Merge branch 'develop' into 'master'

Develop

See merge request !44

.gitlab-ci.yml

@@ -2,7 +2,7 @@
 include:
   - project: 'gazelle/private/gitlab-ci-templates'
     file: 'extends-v2.yaml'
-    ref: 'master'
+    ref: '1.0.0'
 
 # Define stages
 stages:
@@ -13,66 +13,51 @@ stages:
   - publish
   - release
   - upgrade
-  - clean
+  - cleanup
 
 # Define global variables
 variables:
-  P_NAME: "gazelle-objects-checker"
-  P_APP_TYPE: "java"
-  P_CODE_SRC_PATH: "."
   P_MAVEN_IMAGE_TAG: "3.6.3-jdk-11-slim"
 
-# Define jobs
 compile/unit-test:
   stage: build
   extends:
     - .buildJavaMavenTest
-  variables:
-    MAVEN_PHASE: "clean install"
-    P_MAVEN_EXTRA_ARGS: "-DskipITs"
+
+
 
 package:
   stage: build
   extends:
     - .buildJavaMavenPackage
-  needs:
-    - job: compile/unit-test
-      artifacts: true
   variables:
-    P_MAVEN_EXTRA_ARGS: "-DskipTests"
-
-integration-tests:
-  stage: test
-  extends:
-    - .testJavaMavenIntegrationTests
-  needs:
-    - job: compile/unit-test
-      artifacts: false
-  allow_failure: true
-
-static-analysis:
-  stage: test
-  extends:
-    - .testJavaMavenSonarAnalysis
+    P_MAVEN_EXTRA_ARGS: "-DskipTests -DskipITs"
   needs:
     - job: compile/unit-test
       artifacts: true
-  variables:
-    P_MAVEN_EXTRA_ARGS: "-Psonar -DskipTests"
-
 
 install-cache-repo:
   stage: publish
   extends:
     - .publishJavaMavenInstall
+  variables:
+    P_MAVEN_EXTRA_ARGS: "-DskipTests -DskipITs"
   needs:
     - job: package
-      artifacts: false
-  variables:
-    P_MAVEN_EXTRA_ARGS: "-DskipTests"
+      artifacts: true
 
+publish-code:
+  stage: publish
+  extends:
+    - .publishJavaMavenDeploy
+  needs:
+    - job: package
+      artifacts: true
 
 release/code:
   stage: release
   extends:
-    - .releaseCodeForJava
+    - .releaseCodeForJava
\ No newline at end of file
+  when: manual
+  variables:
+    P_MAVEN_JAVADOC_SKIP: "true"

archetype/generated-validator/validator-archetype-instantiator/src/main/java/net/ihe/gazelle/goc/ValidatorInstantiator.java

@@ -10,7 +10,7 @@ public class ValidatorInstantiator {
         String loadMethod;
         String validatorRootClass;
         if ("cdaepsos".equals(configuration)) {
-            validatorRootClass = "net.ihe.gazelle.cdaepsos3.POCDMT000040ClinicalDocument";
+            validatorRootClass = "net.ihe.gazelle.cdaepsos4.POCDMT000040ClinicalDocument";
             loadMethod="load";
         } else {
             validatorRootClass = "net.ihe.gazelle.cda.POCDMT000040ClinicalDocument";

archetype/generated-validator/validator-archetype/src/main/resources/archetype-resources/pom.xml

@@ -201,13 +201,13 @@
             <groupId>net.ihe.gazelle.cdaepsos</groupId>
             <artifactId>cdaepsos-code-jar</artifactId>
             <type>jar</type>
-            <version>1.9</version>
+            <version>1.2.0</version>
         </dependency>
 
         <dependency>
             <groupId>net.ihe.gazelle.cdaepsos</groupId>
             <artifactId>cdaepsos-validator-jar</artifactId>
-            <version>1.0</version>
+            <version>1.1.0</version>
         </dependency>
 
         <dependency>

archetype/generated-validator/validator-archetype/src/main/resources/archetype-resources/src/main/java/net/ihe/gazelle/assembler/__projectName__/MicroDocumentValidation.java

@@ -16,7 +16,7 @@ import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathExpression;
 import javax.xml.xpath.XPathFactory;
 
-import net.ihe.gazelle.cdaepsos3.cdaepsos3.CDAEPSOS3PackValidator;
+import net.ihe.gazelle.cdaepsos4.cdaepsos4.CDAEPSOS4PackValidator;
 import net.ihe.gazelle.cda.cdabasic.CDABASICPackValidator;
 import net.ihe.gazelle.cda.cdadt.CDADTPackValidator;
 import net.ihe.gazelle.cda.cdanblock.CDANBLOCKPackValidator;
@@ -197,7 +197,7 @@ class MicroDocumentValidation {
 		ltp.add(new ${projectNameCapitalyzedFirst}Parser());
 
 		// --conditional validation
-		listConstraintValidatorModule.add(new CDAEPSOS3PackValidator());
+		listConstraintValidatorModule.add(new CDAEPSOS4PackValidator());
 		MicroDocumentValidation.validateWithExtendedCDAValidator(documentContent, listConstraintValidatorModule, ltp, dr);
 
 		${validatorRootClass} clin = null;

archetype/generated-validator/validator-archetype/src/main/resources/archetype-resources/src/main/resources/cdaepsos.properties

-imports=net.ihe.gazelle.medication2.*,net.ihe.gazelle.cdaepsos3.*,net.ihe.gazelle.datatypes.*,net.ihe.gazelle.nblock.*,net.ihe.gazelle.voc.*
+imports=net.ihe.gazelle.medication2.*,net.ihe.gazelle.pharm.*,net.ihe.gazelle.cdaepsos4.*,net.ihe.gazelle.datatypes.*,net.ihe.gazelle.nblock.*,net.ihe.gazelle.voc.*

hl7templates/gocmodel-jar/pom.xml

@@ -322,12 +322,12 @@
         <dependency>
             <groupId>net.ihe.gazelle.model</groupId>
             <artifactId>cda-model</artifactId>
-            <version>3.1.0</version>
+              <version>3.1.1</version>
         </dependency>
         <dependency>
             <groupId>net.ihe.gazelle.model</groupId>
             <artifactId>cdaepsos-model</artifactId>
-            <version>3.1.0</version>
+            <version>3.1.1</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>

hl7templates/hl7templates-generator-jar/src/main/java/net/ihe/gazelle/tempgen/action/AttributeAnalyzer.java

@@ -232,7 +232,7 @@ public class AttributeAnalyzer extends AttributeProcessorImpl {
 
 	@Override
 	public void processIsOptional(Boolean isOptional) {
-		if (isOptional == null || !isOptional.booleanValue()){
+		if ((isOptional == null || !isOptional.booleanValue()) ){
 			List<String> listAttrNames = AttributeUtil.getListAttributesNames(selectedAttribute);
 			for (String attrName : listAttrNames) {
 				if (AttributeUtil.assertAttributeIsNotRequiredByDefault(this.selectedAttribute, attrName)){

hl7templates/hl7templates-generator-jar/src/main/java/net/ihe/gazelle/tempgen/action/HL7TemplatesConverter.java

@@ -152,7 +152,7 @@ public class HL7TemplatesConverter {
             for(Iterator<OwnedRule> itor = currentPe.getOwnedRule().listIterator(); itor.hasNext();){
                 OwnedRule currentOr = itor.next();
                 if(!isOclClean(currentOr)){
-                    log.info("Removing wrong OCL: {}",currentOr.getId());
+                    log.info("Removing wrong OCL: {}",currentOr.getSpecification().getBody());
                     //TamlHandler.removeTAML(currentOr);
                     removedOrIds.add(currentOr.getId());
                     itor.remove();

hl7templates/hl7templates-model-jar/pom.xml

@@ -229,5 +229,6 @@
             <version>1.4.1</version>
         </dependency>
 
+
     </dependencies>
 </project>

hl7templates/hl7templates-model-jar/src/main/java/net/ihe/gazelle/tempmodel/org/decor/art/utils/DecorMarshaller.java

 package net.ihe.gazelle.tempmodel.org.decor.art.utils;
 
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.net.URL;
-import java.net.URLConnection;
+import net.ihe.gazelle.tempmodel.org.decor.art.model.Decor;
+import org.apache.commons.validator.routines.UrlValidator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
 import javax.xml.bind.Unmarshaller;
-
-import org.apache.commons.validator.routines.UrlValidator;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import net.ihe.gazelle.tempmodel.org.decor.art.model.Decor;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.URL;
+import java.net.http.HttpClient;
+import java.net.http.HttpRequest;
+import java.net.http.HttpResponse;
 
 /**
  * 
@@ -27,6 +27,11 @@ public final class DecorMarshaller {
 	
 	
 	private static Logger log = LoggerFactory.getLogger(DecorMarshaller.class);
+
+	private static HttpClient httpClient = HttpClient.newBuilder()
+			.connectTimeout(java.time.Duration.ofSeconds(10))
+			.followRedirects(HttpClient.Redirect.ALWAYS)
+			.build();
 	
 	private DecorMarshaller() {}
 
@@ -65,19 +70,13 @@ public final class DecorMarshaller {
 		InputStream is = null;
 		try {
 			if (UrlValidator.getInstance().isValid(path)) {
-				URL url;
-				
-					url = new URL(path);
-				URLConnection urlConnection = url.openConnection();
-				urlConnection.setConnectTimeout(10000);
-				urlConnection.setReadTimeout(10000);
-				is = urlConnection.getInputStream();
+				is = getInputStreamFromURL(path);
 			}
 			else {
 				is = new FileInputStream(path);
 			}
 			return loadDecor(is);
-		} catch (IOException e) {
+		} catch (IOException | InterruptedException e) {
 			log.error("Error to load decor from url : " + path, e);
 		}finally {
 			if (is != null) {
@@ -106,5 +105,14 @@ public final class DecorMarshaller {
 		mar.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
 		mar.marshal(decor, os);
 	}
-	
+
+	private static InputStream getInputStreamFromURL(String url) throws IOException, InterruptedException {
+		HttpRequest request = HttpRequest.newBuilder()
+				.GET()
+				.uri(java.net.URI.create(url))
+				.build();
+		HttpResponse<InputStream> response = httpClient.send(request, HttpResponse.BodyHandlers.ofInputStream());
+		return response.body();
+	}
+
 }

hl7templates/hl7templates-packager-jar/pom.xml

@@ -198,16 +198,7 @@
             <type>jar</type>
         </dependency>
 
-        <dependency>
-            <groupId>net.ihe.gazelle.model</groupId>
-            <artifactId>cda-model</artifactId>
-            <version>3.1.0</version>
-        </dependency>
-        <dependency>
-            <groupId>net.ihe.gazelle.model</groupId>
-            <artifactId>cdaepsos-model</artifactId>
-            <version>3.1.0</version>
-        </dependency>
+
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-core</artifactId>

hl7templates/hl7templates-packager-jar/src/main/java/net/ihe/gazelle/lib/hl7templatespackager/adapters/ArchetypeInstantiatorMaven.java

@@ -204,9 +204,10 @@ public class ArchetypeInstantiatorMaven implements ArchetypeInstantiator {
             version = System.getProperty("GOC_VERSION");
             if(version == null){
                 log.error("Could not find GOC version, trying to get it from latest release in nexus");
+                version = getLatestGOCVersion();
             }
-            version = getLatestGOCVersion();
         }
+        log.info("GOC version is {}",version);
         return version;
     }
 

settings.xml

@@ -7,5 +7,10 @@
             <username>${ARTIFACT_RELEASE_REPOSITORY_USER}</username>
             <password>${ARTIFACT_RELEASE_REPOSITORY_PASS}</password>
         </server>
+        <server>
+            <id>nexus-snapshots</id>
+            <username>${ARTIFACT_RELEASE_REPOSITORY_USER}</username>
+            <password>${ARTIFACT_RELEASE_REPOSITORY_PASS}</password>
+        </server>
     </servers>
 </settings>