diff --git a/.classpath b/.classpath index d90b917..698778f 100644 --- a/.classpath +++ b/.classpath @@ -1,9 +1,31 @@ - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs index 6916b10..f4217b0 100644 --- a/.settings/org.eclipse.jdt.core.prefs +++ b/.settings/org.eclipse.jdt.core.prefs @@ -1,13 +1,12 @@ -#Fri Jun 22 18:05:41 CEST 2012 eclipse.preferences.version=1 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve -org.eclipse.jdt.core.compiler.compliance=1.6 +org.eclipse.jdt.core.compiler.compliance=1.7 org.eclipse.jdt.core.compiler.debug.lineNumber=generate org.eclipse.jdt.core.compiler.debug.localVariable=generate org.eclipse.jdt.core.compiler.debug.sourceFile=generate org.eclipse.jdt.core.compiler.problem.assertIdentifier=error org.eclipse.jdt.core.compiler.problem.enumIdentifier=error org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning -org.eclipse.jdt.core.compiler.source=1.6 +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/pom.xml b/pom.xml index 0caf28e..0eb0bcf 100644 --- a/pom.xml +++ b/pom.xml @@ -9,12 +9,25 @@ org.gcube.dataanalysis ecological-engine-smart-executor - 1.4.0-SNAPSHOT + 1.5.0-SNAPSHOT Smart Ecological Engine Executor Smart Ecological Engine Executor library https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor + + + + + org.gcube.distribution + gcube-bom + LATEST + pom + import + + + + Gianpaolo Coro @@ -33,16 +46,16 @@ UTF-8 + + org.gcube.data.transfer + data-transfer-library + [1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT) + org.gcube.dataanalysis ecological-engine [1.8.0-SNAPSHOT,2.0.0-SNAPSHOT) - - org.gcube.data.transfer - agent-library - [2.0.0-SNAPSHOT,3.0.0-SNAPSHOT) - org.gcube.contentmanagement storage-manager-core @@ -56,49 +69,23 @@ org.apache.activemq activemq-core - 5.6.0 - - - org.gcube.common - common-authorization - [2.0.0-SNAPSHOT,3.0.0-SNAPSHOT) - provided - - - slf4j-api - org.slf4j - - - common-utils-encryption - org.gcube.core - - + 5.7.0 org.gcube.core common-scope - [1.2.0-SNAPSHOT,2.0.0-SNAPSHOT) - provided - - - slf4j-api - org.slf4j - - - - - + + maven-compiler-plugin 3.1 - 1.6 - 1.6 + 1.7 + 1.7 @@ -109,13 +96,12 @@ true - - - + + + org.apache.maven.plugins maven-assembly-plugin - 2.2 ${distroDirectory}/descriptor.xml diff --git a/src/main/java/org/gcube/dataanalysis/executor/job/management/DistributedProcessingAgentWPS.java b/src/main/java/org/gcube/dataanalysis/executor/job/management/DistributedProcessingAgentWPS.java index 8ec7145..276c1b2 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/job/management/DistributedProcessingAgentWPS.java +++ b/src/main/java/org/gcube/dataanalysis/executor/job/management/DistributedProcessingAgentWPS.java @@ -1,22 +1,17 @@ package org.gcube.dataanalysis.executor.job.management; -import java.io.File; -import java.io.Serializable; import java.util.ArrayList; import java.util.List; -import org.apache.log4j.Logger; import org.gcube.contentmanagement.graphtools.utils.HttpRequest; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools; import org.gcube.dataanalysis.ecoengine.configuration.ALG_PROPS; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE; import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.ResourceLoad; import org.gcube.dataanalysis.ecoengine.connectors.livemonitor.Resources; import org.gcube.dataanalysis.ecoengine.utils.Operations; - -import com.thoughtworks.xstream.XStream; +import org.slf4j.Logger; public class DistributedProcessingAgentWPS { diff --git a/src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java b/src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java index 3b828be..e6e9cdd 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java +++ b/src/main/java/org/gcube/dataanalysis/executor/job/management/GenericWorker.java @@ -13,11 +13,11 @@ import java.net.URLEncoder; import java.nio.charset.StandardCharsets; import java.nio.file.Files; -import org.apache.log4j.Logger; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.contentmanager.storageclient.model.protocol.smp.Handler; import org.gcube.dataanalysis.ecoengine.interfaces.ActorNode; import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm; +import org.slf4j.Logger; public class GenericWorker extends StandardLocalInfraAlgorithm{ diff --git a/src/main/java/org/gcube/dataanalysis/executor/job/management/WPSJobManager.java b/src/main/java/org/gcube/dataanalysis/executor/job/management/WPSJobManager.java index 70809b0..11cc217 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/job/management/WPSJobManager.java +++ b/src/main/java/org/gcube/dataanalysis/executor/job/management/WPSJobManager.java @@ -171,8 +171,7 @@ public class WPSJobManager { } catch (Exception e) { e.printStackTrace(); - AnalysisLogger.getLogger().debug(e); - AnalysisLogger.getLogger().debug("WPSJobManager->Task Number "+taskNumber+" - Process exception: " + e.getLocalizedMessage()); + AnalysisLogger.getLogger().error("WPSJobManager->Task Number {} - Process exception ", taskNumber,e); exitstatus = GenericWorker.TASK_FAILURE; }finally{ diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/WebApplicationPublisher.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/WebApplicationPublisher.java index a8d1596..04aef27 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/WebApplicationPublisher.java +++ b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/WebApplicationPublisher.java @@ -92,8 +92,8 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{ String remotePath = remoteFolder+subpath+"/"; AnalysisLogger.getLogger().debug("Uploading "+key+" -> "+remotePath); - boolean transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath); - if (!transferout){ + long transferout = DataTransferer.transferFileToService(scope, username, transferServiceAddress, transferServicePort, key, remotePath); + if (transferout<=0){ throw new Exception("Error transferring files to the infrastructure "); } i++; @@ -107,9 +107,7 @@ public class WebApplicationPublisher extends StandardLocalInfraAlgorithm{ //get URL addOutputString("Generated Website - Main URL", producedPage); }catch(Exception e){ - e.printStackTrace(); - AnalysisLogger.getLogger().debug(e); - AnalysisLogger.getLogger().debug("An error occurred!"); + AnalysisLogger.getLogger().error("an error occurred!",e); throw e; }finally{ //clean everything diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/BionymLocalTransducer.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/BionymLocalTransducer.java index c6d0b19..651644c 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/BionymLocalTransducer.java +++ b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/BionymLocalTransducer.java @@ -2,6 +2,7 @@ package org.gcube.dataanalysis.executor.nodes.transducers.bionym; import java.io.File; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; @@ -25,7 +26,6 @@ import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Match import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters; import org.gcube.dataanalysis.executor.scripts.OSCommand; -import scala.actors.threadpool.Arrays; public class BionymLocalTransducer implements Transducerer { // BionymFlexibleWorkflowTransducer bionymwf = new BionymFlexibleWorkflowTransducer(); diff --git a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java index 008afb0..044e284 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java +++ b/src/main/java/org/gcube/dataanalysis/executor/nodes/transducers/bionym/abstracts/YasmeenMatcher.java @@ -5,7 +5,6 @@ import java.security.Permission; import java.util.HashMap; import java.util.UUID; -import org.apache.tools.ant.ExitException; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.matchers.LevensteinMatcher; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Matcher; @@ -158,7 +157,7 @@ public abstract class YasmeenMatcher implements Matcher { @Override public void checkExit(int status) { super.checkExit(status); - throw new ExitException(status); + throw new RuntimeException("exit status is "+status); } } } diff --git a/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java b/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java index 0686911..599caa8 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java +++ b/src/main/java/org/gcube/dataanalysis/executor/rscripts/generic/GenericRScript.java @@ -153,8 +153,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm { } } catch (Exception e) { - AnalysisLogger.getLogger().debug(e); - AnalysisLogger.getLogger().debug("Could not delete sandbox folder " + folder.getAbsolutePath()); + AnalysisLogger.getLogger().warn("Could not delete sandbox folder {} ",folder.getAbsolutePath(),e); } if (Rlog != null) { @@ -236,9 +235,7 @@ public abstract class GenericRScript extends StandardLocalInfraAlgorithm { org.gcube.dataanalysis.executor.rscripts.generic.FileUtils.moveFileToDirectory(rowFile, new File(config.getConfigPath()), false); files.add(preparedFile); }catch(Exception e){ - e.printStackTrace(); - AnalysisLogger.getLogger().debug("error in moving file " + rowFile.getAbsolutePath() + " to " + preparedFile); - AnalysisLogger.getLogger().debug(e); + AnalysisLogger.getLogger().error("error in moving file {} to {}",rowFile.getAbsolutePath(),preparedFile,e); throw e; } break; diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/DataTransferer.java b/src/main/java/org/gcube/dataanalysis/executor/util/DataTransferer.java index 0ee6153..17bd8c2 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/util/DataTransferer.java +++ b/src/main/java/org/gcube/dataanalysis/executor/util/DataTransferer.java @@ -1,155 +1,49 @@ package org.gcube.dataanalysis.executor.util; -import static org.gcube.datatransfer.agent.library.proxies.Proxies.transferAgent; - import java.io.File; -import java.net.URI; -import java.net.URL; -import java.net.URLEncoder; -import java.util.ArrayList; -import java.util.concurrent.TimeUnit; +import java.util.Collections; +import java.util.HashMap; +import java.util.Map; + +import org.gcube.data.transfer.library.DataTransferClient; +import org.gcube.data.transfer.library.TransferResult; +import org.gcube.data.transfer.model.Destination; +import org.gcube.data.transfer.model.PluginInvocation; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.blobstorage.service.IClient; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.contentmanager.storageclient.wrapper.AccessType; -import org.gcube.contentmanager.storageclient.wrapper.MemoryType; -import org.gcube.contentmanager.storageclient.wrapper.StorageClient; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.datatransfer.agent.library.AgentLibrary; -import org.gcube.datatransfer.agent.library.exceptions.MonitorTransferException; -import org.gcube.datatransfer.common.agent.Types.storageType; -import org.gcube.datatransfer.common.options.TransferOptions; -import org.gcube.datatransfer.common.outcome.FileTransferOutcome; -import org.gcube.datatransfer.common.outcome.TransferStatus; public class DataTransferer { - public static void main(String[] args) throws Exception { - //String scope = "/d4science.research-infrastructures.eu/gCubeApps"; - - String scope = "/gcube/devsec/devVRE"; - //test only ScopeProvider.instance.set(scope); - //String transferGHN = "dewn04.madgik.di.uoa.gr"; - String transferGHN = "access.d4science.org"; - int transferPort = 8080; - AgentLibrary library = transferAgent().at(transferGHN, transferPort).build(); - - ArrayList input = new ArrayList(); - /* - * File localfile = new File("C:/Users/coro/Dropbox/Public/wind1.tif"); String file = "wind1.tif"; String localfolder = "C:/Users/coro/Dropbox/Public/"; String storagesmpurl = StorageUtils.uploadFilesOnStorage("/gcube/devsec", "gianpaolo.coro",localfolder,file); - * - * System.out.println("URI from storage: "+storagesmpurl); - * - * String urlStorage = "http://dev.d4science.org/uri-resolver/smp?smp-uri="+storagesmpurl+"&fileName="+file; - */ - // String urlStorage = "http://dev.d4science.org/smp?smp-uri=smp://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc=&fileName=wind1.tif"; - //String urlStorage = "http://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc="; - String urlStorage ="http://goo.gl/Vq8QVY"; - - System.out.println("URL for storage: " + urlStorage); - - URI uri = new URI("http://dl.dropboxusercontent.com/u/12809149/wind1.tif"); - // URI uri = new URI(urlStorage); - - // http://dev.d4science.org/uri-resolver/smp?smp-uri=smp://data.gcube.org/gzAv/RparhTHO4yhbF9ItALcRlSJRIiBGmbP5+HKCzc=&fileName=wind1.tif&contentType=tiff - - // URI uri = new URI(storageurl); //localfile.toURI(); - // URI uri = new URI("file:///C:Users/coro/Dropbox/Public/wind1.tif"); - input.add(uri); - - //String outPath = "/tmp"; - String outPath = "/var/www/html/test/"; - String fileToTransfer = "C:\\Users\\coro\\Dropbox\\Public\\3_Aquamaps.jpg"; - //fileToTransfer = "C:\\Users\\coro\\Dropbox\\Public\\3_Aquamaps.jpg"; -// fileToTransfer = "C:/Users/coro/Desktop/DATABASE e NOTE/Experiments/WEB_APP_PUBLISHER/gcube/images/Resource Model.png"; - transferFileToService(scope, "gianpaolo.coro", transferGHN, transferPort,fileToTransfer , outPath); - - - } + private static final Logger logger = LoggerFactory.getLogger(DataTransferer.class); // returns the number of transferred bytes - public static boolean transferFileToService(String scope, String username, String service, int port, String fileAbsolutePath, String remoteFolder) throws Exception { - AnalysisLogger.getLogger().debug("Transferring file " + fileAbsolutePath + " to " + service + ":" + port); -// ScopeProvider.instance.set(scope); + public static long transferFileToService(String scope, String username, String host, int port, String fileAbsolutePath, String remoteFolder) throws Exception { + logger.debug("Transferring file {} to {}:{} " , fileAbsolutePath, host, port ); + + DataTransferClient client=DataTransferClient.getInstanceByEndpoint("http://"+host+":"+port); - AgentLibrary library = transferAgent().at(service, port).build(); - ArrayList input = new ArrayList(); File localFile = new File(fileAbsolutePath); if (!localFile.exists()) throw new Exception("Local file does not exist: " + localFile); - String localfolder = localFile.getParent(); + //String localfolder = localFile.getParent(); String file = localFile.getName(); - AnalysisLogger.getLogger().debug("Uploading file " + file + " onto storage"); -// ScopeProvider.instance.set(scope); - AnalysisLogger.getLogger().info("Loading file on scope: " + scope); - - String storagesmpurl = StorageUtils.uploadFilesOnStorage(scope, username, localfolder, "/",file,true); - //urls for testing - //storagesmpurl = "http://dev.d4science.org/smp?smp-uri="+storagesmpurl+"&fileName="+file; - // String storagesmpurl = "smp://data.gcube.org/sHtVhK4clGtbcWCliQud+5b4PfGx5BW+GmbP5+HKCzc="; - // String storagesmpurl = "http://goo.gl/r6ggMA"; - // String storagesmpurl = "http://dl.dropboxusercontent.com/u/12809149/3_Aquamaps.jpg"; - - AnalysisLogger.getLogger().debug("SMP url generated: " + storagesmpurl); - URI uri = new URI(storagesmpurl); - input.add(uri); - - TransferOptions options = new TransferOptions(); - - options = new TransferOptions(); - options.setOverwriteFile(false); - options.setType(storageType.DataStorage); - options.setUnzipFile(false); - options.setTransferTimeout(3, TimeUnit.HOURS); - AnalysisLogger.getLogger().debug("Transferring..."); - - //old code for sync transfer -// ArrayList outcomes = library.startTransferSync(input, remoteFolder, options); - ArrayList outputURI = new ArrayList(); -// outputURI.add(new URI("file://"+remoteFolder.replace(" ", "_")+file.replace(" ", "_"))); - outputURI.add(new URI("file://"+remoteFolder.replace(" ", "%20")+file.replace(" ", "%20"))); + Map params=new HashMap<>(); + params.put("DESTINATION", remoteFolder); + params.put("SOURCE_PARAMETER", PluginInvocation.DESTINATION_FILE_PATH); + + Destination dest=new Destination(file); - AnalysisLogger.getLogger().debug("Remote file name will be: " + outputURI.get(0)); + TransferResult tranferResult = client.localFile(localFile,dest,Collections.singleton(new PluginInvocation("DECOMPRESS",params))); - String transferId = library.startTransfer(input, outputURI, options); + logger.debug("Transferring..."); - TransferStatus transferStatus = null; + - do { - try { - - Thread.sleep(1000); - transferStatus = TransferStatus.valueOf(library.monitorTransfer(transferId)); - - } catch (MonitorTransferException e) { - e.printStackTrace(); - } - - } while (!transferStatus.hasCompleted()); - - ArrayList outcomes = library.getTransferOutcomes(transferId, FileTransferOutcome.class); - - AnalysisLogger.getLogger().debug("Transferring complete"); - boolean success = false; - String outcomeString = ""; - for (FileTransferOutcome outcome : outcomes) { - AnalysisLogger.getLogger().debug("Outcome " + outcome); - outcomeString = outcome.toString(); - AnalysisLogger.getLogger().debug("Transferred file name " + outcome.fileName()); - AnalysisLogger.getLogger().debug("Transferring success " + outcome.isSuccess()); - AnalysisLogger.getLogger().debug("Transferred bytes " + outcome.getTotal_size()); - AnalysisLogger.getLogger().debug("Transfer time " + outcome.getTransferTime()); - success = outcome.isSuccess(); - } - - if (!success) - throw new Exception("No Bytes were transferred to the Thredds server: "+outcomeString); - - return success; + return tranferResult.getTransferedBytes(); } } diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java b/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java index 50a6eef..3eb3df2 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java +++ b/src/main/java/org/gcube/dataanalysis/executor/util/LocalRScriptsManager.java @@ -17,7 +17,6 @@ import org.gcube.common.scope.api.ScopeProvider; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.executor.scripts.OSCommand; -import org.junit.runner.notification.RunListener; public class LocalRScriptsManager { @@ -91,7 +90,7 @@ public class LocalRScriptsManager { line = br.readLine(); sb.append(line + "\n"); } - AnalysisLogger.getLogger().debug(sb); + AnalysisLogger.getLogger().debug(sb.toString()); uberbuffer.append(sb.toString()); AnalysisLogger.getLogger().debug("---ERRORS---"); br = new BufferedReader(new InputStreamReader(process.getErrorStream())); @@ -102,7 +101,7 @@ public class LocalRScriptsManager { line = br.readLine(); sb.append(line + "\n"); } - AnalysisLogger.getLogger().debug(sb); + AnalysisLogger.getLogger().debug(sb.toString()); uberbuffer.append(sb.toString()); AnalysisLogger.getLogger().debug("---END OF ERRORS---"); } catch (Exception e) { @@ -284,7 +283,8 @@ public class LocalRScriptsManager { } } } - + + /* public static void main1(String[] args) throws Exception { String url = StorageUtils.uploadFilesOnStorage("/gcube/devsec/devVRE", "ecological.engine", "C:\\Users\\coro\\Documents\\", "tacsatmini.csv"); System.out.println(url); @@ -321,5 +321,5 @@ public class LocalRScriptsManager { scriptmanager.executeRScript(config, scriptName, inputFileURL, inputParameters, defaultInputFile, defaultOutputFile, null, true, true, "./"); } - +*/ } diff --git a/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java b/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java index 770e298..3224b81 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java +++ b/src/main/java/org/gcube/dataanalysis/executor/util/RScriptsManager.java @@ -12,8 +12,6 @@ import java.util.HashMap; import java.util.LinkedHashMap; import java.util.List; import java.util.UUID; - -import org.gcube.common.authorization.library.provider.SecurityTokenProvider; import org.gcube.common.scope.api.ScopeProvider; import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; @@ -78,7 +76,7 @@ public class RScriptsManager { line = br.readLine(); sb.append(line + "\n"); } - AnalysisLogger.getLogger().debug(sb); + AnalysisLogger.getLogger().debug(sb.toString()); AnalysisLogger.getLogger().debug("---ERRORS---"); br = new BufferedReader(new InputStreamReader(process.getErrorStream())); @@ -89,7 +87,7 @@ public class RScriptsManager { line = br.readLine(); sb.append(line + "\n"); } - AnalysisLogger.getLogger().debug(sb); + AnalysisLogger.getLogger().debug(sb.toString()); AnalysisLogger.getLogger().debug("---END OF ERRORS---"); } catch (Exception e) { AnalysisLogger.getLogger().debug("---END BY PROCESS INTERRUPTION---"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/CustomRegressor.java b/src/test/java/org/gcube/dataanalysis/executor/tests/CustomRegressor.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/CustomRegressor.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/CustomRegressor.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java similarity index 95% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java index 233f99a..c997073 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym.java @@ -1,6 +1,5 @@ package org.gcube.dataanalysis.executor.tests; -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.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; @@ -13,7 +12,7 @@ public class RegressionTestBiOnym { public static void executeWF(String[] args) throws Exception { // Generate AlgorithmConfiguration config = new AlgorithmConfiguration(); - config.setConfigPath("./cfg/"); + config.setConfigPath("./cfg/"); config.setParam("DatabaseUserName","utente"); config.setParam("DatabasePassword","d4science"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym1Matcher.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym1Matcher.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym1Matcher.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnym1Matcher.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnymProduzione.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnymProduzione.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnymProduzione.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestBiOnymProduzione.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java similarity index 94% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java index 3fa4a3c..3356db3 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestCMSY.java @@ -6,7 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class RegressionTestCMSY { /** diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java similarity index 95% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java index 934b31e..74b234b 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestFAOMSY.java @@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing; public class RegressionTestFAOMSY { diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java similarity index 93% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java index 21f01b9..6f1ebd8 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestGenerators.java @@ -4,9 +4,7 @@ import java.util.List; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.interfaces.Generator; import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class RegressionTestGenerators { /** @@ -20,7 +18,7 @@ public class RegressionTestGenerators { List generators = GeneratorsFactory.getGenerators(testAquamapsSuitable()); generators.get(0).init(); - Regressor.process(generators.get(0)); + CustomRegressor.process(generators.get(0)); generators = null; } diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java similarity index 92% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java index fe09927..adeab75 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestICCATVPA.java @@ -6,8 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.IOHelper; public class RegressionTestICCATVPA { /** diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java similarity index 94% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java index 1686673..473bab8 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestLWR.java @@ -6,7 +6,6 @@ import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class RegressionTestLWR { /** diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java similarity index 88% rename from src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java index 60ef3b0..055bfbf 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/RegressionTestTransducers.java @@ -5,9 +5,7 @@ import java.util.List; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.evaluation.bioclimate.InterpolateTables.INTERPOLATIONFUNCTIONS; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class RegressionTestTransducers { @@ -48,14 +46,14 @@ public static void main(String[] args) throws Exception { */ trans = TransducerersFactory.getTransducerers(testConfigLocal5()); trans.get(0).init(); - Regressor.process(trans.get(0)); + CustomRegressor.process(trans.get(0)); trans = null; } private static AlgorithmConfiguration testConfigLocal() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("BIOCLIMATE_HSPEC"); config.setParam("HSPEC_TABLE_LIST", "hspec_validation"+AlgorithmConfiguration.getListSeparator()+"hspec_validation2"); config.setParam("HSPEC_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test"); @@ -66,7 +64,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal2() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("BIOCLIMATE_HCAF"); config.setParam("HCAF_TABLE_LIST","hcaf_d"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01332632269756"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2016_linear_01336062995861"+AlgorithmConfiguration.getListSeparator()+"hcaf_d_2050"); config.setParam("HCAF_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"); @@ -76,7 +74,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal3() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("BIOCLIMATE_HSPEN"); config.setParam("HSPEN_TABLE_LIST","hspen"+AlgorithmConfiguration.getListSeparator()+"hspen_2016"+AlgorithmConfiguration.getListSeparator()+"hspen_2020"+AlgorithmConfiguration.getListSeparator()+"hspen_2050"); config.setParam("HSPEN_TABLE_NAMES", "test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"+AlgorithmConfiguration.getListSeparator()+"test"); @@ -87,7 +85,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal4() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("HCAF_INTERPOLATION"); config.setParam("FirstHCAF","hcaf_d"); @@ -102,7 +100,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal5() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("OCCURRENCES_MERGER"); config.setParam("longitudeColumn", "decimallongitude"); @@ -125,7 +123,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal6() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("OCCURRENCES_INSEAS_ONEARTH"); config.setParam("longitudeColumn", "decimallongitude"); @@ -140,7 +138,7 @@ public static void main(String[] args) throws Exception { private static AlgorithmConfiguration testConfigLocal7() { - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setAgent("OCCURRENCES_DUPLICATE_DELETER"); config.setParam("longitudeColumn", "decimallongitude"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestAquaMapsJobs.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestAquaMapsJobs.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestAquaMapsJobs.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestAquaMapsJobs.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnym1_0_0.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnym1_0_0.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnym1_0_0.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnym1_0_0.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymEvaluation.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymEvaluation.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymEvaluation.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymEvaluation.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java similarity index 91% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java index 4fdb614..1da8bee 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocal.java @@ -1,15 +1,11 @@ package org.gcube.dataanalysis.executor.tests; -import java.io.File; import java.util.List; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters; @@ -67,7 +63,7 @@ public class TestBiOnymLocal { List types = transducer.getInputParameters(); // System.out.println(types); - Regressor.process(transducer); + CustomRegressor.process(transducer); } } diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java similarity index 87% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java index da2141a..043a680 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestBiOnymLocalFastVersion.java @@ -1,15 +1,11 @@ package org.gcube.dataanalysis.executor.tests; -import java.io.File; import java.util.List; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymLocalTransducer; import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters; @@ -48,7 +44,7 @@ public class TestBiOnymLocalFastVersion { List types = transducer.getInputParameters(); - Regressor.process(transducer); + CustomRegressor.process(transducer); } } diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceMaps.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceMaps.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceMaps.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceMaps.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java similarity index 90% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java index 206baf6..883491f 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_1.java @@ -1,19 +1,14 @@ package org.gcube.dataanalysis.executor.tests; -import java.io.File; - import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.utils.Transformations; import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing; -import org.gcube.dataanalysis.executor.nodes.transducers.OccurrenceMergingNode; public class TestD4ScienceQueueMaps2_1 { public static void main(String[] args) throws Exception { String scope = "/gcube"; - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setConfigPath("./cfg/"); config.setPersistencePath("./"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java similarity index 78% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java index 217cee8..accfe12 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps2_2.java @@ -1,18 +1,6 @@ package org.gcube.dataanalysis.executor.tests; -import java.util.ArrayList; -import java.util.List; - import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType; -import org.gcube.dataanalysis.ecoengine.datatypes.InputTable; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.ServiceType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.ServiceParameters; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; import org.gcube.dataanalysis.executor.generators.D4ScienceDistributedProcessing; public class TestD4ScienceQueueMaps2_2 { @@ -30,7 +18,7 @@ public class TestD4ScienceQueueMaps2_2 { String finalDistributionTable = "hspec_suitable_executorsingle_t3"; // Generate - AlgorithmConfiguration config = Regressor.getConfig(); + AlgorithmConfiguration config = CustomRegressor.getConfig(); config.setParam("DatabaseUserName","utente"); config.setParam("DatabasePassword","d4science"); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps3.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps3.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps3.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMaps3.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMultipleMaps.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMultipleMaps.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMultipleMaps.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestD4ScienceQueueMultipleMaps.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestEmailingSystem.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestEmailingSystem.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestEmailingSystem.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestEmailingSystem.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestGenerator.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestGenerator.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestGenerator.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestGenerator.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestGetRunningExecutor.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestGetRunningExecutor.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestGetRunningExecutor.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestGetRunningExecutor.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java similarity index 92% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java index 0a34198..e0761e0 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestKnitrCompiler.java @@ -8,7 +8,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class TestKnitrCompiler { @@ -35,7 +34,7 @@ public class TestKnitrCompiler { //init the transducerer transducer.init(); //start the process - Regressor.process(transducer); + CustomRegressor.process(transducer); //retrieve the output StatisticalType st = transducer.getOutput(); System.out.println("st:"+((PrimitiveType)st).getContent()); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java similarity index 93% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java index 09de19d..9630385 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestSGVMInterpolation.java @@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class TestSGVMInterpolation { @@ -46,7 +45,7 @@ public class TestSGVMInterpolation { //init the transducerer transducer.init(); //start the process - Regressor.process(transducer); + CustomRegressor.process(transducer); //retrieve the output StatisticalType st = transducer.getOutput(); System.out.println("st:"+((PrimitiveType)st).getContent()); diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestWPSJobs.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestWPSJobs.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestWPSJobs.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestWPSJobs.java diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java similarity index 92% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java index d01d177..b733a09 100644 --- a/src/main/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java +++ b/src/test/java/org/gcube/dataanalysis/executor/tests/TestWebAppPublisher.java @@ -7,7 +7,6 @@ import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; public class TestWebAppPublisher { @@ -35,7 +34,7 @@ public class TestWebAppPublisher { List trans = null; trans = TransducerersFactory.getTransducerers(config); trans.get(0).init(); - Regressor.process(trans.get(0)); + CustomRegressor.process(trans.get(0)); StatisticalType st = trans.get(0).getOutput(); AnalysisLogger.getLogger().debug("ST:" + st); trans = null; diff --git a/src/main/java/org/gcube/dataanalysis/executor/tests/TestsMetaInfo.java b/src/test/java/org/gcube/dataanalysis/executor/tests/TestsMetaInfo.java similarity index 100% rename from src/main/java/org/gcube/dataanalysis/executor/tests/TestsMetaInfo.java rename to src/test/java/org/gcube/dataanalysis/executor/tests/TestsMetaInfo.java diff --git a/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar b/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar deleted file mode 100644 index d1c8e13..0000000 Binary files a/target/ecological-engine-smart-executor-1.0.0-SNAPSHOT.jar and /dev/null differ diff --git a/target/maven-archiver/pom.properties b/target/maven-archiver/pom.properties deleted file mode 100644 index 80368a5..0000000 --- a/target/maven-archiver/pom.properties +++ /dev/null @@ -1,5 +0,0 @@ -#Generated by Maven -#Wed Jun 24 16:37:14 CEST 2015 -version=1.1.0-SNAPSHOT -groupId=org.gcube.dataanalysis -artifactId=ecological-engine-smart-executor diff --git a/target/profile.xml b/target/profile.xml deleted file mode 100644 index 70a5f7d..0000000 --- a/target/profile.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - Library - - Ecological Engine Executor Library - EcologicalEngineExecutor - ecological-engine-smart-executor - 1.0.0 - - - ecological-engine-smart-executor - 1.1.0-SNAPSHOT - - org.gcube.dataanalysis - ecological-engine-smart-executor - 1.1.0-SNAPSHOT - - - ecological-engine-smart-executor-1.1.0-SNAPSHOT.jar - - - - - \ No newline at end of file