Merge pull request #75 from lifs-tools/nosml-tests

Updated to Java 17, added XCMS examples without SML section
lifs-tools · Jul 24, 2024 · 273d951 · 273d951
2 parents 992f3ce + 818f6f3
commit 273d951
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Showing 47 changed files with 15,398 additions and 68 deletions.
diff --git a/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabError.java b/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabError.java
@@ -145,33 +145,19 @@ public ValidationMessage toValidationMessage() throws IllegalStateException {
         ValidationMessage.MessageTypeEnum level = ValidationMessage.MessageTypeEnum.INFO;
         switch (getType().
             getLevel()) {
-            case Error:
-                level = ValidationMessage.MessageTypeEnum.ERROR;
-                break;
-            case Info:
-                level = ValidationMessage.MessageTypeEnum.INFO;
-                break;
-            case Warn:
-                level = ValidationMessage.MessageTypeEnum.WARN;
-                break;
-            default:
-                throw new IllegalStateException("State " + 
+            case Error -> level = ValidationMessage.MessageTypeEnum.ERROR;
+            case Info -> level = ValidationMessage.MessageTypeEnum.INFO;
+            case Warn -> level = ValidationMessage.MessageTypeEnum.WARN;
+            default -> throw new IllegalStateException("State " + 
                     getType().
                     getLevel() + " is not handled in switch/case statement!");
         }
         ValidationMessage.CategoryEnum category = ValidationMessage.CategoryEnum.FORMAT;
         switch(getType().getCategory()) {
-            case Format:
-                category = ValidationMessage.CategoryEnum.FORMAT;
-                break;
-            case Logical:
-                category = ValidationMessage.CategoryEnum.LOGICAL;
-                break;
-            case CrossCheck:
-                category = ValidationMessage.CategoryEnum.CROSS_CHECK;
-                break;
-            default:
-                throw new IllegalStateException("Category " + 
+            case Format -> category = ValidationMessage.CategoryEnum.FORMAT;
+            case Logical -> category = ValidationMessage.CategoryEnum.LOGICAL;
+            case CrossCheck -> category = ValidationMessage.CategoryEnum.CROSS_CHECK;
+            default -> throw new IllegalStateException("Category " + 
                     getType().
                     getCategory()+ " is not handled in switch/case statement!");
         }

diff --git a/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabErrorList.java b/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabErrorList.java
@@ -104,15 +104,17 @@ public boolean add(MZTabError error) throws MZTabErrorOverflowException {
         }
 
         switch(error.getType().getLevel()) {
-            case Info:
+            case Info -> {
                 if(level==MZTabErrorType.Level.Warn || level==MZTabErrorType.Level.Error) {
                     return false;
                 }
-                break;
-            case Warn:
+            }
+            case Warn -> {
                 if(level==MZTabErrorType.Level.Error) {
                     return false;
                 }
+                //ERROR is always being reported
+            }
             //ERROR is always being reported
         }
 
@@ -183,16 +185,16 @@ public MZTabErrorType.Level getLevel() {
         return level;
     }
 
-    /**
-     * Define the level of the errors that are going to be store in the list.
-     * The incoming errors with an equal or highest level will be stored.
-     *
-     * @param level
-     * {@link uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType#level}
-     */
-    public void setLevel(MZTabErrorType.Level level) {
-        this.level = level;
-    }
+//    /**
+//     * Define the level of the errors that are going to be store in the list.
+//     * The incoming errors with an equal or highest level will be stored.
+//     *
+//     * @param level
+//     * {@link uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType#level}
+//     */
+//    public void setLevel(MZTabErrorType.Level level) {
+//        this.level = level;
+//    }
 
     /**
      * Clear all errors stored in the error list.

diff --git a/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabErrorType.java b/api/src/main/java/uk/ac/ebi/pride/jmztab2/utils/errors/MZTabErrorType.java
@@ -110,23 +110,17 @@ protected static MZTabErrorType createInfo(MZTabErrorType.Category category, Str
      */
     private static MZTabErrorType createMZTabError(Category category, Level level, String keyword) {
         if (MZTabStringUtils.isEmpty(keyword)) {
-            throw new NullPointerException(keyword + " can not empty!");
+            throw new NullPointerException(keyword + " can not be empty!");
         }
 
         String prefix = null;
         switch (category) {
-            case Format:
-                prefix = "f_";
-                break;
-            case Logical:
-                prefix = "l_";
-                break;
-            case CrossCheck:
-                prefix = "c_";
-                break;
+            case Format -> prefix = "f_";
+            case Logical -> prefix = "l_";
+            case CrossCheck -> prefix = "c_";
         }
 
-        Integer code = new Integer(MZTabProperties.getProperty(prefix + "code_" + keyword));
+        Integer code = Integer.valueOf(MZTabProperties.getProperty(prefix + "code_" + keyword));
         String original = MZTabProperties.getProperty(prefix + "original_" + keyword);
         String cause = MZTabProperties.getProperty(prefix + "cause_" + keyword);