From 38880c5123586259cd8bf8a6c0ca07632db1ca93 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 4 Mar 2018 16:27:27 +0100
Subject: [PATCH] Added a helper method to process XML results returned by a
 SPARQL end point

---
 .../bioclipse/rdf/business/IRDFManager.java   |  9 +++++++
 .../bioclipse/rdf/business/RDFManager.java    | 27 +++++++++++++++++++
 2 files changed, 36 insertions(+)

diff --git a/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java b/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java
index bdf615c..10790f1 100644
--- a/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java
+++ b/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/IRDFManager.java
@@ -262,6 +262,15 @@ public void saveRDFNTriple(IRDFStore store, String fileName)
     public IStringMatrix sparqlRemote(String url, String SPARQL)
         throws BioclipseException;
 
+    @Recorded
+    @PublishedMethod(
+        params = "String queryResults, String originalQuery",
+        methodSummary = "Parses the XML-formatted SPARQL end point results into an IStringMatrix. "
+        		+ "The originalQuery is used to determine prefixes."
+    )
+    public IStringMatrix processSPARQLXML(byte[] queryResults, String originalQuery)
+        throws BioclipseException;
+
     @Recorded
     @PublishedMethod(
         params = "String url, String SPARQL",
diff --git a/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java b/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java
index 0c2306a..79644e5 100644
--- a/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java
+++ b/plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java
@@ -52,6 +52,7 @@
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFactory;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.Property;
@@ -64,6 +65,7 @@
 import com.hp.hpl.jena.shared.NoReaderForLangException;
 import com.hp.hpl.jena.shared.PrefixMapping;
 import com.hp.hpl.jena.shared.SyntaxError;
+import com.hp.hpl.jena.shared.impl.PrefixMappingImpl;
 import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
 import com.hp.hpl.jena.util.iterator.Filter;
 
@@ -503,6 +505,31 @@ public StringMatrix sparqlRemote(
         return table;
     }
     
+    public StringMatrix processSPARQLXML(
+            byte[] queryResults, String originalQuery, IProgressMonitor monitor) {
+         if (monitor == null) monitor = new NullProgressMonitor();
+
+         monitor.beginTask("Processing XML results returned by a SPARQL end point..", 100);
+    	 PrefixMapping prefixMap = null;
+         if (originalQuery != null) {
+        	 try {
+                 Query query = QueryFactory.create(originalQuery);
+                 prefixMap = query.getPrefixMapping();
+        	 } catch (Exception exception) {
+        		 // could not parse the query for namespaces
+        		 prefixMap = new PrefixMappingImpl();
+        	 }
+         }
+         monitor.worked(20);
+
+         // now the Jena part
+         ResultSet results = ResultSetFactory.fromXML(new ByteArrayInputStream(queryResults));
+         StringMatrix table = StringMatrixHelper.convertIntoTable(prefixMap, results);
+         monitor.worked(80);
+
+         return table;
+     }
+     
     public IRDFStore sparqlConstructRemote(
     		String serviceURL,
     		String sparqlQueryString, IProgressMonitor monitor)