Feature #18993 RStudio Wrapper portlet to support double queries
This commit is contained in:
parent
6cbb9bf96f
commit
0c2ecf2047
18
.classpath
18
.classpath
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@ -1,18 +1,18 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/rstudio-wrapper-portlet-1.3.1-SNAPSHOT/WEB-INF/classes" path="src/main/java">
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<classpathentry kind="src" output="target/rstudio-wrapper-portlet-1.4.0-SNAPSHOT/WEB-INF/classes" path="src/main/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="target/rstudio-wrapper-portlet-1.3.1-SNAPSHOT/WEB-INF/classes" path="target/generated-sources/gwt">
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<classpathentry kind="src" output="target/rstudio-wrapper-portlet-1.4.0-SNAPSHOT/WEB-INF/classes" path="target/generated-sources/gwt">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry excluding="**" kind="src" output="target/rstudio-wrapper-portlet-1.3.1-SNAPSHOT/WEB-INF/classes" path="src/main/resources">
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<classpathentry excluding="**" kind="src" output="target/rstudio-wrapper-portlet-1.4.0-SNAPSHOT/WEB-INF/classes" path="src/main/resources">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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@ -30,16 +30,16 @@
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/rstudio-wrapper-portlet-1.3.1-SNAPSHOT/WEB-INF/classes"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
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<attributes>
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<attribute name="owner.project.facets" value="java"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/rstudio-wrapper-portlet-1.4.0-SNAPSHOT/WEB-INF/classes"/>
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</classpath>
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@ -1,4 +1,4 @@
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eclipse.preferences.version=1
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lastWarOutDir=/Users/massi/Documents/workspace/rstudio-wrapper-portlet/target/rstudio-wrapper-portlet-1.3.1-SNAPSHOT
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lastWarOutDir=${webappDirectory}
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warSrcDir=src/main/webapp
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warSrcDirIsOutput=false
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@ -1,9 +1,9 @@
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eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
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org.eclipse.jdt.core.compiler.compliance=1.7
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org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
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org.eclipse.jdt.core.compiler.compliance=1.8
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org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
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org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
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org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
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org.eclipse.jdt.core.compiler.release=disabled
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org.eclipse.jdt.core.compiler.source=1.7
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org.eclipse.jdt.core.compiler.source=1.8
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@ -1,10 +1,10 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<faceted-project>
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<fixed facet="wst.jsdt.web"/>
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<installed facet="java" version="1.7"/>
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<installed facet="jst.web" version="3.0"/>
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<installed facet="wst.jsdt.web" version="1.0"/>
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<installed facet="jst.jaxrs" version="2.0"/>
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<installed facet="liferay.portlet" version="6.2"/>
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<installed facet="com.gwtplugins.gwt.facet" version="1.0"/>
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<installed facet="java" version="1.8"/>
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</faceted-project>
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8
pom.xml
8
pom.xml
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@ -24,10 +24,10 @@
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<distroDirectory>distro</distroDirectory>
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<liferay.version>6.2.5</liferay.version>
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<liferay.maven.plugin.version>6.2.10.12</liferay.maven.plugin.version>
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<liferay.auto.deploy.dir>/Users/massi/portal/liferay-portal-6.2-ce-ga6/deploy</liferay.auto.deploy.dir>
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<liferay.app.server.deploy.dir>/Users/massi/portal/liferay-portal-6.2-ce-ga6/tomcat-7.0.62/webapps</liferay.app.server.deploy.dir>
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<liferay.app.server.lib.global.dir>/Users/massi/portal/liferay-portal-6.2-ce-ga6/tomcat-7.0.62/lib/ext</liferay.app.server.lib.global.dir>
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<liferay.app.server.portal.dir>/Users/massi/portal/liferay-portal-6.2-ce-ga6/tomcat-7.0.62/webapps/ROOT</liferay.app.server.portal.dir>
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<liferay.auto.deploy.dir>${system.CATALINA_HOME}/../deploy</liferay.auto.deploy.dir>
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<liferay.app.server.deploy.dir>${system.CATALINA_HOME}/webapps</liferay.app.server.deploy.dir>
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<liferay.app.server.lib.global.dir>${system.CATALINA_HOME}/lib/ext</liferay.app.server.lib.global.dir>
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<liferay.app.server.portal.dir>${system.CATALINA_HOME}/webapps/ROOT</liferay.app.server.portal.dir>
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</properties>
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<dependencyManagement>
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<dependencies>
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@ -5,12 +5,17 @@ import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
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import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
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import java.net.MalformedURLException;
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import java.net.URI;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.gcube.common.portal.PortalContext;
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import org.gcube.common.resources.gcore.GCoreEndpoint;
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import org.gcube.common.resources.gcore.GCoreEndpoint.Profile.Endpoint;
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import org.gcube.common.resources.gcore.ServiceEndpoint;
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import org.gcube.common.resources.gcore.utils.Group;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.portlets.user.rstudio_wrapper_portlet.client.RStudioService;
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import org.gcube.portlets.user.rstudio_wrapper_portlet.shared.RStudioInstance;
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@ -37,6 +42,9 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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private static final String RSTUDIO_INSTANCES = "RStudio-Instances";
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private static final String RSTUDIO_URL = "RStudio-URL";
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private static final String RCONNECTOR_EntryName = "org.gcube.data.analysis.rconnector.RConnector";
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private static final String GCORE_SERVICE_NAME = "RConnector";
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private static final String GCORE_SERVICE_CLASS = "DataAnalysis";
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private static final String PATH_TO_RCONNECTOR = "/r-connector/gcube/service/connect";
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private static final String SERVICE_EP_NAME = "RConnector";
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@ -75,13 +83,13 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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_log.debug("calling rConnector with scope = " + scope + " and token = "+token );
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List<ServiceEndpoint> resources = getRStudioServiceEndpoints(scope);
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if (resources.size() == 0){
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_log.warn("There is no Service Endpoint having CATEGORY " + CATEGORY +" and NAME " + SERVICE_EP_NAME + " in this scope. Returning default instance");
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toReturn = rConnector().build().connect().toURL().toExternalForm();
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_log.info("There is no Service Endpoint having CATEGORY " + CATEGORY +" and NAME " + SERVICE_EP_NAME + " in this scope. Passing to the gCore instances");
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toReturn = getRStudioGCoreEndpoint(pContext, userId, curUser, scope, token);
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} else {
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UserManager um = new LiferayUserManager();
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_log.debug("Checking if user " + curUser.getFullname() + " has already an RStudio Instance set ... ");
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String hostedOnSet = null;
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//check if an RStudio instance was previously set (RETRO-COMPATIBILY)
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if (um.readCustomAttr(userId, RSTUDIO_URL) != null && um.readCustomAttr(userId, RSTUDIO_URL).toString().compareTo("") != 0) {
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_log.debug("User had already an RStudio Instance set, upgrading to new version ");
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@ -89,9 +97,9 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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writeRStudioInstanceInScope(um, curUser, scope, hostedOnSet);
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um.saveCustomAttr(userId, RSTUDIO_URL, ""); //reset the old value to blank so that from now on it will read from the new field
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}
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hostedOnSet = getUserRStudioInstances(um,curUser).get(scope);
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_log.info("**** Checking if still exist on this scope: " + scope);
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//if the instance exists and is still available in the given context
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if (hostedOnSet != null && checkRStudioInstanceExistence(curUser, hostedOnSet, resources) ) {
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@ -147,11 +155,105 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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_log.info("returning URL from rConnector = "+toReturn);
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if (!toReturn.startsWith("https")) {
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toReturn = toReturn.replace("http:", "https:");
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toReturn = toReturn.replace(":8080", "");
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toReturn = toReturn.replace(":80", "");
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_log.info("Changed URL from rConnector to support SSL: "+toReturn);
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}
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return toReturn;
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}
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/**
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* new method
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* @param pContext
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* @param userId
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* @param curUser
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* @param scope
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* @param token
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* @return
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*/
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private String getRStudioGCoreEndpoint(PortalContext pContext, long userId, GCubeUser curUser, String scope, String token) {
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String toReturn = "";
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UserManager um = new LiferayUserManager();
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_log.debug("Checking if user " + curUser.getFullname() + " has already an RStudio Instance set ... ");
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String hostedOnSet = null;
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try {
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//check if an RStudio instance was previously set (RETRO-COMPATIBILY)
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if (um.readCustomAttr(userId, RSTUDIO_URL) != null && um.readCustomAttr(userId, RSTUDIO_URL).toString().compareTo("") != 0) {
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_log.debug("User had already an RStudio Instance set, upgrading to new version ");
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hostedOnSet = (String) um.readCustomAttr(userId, RSTUDIO_URL);
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writeRStudioInstanceInScope(um, curUser, scope, hostedOnSet);
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um.saveCustomAttr(userId, RSTUDIO_URL, ""); //reset the old value to blank so that from now on it will read from the new field
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}
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hostedOnSet = getUserRStudioInstances(um,curUser).get(scope);
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_log.info("**** Checking if the user instance " + hostedOnSet+" exists in the VO for this VRE: " + scope);
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//if the instance exists and is still available in the given context
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List<GCoreEndpoint> gCoreResources = getRStudioGCoreEndpoints(scope);
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if (hostedOnSet != null && checkRStudioGCoreInstanceExistence(curUser, hostedOnSet, gCoreResources) ) {
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toReturn = getRConnectorURL(hostedOnSet, token);
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_log.info("User " + curUser.getFullname() + " has RStudio Instance set and is valid, returning rConnector URL " + toReturn);
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}
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else {//need to find the RStudio
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_log.info("User " + curUser.getFullname() + " DOES NOT have RStudio Instance set or the instance previous set no longer exists, calculating allocation ... ");
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HashMap<String, Integer> rStudioDistributionMap = new HashMap<>();
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for (GCoreEndpoint res : gCoreResources) {
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String hostedOn = extractGCoreEndpointHostAndPort(res);
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rStudioDistributionMap.put(hostedOn, 0);
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}
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List<GCubeUser> vreUsers = um.listUsersByGroup(pContext.getCurrentGroupId(getThreadLocalRequest()), false);
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_log.debug("VRE " + scope + " has totalUsers = " + vreUsers.size());
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for (GCubeUser gCubeUser : vreUsers) {
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if (getUserRStudioInstances(um,gCubeUser).get(scope) != null) {
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String hostedOn = getUserRStudioInstances(um,gCubeUser).get(scope);
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if (rStudioDistributionMap.containsKey(hostedOn)) {
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int noToSet = rStudioDistributionMap.get(hostedOn)+1;
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rStudioDistributionMap.put(hostedOn, noToSet);
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}
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}
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}
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_log.info("VRE - RStudio allocaiton map as follows: ");
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int min = 0;
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int i = 0;
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String host2Select = "";
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for (String host : rStudioDistributionMap.keySet()) {
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_log.info("Host " + host + " has # users=" + rStudioDistributionMap.get(host));
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if (i==0) {
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host2Select = host;
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min = rStudioDistributionMap.get(host);
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} else {
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int usersNo = rStudioDistributionMap.get(host);
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if (usersNo < min) {
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_log.info("Host " + host + " has LESS users than " + host2Select + " updating");
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host2Select = host;
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}
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}
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i++;
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}
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writeRStudioInstanceInScope(um, curUser, scope, host2Select);
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_log.debug("User " + curUser.getFullname() + " RStudio gCore Instance set calculated = " + host2Select + " for context " + scope);
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toReturn = getRConnectorURL(host2Select, token);
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_log.debug("User " + curUser.getFullname() + " has RStudio gCore Instance set, returning rConnector URL " + toReturn);
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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return toReturn;
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}
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private List<GCoreEndpoint> getRStudioGCoreEndpoints(String scope) {
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_log.debug("getRStudioGCoreEndpoints on scope="+scope );
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String currScope = ScopeProvider.instance.get();
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ScopeProvider.instance.set(scope);
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SimpleQuery query = queryFor(GCoreEndpoint.class);
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query.addCondition("$resource/Profile/ServiceName/text() eq '"+ GCORE_SERVICE_NAME +"'");
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query.addCondition("$resource/Profile/ServiceClass/text() eq '"+ GCORE_SERVICE_CLASS +"'");
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DiscoveryClient<GCoreEndpoint> client = clientFor(GCoreEndpoint.class);
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List<GCoreEndpoint> toReturn = client.submit(query);
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ScopeProvider.instance.set(currScope);
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return toReturn;
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}
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/**
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*
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* @param um
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@ -204,11 +306,15 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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_log.warn("Could not find an integer after :, using default port 80");
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}
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//http://rstudio-dev.d4science.org:80/r-connector/gcube/service/connect?gcube-token=6fa92d94-6568-4510-8443-a1c5ecdf1c7d-98187548s
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if (port == 443 || port == 8443)
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return "https://"+hostedOn+PATH_TO_RCONNECTOR+"?gcube-token="+token;
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String toReturn = "";
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if (port == 443 || port == 8443) {
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toReturn = "https://"+hostedOn+PATH_TO_RCONNECTOR+"?gcube-token="+token;
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}
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else {
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return "http://"+hostedOn+PATH_TO_RCONNECTOR+"?gcube-token="+token;
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toReturn = "http://"+hostedOn+PATH_TO_RCONNECTOR+"?gcube-token="+token;
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}
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_log.debug("**getRConnectorURL toReturn="+toReturn);
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return toReturn;
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}
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/**
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*
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@ -227,13 +333,32 @@ public class RStudioServiceImpl extends RemoteServiceServlet implements RStudioS
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ScopeProvider.instance.set(currScope);
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return toReturn;
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}
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private static boolean checkRStudioInstanceExistence(GCubeUser curUser, String hostedOn, List<ServiceEndpoint> resources) {
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for (ServiceEndpoint serviceEndpoint : resources)
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if (serviceEndpoint.profile().runtime().hostedOn().equals(hostedOn)) {
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_log.info("**** The instance previously set for user " + curUser.getFullname() + " on " + hostedOn + " is still valid");
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_log.info("---- checkRStudioServiceEndpointExistence: The instance previously set for user " + curUser.getFullname() + " on " + hostedOn + " is still valid");
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return true;
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}
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return false;
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}
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private static boolean checkRStudioGCoreInstanceExistence(GCubeUser curUser, String hostedOn, List<GCoreEndpoint> resources) {
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for (GCoreEndpoint gcoreEndpoint : resources) {
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String instance = extractGCoreEndpointHostAndPort(gcoreEndpoint);
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if (instance.equalsIgnoreCase(hostedOn)) {
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_log.info("**** checkRStudioGCoreInstanceExistence: The instance previously set for user " + curUser.getFullname() + " on " + hostedOn + " is still valid");
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return true;
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}
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}
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return false;
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}
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private static String extractGCoreEndpointHostAndPort(GCoreEndpoint resource) {
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Collection<Endpoint> eps = resource.profile().endpoints().asCollection();
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for (Endpoint ep : eps)
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if (ep.name().equalsIgnoreCase(RCONNECTOR_EntryName))
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return new StringBuilder(ep.uri().getHost()).append(":").append(ep.uri().getPort()).toString();
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return null;
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}
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}
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