Galaxy |

Changeset 18:d3616fac4ca5 (2012-09-20)

Previous changeset 17:c9e01f86b07c (2012-08-20) Next changeset 19:cc270db37d33 (2012-10-06)

Commit message:
Elk support added

modified:
OPPL/README
OPPL/inference.jar
OPPL/inference.xml
OPPL/merge.jar
OPPL/merge.xml
OPPL/oppl.xml
OPPL/oppl_galaxy.jar
OPPL/oppl_query.jar
OPPL/oppl_query.xml
OPPL/query.jar
OPPL/query.xml
OPPL/src/GalaxyOWLAPI.java
OPPL/src/InferenceGalaxy.java
OPPL/src/OPPLGalaxy.java
OPPL/src/OPPLQueryGalaxy.java
OPPL/src/OWLQueryGalaxy.java

added:
OPPL/inference_lib/elk-owlapi.jar
OPPL/inference_lib/log4j-sources.jar
OPPL/inference_lib/log4j.jar
OPPL/merge_lib/elk-owlapi.jar
OPPL/merge_lib/log4j-sources.jar
OPPL/merge_lib/log4j.jar
OPPL/oppl_galaxy_lib/elk-owlapi.jar
OPPL/oppl_galaxy_lib/log4j-sources.jar
OPPL/oppl_galaxy_lib/log4j.jar
OPPL/oppl_query_lib/elk-owlapi.jar
OPPL/oppl_query_lib/log4j-sources.jar
OPPL/oppl_query_lib/log4j.jar
OPPL/query_lib/elk-owlapi.jar
OPPL/query_lib/log4j-sources.jar
OPPL/query_lib/log4j.jar
OPPL/test-data/ontology/single/elk.owl

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/README
--- a/OPPL/README Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/README Thu Sep 20 12:46:36 2012 +0200

@@ -45,11 +45,11 @@
=================

- Support for processing ontologies that import other ontologies loaded
-in galaxy (i.e. to resolve imports within galaxy).
+in Galaxy (i.e. to resolve imports within galaxy).

- Entities rendering definition (URI fragment, rdfs:label, QName, etc).

-- OWLLink, Racer and ELK support.
+- OWLLink and Racer support.

- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf
cell).
@@ -107,6 +107,6 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

-OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.
+OPPL API, OWL API, Pellet, HermiT, Elk and FaCT++ have their own licenses.

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/inference.jar

Binary file OPPL/inference.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/inference.xml
--- a/OPPL/inference.xml Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/inference.xml Thu Sep 20 12:46:36 2012 +0200

@@ -13,6 +13,7 @@
<option value="Pellet" selected="true">Pellet</option>
<option value="HermiT">HermiT</option>
<option value="FaCTPlusPlus">FaCT++</option>
+ <option value="Elk">Elk (Not all axioms supported)</option>
</param>
<param name="axioms" type="select" display="checkboxes" multiple="true" label="Select what axioms to add as asserted">
  <option value="CLASS_ASSERTIONS">CLASS_ASSERTIONS</option>
@@ -37,40 +38,16 @@

**About Inference-Galaxy**

-  Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology.
-
-**Formats**
-
-  Inference-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 OWL (RDF/XML).
+  Inference-Galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology.

**Usage**

-  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. In case the ontology includes imports, they should be resolvable.
-
-  The reasoner can be Pellet, HermiT or FaCT++.
-
-  The inferred axioms to add as asserted axioms can be chosen.
-
-**More information**
-
-  Galaxy public instances with Inference-Galaxy pre-installed:
-
-  http://sele.inf.um.es:8080/
+  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Inference-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. In case the loaded ontology includes OWL imports, Inference-Galaxy will try to resolve them.

-  http://linkeddata2.dia.fi.upm.es:8080
-
-  Links of interest:
-
-  http://owlapi.sourceforge.net/
-
-  http://www.w3.org/TR/owl2-manchester-syntax/
-
-  http://clarkparsia.com/pellet
-
-  http://hermit-reasoner.com/
-
-  http://code.google.com/p/factplusplus/
-
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.
+
+  The inferred axioms to add as asserted axioms can be chosen.
+
**Contact**

   Please send any request or comment to mikel.egana.aranguren@gmail.com.

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/inference_lib/elk-owlapi.jar

Binary file OPPL/inference_lib/elk-owlapi.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/inference_lib/log4j-sources.jar

Binary file OPPL/inference_lib/log4j-sources.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/inference_lib/log4j.jar

Binary file OPPL/inference_lib/log4j.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/merge.jar

Binary file OPPL/merge.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/merge.xml
--- a/OPPL/merge.xml Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/merge.xml Thu Sep 20 12:46:36 2012 +0200

@@ -27,11 +27,13 @@

**About Merge-Galaxy**

-  Merge-Galaxy can be used to merge any imported ontologies into the main ontology, creating a new ontology.
+  Merge-Galaxy can be used to merge any (resolvable) imported ontologies into the main ontology, creating a new ontology.

-**Formats**
-
-  Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load, provided that imports are correctly represented: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is an OWL ontology in RDF/XML format.
+**Usage**
+
+  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. Merge-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.
+
+  An URI can be specified for the new merged ontology. In case non is specified, the following URI will be used: http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl.

**Contact**

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/merge_lib/elk-owlapi.jar

Binary file OPPL/merge_lib/elk-owlapi.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/merge_lib/log4j-sources.jar

Binary file OPPL/merge_lib/log4j-sources.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/merge_lib/log4j.jar

Binary file OPPL/merge_lib/log4j.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl.xml
--- a/OPPL/oppl.xml Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/oppl.xml Thu Sep 20 12:46:36 2012 +0200

@@ -11,20 +11,18 @@



- <command>
- java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null
- </command>
-
-
+ 






- 
+ </command>

@@ -42,12 +40,13 @@

<inputs>
<param name="input" type="data" label="Input ontology file"/>
+ <param format="text" name="OPPL" type="data" label="OPPL file"/>
<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>
+ <option value="Elk">Elk (Not all axioms supported)</option>
</param>
- <param format="text" name="OPPL" type="data" label="OPPL file"/>
<param name="format" type="select" label="Choose ontology output format">
<option value="OWL" selected="true">OWL</option>
<option value="OBO">OBO</option>
@@ -69,29 +68,21 @@

**About OPPL-Galaxy**

-  OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in an ontology, saving time and efforts.
-
-**Formats**
-
-  OPPL-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 available output formats are OBO flat file and OWL (RDF/XML).
+  OPPL-Galaxy can be used to execute an OPPL script against an ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in an ontology, saving time and energy.

**Usage**

-  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool.
-
-  Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.
+  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool. OPPL-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. In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them.
+
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.

-  In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them.
-
-  The output ontology can be OBO or OWL (RDF/XML).
-
-  The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner.
+  The output ontology can be OBO or OWL (RDF/XML).

**More information**

   Galaxy public instances with OPPL-Galaxy pre-installed:

-  http://sele.inf.um.es:8080/
+  http://sele.inf.um.es:9080/

   http://linkeddata2.dia.fi.upm.es:8080

@@ -107,8 +98,6 @@

   http://oppl.sf.net/

-  http://owlapi.sourceforge.net/
-
   http://www.w3.org/TR/owl2-manchester-syntax/

   http://clarkparsia.com/pellet
@@ -117,9 +106,13 @@

   http://code.google.com/p/factplusplus/

+  http://code.google.com/p/elk-reasoner/
+
+  http://owlapi.sourceforge.net/
+
**Citation**

-  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011.
+  Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. In Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, SWAT4LS 2011, pages 12–19, ACM 2012.

**Contact**

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_galaxy.jar

Binary file OPPL/oppl_galaxy.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_galaxy_lib/elk-owlapi.jar

Binary file OPPL/oppl_galaxy_lib/elk-owlapi.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_galaxy_lib/log4j-sources.jar

Binary file OPPL/oppl_galaxy_lib/log4j-sources.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_galaxy_lib/log4j.jar

Binary file OPPL/oppl_galaxy_lib/log4j.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_query.jar

Binary file OPPL/oppl_query.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_query.xml
--- a/OPPL/oppl_query.xml Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/oppl_query.xml Thu Sep 20 12:46:36 2012 +0200

@@ -20,7 +20,7 @@


+ </command>-->

<inputs>
@@ -30,6 +30,7 @@
<option value="Pellet" selected="true">Pellet</option>
<option value="HermiT">HermiT</option>
<option value="FaCTPlusPlus">FaCT++</option>
+ <option value="Elk">Elk (Not all axioms supported)</option>
</param>
<param name="answer_format" type="select" label="Choose how to render the retrieved entities">
<option value="URI" selected="true">URI</option>
@@ -53,11 +54,17 @@

**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.
+  OPPL-Query-Galaxy can be used to execute an OPPL query against an OWL ontology. The result is a two column table with the entities that have been bound by the variables.
+
+**Usage**
+
+  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. 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. In case the loaded ontology includes OWL imports, OPPL-Query-Galaxy will try to resolve them.

-**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.
+  An OPPL query must be provided, e.g. ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing.
+
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.
+
+  The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).

**Contact**

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_query_lib/elk-owlapi.jar

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

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_query_lib/log4j-sources.jar

Binary file OPPL/oppl_query_lib/log4j-sources.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/oppl_query_lib/log4j.jar

Binary file OPPL/oppl_query_lib/log4j.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/query.jar

Binary file OPPL/query.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/query.xml
--- a/OPPL/query.xml Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/query.xml Thu Sep 20 12:46:36 2012 +0200

@@ -16,7 +16,7 @@


+ </command>-->

<inputs>
@@ -26,6 +26,7 @@
<option value="Pellet" selected="true">Pellet</option>
<option value="HermiT">HermiT</option>
<option value="FaCTPlusPlus">FaCT++</option>
+ <option value="Elk">Elk (Not all axioms supported)</option>
</param>
<param name="answer_type" type="select" label="Choose answer type">
<option value="Descendants">Descendant classes</option>
@@ -58,11 +59,19 @@

**About Query-Galaxy**

-  Query-Galaxy can be used to execute a DL query against an OWL ontology (e.g. GO_0007049 or part_of some GO_0007049). The result is a list of entities from the target ontology. How those entities relate to the query can be chosen (A DL query is just an anonymous OWL Class).
+  Query-Galaxy can be used to execute a DL query against an OWL ontology. The result is a list of entities from the target ontology.

-**Formats**
-
-  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.
+**Usage**
+
+  An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. 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. In case the loaded ontology includes OWL imports, Query-Galaxy will try to resolve them.
+
+  A DL query must be provided, e.g. GO_0007049 or part_of some GO_0007049.
+
+  The reasoner can be Pellet, HermiT, FaCT++ or Elk.
+
+  How the retrieved entities relate to the query can be chosen: a DL query is just an anonymous OWL Class, and the retrieved entities can be descendant classes, direct sub-classes, ancestor classes, direct super-classes, equivalent classes, or member individuals.
+
+  The returned entities can be rendered using their URI, their URI fragment, or OBO type URI fragment (e.g. GO_0000022 to GO:0000022).

**Contact**

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/query_lib/elk-owlapi.jar

Binary file OPPL/query_lib/elk-owlapi.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/query_lib/log4j-sources.jar

Binary file OPPL/query_lib/log4j-sources.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/query_lib/log4j.jar

Binary file OPPL/query_lib/log4j.jar has changed

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/src/GalaxyOWLAPI.java
--- a/OPPL/src/GalaxyOWLAPI.java Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/src/GalaxyOWLAPI.java Thu Sep 20 12:46:36 2012 +0200

@@ -12,10 +12,13 @@
import java.util.Scanner;
import java.util.Set;

+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
import org.coode.owlapi.obo.parser.OBOOntologyFormat;
import org.coode.parsers.BidirectionalShortFormProviderAdapter;
import org.semanticweb.HermiT.Reasoner;
+import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.expression.OWLEntityChecker;
import org.semanticweb.owlapi.expression.ParserException;
@@ -110,6 +113,14 @@
reasonerFactory = new Reasoner.ReasonerFactory();
reasoner = reasonerFactory.createReasoner(ontology);
}
+ public void setReasonerElk (){
+ reasonerFactory = new ElkReasonerFactory();
+ Logger.getLogger("org.semanticweb.elk").setLevel(Level.OFF);
+ reasoner = reasonerFactory.createReasoner(ontology);
+ }
+ public void disposeReasoner(){
+ reasoner.dispose();
+ }
public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{
OWLOntologyMerger merger = new OWLOntologyMerger(manager);
// OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology));

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/src/InferenceGalaxy.java
--- a/OPPL/src/InferenceGalaxy.java Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/src/InferenceGalaxy.java Thu Sep 20 12:46:36 2012 +0200

[

@@ -11,7 +11,7 @@

/**
- * @author Mikel Egaña Aranguren
+ * @author Mikel Ega��a Aranguren
*
*/
public class InferenceGalaxy {
@@ -25,7 +25,7 @@
public static void main(String[] args) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException {
// Get the arguments from command-line
String OWLFilePath = args [0];
- String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
+ String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
String axioms_to_inject = args [2]; // CLASS_ASSERTIONS,CLASS_HIERARCHY,DATA_PROPERTY_ASSERTIONS

// CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology.
@@ -54,6 +54,10 @@
else if (reasoner_type.equals("FaCTPlusPlus")){
galaxyowlapi.setReasonerFaCT();
}
+ // Elk
+ else if (reasoner_type.equals("Elk")){
+ galaxyowlapi.setReasonerElk();
+ }
// HermiT
else{
galaxyowlapi.setReasonerHermit();
@@ -70,6 +74,8 @@
injectAxiom (axioms_to_inject, galaxyowlapi);
}

+ galaxyowlapi.disposeReasoner();
+
// Merge imported ontologies if requested
// if(merge.equals("Merge")){
// galaxyowlapi.merge();

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/src/OPPLGalaxy.java
--- a/OPPL/src/OPPLGalaxy.java Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/src/OPPLGalaxy.java Thu Sep 20 12:46:36 2012 +0200

[

@@ -7,13 +7,16 @@
import java.io.IOException;
import java.util.List;
import java.util.Scanner;
+import java.util.logging.Level;
import java.util.logging.Logger;

+//import org.apache.log4j.Level;
import org.coode.oppl.ChangeExtractor;
import org.coode.oppl.OPPLParser;
import org.coode.oppl.OPPLScript;
import org.coode.oppl.ParserFactory;
import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;
+import org.coode.oppl.log.Logging;
import org.coode.parsers.ErrorListener;
import org.coode.parsers.LoggerErrorListener;
import org.semanticweb.owlapi.model.OWLAxiomChange;
@@ -25,8 +28,9 @@

+
/**
- * @author Mikel Egaña Aranguren
+ * @author Mikel Ega��a Aranguren
*
*/
public class OPPLGalaxy {
@@ -40,7 +44,7 @@
public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException {
// Get the arguments from command-line
String OWLFilePath = args [0];
- String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
+ String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|Elk|HermiT

String OPPL_script_file = args [2];
String OWL = args [3]; // OWL|OBO
@@ -61,6 +65,10 @@
else if (reasoner_type.equals("FaCTPlusPlus")){
galaxyowlapi.setReasonerFaCT();
}
+ // Elk
+ else if (reasoner_type.equals("Elk")){
+ galaxyowlapi.setReasonerElk();
+ }
// HermiT
else{
galaxyowlapi.setReasonerHermit();
@@ -83,18 +91,20 @@
// Parse the OPPL script
ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner);
Logger logger = Logger.getLogger(OPPLGalaxy.class.getName());
+// logger.setLevel(Level.OFF);
// Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
+
ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
OPPLParser opplparser = parserFactory.build(errorListener);
OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
-
-

// Execute the script
ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true);
List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
manager.applyChanges(changes);

+ galaxyowlapi.disposeReasoner();
+
// Merge imported ontologies if requested
// if(merge.equals("Merge")){
// galaxyowlapi.merge();

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/src/OPPLQueryGalaxy.java
--- a/OPPL/src/OPPLQueryGalaxy.java Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/src/OPPLQueryGalaxy.java Thu Sep 20 12:46:36 2012 +0200

[

@@ -42,7 +42,7 @@
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 reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk
String Answer_render = args [2]; // URI|URIfragment|URIfragment2OBO
String OPPL_script_source = args [3];

@@ -75,6 +75,10 @@
else if (reasoner_type.equals("FaCTPlusPlus")){
galaxyowlapi.setReasonerFaCT();
}
+ // Elk
+ else if (reasoner_type.equals("Elk")){
+ galaxyowlapi.setReasonerElk();
+ }
// HermiT
else{
galaxyowlapi.setReasonerHermit();
@@ -93,6 +97,8 @@
extractor.visit(OPPLscript);
ConstraintSystem cs = OPPLscript.getConstraintSystem();
Set<BindingNode> nodes = cs.getLeaves();
+
+ galaxyowlapi.disposeReasoner();

Iterator NodesIterator = nodes.iterator();
while(NodesIterator.hasNext()){

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/src/OWLQueryGalaxy.java
--- a/OPPL/src/OWLQueryGalaxy.java Mon Aug 20 11:39:56 2012 +0200
+++ b/OPPL/src/OWLQueryGalaxy.java Thu Sep 20 12:46:36 2012 +0200

[

@@ -19,7 +19,7 @@
public static void main(String[] args) throws OWLOntologyCreationException, ParserException {
// Get the arguments from command-line
String OWLFilePath = args [0]; // /home/pik/UPM/Paper/SWAT4LS_2011/JBS/Workflows_JBS/GO_module_transitive/go_no_trans.owl
- String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT
+ String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT|Elk

String Answer_type = args [2]; // Individuals|EquivalentClasses|DirectSuperClasses|Ancestors|DirectSubClasses|Descendants
String Answer_render = args [3]; // URI|URIfragment|URIfragment2OBO
@@ -41,6 +41,10 @@
else if (reasoner_type.equals("FaCTPlusPlus")){
galaxyowlapi.setReasonerFaCT();
}
+ // Elk
+ else if (reasoner_type.equals("Elk")){
+ galaxyowlapi.setReasonerElk();
+ }
// HermiT
else{
galaxyowlapi.setReasonerHermit();
@@ -52,30 +56,35 @@
// Execute query and print results
if(Answer_type.equals("Individuals")){
Set<OWLNamedIndividual> inds = galaxyowlapi.getIndividuals(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLNamedIndividual ind : inds){
print_result_entity(ind.getIRI(), Answer_render);
}
}
else if (Answer_type.equals("EquivalentClasses")) {
Set<OWLClass> answer_classes = galaxyowlapi.getEquivalentClasses(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLClass cls : answer_classes){
print_result_entity(cls.getIRI(), Answer_render);
}
}
else if (Answer_type.equals("DirectSuperClasses")) {
Set<OWLClass> answer_classes = galaxyowlapi.getDirectSuperClasses(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLClass cls : answer_classes){
print_result_entity(cls.getIRI(), Answer_render);
}
}
else if (Answer_type.equals("Ancestors")) {
Set<OWLClass> answer_classes = galaxyowlapi.getAncestors(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLClass cls : answer_classes){
print_result_entity(cls.getIRI(), Answer_render);
}
}
else if (Answer_type.equals("DirectSubClasses")) {
Set<OWLClass> answer_classes = galaxyowlapi.getDirectSubClasses(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLClass cls : answer_classes){
print_result_entity(cls.getIRI(), Answer_render);
}
@@ -83,6 +92,7 @@
// Descendants
else {
Set<OWLClass> answer_classes = galaxyowlapi.getDescendants(class_expr);
+ galaxyowlapi.disposeReasoner();
for(OWLClass cls : answer_classes){
print_result_entity(cls.getIRI(), Answer_render);
}

diff -r c9e01f86b07c -r d3616fac4ca5 OPPL/test-data/ontology/single/elk.owl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test-data/ontology/single/elk.owl Thu Sep 20 12:46:36 2012 +0200

[

@@ -0,0 +1,106 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY debug "http://www.samuelcroset.com/debug.owl#" >
+    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+]>
+
+
+<rdf:RDF xmlns="http://www.samuelcroset.com/debug.owl#"
+     xml:base="http://www.samuelcroset.com/debug.owl"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:debug="http://www.samuelcroset.com/debug.owl#">
+    <owl:Ontology rdf:about="http://www.samuelcroset.com/debug.owl"/>
+
+
+
+    
+
+
+
+
+    
+
+    <owl:ObjectProperty rdf:about="&debug;eats"/>
+
+
+
+    
+
+
+
+
+    
+
+    <owl:Class rdf:about="&debug;Animal"/>
+
+
+
+    
+
+    <owl:Class rdf:about="&debug;Food"/>
+
+
+
+    
+
+    <owl:Class rdf:about="&debug;Lion">
+        <rdfs:subClassOf rdf:resource="&debug;Animal"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&debug;eats"/>
+                <owl:someValuesFrom rdf:resource="&debug;Meat"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+
+
+    
+
+    <owl:Class rdf:about="&debug;Meat">
+        <rdfs:subClassOf rdf:resource="&debug;Food"/>
+    </owl:Class>
+
+
+
+    
+
+    <owl:Class rdf:about="&debug;MeatEater">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="&debug;Animal"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="&debug;eats"/>
+                        <owl:someValuesFrom rdf:resource="&debug;Meat"/>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+    </owl:Class>
+</rdf:RDF>
+
+
+
+
+