Updated validation output on unexpected exceptions. Bumped jackson.

lifs-tools · Jan 7, 2020 · 529ce40 · 529ce40
1 parent a72a123
commit 529ce40
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Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/pom.xml b/pom.xml
@@ -62,8 +62,8 @@
         <junit.platform.version>1.0.3</junit.platform.version>
         <swagger.version>1.5.16</swagger.version>
         <jersey.version>2.22.2</jersey.version>
-        <jackson.version>2.10.1</jackson.version>
-        <jackson.databind.version>2.10.1</jackson.databind.version>
+        <jackson.version>2.10.2</jackson.version>
+        <jackson.databind.version>2.10.2</jackson.databind.version>
         <jodatime.version>2.9.9</jodatime.version>
         <hibernate.validator.version>6.0.7.Final</hibernate.validator.version>
         <slf4j.version>1.7.25</slf4j.version>

diff --git a/...main/java/de/isas/lipidomics/mztab/validator/webapp/service/validation/IsasValidator.java b/...main/java/de/isas/lipidomics/mztab/validator/webapp/service/validation/IsasValidator.java
@@ -66,7 +66,6 @@ public List<ValidationMessage> validate(Path filepath,
             parser = new MzTabFileParser(filepath.toFile());
             MZTabErrorList errorList = parser.parse(
                     System.out, MZTabErrorType.findLevel(validationLevel), maxErrors);
-            errorList.convertToValidationMessages();
         } catch (Exception e) {
             log.error("Caught Exception in IsasValidator:", e);
             ValidationMessage vm = new ValidationMessage();
@@ -79,7 +78,13 @@ public List<ValidationMessage> validate(Path filepath,
             StringWriter sw = new StringWriter();
             PrintWriter pw = new PrintWriter(sw);
             e.printStackTrace(pw);
-            vm.setMessage(e.getMessage()!=null?e.getMessage():"Caught an Exception while parsing '"+filepath.getFileName()+"'. Please check your file's tabular structure and inspect further validation messages!" + "\n" +sw.toString());
+            StringBuilder message = new StringBuilder();
+            message.append("Basic validation failed for file '").append(filepath.getFileName()).append("'\n");
+            if (e.getMessage() != null) {
+                message.append(" with message: '").append(e.getMessage()).append("'\n");
+            }
+            message.append("Please check your file's structure and inspect further validation messages!\n");
+            vm.setMessage(message.toString());
             validationResults.add(vm);
         } finally {
             if (parser != null) {
@@ -93,7 +98,7 @@ public List<ValidationMessage> validate(Path filepath,
                         List<ValidationMessage> messages = cvValidator.validate(parser.
                                 getMZTabFile());
                         validationResults.addAll(Optional.ofNullable(messages).orElse(Collections.emptyList()));
-                    } catch (JAXBException | IllegalArgumentException iae) {
+                    } catch (Exception iae) {
                         log.error("Caught Exception in IsasValidator, semantic validation:", iae);
                         ValidationMessage vm = new ValidationMessage();
                         vm.setCategory(
@@ -102,7 +107,16 @@ public List<ValidationMessage> validate(Path filepath,
                         vm.setLineNumber(-1l);
                         vm.setMessageType(
                                 ValidationMessage.MessageTypeEnum.ERROR);
-                        vm.setMessage(iae.getMessage());
+                        StringWriter sw = new StringWriter();
+                        PrintWriter pw = new PrintWriter(sw);
+                        iae.printStackTrace(pw);
+                        StringBuilder message = new StringBuilder();
+                        message.append("Semantic validation failed for file '").append(filepath.getFileName()).append("'\n");
+                        if (iae.getMessage() != null) {
+                            message.append(" with message: '").append(iae.getMessage()).append("'\n");
+                        }
+                        message.append("Please check your file's structure and inspect further validation messages!\n");
+                        vm.setMessage(message.toString());
                         validationResults.add(vm);
                     }
                 }