548 lines
22 KiB
Java
548 lines
22 KiB
Java
package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace;
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import java.io.BufferedInputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.InputStream;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.net.URLConnection;
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import java.util.ArrayList;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import org.gcube.common.homelibrary.home.Home;
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import org.gcube.common.homelibrary.home.HomeLibrary;
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import org.gcube.common.homelibrary.home.HomeManager;
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import org.gcube.common.homelibrary.home.HomeManagerFactory;
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import org.gcube.common.homelibrary.home.User;
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import org.gcube.common.homelibrary.home.workspace.Workspace;
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import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
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import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
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import org.gcube.common.homelibrary.home.workspace.folder.FolderItem;
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import org.gcube.common.homelibrary.util.WorkspaceUtil;
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import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper;
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import org.n52.wps.commons.WPSConfig;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class DataspaceManager implements Runnable {
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private static final Logger LOGGER = LoggerFactory.getLogger(DataspaceManager.class);
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public static String dataminerFolder = "DataMiner";
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public static String importedDataFolder = "Input Data Sets";
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public static String computedDataFolder = "Output Data Sets";
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public static String computationsFolder = "Computations";
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AlgorithmConfiguration config;
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ComputationData computation;
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List<StoredData> inputData;
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List<StoredData> outputData;
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List<File> generatedFiles;
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public static String computation_id = "computation_id";
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public static String hostname = "hostname";
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public static String data_id = "data_id";
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public static String data_type = "data_type";
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public static String operator_name = "operator_name";
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public static String operator_id = "operator_id";
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public static String vre = "VRE";
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public static String operator_description = "operator_description";
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public static String data_description = "data_description";
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public static String creation_date = "creation_date";
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public static String start_date = "start_date";
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public static String end_date = "end_date";
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public static String status = "status";
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public static String execution_platform = "execution_platform";
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public static String error = "error";
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public static String IO = "IO";
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public static String operator = "operator_name";
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public static String payload = "payload";
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public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, List<File> generatedFiles) {
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this.config = config;
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this.computation = computation;
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this.inputData = inputData;
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this.outputData = outputData;
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this.generatedFiles = generatedFiles;
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}
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public void run() {
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try {
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LOGGER.debug("Dataspace->Deleting running computation");
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try {
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deleteRunningComputationData();
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} catch (Exception e) {
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LOGGER.debug("Dataspace->No running computation available");
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}
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LOGGER.debug("Dataspace->Writing provenance information");
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writeProvenance(computation, inputData, outputData);
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} catch (Exception e) {
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LOGGER.error("Dataspace-> error writing provenance information ", e);
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}
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}
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public void createFoldersNetwork(Workspace ws, WorkspaceFolder root) throws Exception {
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LOGGER.debug("Dataspace->Creating folders for DataMiner");
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// manage folders: create the folders network
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if (!ws.exists(dataminerFolder, root.getId())) {
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LOGGER.debug("Dataspace->Creating DataMiner main folder");
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root.createFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
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((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
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}
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WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
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if (!ws.exists(importedDataFolder, dataminerFolderWS.getId())) {
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LOGGER.debug("Dataspace->Creating DataMiner imported data folder");
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dataminerFolderWS.createFolder(importedDataFolder, "A folder collecting DataMiner imported data");
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}
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if (!ws.exists(computedDataFolder, dataminerFolderWS.getId())) {
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LOGGER.debug("Dataspace->Creating DataMiner computed data folder");
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dataminerFolderWS.createFolder(computedDataFolder, "A folder collecting DataMiner computed data");
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}
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if (!ws.exists(computationsFolder, dataminerFolderWS.getId())) {
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LOGGER.debug("Dataspace->Creating DataMiner computations folder");
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dataminerFolderWS.createFolder(computationsFolder, "A folder collecting DataMiner computations information");
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}
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}
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public String uploadData(StoredData data, WorkspaceFolder wsFolder) throws Exception {
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return uploadData(data, wsFolder, true);
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}
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public String uploadData(StoredData data, WorkspaceFolder wsFolder, boolean changename) throws Exception {
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LOGGER.debug("Dataspace->Analysing " + data);
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// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder);
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String filenameonwsString = data.name ;
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if (changename)
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filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload, data.type));
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InputStream in = null;
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String url = "";
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try {
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long size = 0;
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if (data.type.equals("text/csv")||data.type.equals("application/d4science")||data.type.equals("image/png")) {
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if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
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LOGGER.debug("Dataspace->Uploading file " + data.payload);
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in = new FileInputStream(new File(data.payload));
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size = new File(data.payload).length();
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} else {
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LOGGER.debug("Dataspace->Uploading via URL " + data.payload);
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int tries = 10;
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for (int i=0;i<tries;i++){
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try {
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URL urlc = new URL(data.payload);
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HttpURLConnection urlConnection = (HttpURLConnection) urlc.openConnection();
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urlConnection.setConnectTimeout(10000);
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urlConnection.setReadTimeout(10000);
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in = new BufferedInputStream(urlConnection.getInputStream());
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}catch(Exception ee){
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LOGGER.warn("Dataspace->Retrying connection to {} number {} ",data.payload,(i+1),ee);
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in =null;
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}
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if (in!=null)
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break;
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else
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Thread.sleep(10000);
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}
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}
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if (in==null)
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throw new Exception("Impossible to open stream from "+data.payload);
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// LOGGER.debug("Dataspace->final file name on ws " + data.name+" description "+data.description);
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LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
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LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
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properties.put(computation_id, data.computationId);
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properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
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properties.put(vre, data.vre);
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properties.put(creation_date, data.creationDate);
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properties.put(operator, data.operator);
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properties.put(data_id, data.id);
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properties.put(data_description, data.description);
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properties.put(IO, data.provenance.name());
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properties.put(data_type, data.type);
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properties.put(payload, url);
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FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size);
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//fileItem.getProperties().addProperties(properties);
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LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
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url = fileItem.getPublicLink(false);
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LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
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data.payload = url;
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try {
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in.close();
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} catch (Exception e) {
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LOGGER.debug("Dataspace->Error creating file " + e.getMessage());
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//LOGGER.debug(e);
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}
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LOGGER.debug("Dataspace->File created " + filenameonwsString);
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} else {
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LOGGER.debug("Dataspace->String parameter " + data.payload);
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url = data.payload;
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}
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} catch (Throwable e) {
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LOGGER.error("Dataspace->Could not retrieve input payload {} ",data.payload,e);
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//LOGGER.debug(e);
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url = "payload was not made available for this dataset";
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data.payload = url;
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}
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return url;
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}
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public List<String> uploadInputData(List<StoredData> inputData, WorkspaceFolder dataminerFolder) throws Exception {
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LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size());
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WorkspaceItem folderItem = dataminerFolder.find(importedDataFolder);
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List<String> urls = new ArrayList<String>();
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if (folderItem != null && folderItem.isFolder()) {
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WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
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for (StoredData input : inputData) {
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WorkspaceItem item = null;
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if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png"))
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item = destinationFolder.find(input.name);
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if (item==null){
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String url = uploadData(input, destinationFolder,false);
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LOGGER.debug("Dataspace->returning property "+url);
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urls.add(url);
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}
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else{
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LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder");
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String url = item.getPublicLink(false);
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LOGGER.debug("Dataspace->returning WS url "+url);
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urls.add(url);
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}
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}
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} else
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LOGGER.debug("Dataspace->folder is not valid");
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LOGGER.debug("Dataspace->finished uploading input data");
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return urls;
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}
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public List<String> uploadOutputData(List<StoredData> outputData, WorkspaceFolder dataminerFolder) throws Exception {
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LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size());
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WorkspaceItem folderItem = dataminerFolder.find(computedDataFolder);
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List<String> urls = new ArrayList<String>();
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if (folderItem != null && folderItem.isFolder()) {
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WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
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for (StoredData output : outputData) {
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String url = uploadData(output, destinationFolder);
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urls.add(url);
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}
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} else
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LOGGER.debug("Dataspace->folder is not valid");
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LOGGER.debug("Dataspace->finished uploading output data");
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return urls;
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}
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public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, WorkspaceFolder dataminerFolder, Workspace ws) throws Exception {
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LOGGER.debug("Dataspace->uploading computation data");
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WorkspaceItem folderItem = dataminerFolder.find(computationsFolder);
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if (folderItem != null && folderItem.isFolder()) {
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// create a folder in here
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LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
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WorkspaceFolder cfolder = ((WorkspaceFolder) folderItem);
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String cfoldername = computation.id;
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WorkspaceFolder newcomputationFolder = null;
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try{
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newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
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}catch(java.lang.ClassCastException e){
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LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
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deleteRunningComputationData();
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newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
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}
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//String itemType = "COMPUTATION";
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// create IO folders
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LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
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newcomputationFolder.createFolder(importedDataFolder, importedDataFolder);
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newcomputationFolder.createFolder(computedDataFolder, computedDataFolder);
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// copy IO in those folders
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LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
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List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
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LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
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List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
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LOGGER.debug("Dataspace->*****adding properties to the folder*****");
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LOGGER.debug("Dataspace->creating Folder Properties");
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// write a computation item for the computation
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LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
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properties.put(computation_id, computation.id);
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properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
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properties.put(vre, computation.vre);
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properties.put(operator_name, config.getAgent());
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properties.put(operator_id, computation.operatorId);
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properties.put(operator_description, computation.operatorDescription);
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properties.put(start_date, computation.startDate);
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properties.put(end_date, computation.endDate);
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properties.put(status, getStatus(computation.status));
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properties.put(execution_platform, computation.infrastructure);
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int ninput = inputurls.size();
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int noutput = outputurls.size();
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LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
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for (int i = 1; i <= ninput; i++) {
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StoredData input = inputData.get(i - 1);
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if (input.payload.contains("|")){
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String payload = input .payload;
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LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload);
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//delete the names that are not useful
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for (StoredData subinput:inputData){
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if (input.description.equals(subinput.description)){
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payload = payload.replace(subinput.name,subinput.payload);
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subinput.name=null;
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}
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}
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input.name = null;
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//delete last pipe character
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if (payload.endsWith("|"))
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payload = payload.substring(0,payload.length()-1);
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LOGGER.debug("Dataspace->Complex input after processing "+payload);
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properties.put("input" + i + "_" + input.description, payload);
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input.payload=payload;
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}
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}
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for (int i = 1; i <= ninput; i++) {
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StoredData input = inputData.get(i - 1);
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if (input.name!=null){
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properties.put("input" + i + "_" + input.name, inputurls.get(i - 1));
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}
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}
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LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
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for (int i = 1; i <= noutput; i++) {
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properties.put("output" + i + "_" + outputData.get(i - 1).name, outputurls.get(i - 1));
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}
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LOGGER.debug("Dataspace->Properties of the folder: " + properties);
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LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs");
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/*
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* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
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*/
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try {
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String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
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File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
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FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
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InputStream sis = new FileInputStream(xmltosave);
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WorkspaceUtil.createExternalFile(newcomputationFolder, computation.id + ".xml", computation.operatorDescription, sis,null,"text/xml",xmltosave.length());
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sis.close();
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xmltosave.delete();
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} catch (Exception e) {
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LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
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}
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//List<String> scopes = new ArrayList<String>();
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//scopes.add(config.getGcubeScope());
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//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
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newcomputationFolder.getProperties().addProperties(properties);
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}
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LOGGER.debug("Dataspace->finished uploading computation data");
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}
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public String buildCompositePayload(List<StoredData> inputData,String payload, String inputName){
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for (StoredData input:inputData){
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if (inputName.equals(input.description)){
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payload = payload.replace(input.name,input.payload);
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}
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}
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return payload;
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}
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public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception {
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LOGGER.debug("Dataspace->connecting to Workspace");
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HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
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HomeManager manager = factory.getHomeManager();
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LOGGER.debug("Dataspace->getting user");
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User user = manager.createUser(computation.user);
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Home home = manager.getHome(user);
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LOGGER.debug("Dataspace->getting root folder");
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Workspace ws = home.getWorkspace();
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WorkspaceFolder root = ws.getRoot();
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LOGGER.debug("Dataspace->create folders network");
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createFoldersNetwork(ws, root);
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WorkspaceFolder dataminerItem = (WorkspaceFolder) root.find(dataminerFolder);
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LOGGER.debug("Dataspace->****uploading input files****");
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uploadInputData(inputData, dataminerItem);
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LOGGER.debug("Dataspace->****uploading output files****");
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uploadOutputData(outputData, dataminerItem);
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LOGGER.debug("Dataspace->****uploading computation files****");
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uploadComputationData(computation, inputData, outputData, dataminerItem, ws);
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LOGGER.debug("Dataspace->provenance management finished");
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LOGGER.debug("Dataspace->deleting generated files");
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AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles);
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LOGGER.debug("Dataspace->generated files deleted");
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}
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public void writeRunningComputationData() throws Exception {
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try {
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deleteRunningComputationData();
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} catch (Exception e) {
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LOGGER.debug("Dataspace->impossible to delete running computation : {} ",e.getMessage());
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}
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// LOGGER.debug("Dataspace->updating computation status");
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// LOGGER.debug("Dataspace->connecting to Workspace");
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HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
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HomeManager manager = factory.getHomeManager();
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// LOGGER.debug("Dataspace->getting user");
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User user = manager.createUser(computation.user);
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Home home = manager.getHome(user);
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// LOGGER.debug("Dataspace->getting root folder");
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Workspace ws = home.getWorkspace();
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WorkspaceFolder root = ws.getRoot();
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// LOGGER.debug("Dataspace->create folders network");
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createFoldersNetwork(ws, root);
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WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
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WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
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// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status);
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String itemType = "COMPUTATION";
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// write a computation item for the computation
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LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
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properties.put(computation_id, computation.id);
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properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
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properties.put(vre, computation.vre);
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properties.put(operator_name, config.getAgent());
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properties.put(operator_description, computation.operatorDescription);
|
|
properties.put(operator_id, computation.operatorId);
|
|
properties.put(start_date, computation.startDate);
|
|
properties.put(end_date, computation.endDate);
|
|
properties.put(status, getStatus(computation.status));
|
|
properties.put(execution_platform, computation.infrastructure);
|
|
if (computation.exception != null && computation.exception.length() > 0)
|
|
properties.put(error, computation.exception);
|
|
|
|
List<String> scopes = new ArrayList<String>();
|
|
scopes.add(config.getGcubeScope());
|
|
ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, computationsFolderItem.getId());
|
|
|
|
LOGGER.debug("Dataspace->finished uploading computation data");
|
|
}
|
|
|
|
public String getStatus(String status){
|
|
double statusD = 0;
|
|
try{
|
|
statusD = Double.parseDouble(status);
|
|
}catch(Exception e){
|
|
return status;
|
|
}
|
|
|
|
if (statusD==100)
|
|
return "completed";
|
|
else if (statusD==-2)
|
|
return "error";
|
|
else if (statusD==-1)
|
|
return "cancelled";
|
|
else
|
|
return status;
|
|
}
|
|
|
|
public void deleteRunningComputationData() throws Exception {
|
|
|
|
LOGGER.debug("Dataspace->deleting computation item");
|
|
LOGGER.debug("Dataspace->connecting to Workspace");
|
|
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
|
|
HomeManager manager = factory.getHomeManager();
|
|
LOGGER.debug("Dataspace->getting user");
|
|
User user = manager.createUser(computation.user);
|
|
Home home = manager.getHome(user);
|
|
LOGGER.debug("Dataspace->getting root folder");
|
|
Workspace ws = home.getWorkspace();
|
|
WorkspaceFolder root = ws.getRoot();
|
|
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
|
|
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
|
|
LOGGER.debug("Dataspace->removing computation data");
|
|
WorkspaceFolder computationsFolderWs = ((WorkspaceFolder) computationsFolderItem);
|
|
WorkspaceItem wi = computationsFolderWs.find(computation.id);
|
|
if (wi!=null){
|
|
LOGGER.debug("Dataspace->Found "+computation.id+" under "+computationsFolderWs.getName()+" - removing");
|
|
wi.remove();
|
|
}
|
|
else
|
|
LOGGER.debug("Dataspace->Warning Could not find "+computation.id+" under "+computationsFolderWs.getName());
|
|
|
|
int maxtries = 3;
|
|
int i =1;
|
|
while (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
|
|
LOGGER.debug("Dataspace->computation data still exist... retrying "+i);
|
|
Thread.sleep(1000);
|
|
computationsFolderWs.find(computation.id).remove();
|
|
i++;
|
|
}
|
|
|
|
LOGGER.debug("Dataspace->finished removing computation data - success "+!ws.exists(computation.id,computationsFolderWs.getId()));
|
|
}
|
|
|
|
public static String getExtension(String payload, String type){
|
|
String extension = "";
|
|
if (type.toLowerCase().equals("text/plain")){}
|
|
else if (payload.toLowerCase().startsWith("http")){
|
|
try {
|
|
URL obj= new URL(payload);
|
|
URLConnection conn = obj.openConnection();
|
|
// get all headers
|
|
Map<String, List<String>> map = conn.getHeaderFields();
|
|
for (Map.Entry<String, List<String>> entry : map.entrySet()) {
|
|
String value = entry.getValue().toString();
|
|
if (value.toLowerCase().contains("filename=")){
|
|
System.out.println("DataSpace->Searching in http header: found "+value);
|
|
extension = value.substring(value.lastIndexOf("."),value.lastIndexOf("\""));
|
|
}
|
|
}
|
|
conn.getInputStream().close();
|
|
} catch (Exception e) {
|
|
System.out.println("DataSpace->Error in the payload http link "+e.getMessage());
|
|
}
|
|
}
|
|
else {
|
|
File paylFile = new File(payload);
|
|
if (paylFile.exists()){
|
|
String paylname = paylFile.getName();
|
|
extension = paylname.substring(paylname.lastIndexOf("."));
|
|
}
|
|
}
|
|
return extension;
|
|
}
|
|
|
|
}
|