fixed uri encoding bug

pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/rna/vocabulary/uri/RnaKbUriPattern.java

@@ -37,6 +37,10 @@ public enum RnaKbUriPattern implements UriPattern, RnaKbNamespace {
 		this.pattern = pattern;
 	}
 
+	public boolean requiresEncoding(){
+		return true;
+	}
+
 	public String getPattern() {
 		return pattern;
 	}

pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/uri/Bio2RdfPdbUriPattern.java

@@ -121,12 +121,12 @@ public enum Bio2RdfPdbUriPattern implements UriPattern, Bio2RdfPdbNamespace {
 	PUBLISHER_NAME(PUBLISHER.pattern + "/name"),
 	GENE_SOURCE_CELL_DEV_STAGE(GENE_SOURCE_CELL.pattern + "/developmentStage"),
 	GENE_SOURCE_ORGANISM_DEV_STAGE(GENE_SOURCE_ORGANISM.pattern + "/developmentStage"),
-	RESIDUE_FORMULA_WEIGH("{0}/formulaWeight"), // {0} => Residue URI
+	RESIDUE_FORMULA_WEIGH("{0}/formulaWeight", false), // {0} => Residue URI
 	RESIDUE_TYPE(DEFAULT_NAMESPACE_RESOURCE + "{0}"), // {0} => residue type name
-	RESIDUE_NUMBER_OF_ATOMS("{0}/numberOfAtoms"), // {0} => Residue URI
-	RESIDUE_NUMBER_OF_NON_HYDROGEN_ATOMS("{0}/numberOfNonHydrogenAtoms"), // {0}
+	RESIDUE_NUMBER_OF_ATOMS("{0}/numberOfAtoms", false), // {0} => Residue URI
+	RESIDUE_NUMBER_OF_NON_HYDROGEN_ATOMS("{0}/numberOfNonHydrogenAtoms", false), // {0}
 	// => Residue URI
-	RESIDUE_FORMULA("{0}/formula"), // {0} => Residue URI
+	RESIDUE_FORMULA("{0}/formula", false), // {0} => Residue URI
 
 	PDB_GRAPH("http://bio2rdf.org/graph/pdb:{0}"),
 	SECONDARY_STRUCTURE(DEFAULT_NAMESPACE_RESOURCE + "{0}/secondaryStructure_{1}"), // {0}
@@ -239,11 +239,21 @@ public enum Bio2RdfPdbUriPattern implements UriPattern, Bio2RdfPdbNamespace {
 	GO("http://bio2rdf.org/go:{0}");
 
 	private final String pattern;
+	private boolean encode;
 
 	private Bio2RdfPdbUriPattern(String pattern) {
+		this(pattern, true);
+	}
+	private Bio2RdfPdbUriPattern(String pattern, boolean encode){
 		this.pattern = pattern;
+		this.encode = encode;
+
 	}
-
+	@Override
+	public boolean requiresEncoding(){
+		return this.encode;
+	}
+	@Override
 	public String getPattern() {
 		return pattern;
 	}

pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/uri/UriBuilder.java

@@ -25,20 +25,27 @@
 import java.text.MessageFormat;
 import java.util.ArrayList;
 
+import javax.management.RuntimeErrorException;
+
 /**
  * @author Alexander De Leon
  */
 public class UriBuilder {
 
 	public String buildUri(UriPattern uriPatterns, String... args) {
-		ArrayList<String> encodedArgs = new ArrayList<String>(args.length);
-		for (String arg : args){
-			try{
-				encodedArgs.add(URLEncoder.encode(arg, "UTF-8"));
-			} catch(UnsupportedEncodingException e){
-				encodedArgs.add(arg);
+		if (uriPatterns.requiresEncoding()) {
+			ArrayList<String> encodedArgs = new ArrayList<String>(args.length);
+			for (String arg : args) {
+
+				try {
+					encodedArgs.add(URLEncoder.encode(arg, "UTF-8"));
+				} catch (UnsupportedEncodingException e) {
+					encodedArgs.add(arg);
+				}
 			}
+			return MessageFormat.format(uriPatterns.getPattern(),
+					encodedArgs.toArray(new Object[encodedArgs.size()]));
 		}
-		return MessageFormat.format(uriPatterns.getPattern(), encodedArgs.toArray(new Object[encodedArgs.size()]));
+		return MessageFormat.format(uriPatterns.getPattern(), (Object[]) args);
 	}
 }

pdb/pdb2rdf-parser/src/main/java/com/dumontierlab/pdb2rdf/parser/vocabulary/uri/UriPattern.java

@@ -26,5 +26,7 @@
 public interface UriPattern {
 
 	String getPattern();
+
+	boolean requiresEncoding();
 
 }