ref 13024: DataMiner - The service must support the https protocol

https://support.d4science.org/issues/13024

Updated DataMiner now support https

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/wps@174937 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -25,6 +25,7 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">

.project

@@ -5,11 +5,31 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>de.walware.statet.r.builders.RSupport</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>de.walware.docmlet.tex.builders.Tex</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
@@ -17,7 +37,14 @@
 		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
+		<nature>org.eclipse.wst.jsdt.core.jsNature</nature>
+		<nature>de.walware.statet.base.StatetNature</nature>
+		<nature>de.walware.statet.r.RNature</nature>
+		<nature>de.walware.docmlet.tex.natures.Tex</nature>
 	</natures>
 </projectDescription>

.settings/.jsdtscope

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry excluding="**/bower_components/*|**/node_modules/*|**/*.min.js" kind="src" path="src/main/webapp"/>
+	<classpathentry kind="src" path="target/m2e-wtp/web-resources"/>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.WebProject">
+		<attributes>
+			<attribute name="hide" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
+	<classpathentry kind="output" path=""/>
+</classpath>

.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +1,8 @@
 eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
 org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.wst.common.component

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="wps">
+        <wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
+        <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
+        <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
+        <dependent-module archiveName="dataminer-1.5.6-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/dataminer/dataminer">
+            <dependency-type>uses</dependency-type>
+        </dependent-module>
+        <property name="context-root" value="wps"/>
+        <property name="java-output-path" value="/wps/target/classes"/>
+    </wb-module>
+</project-modules>

.settings/org.eclipse.wst.common.project.facet.core.prefs.xml

@@ -0,0 +1,7 @@
+<root>
+  <facet id="jst.jaxrs">
+    <node name="libprov">
+      <attribute name="provider-id" value="jaxrs-no-op-library-provider"/>
+    </node>
+  </facet>
+</root>

.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <fixed facet="wst.jsdt.web"/>
+  <installed facet="java" version="1.8"/>
+  <installed facet="jst.web" version="3.0"/>
+  <installed facet="jst.jaxrs" version="2.0"/>
+  <installed facet="wst.jsdt.web" version="1.0"/>
+</faceted-project>

.settings/org.eclipse.wst.jsdt.ui.superType.container

@@ -0,0 +1 @@
+org.eclipse.wst.jsdt.launching.baseBrowserLibrary

.settings/org.eclipse.wst.jsdt.ui.superType.name

@@ -0,0 +1 @@
+Window

.settings/org.eclipse.wst.validation.prefs

@@ -0,0 +1,2 @@
+disabled=06target
+eclipse.preferences.version=1

distro/changelog.xml

@@ -1,7 +1,12 @@
 <ReleaseNotes>
+	<Changeset component="org.gcube.data-analysis.wps.1-1-3"
+		date="2018-12-13">
+		<Change>Added https support [ticket #13024]</Change>
+	</Changeset>
 	<Changeset component="org.gcube.data-analysis.wps.1-1-0"
 		date="2017-09-24">
-		<Change>Dynamic adding, removing and updating of algorithms added</Change>
+		<Change>Dynamic adding, removing and updating of algorithms added
+		</Change>
 		<Change>Moved to SocialNetworkingService 2.0</Change>
 	</Changeset>
 	<Changeset component="org.gcube.data-analysis.wps.1-0-0"

distro/web.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <web-app xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+	xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_3_0.xsd"
-	version="2.4">
+	version="3.0">
 	<display-name>52°North Web Processing Service, Git:
 		1665e1b7b2188755161d4f0f3a6acf562d0444e1 @ 2015-03-21 00:30:20
 	</display-name>

pom.xml

@@ -3,7 +3,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.gcube.data-analysis</groupId>
 	<artifactId>wps</artifactId>
-	<version>1.1.2-SNAPSHOT</version>
+	<version>1.1.3-SNAPSHOT</version>
 	<name>WPS</name>
 
 	<parent>

src/main/java/org/gcube/data/analysis/wps/GetCapabilitiesBuilder.java

@@ -23,42 +23,46 @@ import org.slf4j.LoggerFactory;
 public class GetCapabilitiesBuilder {
 
 	public static String processString = "<wps:Process wps:processVersion=\"1.1.0\">\n\t<ows:Identifier>#CLASS#</ows:Identifier>\n\t<ows:Title>#TITLE#</ows:Title>\n</wps:Process>";
-		
+
-	private static final Logger LOGGER= LoggerFactory.getLogger(GetCapabilitiesBuilder.class);
+	private static final Logger LOGGER = LoggerFactory.getLogger(GetCapabilitiesBuilder.class);
-	
+
-	public String getClassification(String algorithmName, ConfigurationManager configManager) throws Exception{
+	public String getClassification(String algorithmName, ConfigurationManager configManager) throws Exception {
-		//get algorithms classification:
+		// get algorithms classification:
-		LOGGER.debug("Searching for a classification of "+algorithmName);
+		LOGGER.debug("Searching for a classification of " + algorithmName);
-		HashMap<String, List<String>> algorithmsClassification = ProcessorsFactory.getAllFeaturesUser(configManager.getConfig());
+		HashMap<String, List<String>> algorithmsClassification = ProcessorsFactory
+				.getAllFeaturesUser(configManager.getConfig());
 		String rightClassification = "Others";
-		for (String classification:algorithmsClassification.keySet()){
+		for (String classification : algorithmsClassification.keySet()) {
 			List<String> algorithms = algorithmsClassification.get(classification);
-			if (algorithms.contains(algorithmName)){
+			if (algorithms.contains(algorithmName)) {
-				LOGGER.debug("Found classification"+classification);
+				LOGGER.debug("Found classification" + classification);
-				return classification; 
+				return classification;
 			}
 		}
-		LOGGER.debug("No classification found for "+algorithmName);
+		LOGGER.debug("No classification found for " + algorithmName);
 		return rightClassification;
 	}
-	
+
 	public String buildGetCapabilities(Map<String, String[]> parameters) throws Exception {
 
 		LinkedHashMap<String, Object> basicInputs = new LinkedHashMap<String, Object>();
-		//DONE get scope and username from SmartGears to build the get capabilities
+		// DONE get scope and username from SmartGears to build the get
-		/* OLD CODE
+		// capabilities
-		if (parameters != null) {
+		/*
-			if (parameters.get(ConfigurationManager.scopeParameter) != null)
+		 * OLD CODE if (parameters != null) { if
-				basicInputs.put(ConfigurationManager.scopeParameter, parameters.get(ConfigurationManager.scopeParameter)[0]);
+		 * (parameters.get(ConfigurationManager.scopeParameter) != null)
-			if (parameters.get(ConfigurationManager.usernameParameter) != null)
+		 * basicInputs.put(ConfigurationManager.scopeParameter,
-				basicInputs.put(ConfigurationManager.usernameParameter, parameters.get(ConfigurationManager.usernameParameter)[0]);
+		 * parameters.get(ConfigurationManager.scopeParameter)[0]); if
-		} else {// case for testing purposes only
+		 * (parameters.get(ConfigurationManager.usernameParameter) != null)
-			if (AbstractEcologicalEngineMapper.simulationMode){
+		 * basicInputs.put(ConfigurationManager.usernameParameter,
-				basicInputs.put(ConfigurationManager.scopeParameter, ConfigurationManager.defaultScope);
+		 * parameters.get(ConfigurationManager.usernameParameter)[0]); } else
-				basicInputs.put(ConfigurationManager.usernameParameter, ConfigurationManager.defaultUsername);
+		 * {// case for testing purposes only if
-			}
+		 * (AbstractEcologicalEngineMapper.simulationMode){
-		}
+		 * basicInputs.put(ConfigurationManager.scopeParameter,
-		*/
+		 * ConfigurationManager.defaultScope);
+		 * basicInputs.put(ConfigurationManager.usernameParameter,
+		 * ConfigurationManager.defaultUsername); } }
+		 */
 		ConfigurationManager configManager = new ConfigurationManager();
 		TokenManager tokenm = new TokenManager();
 		tokenm.getCredentials();
@@ -68,63 +72,70 @@ public class GetCapabilitiesBuilder {
 		basicInputs.put(ConfigurationManager.scopeParameter, scope);
 		basicInputs.put(ConfigurationManager.usernameParameter, username);
 		basicInputs.put(ConfigurationManager.tokenParameter, token);
-		
+
 		configManager.configAlgorithmEnvironment(basicInputs);
-		LOGGER.debug("Initializing Capabilities Skeleton in scope " + configManager.getScope() + " with user " + configManager.getUsername());
+		LOGGER.debug("Initializing Capabilities Skeleton in scope " + configManager.getScope() + " with user "
+				+ configManager.getUsername());
 		InputStream is = this.getClass().getClassLoader().getResourceAsStream("templates/wpsCapabilitiesSkeleton.xml");
 		String stringTemplate = IOUtils.toString(is, "UTF-8");
-		
+
-		//TODO: GET HOSTNAME AND PORT from container
+		// TODO: GET HOSTNAME AND PORT from container
+		String protocol = WPSConfig.getInstance().getWPSConfig().getServer().getProtocol();
 		String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
 		String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport();
-		stringTemplate = stringTemplate.replace("#HOST#", host).replace("#PORT#", port);
+		stringTemplate = stringTemplate.replace("#PROTOCOL#", protocol).replace("#HOST#", host).replace("#PORT#", port);
+
+		LOGGER.debug("Protocol: "+protocol);
+		LOGGER.debug("Host: " + host);
+		LOGGER.debug("Port: " + port);
 
-		LOGGER.debug("Host: " + host + " Port: " + port);
-		
 		LinkedHashMap<String, String> allalgorithms = new LinkedHashMap<String, String>();
 		/*
-		String packageS = "org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses";
+		 * String packageS =
-		List<Class<?>> classes = null;
+		 * "org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses";
-		try{
+		 * List<Class<?>> classes = null; try{
-			LOGGER.debug("Taking classes from /classes");
+		 * LOGGER.debug("Taking classes from /classes"); classes =
-			classes = GetCapabilitiesChecker.find(packageS);
+		 * GetCapabilitiesChecker.find(packageS); }catch(Exception e){
-		}catch(Exception e){
+		 * LOGGER.debug("Taking classes from the Jar");
-			LOGGER.debug("Taking classes from the Jar");
+		 * classes=GetCapabilitiesChecker.getClassesInSamePackageFromJar(
-			classes=GetCapabilitiesChecker.getClassesInSamePackageFromJar(packageS);
+		 * packageS); }
-		}*/
+		 */
-		
+
-		LOGGER.info("using classloader class {} ",Thread.currentThread().getContextClassLoader().getClass().getSimpleName());
+		LOGGER.info("using classloader class {} ",
-		
+				Thread.currentThread().getContextClassLoader().getClass().getSimpleName());
-		
+
-		Set<Class<?>> algorithmsClass =  GcubeAlgorithmRepository.getAllAlgorithms();
+		Set<Class<?>> algorithmsClass = GcubeAlgorithmRepository.getAllAlgorithms();
-		
+
-		LOGGER.info("class found with annotation Algorithm are {}",algorithmsClass.size());
+		LOGGER.info("class found with annotation Algorithm are {}", algorithmsClass.size());
-		
+
 		for (Class<?> classfind : algorithmsClass) {
-			org.n52.wps.algorithm.annotation.Algorithm algorithmInfo = classfind.getAnnotation(org.n52.wps.algorithm.annotation.Algorithm.class);
+			org.n52.wps.algorithm.annotation.Algorithm algorithmInfo = classfind
+					.getAnnotation(org.n52.wps.algorithm.annotation.Algorithm.class);
 			if (algorithmInfo != null) {
 				LOGGER.debug("Retrieving local declared Algorithm: " + algorithmInfo.title());
 				allalgorithms.put(algorithmInfo.title(), classfind.getName());
-			} 
+			}
 		}
 
 		LOGGER.debug("Getting algorithms from the infrastructure");
 		InfrastructureDialoguer dialoguer = new InfrastructureDialoguer(configManager.getScope());
 		List<String> algorithmsInScope = dialoguer.getAlgorithmsInScope();
-		LOGGER.debug("Found {}  algorithms in scope {} ",algorithmsInScope.size() ,ScopeProvider.instance.get());
+		LOGGER.debug("Found {}  algorithms in scope {} ", algorithmsInScope.size(), ScopeProvider.instance.get());
 		StringBuffer capabilities = new StringBuffer();
-		
+
-		//TO eliminate duplicate coming from IS
+		// TO eliminate duplicate coming from IS
 		Set<String> algorithmsSet = new HashSet<String>(algorithmsInScope);
-		algorithmsSet.addAll(dialoguer.getPrivateAlgorithmsInScope(AuthorizationProvider.instance.get().getClient().getId()));
+		algorithmsSet.addAll(
-		
+				dialoguer.getPrivateAlgorithmsInScope(AuthorizationProvider.instance.get().getClient().getId()));
-		for (String algorithmInScope : algorithmsSet ) {
+
+		for (String algorithmInScope : algorithmsSet) {
 			String classAlgorithm = allalgorithms.get(algorithmInScope);
 			if (classAlgorithm != null) {
 				LOGGER.debug("Approving " + classAlgorithm + " to capabilities ");
-				String algorithmTitle = getClassification(algorithmInScope, configManager)+":"+algorithmInScope;
+				String algorithmTitle = getClassification(algorithmInScope, configManager) + ":" + algorithmInScope;
-//				String algorithmTitle = algorithmInScope;
+				// String algorithmTitle = algorithmInScope;
-				capabilities.append(processString.replace("#TITLE#", algorithmTitle).replace("#CLASS#", classAlgorithm));
+				capabilities
+						.append(processString.replace("#TITLE#", algorithmTitle).replace("#CLASS#", classAlgorithm));
 			}
 		}
 
@@ -133,6 +144,4 @@ public class GetCapabilitiesBuilder {
 		return stringTemplate;
 	}
 
-
-
 }

src/main/webapp/WEB-INF/README

@@ -9,23 +9,23 @@ open-source software toolkit used for building and operating Hybrid Data
 Infrastructures enabling the dynamic deployment of Virtual Research Environments
 by favouring the realisation of reuse oriented policies.
  
-The projects leading to this software have received funding from a series of
+The projects leading to this software have received funding from a series of    
-European Union programmes including:
+European Union programmes including:                                            
-* the Sixth Framework Programme for Research and Technological Development -
+* the Sixth Framework Programme for Research and Technological Development -    
-DILIGENT (grant no. 004260);
+DILIGENT (grant no. 004260);                                                    
-* the Seventh Framework Programme for research, technological development and
+* the Seventh Framework Programme for research, technological development and   
-demonstration - D4Science (grant no. 212488), D4Science-II (grant no.
+demonstration - D4Science (grant no. 212488), D4Science-II (grant no.           
-239019),ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine
+239019),ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine   
-(grant no. 283644);
+(grant no. 283644);                                                             
-* the H2020 research and innovation programme - BlueBRIDGE (grant no. 675680),
+* the H2020 research and innovation programme - BlueBRIDGE (grant no. 675680),  
-EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant
+EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant 
-no. 654119), SoBigData (grant no. 654024), AGINFRA PLUS (grant no. 731001).
+no. 654119), SoBigData (grant no. 654024);
  
  
 Version
 --------------------------------------------------
  
-1.1.1-SNAPSHOT (2018-10-12)
+1.1.3-SNAPSHOT (2018-12-17)
  
 Please see the file named "changelog.xml" in this directory for the release notes.
  

src/main/webapp/WEB-INF/changelog.xml

@@ -1,7 +1,12 @@
 <ReleaseNotes>
+	<Changeset component="org.gcube.data-analysis.wps.1-1-3"
+		date="2018-12-13">
+		<Change>Added https support [ticket #13024]</Change>
+	</Changeset>
 	<Changeset component="org.gcube.data-analysis.wps.1-1-0"
 		date="2017-09-24">
-		<Change>Dynamic adding, removing and updating of algorithms added</Change>
+		<Change>Dynamic adding, removing and updating of algorithms added
+		</Change>
 		<Change>Moved to SocialNetworkingService 2.0</Change>
 	</Changeset>
 	<Changeset component="org.gcube.data-analysis.wps.1-0-0"

src/main/webapp/WEB-INF/descriptor.xml

@@ -9,7 +9,7 @@
 	<baseDirectory>/</baseDirectory>
 	<fileSets>
 		<fileSet>
-			<directory>/home/lucio/workspace/imarine/wps/distro</directory>
+			<directory>/home/giancarlo/workspaceDataMinerService/wps/distro</directory>
 			<outputDirectory>/</outputDirectory>
 			<useDefaultExcludes>true</useDefaultExcludes>
 			<includes>

src/main/webapp/WEB-INF/profile.xml

@@ -10,11 +10,11 @@
 		<Packages>
 			<Software>
 				<Name>wps</Name>
-				<Version>1.1.1-SNAPSHOT</Version>
+				<Version>1.1.3-SNAPSHOT</Version>
 				<MavenCoordinates>
 					<groupId>org.gcube.data-analysis</groupId>
 					<artifactId>wps</artifactId>
-					<version>1.1.1-SNAPSHOT</version>
+					<version>1.1.3-SNAPSHOT</version>
 				</MavenCoordinates>
 				<Files>
 					<File>wps.jar</File>

src/main/webapp/WEB-INF/web.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="utf-8"?>
 <web-app xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
+	xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_3_0.xsd"
-	version="2.4">
+	version="3.0">
 	<display-name>52°North Web Processing Service, Git:
 		1665e1b7b2188755161d4f0f3a6acf562d0444e1 @ 2015-03-21 00:30:20
 	</display-name>