Updated readme with info on building and running. Fixes #2.

README.md

@@ -4,3 +4,57 @@ Given a YAML design pattern following the [DOSDP spec](https://github.com/dosumi
 
 For context, see:
 https://github.com/dosumis/dead_simple_owl_design_patterns/issues/9
+
+## Releases
+dosdp-scala is still somewhat experimental, but pre-packaged releases can be downloaded from [here](https://github.com/balhoff/dosdp-scala/releases).
+
+## Building
+
+Install `sbt` on your system. For Mac OS X, it is easily done using [Homebrew](http://brew.sh): `brew install sbt`
+
+To compile and build the executable package, run:
+
+`sbt stage`
+
+You will find executables for Unix and Windows in `target/universal/stage/bin/`. These depend on the libraries in `target/universal/stage/lib`.
+
+## Usage
+
+```
+Usage
+
+ dosdp-scala [options] : query an ontology for terms matching a Dead Simple OWL Design Pattern
+
+Options
+
+   --ontology    : OWL ontology to query
+   --print-query : Print generated query without running against ontology
+   --reasoner    : Reasoner to use for expanding variable constraints (currently only valid option is `elk`)
+   --template    : DOSDP file (YAML)
+```
+
+Example: `dosdp-scala --template=entity_attribute_location.yaml --print-query`
+
+Output:
+```sparql
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?attribute ?entity ?entity_attribute_location ?location
+WHERE {
+?entity_attribute_location owl:equivalentClass ?935f1722f77e4a5d83a952bd05468061 .
+?935f1722f77e4a5d83a952bd05468061 owl:intersectionOf/rdf:rest*/rdf:first ?589c79cc99244f42aca7ca788c4c5de7 .
+?935f1722f77e4a5d83a952bd05468061 owl:intersectionOf/rdf:rest*/rdf:first ?attribute .
+?935f1722f77e4a5d83a952bd05468061 owl:intersectionOf/rdf:rest/rdf:rest rdf:nil .
+?589c79cc99244f42aca7ca788c4c5de7 owl:onProperty <http://purl.obolibrary.org/obo/RO_0000052> .
+?589c79cc99244f42aca7ca788c4c5de7 owl:someValuesFrom ?c3ce064ef0e54bb580fd6e78c53646b2 .
+?c3ce064ef0e54bb580fd6e78c53646b2 owl:intersectionOf/rdf:rest*/rdf:first ?entity .
+?c3ce064ef0e54bb580fd6e78c53646b2 owl:intersectionOf/rdf:rest*/rdf:first ?1336ea47488043ecb3149ada5d1102ae .
+?c3ce064ef0e54bb580fd6e78c53646b2 owl:intersectionOf/rdf:rest/rdf:rest rdf:nil .
+?1336ea47488043ecb3149ada5d1102ae owl:onProperty <http://purl.obolibrary.org/obo/BFO_0000050> .
+?1336ea47488043ecb3149ada5d1102ae owl:someValuesFrom ?location .
+FILTER(?entity != ?1336ea47488043ecb3149ada5d1102ae)
+FILTER(?attribute != ?589c79cc99244f42aca7ca788c4c5de7)
+}
+```

build.sbt

@@ -12,6 +12,8 @@ scalacOptions := Seq("-unchecked", "-deprecation", "-encoding", "utf8")
 
 scalacOptions in Test ++= Seq("-Yrangepos")
 
+mainClass in Compile := Some("org.monarchinitiative.dosdp.Main")
+
 resolvers += Resolver.bintrayRepo("jeremyrsmith", "maven")
 
 resolvers += "Phenoscape Maven repository" at "http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/maven/repository"

src/main/scala/org/monarchinitiative/dosdp/Main.scala

@@ -20,12 +20,12 @@ import com.hp.hpl.jena.query.QueryExecutionFactory
 import com.hp.hpl.jena.query.ResultSetFormatter
 
 object Main extends CliMain[Unit](
-  name = "dosdp-query",
+  name = "dosdp-scala",
   description = "query an ontology for terms matching a Dead Simple OWL Design Pattern") {
 
   var ontOpt = opt[Option[String]](name = "ontology", description = "OWL ontology to query")
   var templateFile = opt[File](name = "template", default = new File("dosdp.yaml"), description = "DOSDP file (YAML)")
-  var reasonerNameOpt = opt[Option[String]](name = "reasoner", description = "Reasoner to use for expanding variable constraints (currently any reasoner as long as it is `elk`")
+  var reasonerNameOpt = opt[Option[String]](name = "reasoner", description = "Reasoner to use for expanding variable constraints (currently only valid option is `elk`)")
   var printQuery = opt[Boolean](name = "print-query", default = false, description = "Print generated query without running against ontology")
 
   def run: Unit = {

src/main/scala/org/monarchinitiative/dosdp/SPARQL.scala

@@ -17,6 +17,8 @@ import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom
 import org.semanticweb.owlapi.model.OWLSubClassOfAxiom
 
 import com.typesafe.scalalogging.LazyLogging
+import org.semanticweb.owlapi.model.OWLObjectUnionOf
+import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom
 
 object SPARQL extends LazyLogging {
 
@@ -115,6 +117,8 @@ ${triplesFor(dosdp).mkString("\n")}
       val listLengthTriple = s"$node owl:intersectionOf/${and.getOperands.toSeq.map(_ => "rdf:rest").mkString("/")} rdf:nil ."
       (node, (intersectionTriples.toSeq :+ listLengthTriple) ++ operandTriplesList.toSeq.flatten ++ filters)
     }
+    case or: OWLObjectUnionOf => ???
+    case only: OWLObjectAllValuesFrom => ???
   }
 
   private def genVar: String = "?" + UUID.randomUUID.toString.replaceAllLiterally("-", "")