Merge branch 'master' into shalsh-patch

phenoscape · Sep 6, 2019 · 19ac4ad · 19ac4ad
2 parents ce84e7b + 70aa8c1
commit 19ac4ad
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diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,5 @@
 language: scala
 scala:
-  - "2.11.11"
-  - "2.12.4"
+  - "2.12.8"
 jdk:
   - openjdk8
diff --git a/build.sbt b/build.sbt
@@ -10,7 +10,7 @@ mainClass in Compile := Some("org.phenoscape.owl.build.Command")
 
 scalaVersion := "2.12.8"
 
-crossScalaVersions := Seq("2.11.8", "2.12.8")
+crossScalaVersions := Seq("2.12.8")
 
 scalacOptions := Seq("-unchecked", "-deprecation", "-feature", "-encoding", "utf8")
 
@@ -28,21 +28,22 @@ testFrameworks += new TestFramework("utest.runner.Framework")
 
 libraryDependencies ++= {
   Seq(
-    "org.apache.commons" % "commons-lang3" % "3.1",
-    "commons-io" % "commons-io" % "2.4",
-    "org.jdom" % "jdom" % "2.0.2",
-    "net.sourceforge.owlapi" % "owlapi-distribution" % "4.5.8",
-    "org.semanticweb.elk" % "elk-owlapi" % "0.4.3",
-    "com.blazegraph" % "bigdata-core" % "2.1.2",
-    "org.openrdf.sesame" % "sesame-rio" % "2.7.12",
-    "org.phenoscape" %% "scowl" % "1.3",
-    "org.phenoscape" %% "owlet" % "1.6",
-    "org.phenoscape" %% "phenoscape-kb-ingest" % "1.6.1",
-    "log4j" % "log4j" % "1.2.17",
-    "org.apache.directory.studio" % "org.apache.commons.codec" % "1.8",
-    "com.github.pathikrit" %% "better-files" % "3.4.0",
-    "com.lihaoyi" %% "utest" % "0.6.3" % Test,
-    "org.phenoscape" %% "sparql-interpolator" % "1.0"
+    "org.apache.commons"          %  "commons-lang3"            % "3.1",
+    "commons-io"                  %  "commons-io"               % "2.4",
+    "org.jdom"                    %  "jdom"                     % "2.0.2",
+    "net.sourceforge.owlapi"      %  "owlapi-distribution"      % "4.5.8",
+    "org.semanticweb.elk"         %  "elk-owlapi"               % "0.4.3",
+    "com.blazegraph"              %  "bigdata-core"             % "2.1.2",
+    "org.openrdf.sesame"          %  "sesame-rio"               % "2.7.12",
+    "org.phenoscape"              %% "scowl"                    % "1.3.4",
+    "org.phenoscape"              %% "owlet"                    % "1.6",
+    "org.phenoscape"              %% "phenoscape-kb-ingest"     % "1.6.2",
+    "log4j"                       %  "log4j"                    % "1.2.17",
+    "org.apache.directory.studio" %  "org.apache.commons.codec" % "1.8",
+    "com.github.pathikrit"        %% "better-files"             % "3.4.0",
+    "com.lihaoyi"                 %% "utest"                    % "0.6.9" % Test,
+    "org.phenoscape"              %% "sparql-interpolator"      % "1.0",
+    "io.monix"                    %% "monix"                    % "3.0.0-RC2"
 
   )
 }
diff --git a/src/main/scala/org/phenoscape/owl/HomologyTableDemoRolification.scala b/src/main/scala/org/phenoscape/owl/HomologyTableDemoRolification.scala
@@ -1,21 +1,19 @@
 package org.phenoscape.owl
 
-import java.io.File
-import scala.collection.JavaConverters._
-import scala.io.Source
-import org.phenoscape.kb.ingest.util.OBOUtil
+import java.io.{File, FileOutputStream}
+
+import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.lang3.StringUtils
+import org.phenoscape.kb.ingest.util.{OBOUtil, PostCompositionParser}
+import org.phenoscape.owl.Vocab._
 import org.phenoscape.scowl._
 import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model.AddOntologyAnnotation
-import org.semanticweb.owlapi.model.IRI
-import org.semanticweb.owlapi.model.OWLAxiom
-import org.semanticweb.owlapi.model.OWLOntology
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat
+import org.semanticweb.owlapi.model.{AddOntologyAnnotation, IRI, OWLAxiom, OWLOntology}
 import org.semanticweb.owlapi.vocab.DublinCoreVocabulary
 
-import Vocab._
-import org.phenoscape.kb.ingest.util.PostCompositionParser
-import org.apache.commons.codec.digest.DigestUtils
-import org.apache.commons.lang3.StringUtils
+import scala.collection.JavaConverters._
+import scala.io.Source
 
 object HomologyTableDemoRolification extends App {
 
@@ -63,13 +61,13 @@ object HomologyTableDemoRolification extends App {
         val evidence = Individual(s"$uniquePrefix#evidence")
         val pub = factory.getOWLLiteral(items(13).trim)
         if (!negated) {
-          axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (role1.Self)) Annotation (axiom_has_evidence, evidence)
-          axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (role2.Self)) Annotation (axiom_has_evidence, evidence)
-          axioms += (property SubPropertyChain (role1 o factory.getOWLTopObjectProperty o role2)) Annotation (axiom_has_evidence, evidence)
+          axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (role1.Self)) Annotation(axiom_has_evidence, evidence)
+          axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (role2.Self)) Annotation(axiom_has_evidence, evidence)
+          axioms += (property SubPropertyChain (role1 o factory.getOWLTopObjectProperty o role2)) Annotation(axiom_has_evidence, evidence)
         }
         axioms += evidence Type evidenceCode
-        axioms += evidence Annotation (source, pub)
-      case None =>
+        axioms += evidence Annotation(source, pub)
+      case None             =>
         if (!negated) {
           axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (role1.Self))
           axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (role2.Self))
@@ -80,6 +78,6 @@ object HomologyTableDemoRolification extends App {
   }
 
   val output = convertFile(input)
-  manager.saveOntology(output, IRI.create(new File(args(1))))
+  manager.saveOntology(output, new FunctionalSyntaxDocumentFormat(), new FileOutputStream(new File(args(1))))
 
 }
diff --git a/src/main/scala/org/phenoscape/owl/HomologyTableToOWLVAHM.scala b/src/main/scala/org/phenoscape/owl/HomologyTableToOWLVAHM.scala
@@ -1,27 +1,23 @@
 package org.phenoscape.owl
 
-import java.io.File
-
-import scala.collection.JavaConverters._
-import scala.io.Source
+import java.io.{File, FileOutputStream}
 
 import org.apache.commons.codec.digest.DigestUtils
 import org.apache.commons.lang3.StringUtils
-import org.phenoscape.kb.ingest.util.OBOUtil
-import org.phenoscape.kb.ingest.util.PostCompositionParser
+import org.phenoscape.kb.ingest.util.{OBOUtil, PostCompositionParser}
+import org.phenoscape.owl.Vocab._
 import org.phenoscape.scowl._
 import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model.AddOntologyAnnotation
-import org.semanticweb.owlapi.model.IRI
-import org.semanticweb.owlapi.model.OWLAxiom
-import org.semanticweb.owlapi.model.OWLOntology
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat
+import org.semanticweb.owlapi.model.{AddOntologyAnnotation, IRI, OWLAxiom, OWLOntology}
 import org.semanticweb.owlapi.vocab.DublinCoreVocabulary
 
-import Vocab._
+import scala.collection.JavaConverters._
+import scala.io.Source
 
 /**
-  * This corresponds to the AVA homology model in the Phenoscape homology paper.
-  */
+ * This corresponds to the AVA homology model in the Phenoscape homology paper.
+ */
 object HomologyTableToOWLVAHM extends App {
 
   val factory = OWLManager.getOWLDataFactory
@@ -40,7 +36,7 @@ object HomologyTableToOWLVAHM extends App {
   def convertFile(file: Source): OWLOntology = {
     val axioms = (file.getLines.drop(1).flatMap(processEntry)).toSet.asJava
     val ontology = manager.createOntology(axioms, IRI.create("http://purl.org/phenoscape/demo/phenoscape_homology.owl"))
-    manager.applyChange(new AddOntologyAnnotation(ontology, factory.getOWLAnnotation(description, factory.getOWLLiteral("Homology Assertions using the VAHM model"))))
+    manager.applyChange(new AddOntologyAnnotation(ontology, factory.getOWLAnnotation(description, factory.getOWLLiteral("Homology Assertions using the AVA model"))))
     manager.addAxiom(ontology, HistoricalHomologyMemberof InverseOf HasHistoricalHomologyMember)
     manager.addAxiom(ontology, SerialHomologyMemberOf InverseOf HasSerialHomologyMember)
     manager.addAxiom(ontology, InHistoricalHomologyRelationshipWith SubPropertyChain (HistoricalHomologyMemberof o HasHistoricalHomologyMember))
@@ -81,14 +77,14 @@ object HomologyTableToOWLVAHM extends App {
         val evidence = Individual(s"$uniquePrefix#evidence")
         val pub = factory.getOWLLiteral(items(13).trim)
         axioms += evidence Type evidenceCode
-        axioms += evidence Annotation (source, pub)
-        axioms += ancestor Fact (has_evidence, evidence)
+        axioms += evidence Annotation(source, pub)
+        axioms += ancestor Fact(has_evidence, evidence)
       }
     }
     axioms
   }
 
   val output = convertFile(input)
-  manager.saveOntology(output, IRI.create(new File(args(1))))
+  manager.saveOntology(output, new FunctionalSyntaxDocumentFormat(), new FileOutputStream(new File(args(1))))
 
 }
diff --git a/src/main/scala/org/phenoscape/owl/HomologyTableWithTaxa.scala b/src/main/scala/org/phenoscape/owl/HomologyTableWithTaxa.scala
@@ -1,31 +1,23 @@
 package org.phenoscape.owl
 
-import java.io.File
-import java.util.UUID
+import java.io.{File, FileOutputStream}
 
-import scala.collection.JavaConverters._
-import scala.io.Source
-import org.phenoscape.kb.ingest.util.OBOUtil
+import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.lang3.StringUtils
+import org.phenoscape.kb.ingest.util.{OBOUtil, PostCompositionParser}
+import org.phenoscape.owl.Vocab._
 import org.phenoscape.scowl._
 import org.semanticweb.owlapi.apibinding.OWLManager
-import org.semanticweb.owlapi.model.AddImport
-import org.semanticweb.owlapi.model.AddOntologyAnnotation
-import org.semanticweb.owlapi.model.IRI
-import org.semanticweb.owlapi.model.OWLAxiom
-import org.semanticweb.owlapi.model.OWLOntology
+import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat
+import org.semanticweb.owlapi.model.{AddOntologyAnnotation, IRI, OWLAxiom, OWLOntology}
 import org.semanticweb.owlapi.vocab.DublinCoreVocabulary
 
-import Vocab._
-import org.phenoscape.kb.ingest.util.PostCompositionParser
-import org.semanticweb.owlapi.model.OWLClassExpression
-import org.semanticweb.owlapi.model.OWLNamedIndividual
-import org.semanticweb.owlapi.model.OWLIndividual
-import org.apache.commons.codec.digest.DigestUtils
-import org.apache.commons.lang3.StringUtils
+import scala.collection.JavaConverters._
+import scala.io.Source
 
 /**
-  * This corresponds to the REA homology model in the Phenoscape homology paper.
-  */
+ * This corresponds to the REA homology model in the Phenoscape homology paper.
+ */
 object HomologyTableWithTaxa extends App {
 
   val factory = OWLManager.getOWLDataFactory
@@ -45,7 +37,7 @@ object HomologyTableWithTaxa extends App {
   def convertFile(file: Source): OWLOntology = {
     val axioms = (file.getLines.drop(1).flatMap(processEntry)).toSet.asJava
     val ontology = manager.createOntology(axioms, IRI.create("http://purl.org/phenoscape/demo/phenoscape_homology.owl"))
-    manager.applyChange(new AddOntologyAnnotation(ontology, factory.getOWLAnnotation(description, factory.getOWLLiteral("Homology Assertions using the REAHM model"))))
+    manager.applyChange(new AddOntologyAnnotation(ontology, factory.getOWLAnnotation(description, factory.getOWLLiteral("Homology Assertions using the REA model"))))
     ontology
   }
 
@@ -75,23 +67,23 @@ object HomologyTableWithTaxa extends App {
         val evidence = Individual(s"$uniquePrefix#evidence")
         val pub = factory.getOWLLiteral(items(13).trim)
         if (!negated) {
-          axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (property some (structure2 and (in_taxon some taxon2)))) Annotation (axiom_has_evidence, evidence)
-          axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (property some (structure1 and (in_taxon some taxon1)))) Annotation (axiom_has_evidence, evidence)
+          axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (property some (structure2 and (in_taxon some taxon2)))) Annotation(axiom_has_evidence, evidence)
+          axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (property some (structure1 and (in_taxon some taxon1)))) Annotation(axiom_has_evidence, evidence)
         }
         val association = Individual(uniquePrefix)
         axioms += association Type Association
-        axioms += association Fact (has_evidence, evidence)
-        axioms += association Fact (IsNegated, negated)
+        axioms += association Fact(has_evidence, evidence)
+        axioms += association Fact(IsNegated, negated)
         val structure1Ind = Individual(s"$uniquePrefix#structure1")
         val structure2Ind = Individual(s"$uniquePrefix#structure2")
         axioms += structure1Ind Type (structure1 and (in_taxon some taxon1))
         axioms += structure2Ind Type (structure2 and (in_taxon some taxon2))
-        axioms += association Fact (HasSubject, structure1Ind)
-        axioms += association Fact (HasObject, structure2Ind)
-        axioms += association Fact (HasPredicate, Individual(property.getIRI))
+        axioms += association Fact(HasSubject, structure1Ind)
+        axioms += association Fact(HasObject, structure2Ind)
+        axioms += association Fact(HasPredicate, Individual(property.getIRI))
         axioms += evidence Type evidenceCode
-        axioms += evidence Annotation (source, pub)
-      case None =>
+        axioms += evidence Annotation(source, pub)
+      case None             =>
         if (!negated) {
           axioms += ((structure1 and (in_taxon some taxon1)) SubClassOf (property some (structure2 and (in_taxon some taxon2))))
           axioms += ((structure2 and (in_taxon some taxon2)) SubClassOf (property some (structure1 and (in_taxon some taxon1))))
@@ -101,6 +93,6 @@ object HomologyTableWithTaxa extends App {
   }
 
   val output = convertFile(input)
-  manager.saveOntology(output, IRI.create(new File(args(1))))
+  manager.saveOntology(output, new FunctionalSyntaxDocumentFormat(), new FileOutputStream(new File(args(1))))
 
 }
diff --git a/src/main/scala/org/phenoscape/owl/build/Command.scala b/src/main/scala/org/phenoscape/owl/build/Command.scala
@@ -1,28 +1,34 @@
 package org.phenoscape.owl.build
 
 import com.bigdata.rdf.store.DataLoader
-import org.phenoscape.owl.{EvolutionaryProfiles, NegationHierarchyAsserter, TaxonNode}
-import org.semanticweb.owlapi.model.OWLOntology
+import org.phenoscape.owl._
 
 object Command extends App {
 
   val commandArgs = args.drop(1)
   args(0) match {
-    case "build-kb" => PhenoscapeKB.main(commandArgs)
-    case "pairwise-sim" => RunPairwiseOWLSim.main(commandArgs)
-    case "load-triples" => DataLoader.main(commandArgs)
-    case "output-ics" => ComputeICs.main(commandArgs)
-    case "output-profile-sizes" => PrintTaxonAndGeneProfileSizes.main(commandArgs)
-    case "expects-to-triples" => ConvertScoresToTriples.main(commandArgs)
-    case "sparql-select" => RunSPARQLQuery.main(commandArgs)
-    case "sparql-construct" => RunSPARQLConstruct.main(commandArgs)
-    case "sparql-update" => RunSPARQLUpdate.main(commandArgs)
-    case "convert-nexml" => ConvertNeXML.main(commandArgs)
-    case "assert-negation-hierarchy" => NegationHierarchyAsserter.main(commandArgs)
+    case "build-kb"                     => PhenoscapeKB.main(commandArgs)
+    case "pairwise-sim"                 => RunPairwiseOWLSim.main(commandArgs)
+    case "load-triples"                 => DataLoader.main(commandArgs)
+    case "output-ics"                   => ComputeICs.main(commandArgs)
+    case "output-profile-sizes"         => PrintTaxonAndGeneProfileSizes.main(commandArgs)
+    case "expects-to-triples"           => ConvertScoresToTriples.main(commandArgs)
+    case "sparql-select"                => RunSPARQLQuery.main(commandArgs)
+    case "sparql-construct"             => RunSPARQLConstruct.main(commandArgs)
+    case "sparql-update"                => RunSPARQLUpdate.main(commandArgs)
+    case "convert-nexml"                => ConvertNeXML.main(commandArgs)
+    case "assert-negation-hierarchy"    => NegationHierarchyAsserter.main(commandArgs)
     case "output-evolutionary-profiles" => EvolutionaryProfiles.main(commandArgs)
-    case _ => {
-      println(
-        """
+
+    case "homology-table-to-owl"        =>
+      val homologyArgs = commandArgs.drop(1)
+      commandArgs(0).toLowerCase match {
+        case "rea"          => HomologyTableWithTaxa.main(homologyArgs)
+        case "ava"          => HomologyTableToOWLVAHM.main(homologyArgs)
+        case "rolification" => HomologyTableDemoRolification.main(homologyArgs)
+      }
+    case _                              => { println(
+      """
 Valid commands are:
 
 build-kb
@@ -37,6 +43,7 @@ sparql-update
 convert-nexml
 assert-negation-hierarchy
 output-evolutionary-profiles
+homology-table-to-owl
 
 Consult the source code for required parameters.
       """)

diff --git a/src/main/scala/org/phenoscape/owl/build/RunPairwiseOWLSim.scala b/src/main/scala/org/phenoscape/owl/build/RunPairwiseOWLSim.scala
@@ -1,17 +1,15 @@
 package org.phenoscape.owl.build
 
-import java.io.BufferedOutputStream
 import java.io.File
-import java.io.FileOutputStream
 import java.util.Date
-import scala.collection.JavaConverters._
-import org.openrdf.rio.RDFFormat
-import org.openrdf.rio.Rio
-import org.phenoscape.owl.sim.OWLsim
+
 import org.phenoscape.kb.ingest.util.OntUtil
+import org.phenoscape.owl.sim.OWLsim
 import org.semanticweb.owlapi.apibinding.OWLManager
 import org.semanticweb.owlapi.model.OWLNamedIndividual
 
+import scala.collection.JavaConverters._
+
 object RunPairwiseOWLSim extends App {
 
   val taskCount = args(0).toInt
@@ -41,14 +39,6 @@ object RunPairwiseOWLSim extends App {
   val startIndex = (taskNum - 1) * groupSize
   val group = orderedProfiles.drop(startIndex).take(groupSize)
   println("Computing similarity matrix")
-  val similarityMatrix = owlSim.computeAllSimilarityToCorpus(group.toSet)
-  println("Writing results to file")
-  val triplesOutput = new BufferedOutputStream(new FileOutputStream(new File(outfile)))
-  val writer = Rio.createWriter(RDFFormat.TURTLE, triplesOutput)
-  writer.startRDF()
-  similarityMatrix.foreach(writer.handleStatement)
-  writer.endRDF()
-  triplesOutput.close()
+  owlSim.computeAllSimilarityToCorpusDirectOutput(group.toSet, new File(outfile))
   println("Done: " + new Date())
-
 }