Merge pull request #195 from onc-healthit/develop

merge develop into master for release

pom.xml

@@ -71,16 +71,16 @@
 				<version>2.0</version>
 				<scope>provided</scope>
 			</dependency>
+
 			<dependency>
-				<groupId>log4j</groupId>
-				<artifactId>log4j</artifactId>
-				<version>1.2.17</version>
+				<groupId>org.apache.logging.log4j</groupId>
+				<artifactId>log4j-api</artifactId>
+				<version>2.17.2</version>
 			</dependency>
-
 			<dependency>
-				<groupId>log4j</groupId>
-				<artifactId>apache-log4j-extras</artifactId>
-				<version>1.2.17</version>
+				<groupId>org.apache.logging.log4j</groupId>
+				<artifactId>log4j-core</artifactId>
+				<version>2.17.2</version>
 			</dependency>
 			<dependency>
 				<groupId>commons-fileupload</groupId>
@@ -115,7 +115,7 @@
 			<dependency>
 				<groupId>org.hsqldb</groupId>
 				<artifactId>hsqldb</artifactId>
-				<version>2.3.3</version>
+				<version>2.5.2</version>
 			</dependency>
 			<dependency>
 				<groupId>org.hibernate</groupId>
@@ -178,6 +178,30 @@
 			</dependency>
 			<!-- /testing -->
 
+			<!-- authorization/KeyCloak -->
+			<dependency>
+				<groupId>org.json</groupId>
+				<artifactId>json</artifactId>
+				<version>20140107</version>
+			</dependency>			
+			<dependency>
+				<groupId>io.jsonwebtoken</groupId>
+				<artifactId>jjwt-api</artifactId>
+				<version>0.11.2</version>
+			</dependency>
+			<dependency>
+				<groupId>io.jsonwebtoken</groupId>
+				<artifactId>jjwt-impl</artifactId>
+				<version>0.11.2</version>
+				<scope>runtime</scope>
+			</dependency>
+			<dependency>
+				<groupId>io.jsonwebtoken</groupId>
+				<artifactId>jjwt-jackson</artifactId>
+				<version>0.11.1</version>
+				<scope>runtime</scope>
+			</dependency>			
+
 		</dependencies>
 
 

src/main/java/org/sitenv/service/ccda/smartscorecard/authorization/GenerateAccessToken.java

@@ -0,0 +1,64 @@
+package org.sitenv.service.ccda.smartscorecard.authorization;
+
+import java.util.Objects;
+
+import org.json.JSONObject;
+import org.sitenv.service.ccda.smartscorecard.model.ScorecardProperties;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Component;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
+import org.springframework.web.client.HttpClientErrorException;
+import org.springframework.web.client.RestTemplate;
+
+@Component
+public class GenerateAccessToken {
+
+	private static final Logger logger = LoggerFactory.getLogger(GenerateAccessToken.class);
+
+	@Autowired
+	@Qualifier("scorecardProperties")
+	ScorecardProperties scorecardProperties;
+
+	public String getAccessToken() {
+		String accessToken = null;
+		try {
+			RestTemplate restTemplate = new RestTemplate();
+
+			String tokenEndpoint = scorecardProperties.getTokenEndpoint();
+			logger.info("tokenEndpoint: " + tokenEndpoint);
+			String clientId = scorecardProperties.getClientId();
+			logger.info("clientId: " + clientId);
+			String clientSecret = scorecardProperties.getClientSecret();
+
+			HttpHeaders headers = new HttpHeaders();
+			headers.setContentType(MediaType.APPLICATION_FORM_URLENCODED);
+
+			MultiValueMap<String, String> map = new LinkedMultiValueMap<>();
+			map.add("grant_type", "client_credentials");
+			map.add("client_secret", clientSecret);
+			map.add("client_id", clientId);
+			HttpEntity<MultiValueMap<String, String>> request = new HttpEntity<>(map, headers);
+			ResponseEntity<KeyCloakResponse> response = restTemplate.postForEntity(tokenEndpoint, request,
+					KeyCloakResponse.class);
+
+			JSONObject jsonObj = new JSONObject(Objects.requireNonNull(response.getBody()));
+			accessToken = jsonObj.getString("access_token");
+			logger.info("getAccessToken accessToken  status :::::::" + response.getStatusCode());
+		} catch (HttpClientErrorException clienterror) {
+			logger.error("HttpClientErrorException  :::::::" + clienterror.getMessage());
+			clienterror.printStackTrace();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+		return accessToken;
+	}
+
+}

src/main/java/org/sitenv/service/ccda/smartscorecard/authorization/KeyCloakResponse.java

@@ -0,0 +1,33 @@
+package org.sitenv.service.ccda.smartscorecard.authorization;
+
+public class KeyCloakResponse {
+
+    private String access_token;
+    private int expires_in;
+    private String user;
+
+    public String getAccess_token() {
+        return access_token;
+    }
+
+    public void setAccess_token(String access_token) {
+        this.access_token = access_token;
+    }
+
+    public int getExpires_in() {
+        return expires_in;
+    }
+
+    public void setExpires_in(int expires_in) {
+        this.expires_in = expires_in;
+    }
+
+    public String getUser() {
+        return user;
+    }
+
+    public void setUser(String user) {
+        this.user = user;
+    }
+
+}

src/main/java/org/sitenv/service/ccda/smartscorecard/configuration/ApplicationConfiguration.java

@@ -23,8 +23,18 @@ public class ApplicationConfiguration {
 	 * The following value is only looked at if OVERRIDE_SCORECARD_XML_CONFIG is true
 	 * True allows for '2015 Edition Certification Feedback' results
 	 */
-	public static final boolean CERTIFICATION_RESULTS_CALL = true;		
+	public static final boolean CERTIFICATION_RESULTS_CALL = true;
+
+	/**
+	 * The following values are only looked at if OVERRIDE_SCORECARD_XML_CONFIG is true
+	 * True allows defining the authorization detail programmatically vs in the XML config
+	 * This should only be done for local testing purposes as it is dangerous to deploy a secret.
+	 */
+	public static final String TOKEN_ENDPOINT = "";
+	public static final String CLIENT_ID = "";
+	public static final String CLIENT_SECRET = "";
 
+	// TODO: Shouldn't this be updated to SVAP 2022 or later?
 	/**
 	 * The cures update version of the Reference Validator is currently hosted on the C-CDA
 	 * servers. True enables cures validation within the scorecard by switching
@@ -60,7 +70,8 @@ public class ApplicationConfiguration {
 		CODE_IN_VALUESET_SERVICE = "/referenceccdaservice/iscodeinvalueset",
 		CODE_IN_CODESYSTEM_SERVICE = "/referenceccdaservice/iscodeincodesystem",
 		REFERENCE_CCDA_SERVICE = "/referenceccdaservice/",
-		CCDA_SCORECARD_SERVICE = "/scorecard/ccdascorecardservice2",
+		CCDA_SCORECARD_SERVICE_APPLICATION_NAME = "ccdascorecardserviceinternal",
+		CCDA_SCORECARD_SERVICE = "/scorecard/" + CCDA_SCORECARD_SERVICE_APPLICATION_NAME,
 		SAVE_SCORECARD_SERVICE_BACKEND = "/scorecard/savescorecardservicebackend",
 		SAVE_SCORECARD_SERVICE_BACKEND_SUMMARY = "/scorecard/savescorecardservicebackendsummary";	
 
@@ -72,7 +83,7 @@ public class ApplicationConfiguration {
 		CODE_VALUSET_VALIDATION_URL = server + CODE_IN_VALUESET_SERVICE,
 		CODE_CODESYSTEM_VALIDATION_URL = server + CODE_IN_CODESYSTEM_SERVICE,
 		REFERENCE_VALIDATOR_URL = server + REFERENCE_CCDA_SERVICE;
-	// -Scorecard endpoints
+	// -Scorecard endpoints (updating the same server variable to reuse programatically for next config)
 	static {
 		server = ENV.server(EndpointType.Scorecard);
 	}
@@ -153,4 +164,5 @@ public boolean isDevLocalOrCustom() {
 	public static final int CORE_POOL_SIZE = 200;
 	public static final int MAX_POOL_SIZE = 500;
 	public static final int QUEUE_CAPACITY = 10;
+
 }

src/main/java/org/sitenv/service/ccda/smartscorecard/configuration/ApplicationInitializer.java

@@ -8,8 +8,8 @@ public class ApplicationInitializer extends AbstractAnnotationConfigDispatcherSe
 
 	@Override
 	protected Class<?>[] getRootConfigClasses() {
-		return new Class<?>[] { 
-				MvcConfiguration.class,PersistanceConfiguration.class,PersistanceConfigurationPostGres.class};
+		return new Class<?>[] { MvcConfiguration.class, PersistanceConfiguration.class,
+				PersistanceConfigurationPostGres.class };
 	}
 
 	@Override

src/main/java/org/sitenv/service/ccda/smartscorecard/configuration/PersistanceConfiguration.java

@@ -142,6 +142,8 @@ public VocabularyLoaderFactory vocabularyLoaderFactory() {
     @SuppressWarnings("unused")
     public ScorecardProperties scorecardPropertiesLoader(final Environment environment){
     	ScorecardProperties scorecardProperties = new ScorecardProperties();
+
+    	// Basic properties
     	scorecardProperties.setIgConformanceCall(
     			ApplicationConfiguration.OVERRIDE_SCORECARD_XML_CONFIG && ApplicationConfiguration.IG_CONFORMANCE_CALL ? 
     					ApplicationConfiguration.IG_CONFORMANCE_CALL :
@@ -156,6 +158,19 @@ public ScorecardProperties scorecardPropertiesLoader(final Environment environme
     	scorecardProperties.setCertificatinResultsURL(
     			ApplicationConfiguration.OVERRIDE_SCORECARD_XML_CONFIG ? ApplicationConfiguration.REFERENCE_VALIDATOR_URL :    			
     			environment.getProperty("scorecard.certificationResultsUrl"));
+
+    	// NOTE: scorecard.configFile is handled in the scorecardConfigurationLoader method in this file    	
+
+    	// Authorization properties
+    	scorecardProperties.setTokenEndpoint(
+    			ApplicationConfiguration.OVERRIDE_SCORECARD_XML_CONFIG ? ApplicationConfiguration.TOKEN_ENDPOINT :    			
+    			environment.getProperty("scorecard.tokenEndpoint"));
+    	scorecardProperties.setClientId(
+    			ApplicationConfiguration.OVERRIDE_SCORECARD_XML_CONFIG ? ApplicationConfiguration.CLIENT_ID :    			
+    			environment.getProperty("scorecard.clientId"));
+    	scorecardProperties.setClientSecret(
+    			ApplicationConfiguration.OVERRIDE_SCORECARD_XML_CONFIG ? ApplicationConfiguration.CLIENT_SECRET :    			
+    			environment.getProperty("scorecard.clientSecret"));    	
         return scorecardProperties;
     }
 

src/main/java/org/sitenv/service/ccda/smartscorecard/controller/SaveReportController.java

@@ -1254,6 +1254,7 @@ private static String convertFileToString(URI fileURI) {
 		return sb.toString();
 	}	
 
+	// This is for local testing purposes
 	public static void main(String[] args) {
 		String[] filenames = {"highScoringSample", "lowScoringSample", "sampleWithErrors", 
 				"sampleWithSchemaErrors", "sampleWithoutAnyContent", "sampleWithConfErrorAndNoCert"};

src/main/java/org/sitenv/service/ccda/smartscorecard/controller/ScorecardController.java

@@ -5,6 +5,7 @@
 import java.io.IOException;
 
 import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.sitenv.service.ccda.smartscorecard.configuration.ApplicationConfiguration;
 import org.sitenv.service.ccda.smartscorecard.model.ResponseTO;
 import org.sitenv.service.ccda.smartscorecard.processor.ScorecardProcessor;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -18,44 +19,41 @@
 import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.multipart.MultipartFile;
 
-
 @RestController
 public class ScorecardController {
-	
+
 	@Autowired
 	ScorecardProcessor scorecardProcessor;
-
-	@RequestMapping(value = "/ccdascorecardservice2", method = RequestMethod.POST)
-	public @ResponseBody ResponseTO ccdascorecardservice(@RequestParam("ccdaFile") MultipartFile ccdaFile){
+
+	@RequestMapping(value = "/"
+			+ ApplicationConfiguration.CCDA_SCORECARD_SERVICE_APPLICATION_NAME, method = RequestMethod.POST)
+	public @ResponseBody ResponseTO ccdascorecardservice(@RequestParam("ccdaFile") MultipartFile ccdaFile) {
 		return scorecardProcessor.processCCDAFile(ccdaFile);
 	}
-	
+
 	@RequestMapping(value = "/exportscorecarddatatoexcel", method = RequestMethod.GET)
-	public ResponseEntity<InputStreamResource> genrateScorecardData(@RequestParam(value="fromDate", required=false) String fromDate,
-			@RequestParam(value="toDate", required=false) String toDate)throws Exception {
-
-		File file=null;
+	public ResponseEntity<InputStreamResource> genrateScorecardData(
+			@RequestParam(value = "fromDate", required = false) String fromDate,
+			@RequestParam(value = "toDate", required = false) String toDate) throws Exception {
+
+		File file = null;
 		HSSFWorkbook workBook = null;
 		String fileName = "scorecardData.xls";
 		try {
-
 			workBook = scorecardProcessor.generateScorecardData(fromDate, toDate);
 			file = new File(fileName);
 			workBook.write(file);
-
 		} catch (IOException ioe) {
 			ioe.printStackTrace();
 			throw ioe;
 		} catch (Exception e) {
 			e.printStackTrace();
 			throw e;
 		}
-		return ResponseEntity.ok()
-				.contentLength(file.length())
-	            .contentType(MediaType.parseMediaType("application/vnd.ms-excel"))
-	            .header("Content-Disposition","attachment; filename=" + fileName )
-	            .body(new InputStreamResource(new FileInputStream(file)));
-
+		return ResponseEntity.ok().contentLength(file.length())
+				.contentType(MediaType.parseMediaType("application/vnd.ms-excel"))
+				.header("Content-Disposition", "attachment; filename=" + fileName)
+				.body(new InputStreamResource(new FileInputStream(file)));
 	}
 
 }

src/main/java/org/sitenv/service/ccda/smartscorecard/loader/VocabularyLoadRunner.java

@@ -1,6 +1,7 @@
 package org.sitenv.service.ccda.smartscorecard.loader;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.DisposableBean;
 import org.springframework.beans.factory.InitializingBean;
 
@@ -13,7 +14,7 @@
 
 public class VocabularyLoadRunner implements InitializingBean, DisposableBean {
     private VocabularyLoaderFactory vocabularyLoaderFactory;
-    private static Logger logger = Logger.getLogger(VocabularyLoadRunner.class);
+    private static Logger logger = LogManager.getLogger(VocabularyLoadRunner.class);
     private String codeDirectory = null;
     private boolean recursive = true;
     private DataSource dataSource;

src/main/java/org/sitenv/service/ccda/smartscorecard/loader/code/LoincLoader.java

@@ -2,7 +2,8 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.StrBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.sitenv.service.ccda.smartscorecard.loader.BaseVocabularyLoader;
 import org.sitenv.service.ccda.smartscorecard.loader.VocabularyLoader;
 import org.springframework.stereotype.Component;
@@ -18,7 +19,7 @@
 
 @Component(value = "LOINC")
 public class LoincLoader extends BaseVocabularyLoader implements VocabularyLoader {
-    private static Logger logger = Logger.getLogger(LoincLoader.class);
+    private static Logger logger = LogManager.getLogger(LoincLoader.class);
 
     @Override
     public void load(List<File> filesToLoad, Connection connection) {

src/main/java/org/sitenv/service/ccda/smartscorecard/loader/code/TemplateIdLoaderR11.java

@@ -10,15 +10,16 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.StrBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.sitenv.service.ccda.smartscorecard.loader.BaseVocabularyLoader;
 import org.sitenv.service.ccda.smartscorecard.loader.VocabularyLoader;
 import org.springframework.stereotype.Component;
 
 @Component(value = "TEMPLATEIDSR1.1")
 public class TemplateIdLoaderR11 extends BaseVocabularyLoader implements VocabularyLoader {
 
-	private static Logger logger = Logger.getLogger(TemplateIdLoaderR21.class);
+	private static Logger logger = LogManager.getLogger(TemplateIdLoaderR21.class);
 
     @Override
     public void load(List<File> filesToLoad, Connection connection) {

src/main/java/org/sitenv/service/ccda/smartscorecard/loader/code/TemplateIdLoaderR21.java

@@ -10,15 +10,16 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.text.StrBuilder;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.sitenv.service.ccda.smartscorecard.loader.BaseVocabularyLoader;
 import org.sitenv.service.ccda.smartscorecard.loader.VocabularyLoader;
 import org.springframework.stereotype.Component;
 
 @Component(value = "TEMPLATEIDSR2.1")
 public class TemplateIdLoaderR21 extends BaseVocabularyLoader implements VocabularyLoader {
 
-	private static Logger logger = Logger.getLogger(TemplateIdLoaderR21.class);
+	private static Logger logger = LogManager.getLogger(TemplateIdLoaderR21.class);
 
     @Override
     public void load(List<File> filesToLoad, Connection connection) {