Galaxy |

Changeset 15:622cde484f4c (2012-07-12)

Previous changeset 14:68c4ae500a13 (2012-03-31) Next changeset 16:6c25e717c896 (2012-08-02)

Commit message:
Add new tool to perform OPPL queries

modified:
OPPL/FaCT++-OSX-v1.5.2/32bit/libFaCTPlusPlusJNI.jnilib
OPPL/FaCT++-OSX-v1.5.2/64bit/libFaCTPlusPlusJNI.jnilib
OPPL/FaCT++-linux-v1.5.2/32bit/FaCT++
OPPL/FaCT++-linux-v1.5.2/32bit/libFaCTPlusPlusJNI.so
OPPL/FaCT++-linux-v1.5.2/64bit/FaCT++
OPPL/FaCT++-linux-v1.5.2/64bit/libFaCTPlusPlusJNI.so
OPPL/FaCT++-linux-v1.5.2/Models.lisp/create-new-test
OPPL/README
OPPL/src/GalaxyOWLAPI.java
OPPL/test-data/ontology/single/test.owl
OPPL/test-data/oppl_script/test.oppl

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/README
--- a/OPPL/README Sat Mar 31 12:54:09 2012 +0200
+++ b/OPPL/README Thu Jul 12 17:12:00 2012 +0200

@@ -12,9 +12,11 @@
oppl_galaxy_tool.jar
inference.jar
query.jar
+oppl_query.jar
oppl_galaxy_lib/
inference_lib/
query_lib/
+oppl_query_lib/
FaCT++-linux-v1.5.2/
FaCT++-OSX-v1.5.2/

@@ -29,6 +31,7 @@
     <tool file="OPPL/oppl.xml"/>
     <tool file="OPPL/inference.xml"/>
     <tool file="OPPL/query.xml"/>
+    <tool file="OPPL/oppl_query.xml"/>
   </section>

6.- Start Galaxy.
@@ -38,7 +41,7 @@
FORESEEN FEATURES
=================

-General (OPPL, Inference, Query):
+General (OPPL, Inference, Query, OPPL query):

- Support for processing ontologies that import other ontologies loaded
in galaxy.
@@ -61,6 +64,8 @@
- Support for DataPropertyAssertion, DataPropertyHierarchy,
DifferentIndividuals, ...

+OPPL query:
+

KNOWN BUGS AND ISSUES

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query.jar

Binary file OPPL/oppl_query.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/oppl_query.xml Thu Jul 12 17:12:00 2012 +0200

@@ -0,0 +1,68 @@
+<tool id="oppl_query" name="Perform an OPPL query against an ontology" version="1.0.1">
+ <description>It performs a query, expressed in OPPL Syntax, against an OWL ontology</description>
+
+ 
+ 
+ 
+
+ 
+
+ 
+
+ <command>
+ java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null
+ </command>
+
+ 
+
+ 
+ 
+
+ 
+
+
+ <inputs>
+ <param name="ontology" type="data" label="Input ontology file"/>
+ <param name="query" type="text" size="100" value="" label="OPPL Query" />
+ <param name="reasoner" type="select" label="Choose reasoner">
+ <option value="Pellet" selected="true">Pellet</option>
+ <option value="HermiT">HermiT</option>
+ <option value="FaCTPlusPlus">FaCT++</option>
+ </param>
+ <param name="answer_format" type="select" label="Choose how to render the retrieved entities">
+ <option value="URI" selected="true">URI</option>
+ <option value="URIfragment">URI fragment</option>
+ <option value="URIfragment2OBO">OBO type URI fragment (e.g. GO_0000022 to GO:0000022)</option>
+ </param>
+ </inputs>
+ <outputs>
+ <data type="data" format="text" name="output" />
+ </outputs>
+ <tests>
+ <test>
+ <param name="input" value="test.owl"/>
+ <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/>
+ <param name="reasoner" value="Pellet"/>
+ <param name="answer_format" value="URIfragment"/>
+ <output name="out_file" file="query_result"/>
+ </test>
+ </tests>
+ <help>
+
+**About OPPL-Query-Galaxy**
+
+  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology (?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing). The result is a two column table with the entities that have been bound by the variables.
+
+**Formats**
+
+  OPPL-Query-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is a list of terms.
+
+**Contact**
+
+  Please send any request or comment to mikel.egana.aranguren@gmail.com.
+
+ </help>
+
+</tool>

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar

Binary file OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/HermiT.jar

Binary file OPPL/oppl_query_lib/HermiT.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/antlr-runtime-3.2.jar

Binary file OPPL/oppl_query_lib/antlr-runtime-3.2.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/aterm-java-1.6.jar

Binary file OPPL/oppl_query_lib/aterm-java-1.6.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/jgrapht-jdk1.5.jar

Binary file OPPL/oppl_query_lib/jgrapht-jdk1.5.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/org.coode.oppl-API.jar

Binary file OPPL/oppl_query_lib/org.coode.oppl-API.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/owlapi-bin.jar

Binary file OPPL/oppl_query_lib/owlapi-bin.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/parsers.jar

Binary file OPPL/oppl_query_lib/parsers.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-core.jar

Binary file OPPL/oppl_query_lib/pellet-core.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-datatypes.jar

Binary file OPPL/oppl_query_lib/pellet-datatypes.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-el.jar

Binary file OPPL/oppl_query_lib/pellet-el.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-owlapiv3.jar

Binary file OPPL/oppl_query_lib/pellet-owlapiv3.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-query.jar

Binary file OPPL/oppl_query_lib/pellet-query.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/oppl_query_lib/pellet-rules.jar

Binary file OPPL/oppl_query_lib/pellet-rules.jar has changed

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/src/GalaxyOWLAPI.java
--- a/OPPL/src/GalaxyOWLAPI.java Sat Mar 31 12:54:09 2012 +0200
+++ b/OPPL/src/GalaxyOWLAPI.java Thu Jul 12 17:12:00 2012 +0200

@@ -38,7 +38,6 @@
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.reasoner.InferenceType;
-import org.semanticweb.owlapi.reasoner.NodeSet;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.util.BidirectionalShortFormProvider;
@@ -63,7 +62,7 @@
/**
  * A wrapper of the OWL API
  *
- * @author Mikel Egaña Aranguren
+ * @author Mikel Ega��a Aranguren
  */
public class GalaxyOWLAPI {
private OWLOntologyManager manager;

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/src/OPPLQueryGalaxy.java
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/src/OPPLQueryGalaxy.java Thu Jul 12 17:12:00 2012 +0200

[

@@ -0,0 +1,171 @@
+/**
+ *
+ */
+package es.upm.cbgp.opplquery.oppl.galaxy;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Iterator;
+import java.util.Scanner;
+import java.util.Set;
+import java.util.logging.Logger;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.semanticweb.owlapi.expression.ParserException;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLObject;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI;
+
+import org.coode.oppl.ChangeExtractor;
+import org.coode.oppl.ConstraintSystem;
+import org.coode.oppl.OPPLParser;
+import org.coode.oppl.OPPLScript;
+import org.coode.oppl.ParserFactory;
+import org.coode.parsers.ErrorListener;
+import org.coode.parsers.LoggerErrorListener;
+import org.coode.oppl.bindingtree.Assignment;
+import org.coode.oppl.bindingtree.BindingNode;
+import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
+import org.coode.oppl.exceptions.RuntimeExceptionHandler;
+
+public class OPPLQueryGalaxy {
+
+ /**
+ * @param args
+ * @throws OWLOntologyCreationException
+ * @throws ParserException
+ * @throws FileNotFoundException
+ */
+ public static void main(String[] args) throws OWLOntologyCreationException, ParserException, FileNotFoundException {
+ // Get the arguments from command-line
+ String OWLFilePath = args [0]; // /home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/single/test.owl
+ String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
+ String Answer_render = args [2]; // URI|URIfragment|URIfragment2OBO
+ String OPPL_script_sourcee = args [3];
+
+// String OPPL_script_file = args [3];
+// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query.oppl");
+// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl");
+// File OPPL_script_file = new File("/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl");
+
+// String OPPL_script_source = "";
+// Scanner input = new Scanner(OPPL_script_file);
+// while(input.hasNext()) {
+//     String nextToken = input.next();
+//     OPPL_script_source = OPPL_script_source + " " + nextToken;
+// }
+// input.close();
+
+ // Create the manager
+ GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI();
+
+ // Load the main ontology and hope for the imported URIs to be resolvable
+ galaxyowlapi.loadMainOntology(OWLFilePath);
+
+ // Set the reasoner
+
+ // Pellet
+ if(reasoner_type.equals("Pellet")){
+ galaxyowlapi.setReasonerPellet();
+ }
+ // FaCTPlusPlus
+ else if (reasoner_type.equals("FaCTPlusPlus")){
+ galaxyowlapi.setReasonerFaCT();
+ }
+ // HermiT
+ else{
+ galaxyowlapi.setReasonerHermit();
+ }
+
+ OPPL_script_source = completeOPPLScript(OPPL_script_source);
+// System.out.println(OPPL_script_source);
+
+ ParserFactory parserFactory = new ParserFactory(galaxyowlapi.getOWLManager(), galaxyowlapi.getMainOntology(), galaxyowlapi.getReasoner());
+ Logger logger = Logger.getLogger(OPPLQueryGalaxy.class.getName());
+ ErrorListener errorListener = (ErrorListener) new LoggerErrorListener(logger);
+ OPPLParser opplparser = parserFactory.build(errorListener);
+ OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
+ RuntimeExceptionHandler exceptionhandler = new QuickFailRuntimeExceptionHandler();
+ ChangeExtractor extractor = new ChangeExtractor(exceptionhandler, true);
+ extractor.visit(OPPLscript);
+ ConstraintSystem cs = OPPLscript.getConstraintSystem();
+ Set<BindingNode> nodes =  cs.getLeaves();
+
+ Iterator NodesIterator = nodes.iterator();
+ while(NodesIterator.hasNext()){
+ Set Assignments = ((BindingNode)NodesIterator.next()).getAssignments();
+ Iterator AssignmentIterator = Assignments.iterator();
+ while(AssignmentIterator.hasNext()){
+ Assignment assignment = (Assignment)AssignmentIterator.next();
+ System.out.print(assignment.getAssignedVariable().toString());
+ System.out.print("\t");
+ String OWLObjectString = ((OWLObject)assignment.getAssignment()).toString();
+ IRI entityIRI = IRI.create(OWLObjectString.substring(1,OWLObjectString.length()-1));
+ print_result_entity(entityIRI, Answer_render);
+ System.out.print("\n");
+ }
+ }
+ }
+
+ //URI|URIfragment|URIfragment2OBO
+ private static void print_result_entity (IRI iri, String Answer_render){
+ if(Answer_render.equals("URI")){
+ System.out.print(iri);
+ }
+
+ // Weird bug: in eclipse it can print out the IRIs of every entity, but in Galaxy it can't!
+ // done manually
+ else if(Answer_render.equals("URIfragment")){
+ if(iri.toString().contains("#")){
+ System.out.print(iri.getFragment());
+ }
+ else{
+ String [] iri_tokens = iri.toString().split("/");
+ System.out.print(iri_tokens[iri_tokens.length-1]);
+ }
+ }
+ else{
+ if(iri.toString().contains("#")){
+ System.out.print((iri.getFragment()).replace("_", ":"));
+ }
+ else{
+ String [] iri_tokens = iri.toString().split("/");
+ System.out.print((iri_tokens[iri_tokens.length-1]).replace("_", ":"));
+ }
+ }
+ }
+
+ // Very crappy stuff: complete the query to make a whole OPPL script that can be parsed
+ private static String completeOPPLScript (String OPPLQuery){
+
+ // Get the first variable and add at least an axiom to make a whole script
+ Pattern p = Pattern.compile("(\\?\\w+):(CLASS|INDIVIDUAL|OBJECTPROPERTY|DATAPROPERTY|ANNOTATIONPROPERTY|CONSTANT)");
+ Matcher m = p.matcher(OPPLQuery);
+ m.find();
+ if (m.group(2).equals("CLASS")){
+ OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " SubClassOf !A END;";
+ }
+ else if (m.group(2).equals("INDIVIDUAL")){
+ OPPLQuery = OPPLQuery + " BEGIN ADD " + m.group(1) + " !p !b END;";
+ }
+ else if (m.group(2).equals("OBJECTPROPERTY")){
+ OPPLQuery = OPPLQuery + " BEGIN ADD Transitive ?p END;";
+ }
+// else if (m.group(2).equals("DATAPROPERTY")){
+// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
+// }
+// else if (m.group(2).equals("ANNOTATIONPROPERTY")){
+// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
+// }
+// else if (m.group(2).equals("CONSTANT")){
+// OPPLQuery = OPPLQuery + " BEGIN ADD ?whole SubClassOf !A END;";
+// }
+ else{
+ OPPLQuery = "Malformed OPPL query";
+ }
+ return OPPLQuery;
+ }
+}

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/test-data/ontology/single/test.owl
--- a/OPPL/test-data/ontology/single/test.owl Sat Mar 31 12:54:09 2012 +0200
+++ b/OPPL/test-data/ontology/single/test.owl Thu Jul 12 17:12:00 2012 +0200

@@ -32,6 +32,14 @@


+    
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#transitive_prop">
+        <rdf:type rdf:resource="&owl;TransitiveProperty"/>
+    </owl:ObjectProperty>
+
+
+
     

     <owl:ObjectProperty rdf:about="&Ontology1314715036188;part_of"/>
@@ -55,6 +63,12 @@


+    
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+
+
+
     

     <owl:Class rdf:about="&Ontology1314715036188;OPPL_test"/>
@@ -122,9 +136,37 @@
     <owl:Class rdf:about="&Ontology1314715036188;whole">
         <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/>
     </owl:Class>
+
+
+
+    
+
+
+
+
+    
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#A">
+        <rdf:type rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+        <Ontology1314715036188:prop rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#B"/>
+    </owl:NamedIndividual>
+
+
+
+    
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#B">
+        <rdf:type rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+    </owl:NamedIndividual>
</rdf:RDF>

-
+

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/test-data/oppl_script/test.oppl
--- a/OPPL/test-data/oppl_script/test.oppl Sat Mar 31 12:54:09 2012 +0200
+++ b/OPPL/test-data/oppl_script/test.oppl Thu Jul 12 17:12:00 2012 +0200

@@ -4,5 +4,4 @@
?part SubClassOf part_of some ?whole WHERE ?part != Nothing
BEGIN
ADD ?part SubClassOf part_of only ?whole
-END;
-
+END;
\ No newline at end of file

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/test-data/oppl_script/test_oppl_query.oppl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test-data/oppl_script/test_oppl_query.oppl Thu Jul 12 17:12:00 2012 +0200

@@ -0,0 +1,4 @@
+?whole:CLASS,
+?part:CLASS
+SELECT
+?part SubClassOf part_of some ?whole WHERE ?part != Nothing
\ No newline at end of file

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test-data/oppl_script/test_oppl_query_object_ind.oppl Thu Jul 12 17:12:00 2012 +0200

@@ -0,0 +1,4 @@
+?a:INDIVIDUAL,
+?part:CLASS,
+?c:INDIVIDUAL
+SELECT ?a prop ?c
\ No newline at end of file

diff -r 68c4ae500a13 -r 622cde484f4c OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test-data/oppl_script/test_oppl_query_object_prop.oppl Thu Jul 12 17:12:00 2012 +0200

@@ -0,0 +1,2 @@
+?p:OBJECTPROPERTY
+SELECT Transitive ?p
\ No newline at end of file