git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@144486 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/ansiblebridge/AnsibleBridge.java

@@ -203,11 +203,12 @@ public class AnsibleBridge {
 	FileOutputStream fos = new FileOutputStream(n);
 	PrintStream ps = new PrintStream(fos);
 	System.setOut(ps);
-	System.setErr(ps);
+	***REMOVED***System.setErr(ps);
-	worker.apply();
-	System.setOut(console);
 	System.setErr(console);
+
 	worker.apply();
+	***REMOVED***System.setOut(console);
+	***REMOVED***worker.apply();
 	System.out.println("Log stored to to " + n.getAbsolutePath());
         
     ***REMOVED*** destroy the worker
@@ -235,6 +236,8 @@ public class AnsibleBridge {
    */
   public Collection<Role> generateRoles(Dependency d) {
     Collection<Role> roles = new Vector<>();
+    
+    
     if("os".equalsIgnoreCase(d.getType())) {
       OSDependencyPackage pkg = new OSDependencyPackage(d);
       if(pkg!=null) {

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/clients/ISClient.java

@@ -30,7 +30,8 @@ public class ISClient {
       Collection<Host> out = new Vector<>();
       Host h = new Host();
       ***REMOVED***h.setName("bb-dataminer.res.eng.it");
-      h.setName("vm101.ui.savba.sk");
+      ***REMOVED***h.setName("vm101.ui.savba.sk");
+      h.setName("dataminer1-devnext.d4science.org");
       out.add(h);
       return out;
     ***REMOVED*** else {

src/main/java/org/gcube/dataanalysis/dataminer/poolmanager/process/AlgorithmPackageParser.java

@@ -10,6 +10,7 @@ import java.util.Vector;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
+import org.apache.commons.lang.StringEscapeUtils;
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Dependency;
 
@@ -149,24 +150,91 @@ public class AlgorithmPackageParser {
    * @param metadata
    * @return
    */
-  private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
+***REMOVED***  private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
-    Algorithm out = new Algorithm();
+***REMOVED***    Algorithm out = new Algorithm();
-    out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
+***REMOVED***    out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
-    out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
+***REMOVED***    out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
-    out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
+***REMOVED***    out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
-    List<String> dependencies = extractMultipleValues(metadata, METADATA_PACKAGES);
+***REMOVED***    List<String> dependencies = extractMultipleValues(metadata, METADATA_PACKAGES);
-    if (dependencies != null) {
+***REMOVED***    if (dependencies != null) {
-      for (String pkg : dependencies) {
+***REMOVED***      for (String pkg : dependencies) {
-        Dependency dep = new Dependency();
+***REMOVED***        Dependency dep = new Dependency();
-        dep.setName(pkg);
+***REMOVED***        dep.setName(pkg);
-        dep.setType("os");
+***REMOVED***        dep.setType("os");
-        out.addDependency(dep);
+***REMOVED***        out.addDependency(dep);
-      ***REMOVED***
+***REMOVED***      ***REMOVED***
-    ***REMOVED***
+***REMOVED***    ***REMOVED***
-    return out;
+***REMOVED***    return out;
-  ***REMOVED***
+***REMOVED***  ***REMOVED***
 
   
+  private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
+	    Algorithm out = new Algorithm();
+	    out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
+	    out.setDescription(extractSingleValue(metadata, METADATA_ALGORITHM_DESCRIPTION));
+	    out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
+	    List<String> rdependencies = extractMultipleValues(metadata, "r");
+	    if (rdependencies != null) {
+	      for (String pkg : rdependencies) {   
+	        Dependency dep = new Dependency();
+	        
+	        ***REMOVED***if (pkg.startsWith("os:")){
+	        dep.setName(pkg);
+	        dep.setType("cran");
+	        out.addDependency(dep);
+	        ***REMOVED***
+	    ***REMOVED***
+	      
+	    
+	    List<String> osdependencies = extractMultipleValues(metadata, "os");
+	    if (osdependencies != null) {
+	      for (String pkg : osdependencies) {   
+	        Dependency dep = new Dependency();
+	        
+	        ***REMOVED***if (pkg.startsWith("os:")){
+	        dep.setName(pkg);
+	        dep.setType("os");
+	        out.addDependency(dep);
+	        ***REMOVED***
+	    ***REMOVED***  
+	      
+	    
+	    
+	    List<String> cdependencies = extractMultipleValues(metadata, "custom");
+	    if (cdependencies != null) {
+	      for (String pkg : cdependencies) {   
+	        Dependency dep = new Dependency();
+	        
+	        ***REMOVED***if (pkg.startsWith("os:")){
+	        dep.setName(pkg);
+	        dep.setType("custom");
+	        out.addDependency(dep);
+	        ***REMOVED***
+	    ***REMOVED*** 
+	    
+	    
+***REMOVED***	        if (pkg.startsWith("r:")){
+***REMOVED***	        	***REMOVED***String results = StringEscapeUtils.escapeJava(pkg);
+***REMOVED***		        dep.setName(pkg);
+***REMOVED***		        dep.setType("cran");
+***REMOVED***		    ***REMOVED***
+***REMOVED***	        if (pkg.startsWith("custom:")){
+***REMOVED***		        dep.setName(pkg);
+***REMOVED***		        dep.setType("custom");
+***REMOVED***		    ***REMOVED***
+***REMOVED***	        if (!pkg.startsWith("os:")&&!pkg.startsWith("r:")&&!pkg.startsWith("custom:")){
+***REMOVED***		        dep.setName(pkg);
+***REMOVED***		        dep.setType("os");
+***REMOVED***		    ***REMOVED***
+	    
+	      
+	    
+	    return out;
+	  ***REMOVED***
+  
+  
+  
+  
   private static String extractSingleValue(Map<String, List<String>> metadata,
       String key) {
     List<String> l = metadata.get(key);
@@ -177,6 +245,9 @@ public class AlgorithmPackageParser {
     ***REMOVED***
   ***REMOVED***
 
+  
+ 
+  
   private static List<String> extractMultipleValues(
       Map<String, List<String>> metadata, String key) {
     List<String> l = metadata.get(key);

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

@@ -1,8 +1,8 @@
 package org.gcube.dataanalysis.dataminer.poolmanager.rest;
 
-import java.io.File;
 ***REMOVED***
 import java.net.MalformedURLException;
+import java.net.ProxySelector;
 ***REMOVED***
 import java.net.UnknownHostException;
 
@@ -13,12 +13,14 @@ import javax.ws.rs.QueryParam;
 
 ***REMOVED***
 import org.gcube.dataanalysis.dataminer.poolmanager.datamodel.Algorithm;
-import org.gcube.dataanalysis.dataminer.poolmanager.process.AddAlgorithmCommand;
 import org.gcube.dataanalysis.dataminer.poolmanager.service.DataminerPoolManager;
-import org.gcube.dataanalysis.dataminerpoolmanager.AlgorithmPackageParserTest;
+import org.gcube.dataanalysis.dataminer.poolmanager.util.PropertiesBasedProxySelector;
 ***REMOVED***
 ***REMOVED***
 
+
+
+
 @Path("/")
 public class RestPoolManager implements PoolManager {
 
@@ -26,52 +28,46 @@ public class RestPoolManager implements PoolManager {
 
 	private PoolManager service = new DataminerPoolManager();
 
+	
 	@GET
 	@Path("/add")
 	@Produces("text/plain")
-	public String addAlgorithmToVRE(@QueryParam("algorithm") String algorithm, @QueryParam("vre") String vre,
+	public String addAlgorithmToVRE(
-			@QueryParam("name") String name, @QueryParam("description") String description,
+			@QueryParam("algorithm") String algorithm, 
-			@QueryParam("category") String category, @QueryParam("algorithmType") String algorithmType,
+			@QueryParam("vre") String vre,
+			@QueryParam("name") String name,
+			@QueryParam("description") String description,
+			@QueryParam("category") String category,
+			@QueryParam("algorithmType") String algorithmType,
 			@QueryParam("skipJava") String skipJava) throws IOException, InterruptedException {
 		***REMOVED*** TODO Auto-generated method stub
 		LOGGER.debug("Adding algorithm =" + algorithm + " to VRE =" + vre);
 		Algorithm algo = service.extractAlgorithm(algorithm);
-
+		
-		if (algo.getCategory() == null) {
+		if (algo.getCategory() == null){
 			algo.setCategory(category);
-	***REMOVED*** else
+	***REMOVED*** else category = algo.getCategory();
-			category = algo.getCategory();
+		
-		System.out.println("category is: " + category);
+		if (algo.getAlgorithmType() == null){
-
-		if (algo.getAlgorithmType() == null) {
 			algo.setAlgorithmType(algorithmType);
-	***REMOVED*** else
+	***REMOVED*** else algorithmType = algo.getCategory();		
-			algorithmType = algo.getCategory();
+		
-		System.out.println("algorithmType is: " + algorithmType);
+		if (algo.getSkipJava() == null){
-
-		if (algo.getSkipJava() == null) {
 			algo.setSkipJava(skipJava);
-	***REMOVED*** else
+	***REMOVED*** else skipJava = algo.getSkipJava();		
-			skipJava = algo.getSkipJava();
+		
-		System.out.println("skipJava is: " + skipJava);
+		if (algo.getName() == null){
-
-		if (algo.getName() == null) {
 			algo.setCategory(name);
-	***REMOVED*** else
+	***REMOVED*** else name = algo.getName();
-			name = algo.getName();
+				
-		System.out.println("name is: " + name);
+		if (algo.getDescription() == null){
-
+			algo.setDescription(description);;
-		if (algo.getDescription() == null) {
+	***REMOVED*** else description = algo.getDescription();
-			algo.setDescription(description);
-			;
-	***REMOVED*** else
-			description = algo.getDescription();
-		System.out.println("description is: " + description);
 
 		return service.addAlgorithmToVRE(algo, vre);
-
 ***REMOVED***
 
+	
 	@GET
 	@Path("/log")
 	@Produces("text/plain")
@@ -80,6 +76,10 @@ public class RestPoolManager implements PoolManager {
 		LOGGER.debug("Returning Log =" + logUrl);
 		return service.getScriptFromURL(service.getURLfromWorkerLog(logUrl));
 ***REMOVED***
+	
+	
+
+
 
 	@Override
 	public Algorithm extractAlgorithm(String url) throws IOException {
@@ -87,37 +87,58 @@ public class RestPoolManager implements PoolManager {
 		return null;
 ***REMOVED***
 
+
 	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***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");
-		a.addAlgorithmToVRE("http:***REMOVED***data.d4science.org/am84enRYYkZ3dGRjZk9qTytQTndqaFpTOFJtT3RQeGhHbWJQNStIS0N6Yz0",
+		a.addAlgorithmToVRE(
-				"/gcube/devNext/NextNext", null, null, "ICHTHYOP_MODEL", "transducerers", "N");
+		"http:***REMOVED***data.d4science.org/cXhJV0s4b3dUN05jZk9qTytQTndqdmVUdURLOTRHeHpHbWJQNStIS0N6Yz0",
-		***REMOVED*** System.out.println(a.getLogById("dadcb059-69e5-48c3-aa58-3b290ae0419d"));
+		"/gcube/devNext/NextNext",
+		null, null, "test", "transducerers", "N");
+		
+	***REMOVED***System.out.println(a.getLogById("34ac474d-b9df-4929-87e1-2a0ae26cf898"));
 ***REMOVED***
 
+
 	@Override
 	public void getLogId(Algorithm algo, String vre) {
 		***REMOVED*** TODO Auto-generated method stub
-
+		
 ***REMOVED***
 
+
 	@Override
 	public String getScriptFromURL(URL logId) throws IOException {
 		***REMOVED*** TODO Auto-generated method stub
 		return null;
 ***REMOVED***
 
+
 	@Override
 	public String addAlgorithmToVRE(Algorithm algo, String vre) throws IOException, InterruptedException {
 		***REMOVED*** TODO Auto-generated method stub
 		return null;
 ***REMOVED***
 
+
 	@Override
 	public URL getURLfromWorkerLog(String logUrl) throws MalformedURLException, UnknownHostException {
 		***REMOVED*** TODO Auto-generated method stub
 		return null;
 ***REMOVED***
 
+
+
+
+
+	
+
+
+
+
 ***REMOVED***