Merge pull request #157 from onc-healthit/develop

Develop

.java-version

@@ -0,0 +1 @@
+1.8

README.md

@@ -1,6 +1,6 @@
 This document is meant to outline the steps to successfully configure and deploy the reference ccda application.
 
-If you would like to get a test virtual machine up and running quickly, check out https://github.com/mieweb/vagrant-ccda-validator for a Vagrant build. Note: This is a 3rd-party option and is not directly supported by SITE/the ONC. It intends to pull, configure, and deploy the data from our codebase based on these instructions. Otherwise, please continue to follow the full instructions below to create a local, external, or customized instance of the validator.
+If you would like to get a test virtual machine up and running quickly, check out https://github.com/mieweb/vagrant-ccda-validator for a Vagrant build or https://github.com/mieweb/docker-ccda-validator for a docker container. Note: These are 3rd-party options and are not directly supported by SITE/the ONC. They intend to pull, configure, and deploy the data from our codebase based on these instructions. Otherwise, please continue to follow the full instructions below to create a local, external, or customized instance of the validator.
 
 **1. Assumptions**
 

pom.xml

@@ -3,7 +3,7 @@
 
     <groupId>org.sitenv</groupId>
     <artifactId>referenceccdavalidator</artifactId>
-    <version>1.0.65</version>
+    <version>1.0.66</version>
     <packaging>war</packaging>
     <name>Reference CCDA Validator</name>
 
@@ -16,12 +16,12 @@
         <content.validator.version>latestVersion</content.validator.version>
         <!-- MDHT SITE properties -->
         <mdht.models.groupid>mdht.openhealthtools.mdht.cda</mdht.models.groupid>
-        <mdht.models.version>3.0.0.20220126</mdht.models.version>
+        <mdht.models.version>3.0.0.20220825</mdht.models.version>
         <ds4pcontent.groupId>mdht.hl7.ds4p</ds4pcontent.groupId>
 		<ds4pcontent.version>${mdht.models.version}</ds4pcontent.version>		
 		<mdht.plugins.groupId>mdht.eclipse.mdht</mdht.plugins.groupId>
-		<mdht.plugins.version>3.0.0.202201250600</mdht.plugins.version>
-
+		<mdht.plugins.version>3.0.0.202208250500</mdht.plugins.version>
+		<logback.version>1.2.11</logback.version>
  		<!-- MDHT SNAPSHOT properties: Uncomment for local test -->
  		<!--
 		<mdht.models.groupid>org.openhealthtools.mdht.cda</mdht.models.groupid>
@@ -246,25 +246,15 @@
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
             <version>3.12.0</version>
-        </dependency>     
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-            <version>1.7.0</version>
-            <scope>runtime</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-log4j12</artifactId>
-            <version>1.7.0</version>
-            <scope>runtime</scope>
         </dependency>
+
+        <!-- pull in logback-core and slf4j-api -->
         <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.17</version>
-            <scope>runtime</scope>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <version>${logback.version}</version>
         </dependency>
+
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>

src/main/java/org/sitenv/referenceccda/controllers/ReferenceCCDAValidationController.java

@@ -1,6 +1,7 @@
 package org.sitenv.referenceccda.controllers;
 
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.sitenv.referenceccda.dto.ValidationResultsDto;
 import org.sitenv.referenceccda.services.ReferenceCCDAValidationService;
 import org.sitenv.referenceccda.services.VocabularyService;
@@ -32,70 +33,74 @@ public class ReferenceCCDAValidationController {
 
 	private static final String GITHUB_URL = "https://api.github.com/repos/onc-healthit/2015-certification-ccda-testdata/git/trees/master?recursive=1";
 	private static final String DEFAULT_SEVERITY_LEVEL = "INFO";
-	private static Logger logger = Logger.getLogger(ReferenceCCDAValidationController.class);
-	
+	private static Logger logger = LoggerFactory.getLogger(ReferenceCCDAValidationController.class);
+
 	@RequestMapping(value = "/", headers = "content-type=multipart/*", method = RequestMethod.POST)
 	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(value = "curesUpdate", required = false) boolean curesUpdate,  
+			@RequestParam(value = "curesUpdate", required = false) boolean curesUpdate,
+			@RequestParam(value = "svap2022", required = false) boolean svap2022,
 			@RequestParam(defaultValue = VocabularyConstants.Config.DEFAULT, required = false) String vocabularyConfig,
 			@RequestParam(defaultValue = DEFAULT_SEVERITY_LEVEL, required = false) String severityLevel) {
-		
+
 		logger.info("severityLevel requestParam: " + severityLevel);
-		
-		if ((severityLevel == null || severityLevel.equals("")) || 
-				(!severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.INFO.name())  && 
-						!severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.WARNING.name()) && 
-								!severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.ERROR.name())) ) {
+
+		if ((severityLevel == null || severityLevel.equals(""))
+				|| (!severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.INFO.name())
+						&& !severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.WARNING.name())
+						&& !severityLevel.equalsIgnoreCase(VocabularyConstants.SeverityLevel.ERROR.name()))) {
 			severityLevel = DEFAULT_SEVERITY_LEVEL;
 			logger.info("severityLevel was set/overwritten to default: " + severityLevel);
 		}
-		
+
 		SeverityLevel severityLevelEnum = SeverityLevel.valueOf(severityLevel.toUpperCase());
-		logger.info("Final severityLevelEnum.name() " + severityLevelEnum.name());	
-
-
-		return referenceCcdaValidationService.validateCCDA(validationObjective, referenceFileName, ccdaFile, curesUpdate,
-				vocabularyConfig, severityLevelEnum);		
-
+		logger.info("Final severityLevelEnum.name() " + severityLevelEnum.name());
+
+		return referenceCcdaValidationService.validateCCDA(validationObjective, referenceFileName, ccdaFile,
+				curesUpdate, svap2022, vocabularyConfig, severityLevelEnum);
 	}
 
 	@RequestMapping(value = "/getvaluesetsbyoids", method = RequestMethod.GET)
-	public List<VsacValueSet> getValuesetsByOids(@RequestParam(value = "oids", required = true) String[] valuesetOids){
+	public List<VsacValueSet> getValuesetsByOids(@RequestParam(value = "oids", required = true) String[] valuesetOids) {
 		return vocabularyService.getValuesetsByOids(Arrays.asList(valuesetOids));
 	}
 
 	@RequestMapping(value = "/getbycodeincodesystem", method = RequestMethod.GET)
-	public List<Code> getByCodeInCodeSystems(@RequestParam(value = "code", required = true)String code, @RequestParam(value = "codeSystems", required = true) String[] codeSystems){
+	public List<Code> getByCodeInCodeSystems(@RequestParam(value = "code", required = true) String code,
+			@RequestParam(value = "codeSystems", required = true) String[] codeSystems) {
 		return vocabularyService.getByCodeInCodesystems(code, Arrays.asList(codeSystems));
 	}
 
 	@RequestMapping(value = "/getbycodeinvaluesetoid", method = RequestMethod.GET)
-	public List<VsacValueSet> getByCodeInValuesetOid(@RequestParam(value = "code", required = true)String code, @RequestParam(value = "oids", required = true) String[] valuesetOids){
+	public List<VsacValueSet> getByCodeInValuesetOid(@RequestParam(value = "code", required = true) String code,
+			@RequestParam(value = "oids", required = true) String[] valuesetOids) {
 		return vocabularyService.getByCodeInValuesetOids(code, Arrays.asList(valuesetOids));
 	}
 
 	@RequestMapping(value = "/iscodeandisplaynameincodesystem", method = RequestMethod.GET)
-	public boolean isCodeAndDisplayNameFoundInCodeSystems(@RequestParam(value = "code", required = true)String code, @RequestParam(value = "displayName", required = true)String displayName, @RequestParam(value = "codeSystems", required = true) String[] codeSystems){
+	public boolean isCodeAndDisplayNameFoundInCodeSystems(@RequestParam(value = "code", required = true) String code,
+			@RequestParam(value = "displayName", required = true) String displayName,
+			@RequestParam(value = "codeSystems", required = true) String[] codeSystems) {
 		return vocabularyService.isCodeAndDisplayNameFoundInCodeSystems(code, displayName, Arrays.asList(codeSystems));
 	}
 
 	@RequestMapping(value = "/iscodeincodesystem", method = RequestMethod.GET)
-	public boolean isCodeFoundInCodeSystems(@RequestParam(value = "code", required = true)String code, @RequestParam(value = "codeSystems", required = true) String[] codeSystems){
+	public boolean isCodeFoundInCodeSystems(@RequestParam(value = "code", required = true) String code,
+			@RequestParam(value = "codeSystems", required = true) String[] codeSystems) {
 		return vocabularyService.isCodeFoundInCodesystems(code, Arrays.asList(codeSystems));
 	}
 
 	@RequestMapping(value = "/iscodeinvalueset", method = RequestMethod.GET)
-	public boolean isCodeFoundInValuesetOids(@RequestParam(value = "code", required = true)String code, @RequestParam(value = "valuesetOids", required = true) String[] valuesetOids){
+	public boolean isCodeFoundInValuesetOids(@RequestParam(value = "code", required = true) String code,
+			@RequestParam(value = "valuesetOids", required = true) String[] valuesetOids) {
 		return vocabularyService.isCodeFoundInValuesetOids(code, Arrays.asList(valuesetOids));
 	}
 
 	@Cacheable("messagetypeValidationObjectivesAndReferenceFilesMap")
 	@RequestMapping(value = "/senderreceivervalidationobjectivesandreferencefiles", method = RequestMethod.GET)
-	public Map<String, Map<String, List<String>>> getMapOfSenderAndRecieverValidationObjectivesWithReferenceFiles(){
+	public Map<String, Map<String, List<String>>> getMapOfSenderAndRecieverValidationObjectivesWithReferenceFiles() {
 		return vocabularyService.getMapOfSenderAndRecieverValidationObjectivesWithReferenceFiles();
 	}
-
 }

src/main/java/org/sitenv/referenceccda/services/ReferenceCCDAValidationService.java

@@ -8,7 +8,8 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.io.input.BOMInputStream;
 import org.apache.commons.lang3.exception.ExceptionUtils;
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.sitenv.referenceccda.dto.ValidationResultsDto;
 import org.sitenv.referenceccda.dto.ValidationResultsMetaData;
 import org.sitenv.referenceccda.validators.RefCCDAValidationResult;
@@ -27,7 +28,7 @@
 
 @Service
 public class ReferenceCCDAValidationService {
-	private static Logger logger = Logger.getLogger(ReferenceCCDAValidationService.class);
+	private static Logger logger = LoggerFactory.getLogger(ReferenceCCDAValidationService.class);
 
 	private ReferenceCCDAValidator referenceCCDAValidator;
 	private VocabularyCCDAValidator vocabularyCCDAValidator;
@@ -54,29 +55,29 @@ public ReferenceCCDAValidationService(ReferenceCCDAValidator referenceCCDAValida
 
 	public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName,
 			MultipartFile ccdaFile) {
-		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile,false,
+		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, false, false,
 				VocabularyConstants.Config.DEFAULT, SeverityLevel.INFO);
 	}
 
 	public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName,
 			MultipartFile ccdaFile, String vocabularyConfig) {
-		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, false, vocabularyConfig,
+		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, false, false, vocabularyConfig,
 				SeverityLevel.INFO);
 	}
 
 	public ValidationResultsDto validateCCDA(String validationObjective, String referenceFileName,
-			MultipartFile ccdaFile, boolean curesUpdate, String vocabularyConfig, SeverityLevel severityLevel) {
-		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, curesUpdate, vocabularyConfig,
+			MultipartFile ccdaFile, boolean curesUpdate, boolean svap2022, String vocabularyConfig, SeverityLevel severityLevel) {
+		return validateCCDAImplementation(validationObjective, referenceFileName, ccdaFile, curesUpdate, svap2022, vocabularyConfig,
 				severityLevel);
 	}
 
 	private ValidationResultsDto validateCCDAImplementation(String validationObjective, String referenceFileName,
-			MultipartFile ccdaFile, boolean curesUpdate, String vocabularyConfig, SeverityLevel severityLevel) {
+			MultipartFile ccdaFile, boolean curesUpdate, boolean svap2022, String vocabularyConfig, SeverityLevel severityLevel) {
 		ValidationResultsDto resultsDto = new ValidationResultsDto();
 		ValidationResultsMetaData resultsMetaData = new ValidationResultsMetaData();
 		List<RefCCDAValidationResult> validatorResults = new ArrayList<>();
 		try {
-			validatorResults = runValidators(validationObjective, referenceFileName, ccdaFile, curesUpdate, vocabularyConfig,
+			validatorResults = runValidators(validationObjective, referenceFileName, ccdaFile, curesUpdate, svap2022, vocabularyConfig,
 					severityLevel);
 			resultsMetaData = buildValidationMedata(validatorResults, validationObjective, severityLevel);
 			resultsMetaData.setCcdaFileName(ccdaFile.getOriginalFilename());
@@ -110,7 +111,7 @@ private static void processValidateCCDAException(ValidationResultsMetaData resul
 	}
 
 	private List<RefCCDAValidationResult> runValidators(String validationObjective, String referenceFileName,
-			MultipartFile ccdaFile, boolean curesUpdate, String vocabularyConfig, SeverityLevel severityLevel)
+			MultipartFile ccdaFile, boolean curesUpdate, boolean svap2022, String vocabularyConfig, SeverityLevel severityLevel)
 			throws SAXException, Exception {
 		List<RefCCDAValidationResult> validatorResults = new ArrayList<>();
 		InputStream ccdaFileInputStream = null;
@@ -148,7 +149,7 @@ private List<RefCCDAValidationResult> runValidators(String validationObjective,
 				}
 				if (objectiveAllowsContentValidation(validationObjective)) {
 					List<RefCCDAValidationResult> contentResults = doContentValidation(validationObjective,
-							referenceFileName, ccdaFileContents, curesUpdate, severityLevel);
+							referenceFileName, ccdaFileContents, curesUpdate, svap2022, severityLevel);
 					if (contentResults != null && !contentResults.isEmpty()) {
 						logger.info("Adding Content results");
 						validatorResults.addAll(contentResults);
@@ -212,9 +213,10 @@ private ArrayList<RefCCDAValidationResult> doVocabularyValidation(String validat
 	}
 
 	private List<RefCCDAValidationResult> doContentValidation(String validationObjective, String referenceFileName,
-			String ccdaFileContents, boolean curesUpdate, SeverityLevel severityLevel) throws SAXException {
+			String ccdaFileContents, boolean curesUpdate, boolean svap2022, SeverityLevel severityLevel)
+			throws SAXException {
 		logger.info("Attempting Content validation...");
-		return goldMatchingValidator.validateFile(validationObjective, referenceFileName, ccdaFileContents, curesUpdate, severityLevel);
+		return goldMatchingValidator.validateFile(validationObjective, referenceFileName, ccdaFileContents, curesUpdate, svap2022, severityLevel);
 	}
 
 	private ValidationResultsMetaData buildValidationMedata(List<RefCCDAValidationResult> validatorResults,

src/main/java/org/sitenv/referenceccda/validators/BaseCCDAValidator.java

@@ -3,15 +3,16 @@
 import java.io.IOException;
 import java.io.StringReader;
 
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 import org.xml.sax.XMLReader;
 import org.xml.sax.helpers.XMLReaderFactory;
 
 public abstract class BaseCCDAValidator {
     public static final String UTF8_BOM = "\uFEFF";
-    private static Logger logger = Logger.getLogger(BaseCCDAValidator.class);
+    private static Logger logger = LoggerFactory.getLogger(BaseCCDAValidator.class);
 
     protected static void trackXPathsInXML(XPathIndexer xpathIndexer, String xmlString) throws SAXException{    	    	
         XMLReader parser = XMLReaderFactory.createXMLReader();

src/main/java/org/sitenv/referenceccda/validators/content/ReferenceContentValidator.java

@@ -32,24 +32,24 @@ public ReferenceContentValidator(ContentValidatorService contentValidatorService
 	@Override
 	public ArrayList<RefCCDAValidationResult> validateFile(String validationObjective, String referenceFileName,
 			String ccdaFile) throws SAXException {
-		return validateFile(validationObjective, referenceFileName, ccdaFile, false, SeverityLevel.INFO);
+		return validateFile(validationObjective, referenceFileName, ccdaFile, false, false, SeverityLevel.INFO);
 	}
 
 	public ArrayList<RefCCDAValidationResult> validateFile(String validationObjective, String referenceFileName,
-			String ccdaFile, boolean curesUpdate, SeverityLevel severityLevel) throws SAXException {
+			String ccdaFile, boolean curesUpdate, boolean svap2022, SeverityLevel severityLevel) throws SAXException {
 		ArrayList<RefCCDAValidationResult> results = null;
 		if (ccdaFile != null) {
-			results = doValidation(validationObjective, referenceFileName, ccdaFile, curesUpdate, severityLevel);
+			results = doValidation(validationObjective, referenceFileName, ccdaFile, curesUpdate, svap2022, severityLevel);
 		}
 		return results;
 	}
 
 	private ArrayList<RefCCDAValidationResult> doValidation(String validationObjective, String referenceFileName,
-			String ccdaFile, boolean curesUpdate, SeverityLevel severityLevel) throws SAXException {
+			String ccdaFile, boolean curesUpdate, boolean svap2022, SeverityLevel severityLevel) throws SAXException {
 		org.sitenv.contentvalidator.dto.enums.SeverityLevel userSeverityLevelForContentValidation = 
 				org.sitenv.contentvalidator.dto.enums.SeverityLevel.valueOf(severityLevel.name()); 
 		List<ContentValidationResult> validationResults = contentValidatorService.validate(validationObjective,
-				referenceFileName, ccdaFile, curesUpdate, userSeverityLevelForContentValidation);
+				referenceFileName, ccdaFile, curesUpdate, svap2022, userSeverityLevelForContentValidation);
 		ArrayList<RefCCDAValidationResult> results = new ArrayList<>();
 		for (ContentValidationResult result : validationResults) {
 			results.add(createValidationResult(result));

src/main/java/org/sitenv/referenceccda/validators/schema/ReferenceCCDAValidator.java

@@ -9,7 +9,8 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.eclipse.emf.common.util.Diagnostic;
 import org.eclipse.emf.ecore.EClass;
 import org.eclipse.emf.ecore.EObject;
@@ -61,7 +62,7 @@
 @RequestScope
 @Component
 public class ReferenceCCDAValidator extends BaseCCDAValidator implements CCDAValidator {
-	private static Logger logger = Logger.getLogger(ReferenceCCDAValidator.class);
+	private static Logger logger = LoggerFactory.getLogger(ReferenceCCDAValidator.class);
 
 	private static final String IG_ISSUE_ID = "a.consol", MU_ISSUE_ID = "a.mu2con", DS4P_ISSUE_ID = "ds4p";
 	private static final boolean CAPTURE_VALIDATION_STATISTICS = true;