git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/branches/data-analysis/RConnector/2.1@178919 82a268e6-3cf1-43bd-a215-b396298e98cf

.classpath

@@ -15,11 +15,13 @@
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
@@ -30,6 +32,7 @@
 	<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="output" path="target/classes"/>

.project

@@ -5,11 +5,21 @@
 	<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>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
@@ -17,7 +27,11 @@
 		</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>
 	</natures>
 </projectDescription>

distro/changelog.xml

@@ -1,5 +1,8 @@
 <ReleaseNotes>
-	<Changeset component="org.gcube.data-analysis.r-connector.2.1.2" date="2017-03-27">
+    <Changeset component="org.gcube.data-analysis.r-connector.2.1.4" date="2019-03-27">
+		<Change>integration with storageHub</Change>
+	</Changeset> 
+	<Changeset component="org.gcube.data-analysis.r-connector.2.1.3" date="2017-03-27">
 		<Change>add user script is executed also when configfile.csv is not present</Change>
 	</Changeset>
 	<Changeset component="org.gcube.data-analysis.r-connector.2.1.2" date="2017-02-22">

distro/web.xml

@@ -11,6 +11,10 @@
 		<param-name>addUserScript</param-name>
 		<param-value>/usr/local/bin/rusersadd</param-value>
 	</context-param>
+	<context-param>
+		<param-name>unmountScript</param-name>
+		<param-value>/usr/local/bin/rconnector_unmount</param-value>
+	</context-param>
 	<context-param>
 		<param-name>storedKeyPath</param-name>
 		<param-value>/var/lib/rstudio-server/secure-cookie-key</param-value>

pom.xml

@@ -1,9 +1,10 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.gcube.data.analysis</groupId>
 	<artifactId>r-connector</artifactId>
-	<version>2.1.3-SNAPSHOT</version>
+	<version>2.1.4-SNAPSHOT</version>
 	<name>RConnector</name>
 	<description>makes R available in the infrastructure</description>
 
@@ -64,7 +65,12 @@
 			<artifactId>tabulardata-client-library</artifactId>
 			<version>[2.0.0-SNAPSHOT, 3.0.0-SNAPSHOT)</version>
 		</dependency>
-
+		<dependency>
+			<groupId>org.gcube.data-access</groupId>
+			<artifactId>sh-fuse-integration</artifactId>
+			<version>1.0.0-SNAPSHOT</version>
+		</dependency>
+		
 		<!-- jersey -->
 		<dependency>
 			<groupId>javax.ws.rs</groupId>

src/main/java/org/gcube/data/analysis/rconnector/ConfigFileWriter.java

@@ -1,13 +1,13 @@
 package org.gcube.data.analysis.rconnector;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStreamReader;
 
 import javax.inject.Singleton;
 
+import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
+import org.gcube.common.scope.api.ScopeProvider;
+
 import lombok.extern.slf4j.Slf4j;
 
 
@@ -21,38 +21,10 @@ public class ConfigFileWriter {
 			usersHome=usersHome+"/";
 		File userDir = new File(usersHome+login);
 		File configFile= new File(userDir, fileName);
-		executeCommandLine(scriptToExecute,login);
+		Utils.executeCommandLine(scriptToExecute,login, SecurityTokenProvider.instance.get(), ScopeProvider.instance.get());
 		return  writeFile(info, configFile);
 	}
 
-	private String executeCommandLine(String cmd, String login){
-		log.debug("executing command "+cmd+" "+login);
-		Process process = null;
-		String lastline = "";
-		try {
-			
-			ProcessBuilder pb = new ProcessBuilder(cmd, login);
-			process = pb.start();
-			
-			try {
-				process.waitFor();
-			} catch (InterruptedException e) {
-				log.warn("interrupt Exception on process",e);
-			}
-
-			BufferedReader br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
-			String line = br.readLine();
-			while (line!=null){
-				lastline += line;
-				line = br.readLine();
-			}
-		} catch (IOException e) {
-			log.error("error executing command line",e);
-		}
-		log.debug("command result line is "+lastline);
-		return lastline;
-	}
-
 	private boolean writeFile(Info info, File pathToFile){
 		log.debug("writing config file");
 		StringBuffer sb = new StringBuffer();

src/main/java/org/gcube/data/analysis/rconnector/DisconnectResource.java

@@ -1,5 +1,6 @@
 package org.gcube.data.analysis.rconnector;
 
+import javax.inject.Inject;
 import javax.servlet.ServletContext;
 import javax.servlet.http.Cookie;
 import javax.servlet.http.HttpServletRequest;
@@ -10,21 +11,39 @@ import javax.ws.rs.core.Context;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.core.Response;
 
+import org.gcube.common.authorization.library.provider.AuthorizationProvider;
+
 import lombok.extern.slf4j.Slf4j;
 
 @Path("disconnect")
 @Slf4j
 public class DisconnectResource {
 
+			
 	@Context ServletContext context;
 
+	@Inject
+	InfoRetriever infoRetriever;
+	
 	@GET
 	@Produces(MediaType.TEXT_HTML)
 	public Response disconnect(@Context HttpServletRequest req) {
 		log.info("disconnect called ");
 		String rStudioServerAddress = context==null?"":context.getInitParameter("rStudioAddress");
-		log.info(rStudioServerAddress);
+		String scriptToExecute = context.getInitParameter("unmountScript");
+		
+		String login = null;
+		for (Cookie cookie : req.getCookies())
+			if (cookie.getName().equals("user-id"))
+				login = cookie.getValue();
+		
+		if (login==null)
+			return Response.serverError().build();
+		
 		try{
+			
+			Utils.executeCommandLine(scriptToExecute, login);
+			
 			boolean found = false;
 			for (Cookie cookie : req.getCookies())
 				if (cookie.getName().equals("user-id")){ 
@@ -39,8 +58,8 @@ public class DisconnectResource {
 								).build();
 			else return Response.ok(context.getClassLoader().getResourceAsStream("inactivesession.html")).build();
 		}catch(Exception e){
-			e.printStackTrace();
+			log.error("erorr disconnecting from Rstudio",e);
-			return null;
+			return Response.serverError().build();
 		}
 	}
 

src/main/java/org/gcube/data/analysis/rconnector/InfoRetriever.java

@@ -10,8 +10,6 @@ import java.util.regex.Pattern;
 import javax.inject.Inject;
 import javax.inject.Singleton;
 
-import lombok.extern.slf4j.Slf4j;
-
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.database.DatabaseEndpointIdentifier;
 import org.gcube.common.database.DatabaseProvider;
@@ -25,6 +23,8 @@ import org.gcube.data.analysis.tabulardata.model.metadata.common.NamesMetadata;
 import org.gcube.data.analysis.tabulardata.model.metadata.table.DatasetViewTableMetadata;
 import org.gcube.data.analysis.tabulardata.model.table.Table;
 
+import lombok.extern.slf4j.Slf4j;
+
 @Slf4j
 @Singleton
 public class InfoRetriever {
@@ -32,7 +32,6 @@ public class InfoRetriever {
 	@Inject
 	DatabaseProvider databaseProvider;
 	
-	
 	@SuppressWarnings("unchecked")
 	public Info retrieve(String userName, Long tabularResourceId){
 		try {

src/main/java/org/gcube/data/analysis/rconnector/Resource.java

@@ -1,9 +1,11 @@
 package org.gcube.data.analysis.rconnector;
 
 import java.io.File;
+import java.io.IOException;
 import java.net.URI;
 import java.net.URLEncoder;
 import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 import java.util.Calendar;
 import java.util.Locale;
@@ -20,11 +22,12 @@ import javax.ws.rs.core.NewCookie;
 import javax.ws.rs.core.Response;
 import javax.xml.bind.DatatypeConverter;
 
-import lombok.extern.slf4j.Slf4j;
-
 import org.gcube.common.authorization.library.provider.AuthorizationProvider;
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.scope.api.ScopeProvider;
+import org.gcube.data.access.storagehub.fs.StorageHubFS;
+
+import lombok.extern.slf4j.Slf4j;
 
 @Path("connect/")
 @Slf4j
@@ -35,85 +38,89 @@ public class Resource {
 
 	@Inject
 	InfoRetriever infoRetriever;
-	
+
 	@Context ServletContext context;
-	
+
-	
+
 	@Path("/{trId}")
 	@GET
 	public Response connect(@PathParam("trId") Long tabularResourceId) {
 		log.info("connect called with user {} and trID {} in scope {}",AuthorizationProvider.instance.get().getClient().getId(), tabularResourceId, ScopeProvider.instance.get());
+
+		String login = AuthorizationProvider.instance.get().getClient().getId();
 		String usersHome = context.getInitParameter("usersHome");
 		String filename = context.getInitParameter("filename");
 		String scriptToExecute = context.getInitParameter("addUserScript");
-		if (ScopeProvider.instance.get()==null || AuthorizationProvider.instance.get().getClient().getId() == null || tabularResourceId ==null ) return Response.serverError().build();
+		if (ScopeProvider.instance.get()==null || login == null || tabularResourceId ==null ) return Response.serverError().build();
 		Info info;
 		try{
-			info = infoRetriever.retrieve(AuthorizationProvider.instance.get().getClient().getId(), tabularResourceId);
+			info = infoRetriever.retrieve(login, tabularResourceId);
 			log.debug("retrieved info: "+info);
 		}catch(Exception e){
 			log.error("error connecting to r",e);
 			return Response.serverError().build();
 		}
-		if (!writer.write(info, AuthorizationProvider.instance.get().getClient().getId(), usersHome, filename, scriptToExecute)) return Response.serverError().build();
+		if (!writer.write(info, login, usersHome, filename, scriptToExecute)) return Response.serverError().build();
-			
+
-		return createResponse(AuthorizationProvider.instance.get().getClient().getId());	
+		return createResponse(login);	
 	}
 
-	
+
 	@GET
 	public Response connect() {
 		log.info("connect called with user {} in scope {}",AuthorizationProvider.instance.get().getClient().getId(), ScopeProvider.instance.get());
+		String login = AuthorizationProvider.instance.get().getClient().getId();
 		String usersHome = context.getInitParameter("usersHome");
 		String filename = context.getInitParameter("filename");
 		String scriptToExecute = context.getInitParameter("addUserScript");
-		if (AuthorizationProvider.instance.get().getClient().getId() == null ) return Response.serverError().build();
+		if (login == null ) return Response.serverError().build();
 		Info info = new Info();
-		info.setUsername(AuthorizationProvider.instance.get().getClient().getId());
+		info.setUsername(login);
 		info.setToken(SecurityTokenProvider.instance.get());
-		if (!writer.write(info, AuthorizationProvider.instance.get().getClient().getId(), usersHome, filename, scriptToExecute)) return Response.serverError().build();
+		if (!writer.write(info, login, usersHome, filename, scriptToExecute)) return Response.serverError().build();
+
 		return createResponse(AuthorizationProvider.instance.get().getClient().getId());	
 	}
-	
+
 	private Response createResponse(String userName){
 		try{
 			String keyFilePath = context.getInitParameter("storedKeyPath");
 			String rStudioServerAddress = context.getInitParameter("rStudioAddress");
-			
+
 			log.debug("key file path: "+keyFilePath);
 			log.debug("rstudio server address: "+rStudioServerAddress);
-			
+
 			Calendar now = Calendar.getInstance();
 			now.add(Calendar.YEAR, 10);
 			now.add(Calendar.DAY_OF_YEAR, -1);
 			SimpleDateFormat sdf = new SimpleDateFormat("EEE, dd MMM yyyy HH:mm:ss z", Locale.ENGLISH);
 			String format = sdf.format(now.getTime());
-			
+
 			File keyFile = new File(keyFilePath);
 			if (!keyFile.exists())
 				return Response.serverError().build();
-			
+
 			byte[] keyByte = Files.readAllBytes(keyFile.toPath());
-						
+
 			SecretKeySpec keySpec = new SecretKeySpec(keyByte,
-			        "HmacSHA256");
+					"HmacSHA256");
 			Mac mac = Mac.getInstance("HmacSHA256");
 			mac.init(keySpec);
 			byte[] result = mac.doFinal((userName+format).getBytes());
 
 			String encoded = URLEncoder.encode(DatatypeConverter.printBase64Binary(result));
-			
+
 			String cookieValue = userName+"|"+URLEncoder.encode(format).replaceAll("\\+", "%20")+"|"+encoded;
 			NewCookie cookie = new NewCookie("user-id", 
 					cookieValue,
 					"/", rStudioServerAddress, "", -1, false, true );
-			
+
-			
+
 			return Response.seeOther(new URI("http://"+rStudioServerAddress))
 					.cookie(cookie).build();
 		}catch(Exception e){
 			log.error("error creating response", e);
 			return Response.serverError().build();}
 	}
-	
+
 }

src/main/java/org/gcube/data/analysis/rconnector/Utils.java

@@ -0,0 +1,43 @@
+package org.gcube.data.analysis.rconnector;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.Arrays;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class Utils {
+
+	private static Logger log = LoggerFactory.getLogger(Utils.class);
+	
+	protected static String executeCommandLine(String ... args){
+		log.debug("executing command {}",Arrays.asList(args));
+		Process process = null;
+		String lastline = "";
+		try {
+			
+			ProcessBuilder pb = new ProcessBuilder(args);
+			process = pb.start();
+			
+			try {
+				process.waitFor();
+			} catch (InterruptedException e) {
+				log.warn("interrupt Exception on process",e);
+			}
+
+			BufferedReader br = new BufferedReader(new InputStreamReader(process.getErrorStream()));
+			String line = br.readLine();
+			while (line!=null){
+				lastline += line;
+				line = br.readLine();
+			}
+		} catch (IOException e) {
+			log.error("error executing command line",e);
+		}
+		log.debug("command result line is {} ",lastline);
+		return lastline;
+	}
+	
+}

src/main/resources/META-INF/beans.xml

@@ -1,5 +1,3 @@
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
+<?xml version="1.0" encoding="UTF-8"?>
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<beans xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/beans_1_0.xsd">
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee 
-    http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd">
 </beans>