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java index 5acadf9..4d68dc0 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java @@ -105,8 +105,8 @@ private void loadOwlOntology() { //Order matters here - don't change it. mergeOntologies(sourceData.getOntologies()); mergeOntologies(sourceData.getDataOntologies()); - loadDataFromTsv(sourceData.getDataTsvs()); - loadDataFromMap(sourceData.getIndividuals()); + loadIndividualAssociationsFromTsv(sourceData.getIndividualAssociationTsvs()); + loadIndividualAssociationsFromMap(sourceData.getIndividualAssociations()); logger.info("Ontology loaded"); } @@ -138,10 +138,6 @@ private OWLOntology mergeOntologies(Collection uris) { return owlOntology; } - private ChangeApplied addAxiom(OWLAxiom axiom) { - return ontologyManager.addAxiom(owlOntology, axiom); - } - private ChangeApplied addAxioms(Set axioms) { return ontologyManager.addAxioms(owlOntology, axioms); } @@ -179,12 +175,12 @@ private OWLOntology loadOwlOntology(IRI iri) { } } - private OWLOntology loadDataFromTsv(Collection paths) { - paths.forEach(this::loadDataFromTsv); + private OWLOntology loadIndividualAssociationsFromTsv(Collection paths) { + paths.forEach(this::loadIndividualAssociationsFromTsv); return owlOntology; } - private OWLOntology loadDataFromTsv(String path) { + private OWLOntology loadIndividualAssociationsFromTsv(String path) { if (path.endsWith(".gz")) { return loadDataFromTsvGzip(path); } @@ -211,7 +207,7 @@ private OWLOntology loadDataFromTsvGzip(String path) { return owlOntology; } - private void loadDataFromMap(Map> individuals) { + private void loadIndividualAssociationsFromMap(Map> individuals) { if(!individuals.isEmpty()){ logger.info("Loading individuals from map"); } @@ -247,6 +243,10 @@ private void addInstanceOf(String individual, String ontologyClass) { } } + private ChangeApplied addAxiom(OWLAxiom axiom) { + return ontologyManager.addAxiom(owlOntology, axiom); + } + IRI toIri(String id) { return IRI.create(curieUtil.getIri(id).orElse(id)); } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java index 876ff85..e9773a1 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java @@ -20,17 +20,16 @@ private final List dataOntologies; private final Map curies; - //TODO: shouldn't this be individualsTsvs? - private final List dataTsvs; - private final Map> individuals; + private final List individualAssociationTsvs; + private final Map> individualAssociations; //TODO - labels? private OntologySourceData(Builder builder) { this.ontologies = distinctImmutableListOf(builder.ontologies); this.dataOntologies = distinctImmutableListOf(builder.dataOntologies); this.curies = ImmutableMap.copyOf(builder.curies); - this.dataTsvs = distinctImmutableListOf(builder.dataTsvs); - this.individuals = ImmutableMap.copyOf(builder.individuals); + this.individualAssociationTsvs = distinctImmutableListOf(builder.individualAssociationTsvs); + this.individualAssociations = ImmutableMap.copyOf(builder.individualAssociations); } private ImmutableList distinctImmutableListOf(List list) { @@ -49,12 +48,12 @@ private OntologySourceData(Builder builder) { return curies; } - public List getDataTsvs() { - return dataTsvs; + public List getIndividualAssociationTsvs() { + return individualAssociationTsvs; } - public Map> getIndividuals() { - return individuals; + public Map> getIndividualAssociations() { + return individualAssociations; } @Override @@ -65,13 +64,13 @@ public boolean equals(Object o) { return Objects.equals(ontologies, that.ontologies) && Objects.equals(dataOntologies, that.dataOntologies) && Objects.equals(curies, that.curies) && - Objects.equals(dataTsvs, that.dataTsvs) && - Objects.equals(individuals, that.individuals); + Objects.equals(individualAssociationTsvs, that.individualAssociationTsvs) && + Objects.equals(individualAssociations, that.individualAssociations); } @Override public int hashCode() { - return Objects.hash(ontologies, dataOntologies, curies, dataTsvs, individuals); + return Objects.hash(ontologies, dataOntologies, curies, individualAssociationTsvs, individualAssociations); } @Override @@ -80,8 +79,8 @@ public String toString() { "ontologies=" + ontologies + ", dataOntologies=" + dataOntologies + ", curies=" + curies + - ", dataTsvs=" + dataTsvs + - ", individuals=" + individuals + + ", individualAssociationTsvs=" + individualAssociationTsvs + + ", individualAssociations=" + individualAssociations + '}'; } @@ -94,8 +93,8 @@ public static Builder builder() { private List dataOntologies = new ArrayList<>(); //Curies need to be supplied if people are adding data using TSV files or pairwise mappings using curies. private Map curies = Collections.emptyMap(); - private List dataTsvs = new ArrayList<>(); - private Map> individuals = new HashMap<>(); + private List individualAssociationTsvs = new ArrayList<>(); + private Map> individualAssociations = new HashMap<>(); private Builder(){ //use the static method. @@ -162,23 +161,23 @@ public Builder dataOntologies(Collection paths) { return this; } - public Builder dataTsv(String path) { - dataTsvs.add(path); + public Builder individualAssociationsTsv(String path) { + individualAssociationTsvs.add(path); return this; } - public Builder dataTsv(String... paths) { - dataTsvs.addAll(Arrays.asList(paths)); + public Builder individualAssociationsTsv(String... paths) { + individualAssociationTsvs.addAll(Arrays.asList(paths)); return this; } - public Builder dataTsv(Collection paths) { - dataTsvs.addAll(paths); + public Builder individualAssociationsTsv(Collection paths) { + individualAssociationTsvs.addAll(paths); return this; } - public Builder data(Map> mappings) { - individuals.putAll(mappings); + public Builder individualAssociations(Map> mappings) { + individualAssociations.putAll(mappings); return this; } @@ -186,14 +185,14 @@ public OntologySourceData build() { if(ontologies.isEmpty()) { throw new OntologyLoadException("No ontology defined."); } - if (curies.isEmpty() && hasNonOntologyData()) { - throw new OntologyLoadException("Cannot load TSV data sources or pairwise mappings when curies have not been defined."); + if (curies.isEmpty() && hasIndividualAssociationData()) { + throw new OntologyLoadException("Cannot load individual class associations when curies have not been defined."); } return new OntologySourceData(this); } - private boolean hasNonOntologyData() { - return !dataTsvs.isEmpty() || !individuals.isEmpty(); + private boolean hasIndividualAssociationData() { + return !individualAssociationTsvs.isEmpty() || !individualAssociations.isEmpty(); } } } diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java index 8b40f02..7251aae 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java @@ -102,23 +102,23 @@ public Loader loadDataFromOntologies(Collection paths) { return this; } - public Loader loadDataFromTsv(String path) { - sourceDataBuilder.dataTsv(path); + public Loader loadIndividualAssociationsFromTsv(String path) { + sourceDataBuilder.individualAssociationsTsv(path); return this; } - public Loader loadDataFromTsv(String... paths) { - sourceDataBuilder.dataTsv(paths); + public Loader loadIndividualAssociationsFromTsv(String... paths) { + sourceDataBuilder.individualAssociationsTsv(paths); return this; } - public Loader loadDataFromTsv(Collection paths) { - sourceDataBuilder.dataTsv(paths); + public Loader loadIndividualAssociationsFromTsv(Collection paths) { + sourceDataBuilder.individualAssociationsTsv(paths); return this; } - public Loader loadDataFromMap(Map> data) { - sourceDataBuilder.data(data); + public Loader loadIndividualAssociations(Map> data) { + sourceDataBuilder.individualAssociations(data); return this; } diff --git a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/HomologyPhenoPerfIT.java b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/HomologyPhenoPerfIT.java index e8e4270..0cb9276 100644 --- a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/HomologyPhenoPerfIT.java +++ b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/HomologyPhenoPerfIT.java @@ -127,7 +127,7 @@ private void load() throws OWLOntologyCreationException, IOException { kb = OwlKnowledgeBase.loader() .loadCuries(curies) .loadOntology("src/test/resources/ontologies/mammal.obo.gz") - .loadDataFromTsv( + .loadIndividualAssociationsFromTsv( "src/test/resources/data/gene2taxon.tsv.gz", "src/test/resources/data/mouse-pheno.assocs.gz", "src/test/resources/data/human-pheno.assocs.gz") diff --git a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologySourceDataTest.java b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologySourceDataTest.java index b392205..3ccd0ff 100644 --- a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologySourceDataTest.java +++ b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologySourceDataTest.java @@ -47,10 +47,10 @@ public void testItAll() { OntologySourceData sourceData = OntologySourceData.builder() .curies(curies) .ontology("src/test/resources/ontologies/mammal.obo.gz") - .dataTsv("src/test/resources/data/gene2taxon.tsv.gz") - .dataTsv("src/test/resources/data/mouse-pheno.assocs.gz") - .dataTsv("src/test/resources/data/human-pheno.assocs.gz") - .data(individuals) + .individualAssociationsTsv("src/test/resources/data/gene2taxon.tsv.gz") + .individualAssociationsTsv("src/test/resources/data/mouse-pheno.assocs.gz") + .individualAssociationsTsv("src/test/resources/data/human-pheno.assocs.gz") + .individualAssociations(individuals) .build(); System.out.println(sourceData); @@ -60,7 +60,7 @@ public void testItAll() { public void testThrowsExceptionWhenCuriesEmptyAndDataIncludedFromTsv() { OntologySourceData sourceData = OntologySourceData.builder() - .dataTsv("src/test/resources/data/gene2taxon.tsv.gz") + .individualAssociationsTsv("src/test/resources/data/gene2taxon.tsv.gz") .build(); System.out.println(sourceData); diff --git a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologyTest.java b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologyTest.java index a1c6e30..8fcd0a2 100644 --- a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologyTest.java +++ b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologyTest.java @@ -33,7 +33,7 @@ private Ontology getBobOnlyOntology() { OntologySourceData sourceData = OntologySourceData.builder() .ontology("src/test/resources/species-no-individuals.owl") .curies(curies) - .data(data) + .individualAssociations(data) .build(); return Ontology.load(sourceData); @@ -61,7 +61,7 @@ public void testAddNullIndividuals() { OntologySourceData sourceData = OntologySourceData.builder() .ontology("src/test/resources/species-no-individuals.owl") .curies(curies) - .data(data) + .individualAssociations(data) .build(); Ontology.load(sourceData); @@ -77,7 +77,7 @@ public void testAddNullClasses() { OntologySourceData sourceData = OntologySourceData.builder() .ontology("src/test/resources/species-no-individuals.owl") .curies(curies) - .data(data) + .individualAssociations(data) .build(); Ontology.load(sourceData); @@ -97,7 +97,7 @@ public void testAddIndividuals() { OntologySourceData sourceData = OntologySourceData.builder() .ontology("src/test/resources/species-no-individuals.owl") .curies(curies) - .data(data) + .individualAssociations(data) .build(); Ontology ontology = Ontology.load(sourceData); diff --git a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBaseTest.java b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBaseTest.java index e25c085..484f9ba 100644 --- a/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBaseTest.java +++ b/owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBaseTest.java @@ -76,7 +76,7 @@ public void testLoadRemoteOntology() { @Test(expected = OntologyLoadException.class) public void testLoadGzippedDataFileNoOntology() { BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader() - .loadDataFromTsv("src/test/resources/data/human-pheno.assocs.gz") + .loadIndividualAssociationsFromTsv("src/test/resources/data/human-pheno.assocs.gz") .createKnowledgeBase(); } @@ -102,8 +102,9 @@ public void loadDataFromOntologies() { public void loadDataFromTsv() { BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader() .loadCuries(curies()) - .loadOntology("src/test/resources/species-no-individuals.owl") - .loadDataFromTsv("src/test/resources/data/species-individuals.tsv") +// .loadOntology("src/test/resources/species-no-individuals.owl") + .loadOntology("src/test/resources/species.owl") + .loadIndividualAssociationsFromTsv("src/test/resources/data/species-individuals.tsv") .createKnowledgeBase(); } @@ -112,7 +113,7 @@ public void loadDataFromGzippedTsv() { BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader() .loadCuries(curies()) .loadOntology("src/test/resources/ontologies/mammal.obo.gz") - .loadDataFromTsv("src/test/resources/data/human-pheno.assocs.gz") + .loadIndividualAssociationsFromTsv("src/test/resources/data/human-pheno.assocs.gz") .createKnowledgeBase(); } @@ -121,7 +122,7 @@ public void loadDataFromTsvCollection() { BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader() .loadCuries(curies()) .loadOntology("src/test/resources/ontologies/mammal.obo.gz") - .loadDataFromTsv(Arrays.asList( + .loadIndividualAssociationsFromTsv(Arrays.asList( "src/test/resources/data/gene2taxon.tsv.gz", "src/test/resources/data/mouse-pheno.assocs.gz", "src/test/resources/data/human-pheno.assocs.gz")) @@ -154,7 +155,7 @@ public void loadDataFromMap() { BMKnowledgeBase knowledgeBase = BMKnowledgeBase.owlLoader() .loadOntology("src/test/resources/species-no-individuals.owl") .loadCuries(curies) - .loadDataFromMap(data) + .loadIndividualAssociations(data) .createKnowledgeBase(); System.out.println("knowledgebase individuals are: " + knowledgeBase.getIndividualIdsInSignature()); diff --git a/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java b/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java index 8a19ef4..dde9e3b 100644 --- a/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java +++ b/owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java @@ -28,7 +28,7 @@ public KnowledgeBaseModule(Collection ontologyUris, Collection o ontologyUris.forEach(logger::info); logger.info("Loading ontologyDataUris:"); ontologyDataUris.forEach(logger::info); - logger.info("Loading dataTsvs:"); + logger.info("Loading individual associations Tsvs:"); dataTsvs.forEach(logger::info); logger.info("Loading curies:"); curies.entrySet().forEach(logger::info); @@ -37,7 +37,7 @@ public KnowledgeBaseModule(Collection ontologyUris, Collection o this.bmKnowledgeBase = OwlKnowledgeBase.loader() .loadOntologies(ontologyUris) .loadDataFromOntologies(ontologyDataUris) - .loadDataFromTsv(dataTsvs) + .loadIndividualAssociationsFromTsv(dataTsvs) .loadCuries(curies) .createKnowledgeBase();