Merge pull request #94 from PRIDE-Archive/mzML1.2.0

supporting mzML 1.2.0
PRIDE-Archive · Jun 30, 2020 · aa8b209 · aa8b209
2 parents a9fae3f + 7dfb8e0
commit aa8b209
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 3 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
@@ -46,7 +46,8 @@ public class FileScanAndValidationTask extends TaskAdapter<DataFileValidationMes
 
     private static final Logger logger = LoggerFactory.getLogger(FileScanAndValidationTask.class);
 
-    private static final String MZIDENTML_ACCEPTED_VERSION = "1.1.0";
+    private static final String MZIDENTML_ACCEPTED_VERSION_1_1_0 = "1.1.0";
+    private static final String MZIDENTML_ACCEPTED_VERSION_1_2_0 = "1.2.0";
     public static final Pattern MZIDENTML_PEAK_LIST_FILE_PATTERN = Pattern.compile("^[^<]*<SpectraData[^>]*location=\"([^\"]+)\"[^>]*>.*$");
     public static final String MZIDENTML_PEAK_LIST_FILE_END = "</SpectraData>";
     public static final String PRIDEXML_SAMPLE_DESCRIPTION_BEGIN = "<sampleDescription";
@@ -738,7 +739,7 @@ private List<DataFile> runMzIdentMLVersionValidation(List<DataFile> dataFiles) t
                 boolean correctVersion = false;
                 for (int i = 0; i < 5; i++) {
                     String line = fileReader.readLine();
-                    if (line.contains("version=\"" + MZIDENTML_ACCEPTED_VERSION + "\"")) {
+                    if (line.contains("version=\"" + MZIDENTML_ACCEPTED_VERSION_1_1_0 + "\"") || line.contains("version=\"" + MZIDENTML_ACCEPTED_VERSION_1_2_0 + "\"")) {
                         correctVersion = true;
                         break;
                     }

diff --git a/src/main/java/uk/ac/ebi/pride/gui/util/WarningMessageGenerator.java b/src/main/java/uk/ac/ebi/pride/gui/util/WarningMessageGenerator.java
@@ -46,7 +46,7 @@ public static String getMultipleResultFileFormatWarning(String formatA, String f
     public static String getInvalidMzIdentMLVersionWarning(List<DataFile> mzIdentMLFiles) {
         StringBuilder errMsg = new StringBuilder();
         errMsg.append("<html>");
-        errMsg.append("<b>The following mzIdentML are not version 1.1.0 </b><br/>");
+        errMsg.append("<b>The following mzIdentML are not version 1.1.0 or 1.2.0 </b><br/>");
         for (DataFile mzIdentMLFile : mzIdentMLFiles) {
             errMsg.append("<li>");
             errMsg.append(mzIdentMLFile.getFile().getName());