pom.xml

@@ -24,6 +24,12 @@
 	</properties>
 
 	<dependencies>
+	<dependency>
+			<groupId>org.gcube.core</groupId>
+			<artifactId>common-smartgears</artifactId>
+						<!--  <version>[1.0.0-SNAPSHOT,1.2.7)</version>-->
+			<scope>provided</scope>
+		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/AlgoResource.java

@@ -0,0 +1,22 @@
+package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
+
+public class AlgoResource  {
+
+	protected String id;
+
+	public AlgoResource() {
+***REMOVED***
+
+	public AlgoResource(String id) {
+		this.id = id;
+***REMOVED***
+
+	public String getId() {
+		return this.id;
+***REMOVED***
+
+	public void setId(String id) {
+		this.id = id;
+***REMOVED***
+
+***REMOVED***

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/datamodel/Algorithm.java

@@ -3,8 +3,35 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
 import java.util.Collection;
 import java.util.Vector;
 
-public class Algorithm {
 
+public class Algorithm extends AlgoResource {
+
+	
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((id == null) ? 0 : id.hashCode());
+		return result;
+***REMOVED***
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		Algorithm other = (Algorithm) obj;
+		if (id == null) {
+			if (other.id != null)
+				return false;
+	***REMOVED*** else if (!id.equals(other.id))
+			return false;
+		return true;
+***REMOVED***
+	
   private String name;
 
   private String description;

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/PoolManager.java

@@ -31,6 +31,7 @@ package org.gcube.dataanalysis.dataminer.poolmanager.rest;
 import java.net.MalformedURLException;
 ***REMOVED***
 import java.net.UnknownHostException;
+import java.util.Set;
 
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
 
@@ -47,6 +48,12 @@ public interface PoolManager {
 
 	String getScriptFromURL(URL logId) throws IOException;
 
-	URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException; 
+	URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException;
+	
+	void addAlgToIs(Algorithm algo);
+	
+	Set<Algorithm> getAlgoFromIs();
+	
+	Algorithm getAlgoById(String id); 
 	
 ***REMOVED***

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/rest/RestPoolManager.java

@@ -147,12 +147,16 @@ import java.net.MalformedURLException;
 import java.net.ProxySelector;
 ***REMOVED***
 import java.net.UnknownHostException;
+import java.util.Random;
+import java.util.Set;
+import java.util.UUID;
 
 import javax.ws.rs.GET;
 import javax.ws.rs.Path;
 import javax.ws.rs.Produces;
 import javax.ws.rs.QueryParam;
 
+import org.apache.commons.lang.math.RandomUtils;
 ***REMOVED***
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
 import org.gcube.dataanalysis.dataminer.poolmanager.service.DataminerPoolManager;
@@ -175,7 +179,7 @@ public class RestPoolManager implements PoolManager {
   /hosts/<hostname> POST  ***REMOVED*** add an algorithm to the given host
   */
 
-	@GET
+  @GET
   @Path("/scopes/add")
   @Produces("text/plain")
   public String addAlgorithmToVRE(
@@ -187,6 +191,7 @@ public class RestPoolManager implements PoolManager {
       @QueryParam("algorithmType") String algorithmType,
       @QueryParam("skipJava") String skipJava) throws IOException, InterruptedException {
     Algorithm algo= this.getAlgorithm(algorithm, vre, null, name, description, category, algorithmType, skipJava);
+    ***REMOVED***service.addAlgToIs(algo);
     return service.addAlgorithmToVRE(algo, vre);
   ***REMOVED***
 
@@ -202,6 +207,7 @@ public class RestPoolManager implements PoolManager {
       @QueryParam("algorithmType") String algorithmType,
       @QueryParam("skipJava") String skipJava) throws IOException, InterruptedException {
     Algorithm algo= this.getAlgorithm(algorithm, null, hostname, name, description, category, algorithmType, skipJava);
+    service.addAlgToIs(algo);
     return service.addAlgorithmToHost(algo, hostname);
   ***REMOVED***
 
@@ -218,6 +224,7 @@ public class RestPoolManager implements PoolManager {
     ***REMOVED*** TODO Auto-generated method stub
     LOGGER.debug("Adding algorithm =" + algorithm + " to VRE =" + vre);
     Algorithm algo = service.extractAlgorithm(algorithm);
+    algo.setId(name+"@"+UUID.randomUUID());
     
     if (algo.getCategory() == null){
       algo.setCategory(category);
@@ -303,28 +310,30 @@ public class RestPoolManager implements PoolManager {
 
 
 	public static void main(String[] args) throws IOException, InterruptedException {
-		RestPoolManager a = new RestPoolManager();
 		***REMOVED***System.out.println(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager");
-		
-		
 	    ***REMOVED***ProxySelector.setDefault(new PropertiesBasedProxySelector("/home/ngalante/.proxy-settings"));
 		
 		ScopeProvider.instance.set("/gcube/devNext/NextNext");
-***REMOVED***		a.addAlgorithmToVRE(
-***REMOVED***		"http:***REMOVED***data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
-***REMOVED***		"/gcube/devNext/NextNext",
-***REMOVED***		null, null, "test", "transducerers", "N");
 		
+		***REMOVED***PoolManager aa = new DataminerPoolManager();
+		***REMOVED***System.out.println(aa.getAlgoById("ICHTHYOP_MODEL_ONE_BY_ONE@3141d3aa-5f93-409f-b6f8-9fae0a6c0ee3"));
+		***REMOVED***System.out.println(aa.getAlgoFromIs());
+
 		
+		RestPoolManager a = new RestPoolManager();
+		***REMOVED***a.addAlgorithmToVRE(
+		***REMOVED***"http:***REMOVED***data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
+		***REMOVED***"/gcube/devNext/NextNext",
+		***REMOVED***null, null, "test", "transducerers", "N");
+				
 		a.addAlgorithmToHost(
-				"http:***REMOVED***data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
-				"dataminer1-devnext.d4science.org",
-				null, null, "test", "transducerers", "N");
-		
-	***REMOVED***System.out.println(a.getLogById("34ac474d-b9df-4929-87e1-2a0ae26cf898"));
+		"http:***REMOVED***data.d4science.org/S2h1RHZGd0JpWnBjZk9qTytQTndqcDRLVHNrQUt6QjhHbWJQNStIS0N6Yz0",
+		"dataminer1-devnext.d4science.org",
+		"ICHTHYOP_MODEL_ONE_BY_ONE", null, "ICHTHYOP_MODEL", "transducerers", "N");
 ***REMOVED***
 
 
+
 	@Override
 	public void getLogId(Algorithm algo, String vre) {
 		***REMOVED*** TODO Auto-generated method stub
@@ -358,6 +367,27 @@ public class RestPoolManager implements PoolManager {
 		return null;
 ***REMOVED***
 
+	@Override
+	public void addAlgToIs(Algorithm algo) {
+		***REMOVED*** TODO Auto-generated method stub
+		
+***REMOVED***
+
+
+
+
+	@Override
+	public Set<Algorithm> getAlgoFromIs() {
+		***REMOVED*** TODO Auto-generated method stub
+		return null;
+***REMOVED***
+
+	@Override
+	public Algorithm getAlgoById(String id) {
+		***REMOVED*** TODO Auto-generated method stub
+		return null;
+***REMOVED***
+
 
 
 ***REMOVED***

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/service/DataminerPoolManager.java

@@ -262,16 +262,29 @@
 ***REMOVED******REMOVED***
 package org.gcube.dataanalysis.dataminer.poolmanager.service;
 
+import static org.gcube.resources.discovery.icclient.ICFactory.clientFor;
+import static org.gcube.resources.discovery.icclient.ICFactory.queryFor;
+
 ***REMOVED***
 import java.io.File;
 ***REMOVED***
 ***REMOVED***
+import java.io.StringWriter;
 import java.net.MalformedURLException;
 ***REMOVED***
 import java.net.URLConnection;
 import java.net.UnknownHostException;
+import java.util.Arrays;
+import java.util.HashSet;
+***REMOVED***
+import java.util.Set;
 import java.util.UUID;
 
+import org.gcube.common.resources.gcore.GenericResource;
+import org.gcube.common.resources.gcore.HostingNode;
+import org.gcube.common.resources.gcore.Resources;
+import org.gcube.common.resources.gcore.Software.Profile.Dependency;
+***REMOVED***
 import org.gcube.dataanalysis.dataminer.poolmanager.ansiblebridge.AnsibleBridge;
 import org.gcube.dataanalysis.dataminer.poolmanager.clients.ISClient;
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
@@ -280,289 +293,390 @@ import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.AlgorithmSet;
 ***REMOVED***
 import org.gcube.dataanalysis.dataminer.poolmanager.process.AlgorithmPackageParser;
 import org.gcube.dataanalysis.dataminer.poolmanager.rest.PoolManager;
+import org.gcube.informationsystem.publisher.AdvancedScopedPublisher;
+import org.gcube.informationsystem.publisher.RegistryPublisherFactory;
+import org.gcube.informationsystem.publisher.ScopedPublisher;
+import org.gcube.informationsystem.publisher.exception.RegistryNotFoundException;
+import org.gcube.resources.discovery.client.api.DiscoveryClient;
+import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
+
 ***REMOVED***
 ***REMOVED***
 
 public class DataminerPoolManager implements PoolManager {
 
-	
 	private static final Logger LOGGER = LoggerFactory.getLogger(DataminerPoolManager.class);
 
-	
-***REMOVED***  static Collection<Algorithm> algorithms;
-***REMOVED***  
-***REMOVED***  static Collection<AlgorithmSet> sets;
-***REMOVED***
-***REMOVED***  static {
-***REMOVED***    algorithms = new Vector<>();
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  public DataminerPoolManager() {
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  /**
-***REMOVED***   * Add a new algorithm to the set of known ones. No further action is expected
-***REMOVED***   * on the pool.
-***REMOVED***   */
-***REMOVED***  public void publishAlgorithm(Algorithm algorithm) {
-***REMOVED***    algorithms.add(algorithm);
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  /**
-***REMOVED***   * Re-deploy the given algorithm wherever it's installed
-***REMOVED***   * 
-***REMOVED***   * @param algorithm
-***REMOVED***   */
-***REMOVED***  /*
-***REMOVED***   * public void updateAlgorithm(Algorithm algorithm) { ***REMOVED*** TODO implement this ***REMOVED***
-***REMOVED***   */
-***REMOVED***
-***REMOVED***  /**
-***REMOVED***   * Add the give algorithm to the given set
-***REMOVED***   * 
-***REMOVED***   * @param algorithmId
-***REMOVED***   * @param setId
-***REMOVED***   */
-***REMOVED***  public void addAlgorithmToSet(String algorithmName, String setName) {
-***REMOVED***    AlgorithmSet set = this.getAlgorithmSet(setName);
-***REMOVED***    Algorithm algorithm = this.getAlgorithm(algorithmName);
-***REMOVED***    if (set != null && algorithm != null) {
-***REMOVED***      set.addAlgorithm(algorithm);
-***REMOVED***      this.updateClusters();
-***REMOVED***    ***REMOVED***
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  /**
-***REMOVED***   * Apply the given set of algorithms to the given cluster
-***REMOVED***   * 
-***REMOVED***   * @param setId
-***REMOVED***   * @param clusterId
-***REMOVED***   */
-***REMOVED***  public void applyAlgorithmSetToCluster(String setName, String clusterName) {
-***REMOVED***    AlgorithmSet set = this.getAlgorithmSet(setName);
-***REMOVED***    Cluster cluster = new ISClient().getCluster(clusterName);
-***REMOVED***    if (set != null && cluster != null) {
-***REMOVED***      cluster.addAlgorithmSet(set);
-***REMOVED***      this.updateClusters();
-***REMOVED***    ***REMOVED***
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  private AlgorithmSet getAlgorithmSet(String name) {
-***REMOVED***    for (AlgorithmSet set : sets) {
-***REMOVED***      if (name.equals(set.getName())) {
-***REMOVED***        return set;
-***REMOVED***      ***REMOVED***
-***REMOVED***    ***REMOVED***
-***REMOVED***    return null;
-***REMOVED***  ***REMOVED***
-***REMOVED***
-***REMOVED***  private Algorithm getAlgorithm(String name) {
-***REMOVED***    for (Algorithm a : algorithms) {
-***REMOVED***      if (name.equals(a.getName())) {
-***REMOVED***        return a;
-***REMOVED***      ***REMOVED***
-***REMOVED***    ***REMOVED***
-***REMOVED***    return null;
-***REMOVED***  ***REMOVED***
+	***REMOVED*** static Collection<Algorithm> algorithms;
+	***REMOVED***
+	***REMOVED*** static Collection<AlgorithmSet> sets;
+	***REMOVED***
+	***REMOVED*** static {
+	***REMOVED*** algorithms = new Vector<>();
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** public DataminerPoolManager() {
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** /**
+	***REMOVED*** * Add a new algorithm to the set of known ones. No further action is
+	***REMOVED*** expected
+	***REMOVED*** * on the pool.
+	***REMOVED*** */
+	***REMOVED*** public void publishAlgorithm(Algorithm algorithm) {
+	***REMOVED*** algorithms.add(algorithm);
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** /**
+	***REMOVED*** * Re-deploy the given algorithm wherever it's installed
+	***REMOVED*** *
+	***REMOVED*** * @param algorithm
+	***REMOVED*** */
+	***REMOVED*** /*
+	***REMOVED*** * public void updateAlgorithm(Algorithm algorithm) { ***REMOVED*** TODO implement
+	***REMOVED*** this ***REMOVED***
+	***REMOVED*** */
+	***REMOVED***
+	***REMOVED*** /**
+	***REMOVED*** * Add the give algorithm to the given set
+	***REMOVED*** *
+	***REMOVED*** * @param algorithmId
+	***REMOVED*** * @param setId
+	***REMOVED*** */
+	***REMOVED*** public void addAlgorithmToSet(String algorithmName, String setName) {
+	***REMOVED*** AlgorithmSet set = this.getAlgorithmSet(setName);
+	***REMOVED*** Algorithm algorithm = this.getAlgorithm(algorithmName);
+	***REMOVED*** if (set != null && algorithm != null) {
+	***REMOVED*** set.addAlgorithm(algorithm);
+	***REMOVED*** this.updateClusters();
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** /**
+	***REMOVED*** * Apply the given set of algorithms to the given cluster
+	***REMOVED*** *
+	***REMOVED*** * @param setId
+	***REMOVED*** * @param clusterId
+	***REMOVED*** */
+	***REMOVED*** public void applyAlgorithmSetToCluster(String setName, String
+	***REMOVED*** clusterName) {
+	***REMOVED*** AlgorithmSet set = this.getAlgorithmSet(setName);
+	***REMOVED*** Cluster cluster = new ISClient().getCluster(clusterName);
+	***REMOVED*** if (set != null && cluster != null) {
+	***REMOVED*** cluster.addAlgorithmSet(set);
+	***REMOVED*** this.updateClusters();
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** private AlgorithmSet getAlgorithmSet(String name) {
+	***REMOVED*** for (AlgorithmSet set : sets) {
+	***REMOVED*** if (name.equals(set.getName())) {
+	***REMOVED*** return set;
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** return null;
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED*** private Algorithm getAlgorithm(String name) {
+	***REMOVED*** for (Algorithm a : algorithms) {
+	***REMOVED*** if (name.equals(a.getName())) {
+	***REMOVED*** return a;
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** return null;
+	***REMOVED*** ***REMOVED***
 
-	
+	***REMOVED***
+	***REMOVED*** public void getLogId(final Algorithm algorithm, final String vre) {
+	***REMOVED*** new Thread() {
+	***REMOVED*** public void run() {
+	***REMOVED*** while (true) {
+	***REMOVED*** try {
+	***REMOVED*** addAlgorithmToVRE(algorithm, vre);
+	***REMOVED*** ***REMOVED*** catch (Exception e) {
+	***REMOVED*** ***REMOVED***log here
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** ***REMOVED***.start();
+	***REMOVED*** ***REMOVED***
+	***REMOVED***
+	***REMOVED***
 
+	***REMOVED*** public String getLogId(){
+	***REMOVED*** PrintStream console = System.out;
+	***REMOVED*** File path = new File(worker.getWorkdir() + File.separator + "logs");
+	***REMOVED*** path.mkdirs();
+	***REMOVED*** File n = new File(path + File.separator + worker.getWorkerId());
+	***REMOVED*** FileOutputStream fos = new FileOutputStream(n);
+	***REMOVED*** PrintStream ps = new PrintStream(fos);
+	***REMOVED*** System.setOut(ps);
+	***REMOVED*** worker.apply();
+	***REMOVED*** System.setOut(console);
+	***REMOVED*** worker.apply();
+	***REMOVED*** System.out.println("Log stored to to " + n.getAbsolutePath());
+	***REMOVED*** ***REMOVED***
 
-***REMOVED***	     
-***REMOVED***	public void getLogId(final Algorithm algorithm, final String vre) {
-***REMOVED***	    new Thread() {
-***REMOVED***	        public void run() {
-***REMOVED***	            while (true) {
-***REMOVED***	                try {
-***REMOVED***	                	addAlgorithmToVRE(algorithm, vre);
-***REMOVED***	                ***REMOVED*** catch (Exception e) {
-***REMOVED***	                    ***REMOVED***log here
-***REMOVED***	                ***REMOVED***
-***REMOVED***	            ***REMOVED***
-***REMOVED***	        ***REMOVED***
-***REMOVED***	    ***REMOVED***.start();
-***REMOVED******REMOVED***	
-***REMOVED***	
-***REMOVED***	
-	
-***REMOVED***	public String getLogId(){
-***REMOVED***		PrintStream console = System.out;
-***REMOVED***	    File path = new File(worker.getWorkdir() + File.separator + "logs");
-***REMOVED***		path.mkdirs();
-***REMOVED***		File n = new File(path + File.separator + worker.getWorkerId());
-***REMOVED***		FileOutputStream fos = new FileOutputStream(n);
-***REMOVED***		PrintStream ps = new PrintStream(fos);
-***REMOVED***		System.setOut(ps);
-***REMOVED***		worker.apply();
-***REMOVED***		System.setOut(console);
-***REMOVED***		worker.apply();
-***REMOVED***		System.out.println("Log stored to to " + n.getAbsolutePath());
-***REMOVED******REMOVED***
-	
-	
-	
-	
-***REMOVED***   public String getLogById(String id) throws IOException {
-***REMOVED***	   String strLine = null;
-***REMOVED***	   try{
-***REMOVED***		   FileInputStream fstream = new FileInputStream("/tmp/dataminer-pool-manager/work/"+id+"/logs/"+id);
-***REMOVED***		   BufferedReader br = new BufferedReader(new InputStreamReader(fstream));
-***REMOVED***		   /* read log line by line */
-***REMOVED***		   while ((strLine = br.readLine()) != null)   {
-***REMOVED***		     /* parse strLine to obtain what you want */
-***REMOVED***		     System.out.println (strLine);
-***REMOVED***		   ***REMOVED***
-***REMOVED***		   br.close();
-***REMOVED***	***REMOVED*** catch (Exception e) {
-***REMOVED***		     System.err.println("Error: " + e.getMessage());
-***REMOVED***	***REMOVED***
-***REMOVED***	return strLine; 
-***REMOVED******REMOVED***
-	
+	***REMOVED*** public String getLogById(String id) throws IOException {
+	***REMOVED*** String strLine = null;
+	***REMOVED*** try{
+	***REMOVED*** FileInputStream fstream = new
+	***REMOVED*** FileInputStream("/tmp/dataminer-pool-manager/work/"+id+"/logs/"+id);
+	***REMOVED*** BufferedReader br = new BufferedReader(new InputStreamReader(fstream));
+	***REMOVED*** /* read log line by line */
+	***REMOVED*** while ((strLine = br.readLine()) != null) {
+	***REMOVED*** /* parse strLine to obtain what you want */
+	***REMOVED*** System.out.println (strLine);
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** br.close();
+	***REMOVED*** ***REMOVED*** catch (Exception e) {
+	***REMOVED*** System.err.println("Error: " + e.getMessage());
+	***REMOVED*** ***REMOVED***
+	***REMOVED*** return strLine;
+	***REMOVED*** ***REMOVED***
 
-   public String getScriptFromURL(URL url) throws IOException {
-	    if (url == null) {
-	      return null;
-	    ***REMOVED***
-	    URLConnection yc = url.openConnection();
-	    BufferedReader input = new BufferedReader(new InputStreamReader(
-	        yc.getInputStream()));
-	    String line;
-	    StringBuffer buffer = new StringBuffer();
-	    while ((line = input.readLine()) != null) {
-	      buffer.append(line + "\n");
-	    ***REMOVED***
-	    String bufferScript = buffer.substring(0, buffer.length());
-	    input.close();
-	    return bufferScript;
-	  ***REMOVED***
-	
-   
-   
-   
-	
-  /**
-   * Publish the given algorithm in the given VRE
-   * 
-   * @param algorithmName
-   * @param vre
-   * 
-   */
-  public String addAlgorithmToVRE(Algorithm algorithm, final String vre)
-      throws IOException {
-    ***REMOVED*** create a fake algorithm set
-    final AlgorithmSet algoSet = new AlgorithmSet();
-    algoSet.setName("fake");
-    algoSet.addAlgorithm(algorithm);
-    final String uuid = UUID.randomUUID().toString();
+	public String getScriptFromURL(URL url) throws IOException {
+		if (url == null) {
+			return null;
+	***REMOVED***
+		URLConnection yc = url.openConnection();
+		BufferedReader input = new BufferedReader(new InputStreamReader(yc.getInputStream()));
+		String line;
+		StringBuffer buffer = new StringBuffer();
+		while ((line = input.readLine()) != null) {
+			buffer.append(line + "\n");
+	***REMOVED***
+		String bufferScript = buffer.substring(0, buffer.length());
+		input.close();
+		return bufferScript;
+***REMOVED***
 
-    new Thread(new Runnable() {
-      @Override
-      public void run() {
-        ***REMOVED*** TODO Auto-generated method stub
-        try {
-          addAlgorithmsToVRE(algoSet, vre, uuid);
-        ***REMOVED*** catch (IOException e) {
-          ***REMOVED*** TODO Auto-generated catch block
-          e.printStackTrace();
-        ***REMOVED***
-      ***REMOVED***
-    ***REMOVED***).start();
-    ***REMOVED*** this line will execute immediately, not waiting for your task to complete
-    System.out.println(uuid);
-    return uuid;
-  ***REMOVED***
-  
-  public String addAlgorithmToHost(Algorithm algorithm, final String hostname)
-      throws IOException {
-    ***REMOVED*** create a fake algorithm set
-    final AlgorithmSet algoSet = new AlgorithmSet();
-    algoSet.setName("fake");
-    algoSet.addAlgorithm(algorithm);
-    final String uuid = UUID.randomUUID().toString();
+	/**
+	 * Publish the given algorithm in the given VRE
+	 * 
+	 * @param algorithmName
+	 * @param vre
+	 * 
+	 */
+	public String addAlgorithmToVRE(Algorithm algorithm, final String vre) throws IOException {
+		***REMOVED*** create a fake algorithm set
+		final AlgorithmSet algoSet = new AlgorithmSet();
+		algoSet.setName("fake");
+		algoSet.addAlgorithm(algorithm);
+		final String uuid = UUID.randomUUID().toString();
 
-    new Thread(new Runnable() {
-      @Override
-      public void run() {
-        ***REMOVED*** TODO Auto-generated method stub
-        try {
-          addAlgorithmsToHost(algoSet, hostname, uuid);
-        ***REMOVED*** catch (IOException e) {
-          ***REMOVED*** TODO Auto-generated catch block
-          e.printStackTrace();
-        ***REMOVED***
-      ***REMOVED***
-    ***REMOVED***).start();
-    ***REMOVED*** this line will execute immediately, not waiting for your task to complete
-    System.out.println(uuid);
-    return uuid;
-  ***REMOVED***  
-  
-  
-  public URL getURLfromWorkerLog(String a) throws MalformedURLException, UnknownHostException{
-		
-		File path = new File(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager/work/"+a+File.separator+"logs");
+		new Thread(new Runnable() {
+			@Override
+			public void run() {
+				***REMOVED*** TODO Auto-generated method stub
+				try {
+					addAlgorithmsToVRE(algoSet, vre, uuid);
+			***REMOVED*** catch (IOException e) {
+					***REMOVED*** TODO Auto-generated catch block
+					e.printStackTrace();
+			***REMOVED***
+		***REMOVED***
+	***REMOVED***).start();
+		***REMOVED*** this line will execute immediately, not waiting for your task to
+		***REMOVED*** complete
+		System.out.println(uuid);
+		return uuid;
+***REMOVED***
+
+	public String addAlgorithmToHost(Algorithm algorithm, final String hostname) throws IOException {
+		***REMOVED*** create a fake algorithm set
+		final AlgorithmSet algoSet = new AlgorithmSet();
+		algoSet.setName("fake");
+		algoSet.addAlgorithm(algorithm);
+		final String uuid = UUID.randomUUID().toString();
+
+		new Thread(new Runnable() {
+			@Override
+			public void run() {
+				***REMOVED*** TODO Auto-generated method stub
+				try {
+					addAlgorithmsToHost(algoSet, hostname, uuid);
+			***REMOVED*** catch (IOException e) {
+					***REMOVED*** TODO Auto-generated catch block
+					e.printStackTrace();
+			***REMOVED***
+		***REMOVED***
+	***REMOVED***).start();
+		***REMOVED*** this line will execute immediately, not waiting for your task to
+		***REMOVED*** complete
+		System.out.println(uuid);
+		return uuid;
+***REMOVED***
+
+	public URL getURLfromWorkerLog(String a) throws MalformedURLException, UnknownHostException {
+
+		File path = new File(System.getProperty("user.home") + File.separator + "/gcube/dataminer-pool-manager/work/"
+				+ a + File.separator + "logs");
 		path.mkdirs();
-		File n = new File(path + File.separator +a);
-        ***REMOVED***String addr = InetAddress.getLocalHost().getHostAddress();
-		
+		File n = new File(path + File.separator + a);
+		***REMOVED*** String addr = InetAddress.getLocalHost().getHostAddress();
+
 		return new File(n.getPath()).toURI().toURL();
-	  ***REMOVED***
-   
-  
-
-  public String addAlgorithmsToVRE(AlgorithmSet algorithms, String vre, String uuid) throws IOException {
-    
-    ***REMOVED*** create the cluster (dataminers in the vre)
-    Cluster cluster = new Cluster();
-    for(Host h:new ISClient().listDataminersInVRE()) {
-      cluster.addHost(h);
-    ***REMOVED***
-
-    ***REMOVED*** apply the changes
-    AnsibleBridge a = new AnsibleBridge();
-    return a.applyAlgorithmSetToCluster(algorithms, cluster,uuid).getWorkerId();
-    
-  ***REMOVED***
-  
-  public String addAlgorithmsToHost(AlgorithmSet algorithms, String hostname, String uuid) throws IOException {
-    
-    ***REMOVED*** create the cluster (dataminers in the vre)
-    Cluster cluster = new Cluster();
-    cluster.addHost(new ISClient().getDataminer(hostname));
-***REMOVED***    for(Host h:new ISClient().listDataminersInVRE()) {
-***REMOVED***      cluster.addHost(h);
-***REMOVED***    ***REMOVED***
-
-    ***REMOVED*** apply the changes
-    AnsibleBridge a = new AnsibleBridge();
-    return a.applyAlgorithmSetToCluster(algorithms, cluster,uuid).getWorkerId();
-    
-  ***REMOVED***
-
-
-  public Algorithm extractAlgorithm(String url) throws IOException {
-	    return new AlgorithmPackageParser().parsePackage(url);
-	  ***REMOVED***
-
-
-@Override
-public void getLogId(Algorithm algo, String vre) {
-	***REMOVED*** TODO Auto-generated method stub
-	
 ***REMOVED***
 
+	public String addAlgorithmsToVRE(AlgorithmSet algorithms, String vre, String uuid) throws IOException {
+
+		***REMOVED*** create the cluster (dataminers in the vre)
+		Cluster cluster = new Cluster();
+		for (Host h : new ISClient().listDataminersInVRE()) {
+			cluster.addHost(h);
+	***REMOVED***
+
+		***REMOVED*** apply the changes
+		AnsibleBridge a = new AnsibleBridge();
+		return a.applyAlgorithmSetToCluster(algorithms, cluster, uuid).getWorkerId();
 
-@Override
-public String getLogById(String logId) throws IOException {
-	***REMOVED*** TODO Auto-generated method stub
-	return null;
 ***REMOVED***
 
+	public String addAlgorithmsToHost(AlgorithmSet algorithms, String hostname, String uuid) throws IOException {
 
+		***REMOVED*** create the cluster (dataminers in the vre)
+		Cluster cluster = new Cluster();
+		cluster.addHost(new ISClient().getDataminer(hostname));
+		***REMOVED*** for(Host h:new ISClient().listDataminersInVRE()) {
+		***REMOVED*** cluster.addHost(h);
+		***REMOVED*** ***REMOVED***
 
+		***REMOVED*** apply the changes
+		AnsibleBridge a = new AnsibleBridge();
+		return a.applyAlgorithmSetToCluster(algorithms, cluster, uuid).getWorkerId();
 
-  
 ***REMOVED***
 
+	public Algorithm extractAlgorithm(String url) throws IOException {
+		return new AlgorithmPackageParser().parsePackage(url);
+***REMOVED***
 
+	@Override
+	public void getLogId(Algorithm algo, String vre) {
+		***REMOVED*** TODO Auto-generated method stub
+
+***REMOVED***
+
+	@Override
+	public String getLogById(String logId) throws IOException {
+		***REMOVED*** TODO Auto-generated method stub
+		return null;
+***REMOVED***
+
+	***REMOVED*** 2017 March 29
+
+	public void unPublishScopedResource(GenericResource resource) throws RegistryNotFoundException, Exception {
+		ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
+		AdvancedScopedPublisher advancedScopedPublisher = new AdvancedScopedPublisher(scopedPublisher);
+		String id = resource.id();
+		LOGGER.debug("Trying to remove {***REMOVED*** with ID {***REMOVED*** from {***REMOVED***", resource.getClass().getSimpleName(), id,
+				ScopeProvider.instance.get());
+		***REMOVED*** scopedPublisher.remove(resource, scopes);
+		advancedScopedPublisher.forceRemove(resource);
+		LOGGER.debug("{***REMOVED*** with ID {***REMOVED*** removed successfully", resource.getClass().getSimpleName(), id);
+***REMOVED***
+
+	public void publishScopedResource(GenericResource a, List<String> scopes)
+			throws RegistryNotFoundException, Exception {
+		StringWriter stringWriter = new StringWriter();
+		Resources.marshal(a, stringWriter);
+
+		ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
+		try {
+			System.out.println(scopes);
+			System.out.println(stringWriter);
+			scopedPublisher.create(a, scopes);
+	***REMOVED*** catch (RegistryNotFoundException e) {
+			System.out.println(e);
+			throw e;
+	***REMOVED***
+***REMOVED***
+
+	@Override
+	public void addAlgToIs(Algorithm algo) {
+		GenericResource a = new GenericResource();
+		a.newProfile().name(algo.getName()).type("DataMinerAlgorithms").description(algo.getDescription());
+		a.profile().newBody(this.getAlgoBody(algo));
+		try {
+			publishScopedResource(a, Arrays.asList(new String[] { ScopeProvider.instance.get() ***REMOVED***));
+	***REMOVED*** catch (Exception e) {
+			e.printStackTrace();
+	***REMOVED***
+***REMOVED***
+
+	private String getAlgoBody(Algorithm algo) {
+		return "<id>" + algo.getId() + "</id>" + "\n" + "<category>" + algo.getCategory() + "</category>" + "\n"
+				+ "<clazz>" + algo.getClazz() + "</clazz>" + "\n" + "<algorithmType>" + algo.getAlgorithmType()
+				+ "</algorithmType>" + "\n" + "<skipJava>" + algo.getSkipJava() + "</skipJava>" + "\n" + "<packageURL>"
+				+ algo.getPackageURL() + "</packageURL>" + "\n" + "<dependencies>"
+				+ algo.getDependencies().iterator().next().getName() + "</dependencies>";
+***REMOVED***
+
+	public void updateAlg(Algorithm algo) {
+
+		ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
+
+		SimpleQuery query = queryFor(GenericResource.class);
+		query.addCondition("$resource/Profile/Name/text() eq '" + algo.getName() + "'").setResult("$resource");
+		DiscoveryClient<GenericResource> client = clientFor(GenericResource.class);
+		List<GenericResource> ds = client.submit(query);
+		if (ds.isEmpty()) {
+			return;
+	***REMOVED***
+		GenericResource a = ds.get(0);
+		a.profile().newBody(this.getAlgoBody(algo));
+		try {
+			scopedPublisher.update(a);
+	***REMOVED*** catch (RegistryNotFoundException e) {
+			e.printStackTrace();
+	***REMOVED***
+***REMOVED***
+
+	private Algorithm convertAlgo(GenericResource a) {
+		Algorithm out = new Algorithm();
+
+		out.setId(a.profile().body().getElementsByTagName("id").item(0).getTextContent());
+		out.setAlgorithmType(a.profile().body().getElementsByTagName("algorithmType").item(0).getTextContent());
+		out.setCategory(a.profile().body().getElementsByTagName("category").item(0).getTextContent());
+		out.setClazz(a.profile().body().getElementsByTagName("clazz").item(0).getTextContent());
+		out.setName(a.profile().name());
+		out.setPackageURL(a.profile().body().getElementsByTagName("packageURL").item(0).getTextContent());
+		out.setSkipJava(a.profile().body().getElementsByTagName("skipJava").item(0).getTextContent());
+		out.setDescription(a.profile().description());
+
+		Set<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency> deps = new HashSet<org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency>();
+		for (int i = 0; i < a.profile().body().getElementsByTagName("dependencies").getLength(); i++) {
+			org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency d1 = new org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency();
+			d1.setName(a.profile().body().getElementsByTagName("dependencies").item(i).getTextContent());
+			deps.add(d1);
+	***REMOVED***
+		out.setDependencies(deps);
+***REMOVED***
+***REMOVED***
+
+	public Algorithm getAlgoById(String id) {
+		for (Algorithm aa : this.getAlgoFromIs()) {
+			if (aa.getId().equals(id)) {				
+				return aa;
+		***REMOVED***
+	***REMOVED***
+		return null;
+***REMOVED***
+
+	@Override
+	public Set<Algorithm> getAlgoFromIs() {
+		***REMOVED*** TODO Auto-generated method stub
+
+		Set<Algorithm> out = new HashSet<Algorithm>();
+		SimpleQuery query = queryFor(GenericResource.class);
+		query.addCondition("$resource/Profile/SecondaryType/text() eq 'DataMinerAlgorithms'").setResult("$resource");
+		DiscoveryClient<GenericResource> client = clientFor(GenericResource.class);
+		List<GenericResource> ds = client.submit(query);
+		for (GenericResource a : ds) {
+			out.add(this.convertAlgo(a));
+	***REMOVED***
+***REMOVED***
+***REMOVED***
+
+***REMOVED***