Merge pull request #87 from lifs-tools/fix-metadata-objects-validation

Updated Metadata Assay name and Study name validation.
lifs-tools · Jul 26, 2024 · a6bebdb · a6bebdb
2 parents 506d5b3 + afd74af
commit a6bebdb
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Showing 4 changed files with 29 additions and 9 deletions.
diff --git a/io/src/main/java/org/lifstools/mztab2/io/validators/AssayValidator.java b/io/src/main/java/org/lifstools/mztab2/io/validators/AssayValidator.java
@@ -25,7 +25,7 @@
 import uk.ac.ebi.pride.jmztab2.utils.parser.MZTabParserContext;
 
 /**
- * Validates that the quantification method section is present in metadata.
+ * Validates that the assay section is present in metadata.
  *
  * @author nilshoffmann
  */
@@ -42,6 +42,11 @@ public List<MZTabError> validateRefine(Metadata metadata, MZTabParserContext par
         }
 
         for (Integer id : assayMap.keySet()) {
+            if (assayMap.get(id).getName() == null || assayMap.get(id).getName().isBlank()) {
+                errorList.add(new MZTabError(
+                        LogicalErrorType.NotDefineInMetadata, -1,
+                        Metadata.Properties.assay + "[" + id + "]" + "\t<" + Assay.Properties.name + ">"));
+            }
             if (assayMap.get(id).
                     getMsRunRef() == null || assayMap.get(id).
                             getMsRunRef().isEmpty()) {

diff --git a/io/src/main/java/org/lifstools/mztab2/io/validators/StudyVariableValidator.java b/io/src/main/java/org/lifstools/mztab2/io/validators/StudyVariableValidator.java
@@ -55,18 +55,19 @@ public List<MZTabError> validateRefine(Metadata metadata, MZTabParserContext par
                     if (sv == null) {
                         errorList.add(new MZTabError(
                                 LogicalErrorType.NotDefineInMetadata, -1,
-                                Metadata.Properties.studyVariable + "[" + id + "]" + "\t" + "<NAME>"));
+                                Metadata.Properties.studyVariable + "[" + id + "]" + "\t<" + StudyVariable.Properties.name + ">"));
                     } else {
                         if (sv.getName() == null) {
                             errorList.add(new MZTabError(
                                     LogicalErrorType.NotDefineInMetadata, -1,
-                                    Metadata.Properties.studyVariable + "[" + id + "]" + "\t" + "<NAME>"));
+                                    Metadata.Properties.studyVariable + "[" + id + "]" + "\t<" + StudyVariable.Properties.name + ">"));
                         } else {
                             if (sv.getName().equals("undefined")) {
                                 if (undefinedDefined) {
                                     errorList.add(new MZTabError(
                                             LogicalErrorType.UndefinedStudyVariableNameOnceOnly, -1,
-                                            Metadata.Properties.studyVariable + "[" + id + "]" + "\t" + "<NAME>"));
+                                            Metadata.Properties.studyVariable + "[" + id + "]" + "\t<" + StudyVariable.Properties.name
+                                            + ">"));
                                 } else {
                                     undefinedDefined = true;
                                 }
@@ -76,7 +77,7 @@ public List<MZTabError> validateRefine(Metadata metadata, MZTabParserContext par
                                 getDescription() == null) {
                             errorList.add(new MZTabError(
                                     LogicalErrorType.NotDefineInMetadata, -1,
-                                    Metadata.Properties.studyVariable + "[" + id + "]-" + StudyVariable.Properties.description + "\t" + "<DESCRIPTION>"));
+                                    Metadata.Properties.studyVariable + "[" + id + "]-" + StudyVariable.Properties.description));
                         }
                         if (sv.
                                 getAssayRefs() == null || sv.getAssayRefs().

diff --git a/io/src/test/java/org/lifstools/mztab2/io/validators/AssayValidatorTest.java b/io/src/test/java/org/lifstools/mztab2/io/validators/AssayValidatorTest.java
@@ -47,6 +47,20 @@ public void testValidateRefineNullAssay() {
         assertEquals(expResult.size(), result.size());
         assertEquals(expResult.get(0).toString(), result.get(0).toString());
     }
+
+    @Test
+    public void testValidateMissingName() {
+        Metadata metadata = new Metadata();
+        metadata.addAssayItem(new Assay().id(1));
+        MZTabParserContext parserContext = new MZTabParserContext();
+        AssayValidator instance = new AssayValidator();
+        List<MZTabError> expResult = Arrays.asList(new MZTabError(
+                LogicalErrorType.NotDefineInMetadata, -1,
+                Metadata.Properties.assay + ""));
+        List<MZTabError> result = instance.validateRefine(metadata, parserContext);
+        assertEquals(expResult.size(), result.size());
+        assertEquals(expResult.get(0).toString(), result.get(0).toString());
+    }
 
     /**
      * Test of validateRefine method for assay requiring a linked ms run, of

diff --git a/io/src/test/java/org/lifstools/mztab2/io/validators/StudyVariableValidatorTest.java b/io/src/test/java/org/lifstools/mztab2/io/validators/StudyVariableValidatorTest.java
@@ -95,13 +95,13 @@ public void testTwoStudyVariableMultipleAssaysMissingNamesAndMissingDescription(
         List<MZTabError> expResult = Arrays.asList(
                 new MZTabError(
                         LogicalErrorType.NotDefineInMetadata, -1,
-                        Metadata.Properties.studyVariable + "[" + 1 + "]" + "\t" + "<NAME>"),
+                        Metadata.Properties.studyVariable + "[" + 1 + "]" + "\t<" + StudyVariable.Properties.name+">"),
                 new MZTabError(
                         LogicalErrorType.NotDefineInMetadata, -1,
-                        Metadata.Properties.studyVariable + "[" + 2 + "]" + "\t" + "<NAME>"),
+                        Metadata.Properties.studyVariable + "[" + 2 + "]" + "\t<" + StudyVariable.Properties.name+">"),
                 new MZTabError(
                         LogicalErrorType.NotDefineInMetadata, -1,
-                        Metadata.Properties.studyVariable + "[" + 2 + "]-" + StudyVariable.Properties.description + "\t" + "<DESCRIPTION>")
+                        Metadata.Properties.studyVariable + "[" + 2 + "]-" + StudyVariable.Properties.description)
         );
         List<MZTabError> result = instance.validateRefine(metadata, parserContext);
         assertEquals(expResult.size(), result.size());
@@ -134,7 +134,7 @@ public void testTwoStudyVariableMultipleAssaysMultipleUndefinedStudyVariables()
         List<MZTabError> expResult = Arrays.asList(
                 new MZTabError(
                         LogicalErrorType.UndefinedStudyVariableNameOnceOnly, -1,
-                        Metadata.Properties.studyVariable + "[" + 2 + "]" + "\t" + "<NAME>")
+                        Metadata.Properties.studyVariable + "[" + 2 + "]" + "\t<" + StudyVariable.Properties.name+">")
         );
         List<MZTabError> result = instance.validateRefine(metadata, parserContext);
         assertEquals(expResult.size(), result.size());