changeset 0:137f9a4a6337 draft

First version to init the repo, still README etc to add but it works

Binary file SPARQLGalaxy.jar has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SPARQLGalaxy.xml	Thu Oct 25 12:17:40 2012 -0400
@@ -0,0 +1,56 @@
+<tool id="SPARQLGalaxy" name="Execute an SPARQL query against an OWL ontology" version="1.0.1">
+	<description>It executes an SPARQL query against the input OWL ontology and generates a two column tab file with the variables and bound entities</description>
+	<command>
+	  java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/SPARQLGalaxy.jar $ontology $query_file > $output 2>/dev/null 
+	</command>
+	<inputs>
+		<param name="ontology" type="data" label="Input ontology file"/>
+		<param name="query_file" type="data" label="Input SPARQL query file"/>
+	</inputs>
+	<outputs>
+		<data format="text" name="output" />
+	</outputs>
+	<!--<tests>
+		<test>
+			<param name="input" value="test.owl"/>
+			<param name="OPPL" value="test.oppl"/>
+			<param name="format" value="OWL"/>
+			<param name="reasoner" value="Pellet"/>
+			<output name="out_file" file="test_new.owl"/>	
+		</test>
+	</tests>-->
+	<help>
+
+**Usage**
+
+  An OWL ontology in RDF/XML syntax and a plain text file with the SPARQL are needed. See bundle for examples.
+
+**More information**
+
+  Galaxy public instance with SPARQL-Galaxy pre-installed:
+  
+  http://biordf.org:8090/
+  
+  SPARQL: 
+  
+  http://www.w3.org/standards/techs/sparql
+ 
+  JENA:
+  
+  http://jena.apache.org/
+  
+**Authors and funding**
+
+  Alejandro Rodríguez González is funded by the Isaac Peral Programme and developed the Java wrapper for JENA.
+  
+  Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme and developed the XML file for this tool.
+  
+  They both belong to the Biological Informatics group of the CBGP, Spain (http://wilkinsonlab.info/).
+
+**Contact**
+
+  Please send any request or comment to [e-mail].
+
+	</help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/es/cbgp/galaxy/sparql/jena/OntologyManager.java	Thu Oct 25 12:17:40 2012 -0400
@@ -0,0 +1,32 @@
+package es.cbgp.galaxy.sparql.jena;
+
+import java.io.File;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+public class OntologyManager {
+
+	private String ontFile;
+	private String sparqlFile;
+	private OntModel model;
+	private SPARQLQueryEngine sqe;
+
+	public OntologyManager(String of, String sf) throws Exception {
+		this.ontFile = of;
+		this.sparqlFile = sf;
+		init();
+	}
+
+	private void init() throws Exception {
+		this.model = ModelFactory.createOntologyModel();
+		this.model.read(new File(ontFile).toURI().toString());
+	}
+
+	public void executeQuery() throws Exception {
+		this.sqe = new SPARQLQueryEngine(model);
+		this.sqe.setQueryFile(sparqlFile);
+		String ret = sqe.executeQuery();
+		System.out.println(ret);
+	}
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/es/cbgp/galaxy/sparql/jena/SPARQLQueryEngine.java	Thu Oct 25 12:17:40 2012 -0400
@@ -0,0 +1,66 @@
+package es.cbgp.galaxy.sparql.jena;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.util.Iterator;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.query.*;
+import com.hp.hpl.jena.shared.Lock;
+
+public class SPARQLQueryEngine {
+
+	private OntModel queryModel;
+	private String sparqlFile;
+
+	public SPARQLQueryEngine(OntModel om) {
+		this.queryModel = om;
+	}
+
+	public String executeQuery() throws Exception {
+		String finalQuery = loadQueryFromFile();
+		// System.out.println("Final query: " + finalQuery);
+		Query query = null;
+		QueryExecution qexec = null;
+		try {
+			queryModel.enterCriticalSection(Lock.READ);
+			query = QueryFactory.create(finalQuery);
+			qexec = QueryExecutionFactory.create(query, queryModel);
+			ResultSet results = qexec.execSelect();
+			String res = "";
+			while (results.hasNext()) {
+				QuerySolution qs = results.next();
+				Iterator<String> vars = qs.varNames();
+				while (vars.hasNext()) {
+					String var = vars.next();
+					if (!qs.getResource(var).isAnon()) {
+						res += "?" + var + "\t" + qs.getResource(var) + "\n";
+					}
+				}
+			}
+			return res;
+		} catch (Exception e) {
+			e.printStackTrace();
+		} finally {
+			queryModel.leaveCriticalSection();
+			if (qexec != null) {
+				qexec.close();
+			}
+		}
+		return null;
+	}
+
+	private String loadQueryFromFile() throws Exception {
+		String query = "";
+		BufferedReader bL = new BufferedReader(new FileReader(this.sparqlFile));
+		while (bL.ready()) {
+			query += bL.readLine();
+		}
+		bL.close();
+		return query;
+	}
+
+	public void setQueryFile(String sparqlFile) {
+		this.sparqlFile = sparqlFile;
+	}
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/es/cbgp/galaxy/sparql/main/Main.java	Thu Oct 25 12:17:40 2012 -0400
@@ -0,0 +1,54 @@
+package es.cbgp.galaxy.sparql.main;
+
+import java.io.File;
+
+import es.cbgp.galaxy.sparql.jena.OntologyManager;
+
+public class Main {
+
+	public Main(String args[]) {
+		Result r = check(args);
+		if (r.getBoolValue()) {
+			String ontFile = args[0];
+			String sparqlFile = args[1];
+			run(ontFile, sparqlFile);
+		} else {
+			System.err.println("Error: " + r.getMessage());
+		}
+	}
+
+	private void run(String ontFile, String sparqlFile) {
+		try {
+			OntologyManager om = new OntologyManager(ontFile, sparqlFile);
+			om.executeQuery();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	private Result check(String[] args) {
+		if (args.length == 2) {
+			String fo = args[0];
+			String fs = args[1];
+			if (new File(fo).exists()) {
+				if (new File(fs).exists()) {
+					return new Result(true);
+				} else {
+					return new Result(false,
+							"Ontology file exists. SPARQL file not!");
+				}
+			}
+			return new Result(false, "Ontology file not exists!");
+		}
+		return new Result(false,
+				"Incorrect number of parameters. Necessary 2: " + args.length);
+	}
+
+	public static void main(String[] args) {
+		/*
+		 * Input: ontologia "SELECT .... blala"
+		 */
+		new Main(args);
+	}
+
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/es/cbgp/galaxy/sparql/main/Result.java	Thu Oct 25 12:17:40 2012 -0400
@@ -0,0 +1,23 @@
+package es.cbgp.galaxy.sparql.main;
+
+public class Result {
+	private boolean boolValue;
+	private String message;
+
+	public Result(boolean b, String m) {
+		this.boolValue = b;
+		this.message = m;
+	}
+
+	public Result(boolean b) {
+		this.boolValue = b;
+	}
+
+	public String getMessage() {
+		return this.message;
+	}
+
+	public boolean getBoolValue() {
+		return this.boolValue;
+	}
+}