From f2d09f6b8c7c4df8814116fff74ba43ffa2d0687 Mon Sep 17 00:00:00 2001
From: selva <selva@ebi.ac.uk>
Date: Fri, 28 Aug 2020 07:29:54 +0100
Subject: [PATCH 1/2] mztab reference peak/raw

---
 .../gui/task/FileScanAndValidationTask.java   | 29 ++++++++++++++-----
 1 file changed, 22 insertions(+), 7 deletions(-)

diff --git a/src/main/java/uk/ac/ebi/pride/gui/task/FileScanAndValidationTask.java b/src/main/java/uk/ac/ebi/pride/gui/task/FileScanAndValidationTask.java
index f9765d5a..7d0a2abe 100755
--- a/src/main/java/uk/ac/ebi/pride/gui/task/FileScanAndValidationTask.java
+++ b/src/main/java/uk/ac/ebi/pride/gui/task/FileScanAndValidationTask.java
@@ -18,7 +18,11 @@
 import uk.ac.ebi.pride.data.validation.SubmissionValidator;
 import uk.ac.ebi.pride.data.validation.ValidationMessage;
 import uk.ac.ebi.pride.data.validation.ValidationReport;
-import uk.ac.ebi.pride.gui.util.*;
+import uk.ac.ebi.pride.gui.util.Constant;
+import uk.ac.ebi.pride.gui.util.DataFileValidationMessage;
+import uk.ac.ebi.pride.gui.util.PrideConverterSupport;
+import uk.ac.ebi.pride.gui.util.ValidationState;
+import uk.ac.ebi.pride.gui.util.WarningMessageGenerator;
 import uk.ac.ebi.pride.jaxb.model.CvParam;
 import uk.ac.ebi.pride.jaxb.model.SampleDescription;
 import uk.ac.ebi.pride.jaxb.xml.unmarshaller.PrideXmlUnmarshaller;
@@ -26,10 +30,20 @@
 import uk.ac.ebi.pride.toolsuite.gui.task.TaskAdapter;
 
 import javax.xml.bind.JAXBException;
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -341,17 +355,18 @@ private Map<DataFile, Set<String>> checkMzTabFileReferences(List<DataFile> mzTab
                         errorEntry = mzTabFile.getMzTabDocument().getMetaData().getMsRunEntry(msRunIndex).getLocation().toString();
                     } else {
                         // The file is in the list of files part of the current submission process
-                        // Check that the referenced file is a Raw file
-                        if (dataFiles.get(referencedFile.toLowerCase()).getFileType() != ProjectFileType.RAW) {
+                        // Check that the referenced file is a Peak List / RAW file
+                        ProjectFileType referencedDataFileType = dataFiles.get(referencedFile.toLowerCase()).getFileType();
+                        if (referencedDataFileType != ProjectFileType.PEAK && referencedDataFileType != ProjectFileType.RAW) {
                             // Flag the error
                             errorFlagged = true;
                             // Log the error
                             errorLogMsg = "mzTab file '" + mzTabFile.getFilePath()
-                                    + "' references NON-RAW file '"
+                                    + "' references NON-Peak List/RAW file '"
                                     + referencedFile
                                     + "', which is NOT ALLOWED";
                             // Report the error
-                            errorEntry = "NON-RAW file '"
+                            errorEntry = "NON-Peak List/RAW referenced file '"
                                     + referencedFile
                                     + "', is NOT ALLOWED";
                         }

From 58d99ada125d8970709f6fcdc672d2c4845a8cb7 Mon Sep 17 00:00:00 2001
From: selva <selva@ebi.ac.uk>
Date: Fri, 28 Aug 2020 07:50:24 +0100
Subject: [PATCH 2/2] major version

---
 README.md | 2 +-
 pom.xml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 7159b5c0..fb5c7302 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ PX Submission Tool is a desktop application to submit the data to proteomeXchang
 
 # Quick Download 
 
-[<img src="https://raw.githubusercontent.com/PRIDE-Toolsuite/pride-inspector/master/wiki/download.png">](https://github.com/PRIDE-Archive/px-submission-tool/releases/download/2.4.18/px-submission-tool-2.4.18.zip)
+[<img src="https://raw.githubusercontent.com/PRIDE-Toolsuite/pride-inspector/master/wiki/download.png">](https://github.com/PRIDE-Archive/px-submission-tool/releases/download/2.5.0/px-submission-tool-2.5.0.zip)
 
 Please unzip and run `px-submission-tool-<version number>.jar` file!
 
diff --git a/pom.xml b/pom.xml
index 33639fd4..92bf810b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
     <groupId>uk.ac.ebi.pride.px</groupId>
     <artifactId>px-submission-tool</artifactId>
     <packaging>jar</packaging>
-    <version>2.4.18</version>
+    <version>2.5.0</version>
     <name>px-submission-tool</name>
     <url>https://github.com/proteomexchange/px-submission-tool</url>