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Merge pull request #65 from phenoscape/cleanup
Lots of cleanup.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| sbt.version=1.1.6 | ||
| sbt.version=1.3.10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,2 @@ | ||
| addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % "1.3.15") | ||
| addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % "1.7.1") | ||
| addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.3.4") |
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16 changes: 7 additions & 9 deletions
16
src/main/scala/org/phenoscape/owl/DevelopsFromRuleGenerator.scala
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11 changes: 3 additions & 8 deletions
11
src/main/scala/org/phenoscape/owl/EQCharactersGenerator.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,92 +1,85 @@ | ||
| package org.phenoscape.owl | ||
|
|
||
| import scala.collection.JavaConverters._ | ||
| import org.phenoscape.scowl._ | ||
| import org.semanticweb.owlapi.apibinding.OWLManager | ||
| import org.semanticweb.elk.owlapi.ElkReasonerFactory | ||
| import org.semanticweb.owlapi.model.IRI | ||
| import org.apache.log4j.BasicConfigurator | ||
| import org.apache.log4j.Logger | ||
| import org.apache.log4j.Level | ||
| import java.io.File | ||
| import java.io.{BufferedOutputStream, File, FileOutputStream} | ||
| import java.util.Date | ||
| import org.semanticweb.owlapi.model.OWLClass | ||
| import org.semanticweb.owlapi.model.OWLAxiom | ||
| import java.io.FileOutputStream | ||
| import java.io.BufferedOutputStream | ||
| import java.util.zip.GZIPOutputStream | ||
| import org.semanticweb.owlapi.model.AddImport | ||
|
|
||
| import org.phenoscape.owl.Vocab._ | ||
| import org.phenoscape.scowl._ | ||
| import org.semanticweb.elk.owlapi.ElkReasonerFactory | ||
| import org.semanticweb.owlapi.apibinding.OWLManager | ||
| import org.semanticweb.owlapi.model.parameters.Imports | ||
| import org.semanticweb.owlapi.model.{AddImport, IRI, OWLAxiom, OWLClass} | ||
| import org.semanticweb.owlapi.reasoner.InferenceType | ||
| import Vocab._ | ||
|
|
||
| import scala.collection.JavaConverters._ | ||
|
|
||
| //takes at least 200 GB memory | ||
| object EQCreator { | ||
|
|
||
| def main(args: Array[String]): Unit = { | ||
| BasicConfigurator.configure(); | ||
| Logger.getRootLogger().setLevel(Level.ERROR); | ||
| println(new Date() + ": starting"); | ||
| val manager = OWLManager.createOWLOntologyManager(); | ||
| val factory = manager.getOWLDataFactory(); | ||
| val eqs = manager.createOntology(); | ||
| manager.addAxiom(eqs, factory.getOWLTransitiveObjectPropertyAxiom(has_part)); | ||
| manager.addAxiom(eqs, factory.getOWLReflexiveObjectPropertyAxiom(has_part)); | ||
| manager.addAxiom(eqs, factory.getOWLTransitiveObjectPropertyAxiom(part_of)); | ||
| manager.addAxiom(eqs, factory.getOWLReflexiveObjectPropertyAxiom(part_of)); | ||
| manager.addAxiom(eqs, factory.getOWLInverseObjectPropertiesAxiom(has_part, part_of)); | ||
| val uberon = manager.loadOntologyFromOntologyDocument(new File("uberon.owl")); | ||
| val pato = manager.loadOntologyFromOntologyDocument(new File("pato.owl")); | ||
| manager.applyChange(new AddImport(eqs, factory.getOWLImportsDeclaration(uberon.getOntologyID.getOntologyIRI.get))); | ||
| manager.applyChange(new AddImport(eqs, factory.getOWLImportsDeclaration(pato.getOntologyID.getOntologyIRI.get))); | ||
| val anatomicalEntity = Class(IRI.create("http://purl.obolibrary.org/obo/UBERON_0001062")); | ||
| val qualityRoot = Class(IRI.create("http://purl.obolibrary.org/obo/PATO_0000001")); | ||
| val uberonReasoner = new ElkReasonerFactory().createReasoner(uberon); | ||
| val patoReasoner = new ElkReasonerFactory().createReasoner(pato); | ||
| val anatomicalEntities = uberonReasoner.getSubClasses(anatomicalEntity, false).getFlattened(); | ||
| uberonReasoner.dispose(); | ||
| val qualities = patoReasoner.getSubClasses(qualityRoot, false).getFlattened(); | ||
| patoReasoner.dispose(); | ||
| println(new Date() + ": building"); | ||
| println(new Date() + ": starting") | ||
| val manager = OWLManager.createOWLOntologyManager() | ||
| val factory = manager.getOWLDataFactory | ||
| val eqs = manager.createOntology() | ||
| manager.addAxiom(eqs, factory.getOWLTransitiveObjectPropertyAxiom(has_part)) | ||
| manager.addAxiom(eqs, factory.getOWLReflexiveObjectPropertyAxiom(has_part)) | ||
| manager.addAxiom(eqs, factory.getOWLTransitiveObjectPropertyAxiom(part_of)) | ||
| manager.addAxiom(eqs, factory.getOWLReflexiveObjectPropertyAxiom(part_of)) | ||
| manager.addAxiom(eqs, factory.getOWLInverseObjectPropertiesAxiom(has_part, part_of)) | ||
| val uberon = manager.loadOntologyFromOntologyDocument(new File("uberon.owl")) | ||
| val pato = manager.loadOntologyFromOntologyDocument(new File("pato.owl")) | ||
| manager.applyChange(new AddImport(eqs, factory.getOWLImportsDeclaration(uberon.getOntologyID.getOntologyIRI.get))) | ||
| manager.applyChange(new AddImport(eqs, factory.getOWLImportsDeclaration(pato.getOntologyID.getOntologyIRI.get))) | ||
| val anatomicalEntity = Class(IRI.create("http://purl.obolibrary.org/obo/UBERON_0001062")) | ||
| val qualityRoot = Class(IRI.create("http://purl.obolibrary.org/obo/PATO_0000001")) | ||
| val uberonReasoner = new ElkReasonerFactory().createReasoner(uberon) | ||
| val patoReasoner = new ElkReasonerFactory().createReasoner(pato) | ||
| val anatomicalEntities = uberonReasoner.getSubClasses(anatomicalEntity, false).getFlattened | ||
| uberonReasoner.dispose() | ||
| val qualities = patoReasoner.getSubClasses(qualityRoot, false).getFlattened | ||
| patoReasoner.dispose() | ||
| println(new Date() + ": building") | ||
| for { | ||
| entity <- anatomicalEntities.asScala | ||
| quality <- qualities.asScala | ||
| } manager.addAxiom(eqs, createEQ(entity, quality)); | ||
| println(new Date() + ": saving EQs"); | ||
| val outputStream = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(new File(args(0) + ".gz")))); | ||
| manager.saveOntology(eqs, outputStream); | ||
| outputStream.close(); | ||
| println(new Date() + ": done saving"); | ||
| val hierarchy = manager.createOntology(); | ||
| println(new Date() + ": starting classification"); | ||
| val eqReasoner = new ElkReasonerFactory().createReasoner(eqs); | ||
| eqReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY); // | ||
| println(new Date() + ": done classification"); | ||
| //MaterializeInferences.materializeInferences(hierarchy, eqReasoner); | ||
| println(new Date() + ": starting axiom generation"); | ||
| val allClasses = eqs.getClassesInSignature(true).asScala; | ||
| } manager.addAxiom(eqs, createEQ(entity, quality)) | ||
| println(new Date() + ": saving EQs") | ||
| val outputStream = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(new File(args(0) + ".gz")))) | ||
| manager.saveOntology(eqs, outputStream) | ||
| outputStream.close() | ||
| println(new Date() + ": done saving") | ||
| val hierarchy = manager.createOntology() | ||
| println(new Date() + ": starting classification") | ||
| val eqReasoner = new ElkReasonerFactory().createReasoner(eqs) | ||
| eqReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY) // | ||
| println(new Date() + ": done classification") | ||
| //MaterializeInferences.materializeInferences(hierarchy, eqReasoner) | ||
| println(new Date() + ": starting axiom generation") | ||
| val allClasses = eqs.getClassesInSignature(Imports.INCLUDED).asScala | ||
| for (owlClass <- allClasses) { | ||
| val newAxioms = eqReasoner | ||
| .getSuperClasses(owlClass, true) | ||
| .getFlattened() | ||
| .getFlattened | ||
| .asScala | ||
| .map(owlClass SubClassOf _) | ||
| .filterNot(eqs.containsAxiom(_, true)); | ||
| manager.addAxioms(hierarchy, newAxioms.asJava); | ||
| .filterNot(eqs.containsAxiom(_, true)) | ||
| manager.addAxioms(hierarchy, newAxioms.asJava) | ||
| } | ||
| println(new Date() + ": done axiom generation"); | ||
| println(new Date() + ": saving hierarchy"); | ||
| println(new Date() + ": done axiom generation") | ||
| println(new Date() + ": saving hierarchy") | ||
| val hierarchyOutputStream = new GZIPOutputStream( | ||
| new BufferedOutputStream(new FileOutputStream(new File(args(1) + ".gz"))) | ||
| ); | ||
| manager.saveOntology(hierarchy, hierarchyOutputStream); | ||
| hierarchyOutputStream.close(); | ||
| println(new Date() + ": done saving"); | ||
| System.exit(0); | ||
| ) | ||
| manager.saveOntology(hierarchy, hierarchyOutputStream) | ||
| hierarchyOutputStream.close() | ||
| println(new Date() + ": done saving") | ||
| System.exit(0) | ||
| } | ||
|
|
||
| def createEQ(entity: OWLClass, quality: OWLClass): OWLAxiom = { | ||
| val eqClass = Class(IRI.create(entity.getIRI().toString() + "+" + quality.getIRI().toString())); | ||
| eqClass EquivalentTo (has_part some ((part_of some entity) and (bearer_of some quality))); | ||
| val eqClass = Class(IRI.create(entity.getIRI.toString + "+" + quality.getIRI.toString)) | ||
| eqClass EquivalentTo (has_part some ((part_of some entity) and (bearer_of some quality))) | ||
| } | ||
|
|
||
| } |
12 changes: 6 additions & 6 deletions
12
src/main/scala/org/phenoscape/owl/ExtractNamedClassHierarchy.scala
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