From b19e2bbfd00d5b92e3f27b9ead5b9aa76064dfaa Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Fri, 5 Jul 2024 09:59:43 +0200
Subject: [PATCH 1/2] enabling mzid1.2 import

---
 .../intermediate/compiler/PIACompiler.java    | 26 +++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/PIACompiler.java b/src/main/java/de/mpc/pia/intermediate/compiler/PIACompiler.java
index 0aa3d41..86ecf7a 100755
--- 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");
 

From ca3cae56c9fa9e64e4eac782f34966b4433bd318 Mon Sep 17 00:00:00 2001
From: julianu <julian.uszkoreit@rub.de>
Date: Fri, 5 Jul 2024 10:16:25 +0200
Subject: [PATCH 2/2] bumping version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 63ef864..6aa694d 100644
--- 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>