Add severityLevel to API, support MDHT results, add tests, update UI

-SITE-3008 ETT GG/Github Issues Ref Val: "Configure Validator to Exclude Warnings & Info"
onc-healthit · Jun 19, 2019 · 2903f55 · 2903f55
1 parent b2dce3c
commit 2903f55
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Showing 7 changed files with 1,329 additions and 939 deletions.
diff --git a/pom.xml b/pom.xml
@@ -12,7 +12,7 @@
         <java.version>1.7</java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <code.validator.version>1.0.20</code.validator.version>
+        <code.validator.version>1.0.21-SNAPSHOT</code.validator.version>
         <content.validator.version>1.0.19</content.validator.version>
         <!-- MDHT properties -->
         <mdht.models.version>3.0.8.20180531</mdht.models.version>

diff --git a/src/main/java/org/sitenv/referenceccda/controllers/ReferenceCCDAValidationController.java b/src/main/java/org/sitenv/referenceccda/controllers/ReferenceCCDAValidationController.java
@@ -4,6 +4,7 @@
 import org.sitenv.referenceccda.services.ReferenceCCDAValidationService;
 import org.sitenv.referenceccda.services.VocabularyService;
 import org.sitenv.vocabularies.constants.VocabularyConstants;
+import org.sitenv.vocabularies.constants.VocabularyConstants.SeverityLevel;
 import org.sitenv.vocabularies.validation.entities.Code;
 import org.sitenv.vocabularies.validation.entities.VsacValueSet;
 import org.sitenv.vocabularies.validation.services.VocabularyValidationService;
@@ -35,9 +36,15 @@ public ValidationResultsDto doValidation(
 			@RequestParam(value = "validationObjective", required = true) String validationObjective,
 			@RequestParam(value = "referenceFileName", required = true) String referenceFileName,
 			@RequestParam(value = "ccdaFile", required = true) MultipartFile ccdaFile,
-			@RequestParam(defaultValue = VocabularyConstants.Config.DEFAULT, required = false) String vocabularyConfig) {
+			@RequestParam(defaultValue = VocabularyConstants.Config.DEFAULT, required = false) String vocabularyConfig,
+			@RequestParam(defaultValue = "info", required = false) String severityLevel) {		
+		if (severityLevel == null || severityLevel.equals("")) {
+			severityLevel = "info";
+		}
+		SeverityLevel severityLevelEnum = SeverityLevel.valueOf(severityLevel.toUpperCase());
+
 		return referenceCcdaValidationService.validateCCDA(validationObjective, referenceFileName, ccdaFile, 
-				vocabularyConfig);
+				vocabularyConfig, severityLevelEnum);		
 	}
 
 	@RequestMapping(value = "/getvaluesetsbyoids", method = RequestMethod.GET)

diff --git a/src/main/java/org/sitenv/referenceccda/services/ReferenceCCDAValidationService.java b/src/main/java/org/sitenv/referenceccda/services/ReferenceCCDAValidationService.java
@@ -18,6 +18,7 @@
 import org.sitenv.referenceccda.validators.schema.ValidationObjectives;
 import org.sitenv.referenceccda.validators.vocabulary.VocabularyCCDAValidator;
 import org.sitenv.vocabularies.constants.VocabularyConstants;
+import org.sitenv.vocabularies.constants.VocabularyConstants.SeverityLevel;
 import org.sitenv.vocabularies.validation.dto.GlobalCodeValidatorResults;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
@@ -52,21 +53,26 @@ public ReferenceCCDAValidationService(ReferenceCCDAValidator referenceCCDAValida
     }
 
     public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName, MultipartFile ccdaFile) {
-    	return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, VocabularyConstants.Config.DEFAULT);
+    	return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, VocabularyConstants.Config.DEFAULT, SeverityLevel.INFO);
     }
 
     public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName, MultipartFile ccdaFile, 
     		String vocabularyConfig) {
-    	return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, vocabularyConfig);
+    	return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, vocabularyConfig, SeverityLevel.INFO);
     }
 
+    public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName, MultipartFile ccdaFile, 
+    		String vocabularyConfig, SeverityLevel severityLevel) {
+    	return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, vocabularyConfig, severityLevel);
+    }    
+
     private ValidationResultsDto validateCCDAImplementation(String validationObjective, String referenceFileName, 
-    		MultipartFile ccdaFile, String vocabularyConfig) {
+    		MultipartFile ccdaFile, String vocabularyConfig, SeverityLevel severityLevel) {
         ValidationResultsDto resultsDto = new ValidationResultsDto();
         ValidationResultsMetaData resultsMetaData = new ValidationResultsMetaData();
         List<RefCCDAValidationResult> validatorResults = new ArrayList<>();
         try {
-            validatorResults = runValidators(validationObjective, referenceFileName, ccdaFile, vocabularyConfig);
+            validatorResults = runValidators(validationObjective, referenceFileName, ccdaFile, vocabularyConfig, severityLevel);
             resultsMetaData = buildValidationMedata(validatorResults, validationObjective);
             resultsMetaData.setCcdaFileName(ccdaFile.getOriginalFilename());
             resultsMetaData.setCcdaFileContents(new String(ccdaFile.getBytes()));
@@ -103,7 +109,7 @@ private static void processValidateCCDAException(ValidationResultsMetaData resul
 	}
 
     private List<RefCCDAValidationResult> runValidators(String validationObjective, String referenceFileName,
-                                                        MultipartFile ccdaFile, String vocabularyConfig) 
+                                                        MultipartFile ccdaFile, String vocabularyConfig, SeverityLevel severityLevel) 
                                                         		throws SAXException, Exception {
         List<RefCCDAValidationResult> validatorResults = new ArrayList<>();
         InputStream ccdaFileInputStream = null;
@@ -117,7 +123,7 @@ private List<RefCCDAValidationResult> runValidators(String validationObjective,
             }
             String ccdaFileContents = IOUtils.toString(bomInputStream, "UTF-8");
 
-            List<RefCCDAValidationResult> mdhtResults = doMDHTValidation(validationObjective, referenceFileName, ccdaFileContents);
+            List<RefCCDAValidationResult> mdhtResults = doMDHTValidation(validationObjective, referenceFileName, ccdaFileContents, severityLevel);
             if(mdhtResults != null && !mdhtResults.isEmpty()) {
             	logger.info("Adding MDHT results");
             	validatorResults.addAll(mdhtResults);
@@ -183,9 +189,10 @@ private boolean objectiveAllowsContentValidation(String validationObjective) {
 				ValidationObjectives.ALL_UNIQUE_CONTENT_ONLY);
 	}
 
-    private List<RefCCDAValidationResult> doMDHTValidation(String validationObjective, String referenceFileName, String ccdaFileContents) throws SAXException, Exception {
+	private List<RefCCDAValidationResult> doMDHTValidation(String validationObjective, String referenceFileName,
+			String ccdaFileContents, SeverityLevel severityLevel) throws SAXException, Exception {
     	logger.info("Attempting MDHT validation...");
-        return referenceCCDAValidator.validateFile(validationObjective, referenceFileName, ccdaFileContents);
+        return referenceCCDAValidator.validateFile(validationObjective, referenceFileName, ccdaFileContents, severityLevel);
     }
 
 	private ArrayList<RefCCDAValidationResult> doVocabularyValidation(String validationObjective,