git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@146429 82a268e6-3cf1-43bd-a215-b396298e98cf

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  ***REMOVED***
+
+	protected String id;
+
+	public AlgoResource() ***REMOVED***
+***REMOVED***
+
+	public AlgoResource(String id) ***REMOVED***
+		this.id = id;
+***REMOVED***
+
+	public String getId() ***REMOVED***
+		return this.id;
+***REMOVED***
+
+	public void setId(String id) ***REMOVED***
+		this.id = id;
+***REMOVED***
+
+***REMOVED***

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

@@ -3,7 +3,34 @@ package org.gcube.dataanalysis.dataminer.poolmanager.datamodel;
 import java.util.Collection;
 import java.util.Vector;
 
-public class Algorithm ***REMOVED***
+
+public class Algorithm extends AlgoResource ***REMOVED***
+
+	
+***REMOVED***
+	public int hashCode() ***REMOVED***
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((id == null) ? 0 : id.hashCode());
+		return result;
+***REMOVED***
+
+***REMOVED***
+	public boolean equals(Object obj) ***REMOVED***
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		Algorithm other = (Algorithm) obj;
+		if (id == null) ***REMOVED***
+			if (other.id != null)
+				return false;
+	***REMOVED*** else if (!id.equals(other.id))
+			return false;
+		return true;
+***REMOVED***
 	
   private String name;
 

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

@@ -27,6 +27,7 @@
 
 ***REMOVED***
 
+***REMOVED***
 ***REMOVED***
 ***REMOVED***
 ***REMOVED***
@@ -49,4 +50,10 @@ public interface PoolManager ***REMOVED***
 
 	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/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;
+
 import java.io.BufferedReader;
 import java.io.File;
 ***REMOVED***
 import java.io.InputStreamReader;
+import java.io.StringWriter;
 ***REMOVED***
 ***REMOVED***
 import java.net.URLConnection;
 ***REMOVED***
+import java.util.Arrays;
+import java.util.HashSet;
+***REMOVED***
+***REMOVED***
 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;
 ***REMOVED***
@@ -280,15 +293,20 @@ import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Cluster;
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Host;
 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 ***REMOVED***
 
-	
 	private static final Logger LOGGER = LoggerFactory.getLogger(DataminerPoolManager.class);
 
-	
 	***REMOVED*** static Collection<Algorithm> algorithms;
 	***REMOVED***
 	***REMOVED*** static Collection<AlgorithmSet> sets;
@@ -301,7 +319,8 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** ***REMOVED***
 	***REMOVED***
 	***REMOVED*** /**
-***REMOVED***   * Add a new algorithm to the set of known ones. No further action is expected
+	***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***
@@ -314,7 +333,8 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** * @param algorithm
 	***REMOVED*** */
 	***REMOVED*** /*
-***REMOVED***   * public void updateAlgorithm(Algorithm algorithm) ***REMOVED*** ***REMOVED*** TODO implement this ***REMOVED***
+	***REMOVED*** * public void updateAlgorithm(Algorithm algorithm) ***REMOVED*** ***REMOVED*** TODO implement
+	***REMOVED*** this ***REMOVED***
 	***REMOVED*** */
 	***REMOVED***
 	***REMOVED*** /**
@@ -338,7 +358,8 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** * @param setId
 	***REMOVED*** * @param clusterId
 	***REMOVED*** */
-***REMOVED***  public void applyAlgorithmSetToCluster(String setName, String clusterName) ***REMOVED***
+	***REMOVED*** public void applyAlgorithmSetToCluster(String setName, String
+	***REMOVED*** clusterName) ***REMOVED***
 	***REMOVED*** AlgorithmSet set = this.getAlgorithmSet(setName);
 	***REMOVED*** Cluster cluster = new ISClient().getCluster(clusterName);
 	***REMOVED*** if (set != null && cluster != null) ***REMOVED***
@@ -365,9 +386,6 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** return null;
 	***REMOVED*** ***REMOVED***
 
-	
-
-
 	***REMOVED***
 	***REMOVED*** public void getLogId(final Algorithm algorithm, final String vre) ***REMOVED***
 	***REMOVED*** new Thread() ***REMOVED***
@@ -399,13 +417,11 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** System.out.println("Log stored to to " + n.getAbsolutePath());
 	***REMOVED*** ***REMOVED***
 
-	
-	
-	
 	***REMOVED*** public String getLogById(String id) throws IOException ***REMOVED***
 	***REMOVED*** String strLine = null;
 	***REMOVED*** try***REMOVED***
-***REMOVED***		   FileInputStream fstream = new FileInputStream("/tmp/dataminer-pool-manager/work/"+id+"/logs/"+id);
+	***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***
@@ -419,14 +435,12 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 	***REMOVED*** return strLine;
 	***REMOVED*** ***REMOVED***
 
-
 	public String getScriptFromURL(URL url) throws IOException ***REMOVED***
 		if (url == null) ***REMOVED***
-	      return null;
+	***REMOVED***
 	***REMOVED***
 		URLConnection yc = url.openConnection();
-	    BufferedReader input = new BufferedReader(new InputStreamReader(
+		BufferedReader input = new BufferedReader(new InputStreamReader(yc.getInputStream()));
-	        yc.getInputStream()));
 		String line;
 		StringBuffer buffer = new StringBuffer();
 		while ((line = input.readLine()) != null) ***REMOVED***
@@ -437,19 +451,14 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 		return bufferScript;
 ***REMOVED***
 
-   
+***REMOVED****
-   
-   
-	
-  /**
 	 * Publish the given algorithm in the given VRE
 	 * 
 	 * @param algorithmName
 	 * @param vre
 	 * 
-   */
+***REMOVED***
-  public String addAlgorithmToVRE(Algorithm algorithm, final String vre)
+	public String addAlgorithmToVRE(Algorithm algorithm, final String vre) throws IOException ***REMOVED***
-      throws IOException ***REMOVED***
 		***REMOVED*** create a fake algorithm set
 		final AlgorithmSet algoSet = new AlgorithmSet();
 		algoSet.setName("fake");
@@ -457,9 +466,9 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 		final String uuid = UUID.randomUUID().toString();
 
 		new Thread(new Runnable() ***REMOVED***
-      @Override
+	***REMOVED***
 			public void run() ***REMOVED***
-        ***REMOVED*** TODO Auto-generated method stub
+		***REMOVED***
 				try ***REMOVED***
 					addAlgorithmsToVRE(algoSet, vre, uuid);
 			***REMOVED*** catch (IOException e) ***REMOVED***
@@ -468,13 +477,13 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 			***REMOVED***
 		***REMOVED***
 	***REMOVED***).start();
-    ***REMOVED*** this line will execute immediately, not waiting for your task to complete
+		***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)
+	public String addAlgorithmToHost(Algorithm algorithm, final String hostname) throws IOException ***REMOVED***
-      throws IOException ***REMOVED***
 		***REMOVED*** create a fake algorithm set
 		final AlgorithmSet algoSet = new AlgorithmSet();
 		algoSet.setName("fake");
@@ -482,9 +491,9 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 		final String uuid = UUID.randomUUID().toString();
 
 		new Thread(new Runnable() ***REMOVED***
-      @Override
+	***REMOVED***
 			public void run() ***REMOVED***
-        ***REMOVED*** TODO Auto-generated method stub
+		***REMOVED***
 				try ***REMOVED***
 					addAlgorithmsToHost(algoSet, hostname, uuid);
 			***REMOVED*** catch (IOException e) ***REMOVED***
@@ -493,15 +502,16 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 			***REMOVED***
 		***REMOVED***
 	***REMOVED***).start();
-    ***REMOVED*** this line will execute immediately, not waiting for your task to complete
+		***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 ***REMOVED***
 
-		File path = new File(System.getProperty("user.home")+File.separator+"/gcube/dataminer-pool-manager/work/"+a+File.separator+"logs");
+		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();
@@ -509,8 +519,6 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 		return new File(n.getPath()).toURI().toURL();
 ***REMOVED***
 
-  
-
 	public String addAlgorithmsToVRE(AlgorithmSet algorithms, String vre, String uuid) throws IOException ***REMOVED***
 
 		***REMOVED*** create the cluster (dataminers in the vre)
@@ -540,29 +548,135 @@ public class DataminerPoolManager implements PoolManager ***REMOVED***
 
 ***REMOVED***
 
-
 	public Algorithm extractAlgorithm(String url) throws IOException ***REMOVED***
 		return new AlgorithmPackageParser().parsePackage(url);
 ***REMOVED***
 
-
+***REMOVED***
-@Override
 	public void getLogId(Algorithm algo, String vre) ***REMOVED***
-	***REMOVED*** TODO Auto-generated method stub
+***REMOVED***
 
 ***REMOVED***
 
-
+***REMOVED***
-@Override
 	public String getLogById(String logId) throws IOException ***REMOVED***
-	***REMOVED*** TODO Auto-generated method stub
+***REMOVED***
-	return null;
+***REMOVED***
 ***REMOVED***
 
+	***REMOVED*** 2017 March 29
 
-
+	public void unPublishScopedResource(GenericResource resource) throws RegistryNotFoundException, Exception ***REMOVED***
-
+		ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
-  
+		AdvancedScopedPublisher advancedScopedPublisher = new AdvancedScopedPublisher(scopedPublisher);
+		String id = resource.id();
+		LOGGER.debug("Trying to remove ***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** from ***REMOVED******REMOVED***", resource.getClass().getSimpleName(), id,
+				ScopeProvider.instance.get());
+		***REMOVED*** scopedPublisher.remove(resource, scopes);
+		advancedScopedPublisher.forceRemove(resource);
+		LOGGER.debug("***REMOVED******REMOVED*** with ID ***REMOVED******REMOVED*** removed successfully", resource.getClass().getSimpleName(), id);
 ***REMOVED***
 
+	public void publishScopedResource(GenericResource a, List<String> scopes)
+			throws RegistryNotFoundException, Exception ***REMOVED***
+		StringWriter stringWriter = new StringWriter();
+		Resources.marshal(a, stringWriter);
 
+		ScopedPublisher scopedPublisher = RegistryPublisherFactory.scopedPublisher();
+		try ***REMOVED***
+			System.out.println(scopes);
+			System.out.println(stringWriter);
+			scopedPublisher.create(a, scopes);
+	***REMOVED*** catch (RegistryNotFoundException e) ***REMOVED***
+			System.out.println(e);
+			throw e;
+	***REMOVED***
+***REMOVED***
+
+***REMOVED***
+	public void addAlgToIs(Algorithm algo) ***REMOVED***
+		GenericResource a = new GenericResource();
+		a.newProfile().name(algo.getName()).type("DataMinerAlgorithms").description(algo.getDescription());
+		a.profile().newBody(this.getAlgoBody(algo));
+		try ***REMOVED***
+			publishScopedResource(a, Arrays.asList(new String[] ***REMOVED*** ScopeProvider.instance.get() ***REMOVED***));
+	***REMOVED*** catch (Exception e) ***REMOVED***
+			e.printStackTrace();
+	***REMOVED***
+***REMOVED***
+
+	private String getAlgoBody(Algorithm algo) ***REMOVED***
+		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) ***REMOVED***
+
+		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()) ***REMOVED***
+			return;
+	***REMOVED***
+		GenericResource a = ds.get(0);
+		a.profile().newBody(this.getAlgoBody(algo));
+		try ***REMOVED***
+			scopedPublisher.update(a);
+	***REMOVED*** catch (RegistryNotFoundException e) ***REMOVED***
+			e.printStackTrace();
+	***REMOVED***
+***REMOVED***
+
+	private Algorithm convertAlgo(GenericResource a) ***REMOVED***
+		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++) ***REMOVED***
+			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);
+		return out;
+***REMOVED***
+
+	public Algorithm getAlgoById(String id) ***REMOVED***
+		for (Algorithm aa : this.getAlgoFromIs()) ***REMOVED***
+			if (aa.getId().equals(id)) ***REMOVED***				
+				return aa;
+		***REMOVED***
+	***REMOVED***
+***REMOVED***
+***REMOVED***
+
+***REMOVED***
+	public Set<Algorithm> getAlgoFromIs() ***REMOVED***
+***REMOVED***
+
+		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) ***REMOVED***
+			out.add(this.convertAlgo(a));
+	***REMOVED***
+		return out;
+***REMOVED***
+
+***REMOVED***