Merge pull request medbioinf#206 from julianu/main

enabling mzid1.2 import
julianu · Jul 5, 2024 · a17b10c · a17b10c
2 parents 79b00bf + ca3cae5
commit a17b10c
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 3 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 
 	<groupId>de.mpc.pia</groupId>
 	<artifactId>pia</artifactId>
-	<version>1.5.1</version>
+	<version>1.5.2</version>
 	<name>PIA - Protein Inference Algorithms</name>
 	<url>https://github.com/mpc-bioinformatics/pia</url>
 

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/PIACompiler.java b/src/main/java/de/mpc/pia/intermediate/compiler/PIACompiler.java
@@ -12,6 +12,7 @@
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Map;
@@ -21,6 +22,7 @@
 import javax.xml.bind.JAXBElement;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
+import javax.xml.namespace.NamespaceContext;
 import javax.xml.namespace.QName;
 import javax.xml.stream.FactoryConfigurationError;
 import javax.xml.stream.XMLOutputFactory;
@@ -135,13 +137,13 @@ public abstract class PIACompiler {
     private static String nsjPiaXML = "http://www.medizinisches-proteom-center.de/PIA/piaintermediate";
 
     /** prefixdeclaration for jPiaXML */
-    private static String prefixjPiaXML = "ns3";
+    private static String prefixjPiaXML = "pia";
 
     /** namespace declaration for mzIdentML */
     private static String nsMzIdentML = "http://psidev.info/psi/pi/mzIdentML/1.1";
 
     /** prefix declaration for mzIdentML */
-    private static String prefixMzIdentML = "ns2";
+    private static String prefixMzIdentML = "mzid";
 
     /** encoding specification */
     private static String encoding = "UTF-8";
@@ -933,6 +935,26 @@ public final void writeOutXML(OutputStream outputStream) {
             XMLOutputFactory xmlof = XMLOutputFactory.newInstance();
             XMLStreamWriter xmlOut = new IndentingXMLStreamWriter(xmlof.createXMLStreamWriter(out));
 
+            // take care of the namespace in the PIA XML files -> basically set them fixed to PIA and mzid 1.1
+            xmlOut.setNamespaceContext(new NamespaceContext() {
+                public Iterator<String> getPrefixes(String namespaceURI) {
+                    return null;
+                }
+
+                public String getPrefix(String namespaceURI) {
+                    if (namespaceURI.equals(nsjPiaXML)) {
+                        return prefixjPiaXML;
+                    } else if (namespaceURI.contains("mzIdentML")) {
+                        return prefixMzIdentML;
+                    }
+                    return "";
+                }
+
+                public String getNamespaceURI(String prefix) {
+                    return "";
+                }
+            });
+
             // xml header
             xmlOut.writeStartDocument(encoding, "1.0");