Merge pull request 'feature/23054' (!2) from feature/23054 into master

Reviewed-on: #2

CHANGELOG.md

@@ -1,92 +1,67 @@
-This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-
 # Changelog for "dataminer"
 
 ## [v1.8.1-SNAPSHOT] - 2022-03-21
 
-### Fixes
+- Update wps service to support not writing of the computation status to the user's workspace [#23054]
-
 - Fixed protocol parameter when persistence is disabled
 
 
 ## [v1.8.0] - 2022-01-24
 
-### Fixes
-
 - Fixed max computations support [#22700]
 
 
 ## [v1.7.1] - 2021-05-24
 
-### Fixes
-
 - Fixed obsolete short urls [#20971]
 
 
 ## [v1.7.0] - 2020-11-20
 
-### Fixes
-
 - import range modified to resolve old repositories invalid url
 
-## [v1.6.0] - 2020-05-12
 
-### Fixes
+## [v1.6.0] - 2020-05-12
 
 - Added storagehub retry in InputsManager class, getLocalFile method [#19253]
 
 
-
 ## [v1.5.9] - 2019-11-20
 
-### Fixes
-
 - Fixed Content-Type support for files in the results of computations [#18096]
 
 
-
 ## [v1.5.8] - 2019-10-01
 
-### Fixes
-
 - Fixed https link for output parameter [#17659]
 
 
-
 ## [v1.5.7] - 2019-03-01
 
-### Features
-
 - Updated https support [#13024]
 
 
 
 ## [v1.5.2] - 2017-12-13
 
-### Fixes
-
 - added the right extension on output file
 - lock file created on execution
 
 
-
 ## [v1.5.1] - 2017-09-14
 
-### Features
-
 - added accounting on algorithm execution
 
 
-
 ## [v1.5.0] - 2017-07-31
 
-### Features
-
 - service interface classes moved to wps project
 
 
-
 ## [v1.1.0] - 2016-10-03
 
 - First Release
 
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/AbstractEcologicalEngineMapper.java

@@ -53,12 +53,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 	private static final int COMPUTATION_WAIT_FOR_RUN_REQUEST = 20000;
 
 	/**
-	 * Deploying procedure: 1 - modify configuration files 2 - modify resource
+	 * Deploying procedure: 1 - modify configuration files 2 - modify resource file:
-	 * file: resources/templates/setup.cfg 3 - generate classes with
+	 * resources/templates/setup.cfg 3 - generate classes with ClassGenerator 4 -
-	 * ClassGenerator 4 - add new classes in the wps_config.xml on the wps web
+	 * add new classes in the wps_config.xml on the wps web app config folder 5 -
-	 * app config folder 5 - produce the Jar file of this project 6 - copy the
+	 * produce the Jar file of this project 6 - copy the jar file in the lib folder
-	 * jar file in the lib folder of the wps web app change the server
+	 * of the wps web app change the server parameters in the wps_config.xml file
-	 * parameters in the wps_config.xml file
 	 */
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(AbstractEcologicalEngineMapper.class);
@@ -538,15 +537,25 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 	}
 
 	private boolean checkWriteAuthorization(String username) {
-		if (env != null && env.getShubUsersExcluded() != null) {
+		if (env != null) {
-			if (env.getShubUsersExcluded().isEmpty()) {
+			if (env.getShubUsersExcluded() != null) {
-				return false;
+				if (env.getShubUsersExcluded().isEmpty()) {
-			}
+					// all users write
-			if (env.getShubUsersExcluded().contains(username)) {
+					return true;
+				}
+				if (env.getShubUsersExcluded().contains(username)) {
+					return false;
+				} else {
+					// username write
+					return true;
+				}
+			} else {
+				//This is the * case, no users write.
 				return false;
 			}
+		} else {
+			return false;
 		}
-		return true;
 	}
 
 	private void accountAlgorithmExecution(long start, long end, OperationResult result) {

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/DataspaceManager.java

@@ -64,7 +64,7 @@ public class DataspaceManager implements Runnable {
 	public static String payload = "payload";
 
 	private String statusComputationName;
-	private static final String STATUS_POSTFIX="-STATUS";
+	private static final String STATUS_POSTFIX = "-STATUS";
 
 	public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
 			List<StoredData> outputData, List<File> generatedFiles) {
@@ -73,7 +73,7 @@ public class DataspaceManager implements Runnable {
 		this.inputData = inputData;
 		this.outputData = outputData;
 		this.generatedFiles = generatedFiles;
-		this.statusComputationName =  this.computation.id+STATUS_POSTFIX;
+		this.statusComputationName = this.computation.id + STATUS_POSTFIX;
 
 		LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
 				+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
@@ -142,25 +142,26 @@ public class DataspaceManager implements Runnable {
 	}
 
 	public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
-		LOGGER.debug("Dataspace->Analysing " + data);
+		LOGGER.debug("Dataspace->Uploaddata:"
+				+ " [data={},destinationFolder={}, changename={}] ", data, destinationFolder,
+				changename);
 		// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
 		// wsFolder);
 		String filenameonwsString = data.name;
 		if (changename)
-			filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
+			filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload));
-					getExtension(data.payload));
 
 		InputStream in = null;
 		String url = "";
 		try {
-			//long size = 0;
+			// long size = 0;
 			if (data.type.equals("text/csv") || data.type.equals("application/d4science")
 					|| data.type.equals("image/png")) {
 
 				if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
 					LOGGER.debug("Dataspace->Uploading file {}", data.payload);
 					in = new FileInputStream(new File(data.payload));
-					//size = new File(data.payload).length();
+					// size = new File(data.payload).length();
 				} else {
 					LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
 					int tries = 10;
@@ -188,7 +189,7 @@ public class DataspaceManager implements Runnable {
 
 				// LOGGER.debug("Dataspace->final file name on ws " +
 				// data.name+" description "+data.description);
-				LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
+				LOGGER.debug("Dataspace->WS OP saving the following file on the WS: " + filenameonwsString);
 				Map<String, Object> properties = new LinkedHashMap<String, Object>();
 
 				properties.put(computation_id, data.computationId);
@@ -203,9 +204,11 @@ public class DataspaceManager implements Runnable {
 				properties.put(payload, url);
 
 				FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
-				fileContainer.setMetadata(new Metadata(properties));
+				LOGGER.debug("Dataspace->WS OP file uploaded on WS: " + filenameonwsString);
+				Metadata metadata = new Metadata(properties);
+				fileContainer.setMetadata(metadata);
 
-				LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
+				LOGGER.debug("Dataspace->WS OP file set metadata: " + metadata);
 
 				url = fileContainer.getPublicLink().toString();
 				LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
@@ -395,10 +398,9 @@ public class DataspaceManager implements Runnable {
 		}
 		/*
 		 * List<String> scopes = new ArrayList<String>();
-		 * scopes.add(config.getGcubeScope());
+		 * scopes.add(config.getGcubeScope()); ws.createGcubeItem(computation.id,
-		 * ws.createGcubeItem(computation.id, computation.operatorDescription,
+		 * computation.operatorDescription, scopes, computation.user, itemType,
-		 * scopes, computation.user, itemType, properties,
+		 * properties, newcomputationFolder.getId());
-		 * newcomputationFolder.getId());
 		 */
 		newcomputationFolder.setMetadata(new Metadata(properties));
 
@@ -465,8 +467,8 @@ public class DataspaceManager implements Runnable {
 
 		List<String> scopes = new ArrayList<String>();
 		scopes.add(config.getGcubeScope());
-		
+
-		//TODO: update gcubeItem not recreate it...
+		// TODO: update gcubeItem not recreate it...
 		GCubeItem gcubeItem = new GCubeItem();
 		gcubeItem.setName(this.statusComputationName);
 		gcubeItem.setDescription(computation.operatorDescription);
@@ -509,7 +511,8 @@ public class DataspaceManager implements Runnable {
 				.getContainers().get(0);
 		LOGGER.debug("Dataspace->removing computation data");
 
-		List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName).getContainers();
+		List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName)
+				.getContainers();
 		if (!wi.isEmpty()) {
 			for (ItemContainer<? extends Item> container : wi) {
 				boolean retry = false;
@@ -517,25 +520,23 @@ public class DataspaceManager implements Runnable {
 					try {
 						container.forceDelete();
 						retry = false;
-					}catch (ItemLockedException e) {
+					} catch (ItemLockedException e) {
 						LOGGER.warn("item locked, retrying");
 						Thread.sleep(1000);
 						retry = true;
 					}
-				}while (retry);
+				} while (retry);
 			}
 		} else
 			LOGGER.debug("Dataspace->Warning Could not find {} under {}", this.statusComputationName,
 					computationContainer.get().getName());
 
-
 		/*
 		 * TODO: ASK GIANPAOLO int maxtries = 3; int i =1; while
-		 * (ws.exists(computation.id,computationsFolderWs.getId()) &&
+		 * (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
-		 * i<maxtries){
+		 * LOGGER.debug("Dataspace->computation data still exist... retrying "+i );
-		 * LOGGER.debug("Dataspace->computation data still exist... retrying "+i
+		 * Thread.sleep(1000); computationsFolderWs.find(computation.id).remove(); i++;
-		 * ); Thread.sleep(1000);
+		 * }
-		 * computationsFolderWs.find(computation.id).remove(); i++; }
 		 */
 
 		LOGGER.debug("Dataspace->finished removing computation data ");
@@ -544,7 +545,7 @@ public class DataspaceManager implements Runnable {
 	// TODO
 	public static String getExtension(String payload) {
 		LOGGER.debug("DataSpace->Get Extension from: " + payload);
-		String extension="";
+		String extension = "";
 		if (payload.toLowerCase().startsWith("http")) {
 			try {
 				URL obj = new URL(payload);