Aligned Trunk to Branch
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@174213 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
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@ -388,7 +388,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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time("Ecological Engine Algorithm selection");
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// adding service parameters to the configuration
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LOGGER.info("5 - Adding Service parameters to the configuration");
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inputsManager.addInputServiceParameters(getInputParameters(algorithm), infrastructureDialoguer);
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List<StatisticalType> dataminerInputParameters = getInputParameters(algorithm);
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LOGGER.debug("Dataminer Algo Default InputParameters: "+dataminerInputParameters);
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inputsManager.addInputServiceParameters(dataminerInputParameters, infrastructureDialoguer);
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time("Service parameters added to the algorithm");
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// merging wps with ecological engine parameters - modifies the
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// config
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@ -396,7 +398,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
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// build computation Data
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currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
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inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo);
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inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
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generatedInputTables = inputsManager.getGeneratedTables();
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generatedFiles = inputsManager.getGeneratedInputFiles();
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time("Setup and download of input parameters with tables creation");
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@ -447,13 +449,13 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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time("Output preparation for WPS document (no storage manager)");
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outputmanager.shutdown();
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// delete all temporary tables
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LOGGER.info("12 - Deleting possible generated temporary tables");
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LOGGER.debug("Final Computation Output: " + outputs);
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LOGGER.debug("12 - Final Computation Output");
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LOGGER.debug("Outputs: "+ outputs);
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endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
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if (!isCancelled()) {
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LOGGER.debug("Save Computation Data");
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saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
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} else {
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LOGGER.debug("Computation interrupted - no update");
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@ -542,8 +544,13 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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}
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private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent, List<File> generatedFiles) {
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LOGGER.debug("Save Computation On WS");
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LOGGER.debug("InputData: "+inputData);
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LOGGER.debug("OutputData: "+outputData);
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LOGGER.debug("Agent: "+agent);
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LOGGER.debug("Generated files: "+generatedFiles);
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LOGGER.debug("Provenance manager started for operator " + this.getClass().getCanonicalName());
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ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());
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// post on WS
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DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
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@ -41,7 +41,7 @@ import org.slf4j.LoggerFactory;
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public class InputsManager {
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private static final Logger LOGGER = LoggerFactory.getLogger(InputsManager.class);
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private static final Logger LOGGER = LoggerFactory.getLogger(InputsManager.class);
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LinkedHashMap<String, Object> inputs;
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List<String> generatedTables;
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@ -51,11 +51,11 @@ public class InputsManager {
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String computationId;
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List<StoredData> provenanceData = new ArrayList<StoredData>();
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public List<StoredData> getProvenanceData() {
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return provenanceData;
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}
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public static String inputsSeparator = "\\|";
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public AlgorithmConfiguration getConfig() {
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@ -92,30 +92,35 @@ public class InputsManager {
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config.setParam("DatabaseURL", supportDatabaseInfo.url);
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}
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public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo) throws Exception {
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public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo,
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List<StatisticalType> dataminerInputParameters) throws Exception {
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LOGGER.debug("Merge WPS And Ecological Inputs");
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// browse input parameters from WPS
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for (String inputName : inputs.keySet()) {
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Object input = inputs.get(inputName);
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LOGGER.debug("Managing Input Parameter with Name "+ inputName);
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LOGGER.debug("Managing Input Parameter with Name " + inputName);
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// case of simple input
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if (input instanceof String) {
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LOGGER.debug("Simple Input: "+ input);
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LOGGER.debug("Simple Input: " + input);
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// manage lists
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String inputAlgoOrig = ((String) input).trim();
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String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator, AlgorithmConfiguration.listSeparator);
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String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator,
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AlgorithmConfiguration.listSeparator);
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LOGGER.debug("Simple Input Transformed: " + inputAlgo);
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config.setParam(inputName, inputAlgo);
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saveInputData(inputName,inputName,inputAlgoOrig);
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saveInputData(inputName, inputName, inputAlgoOrig);
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}
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// case of Complex Input
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else if (input instanceof GenericFileData) {
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LOGGER.debug("Complex Input: " + input);
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LOGGER.debug("Complex Input");
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// retrieve payload
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GenericFileData files = ((GenericFileData) input);
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LOGGER.debug("GenericFileData: [fileExtension=" + files.getFileExtension() + ", mimeType="
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+ files.getMimeType() + "]");
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List<File> localfiles = getLocalFiles(files,inputName);
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List<File> localfiles = getLocalFiles(files, inputName, dataminerInputParameters);
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String inputtables = "";
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int nfiles = localfiles.size();
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StringBuffer sb = new StringBuffer();
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@ -128,10 +133,11 @@ public class InputsManager {
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if (inputTableTemplates.get(inputName) != null) {
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LOGGER.debug("Creating table: " + tableName);
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createTable(tableName, tableFile, config, supportDatabaseInfo, inputTableTemplates.get(inputName));
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createTable(tableName, tableFile, config, supportDatabaseInfo,
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inputTableTemplates.get(inputName));
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generatedTables.add(tableName);
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}
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//case of non-table input file, e.g. FFANN
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// case of non-table input file, e.g. FFANN
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else
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tableName = tableFile.getAbsolutePath();
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if (i > 0)
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@ -140,13 +146,13 @@ public class InputsManager {
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inputtables += tableName;
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saveInputData(tableFile.getName(), inputName, tableFile.getAbsolutePath());
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if (i>0)
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if (i > 0)
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sb.append("|");
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sb.append(tableFile.getName());
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}
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sb.append("|");
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if (nfiles>0)
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if (nfiles > 0)
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saveInputData(inputName, inputName, sb.toString());
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// the only possible complex input is a table - check the WPS
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@ -157,15 +163,15 @@ public class InputsManager {
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}
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public boolean isXML(String fileContent){
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public boolean isXML(String fileContent) {
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if (fileContent.startsWith("<"))
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return true;
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else
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else
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return false;
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}
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public String readOneLine(String filename){
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public String readOneLine(String filename) {
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try {
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BufferedReader in = new BufferedReader(new FileReader(new File(filename)));
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@ -173,7 +179,7 @@ public class InputsManager {
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String vud = "";
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while ((line = in.readLine()) != null) {
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if (line.trim().length()>0){
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if (line.trim().length() > 0) {
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vud = line.trim();
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break;
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}
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@ -183,47 +189,54 @@ public class InputsManager {
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} catch (Exception e) {
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e.printStackTrace();
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return null;
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}
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}
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}
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public String inputNameFromHttpHeader(String url) throws Exception{
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public String inputNameFromHttpHeader(String url) throws Exception {
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LOGGER.debug("Search filename in http header from: " + url);
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URL obj = new URL(url);
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URLConnection conn = obj.openConnection();
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String filename=null;
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String filename = null;
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// get all headers
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Map<String, List<String>> map = conn.getHeaderFields();
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LOGGER.debug("Getting file name from http header");
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for (Map.Entry<String, List<String>> entry : map.entrySet()) {
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String value = entry.getValue().toString();
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if (value.toLowerCase().contains("filename=")){
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LOGGER.debug("Searching in http header: found file name in header value {}",value);
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filename=value.substring(value.indexOf("=")+1);
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filename=filename.replace("\"", "").replace("]", "");
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LOGGER.debug("Searching in http header: retrieved file name {}",filename);
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LOGGER.debug("Header value: " + value);
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if (value.toLowerCase().contains("filename")) {
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LOGGER.debug("Searching in http header: found file name in header value {}", value);
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filename = value.substring(value.indexOf("=") + 1);
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filename = filename.replace("\"", "").replace("]", "");
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LOGGER.debug("Searching in http header: retrieved file name {}", filename);
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break;
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}
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}
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LOGGER.debug("Filename retrieved from http header: " + filename);
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return filename;
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}
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public List<File> getLocalFiles(GenericFileData files,String inputName) throws Exception {
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public List<File> getLocalFiles(GenericFileData files, String inputName,
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List<StatisticalType> dataminerInputParameters) throws Exception {
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LOGGER.debug("GetLocalFiles: [files: " + files + ", inputName: " + inputName + "]");
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// download input
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List<File> filesList = new ArrayList<File>();
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File f = files.getBaseFile(false);
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LOGGER.debug("Retrieving file content as a URL link: " + f.getAbsolutePath());
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//TODO DO NOT READ FILE INTO MEMORY
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LOGGER.debug("Retrieving local files: " + f.getAbsolutePath());
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// TODO DO NOT READ FILE INTO MEMORY
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// read file content
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String fileLink = readOneLine(f.getAbsolutePath());
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LOGGER.debug("File link: {} ...",fileLink.substring(0,Math.min(fileLink.length(),10)));
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LOGGER.debug("Check File is link: {} ...", fileLink.substring(0, Math.min(fileLink.length(), 10)));
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String fileName = "";
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// case of a http link
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if (fileLink!=null && (fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:"))) {
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if (fileLink != null
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&& (fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:"))) {
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// manage the case of multiple files
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LOGGER.debug("Complex Input payload is link");
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LOGGER.debug("Retrieving files from url: " + fileLink);
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String[] remotefiles = fileLink.split(inputsSeparator);
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for (String subfilelink : remotefiles) {
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subfilelink = subfilelink.trim();
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LOGGER.debug("Managing link: {}",subfilelink);
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LOGGER.debug("Managing link: {}", subfilelink);
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if (subfilelink.length() == 0)
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continue;
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InputStream is = null;
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@ -234,15 +247,18 @@ public class InputsManager {
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// retrieve payload: for test purpose only
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String fileNameTemp = inputNameFromHttpHeader(subfilelink);
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LOGGER.debug("the fileNameTemp is {}",fileNameTemp);
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if (fileNameTemp==null)
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fileName = String.format("%s_(%s).%s",inputName, computationId, FilenameUtils.getExtension(inputName));
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else
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fileName = String.format("%s_(%s).%s",fileNameTemp, computationId, FilenameUtils.getExtension(fileNameTemp));
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LOGGER.debug("the name of the generated file is {}",fileName);
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LOGGER.debug("the fileNameTemp is {}", fileNameTemp);
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if (fileNameTemp != null && !fileNameTemp.isEmpty()) {
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fileName = String.format("%s_(%s).%s", inputName, computationId,
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FilenameUtils.getExtension(fileNameTemp));
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} else {
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fileName = String.format("%s_(%s).%s", inputName, computationId,
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FilenameUtils.getExtension(inputName));
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}
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LOGGER.debug("the name of the generated file is {}", fileName);
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File of = new File(config.getPersistencePath(), fileName);
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FileOutputStream fos = new FileOutputStream(of);
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IOUtils.copy(is, fos);
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@ -254,35 +270,54 @@ public class InputsManager {
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LOGGER.debug("Created local file: {}", of.getAbsolutePath());
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}
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} else {
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LOGGER.debug("Complex Input payload is the filelink");
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LOGGER.debug("Complex Input payload is file");
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fileName = f.getName();
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LOGGER.debug("Retriving local input from file: {}", fileName);
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String fileExt=null;
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if (isXML(fileLink))
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{
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LOGGER.debug("Retrieving local input from file: {}", fileName);
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String fileExt = null;
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if (isXML(fileLink)) {
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String xmlFile = f.getAbsolutePath();
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String csvFile = xmlFile+".csv";
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LOGGER.debug("Transforming XML file into a csv: {} ",csvFile);
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String csvFile = xmlFile + ".csv";
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LOGGER.debug("Transforming XML file into a csv: {} ", csvFile);
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GML2CSV.parseGML(xmlFile, csvFile);
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LOGGER.debug("GML Parsed: {} [..]",readOneLine(csvFile));
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LOGGER.debug("GML Parsed: {} [..]", readOneLine(csvFile));
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f = new File(csvFile);
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fileExt = "csv";
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}
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else{
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LOGGER.debug("The file is a csv: {}",f.getAbsolutePath());
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} else {
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LOGGER.debug("The file is a csv: {}", f.getAbsolutePath());
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fileExt = FilenameUtils.getExtension(fileName);
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}
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String absFile = new File(f.getParent(), String.format("%s_(%s).%s",inputName,computationId, fileExt)).getAbsolutePath();
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LOGGER.debug("Renaming to: "+absFile);
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LOGGER.debug("Retrieve default extension");
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String fileDefaultValue = null;
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for (StatisticalType defaultInputParameter : dataminerInputParameters) {
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if (defaultInputParameter.getName().compareTo(inputName) == 0) {
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fileDefaultValue = defaultInputParameter.getDefaultValue();
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break;
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}
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}
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LOGGER.debug("Parameter default value retrieved: " + fileDefaultValue);
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if (fileDefaultValue != null && !fileDefaultValue.isEmpty()) {
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int lastPointIndex = fileDefaultValue.lastIndexOf(".");
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if (lastPointIndex > -1 && lastPointIndex < (fileDefaultValue.length() - 1)) {
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fileExt = fileDefaultValue.substring(lastPointIndex + 1);
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LOGGER.debug("Default Extension retrieved: " + fileExt);
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}
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}
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LOGGER.debug("Use extension: " + fileExt);
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String absFile = new File(f.getParent(), String.format("%s_(%s).%s", inputName, computationId, fileExt))
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.getAbsolutePath();
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LOGGER.debug("Renaming to: " + absFile);
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System.gc();
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boolean renamed = f.renameTo(new File(absFile));
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if (renamed)
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f = new File(absFile);
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LOGGER.debug("The file has been renamed as : {} - {}",f.getAbsolutePath(),renamed);
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LOGGER.debug("The file has been renamed as : {} - {}", f.getAbsolutePath(), renamed);
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filesList.add(f);
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}
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@ -290,7 +325,8 @@ public class InputsManager {
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return filesList;
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}
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public void createTable(String tableName, File tableFile, AlgorithmConfiguration config, DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception {
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public void createTable(String tableName, File tableFile, AlgorithmConfiguration config,
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DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception {
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// creating table
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LOGGER.debug("Complex Input size after download: " + tableFile.length());
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@ -316,11 +352,13 @@ public class InputsManager {
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TableTemplatesMapper mapper = new TableTemplatesMapper();
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String createstatement = mapper.generateCreateStatement(tableName, templatename, tableStructure);
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LOGGER.debug("Creating table: " + tableName);
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DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
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DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
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DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username,
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supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
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DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true,
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supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
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} catch (Exception e) {
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LOGGER.error("Error in database transaction " ,e);
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LOGGER.error("Error in database transaction ", e);
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throw new Exception("Error in creating the table for " + tableName + ": " + e.getLocalizedMessage());
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} finally {
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DatabaseUtils.closeDBConnection(dbConnection);
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@ -376,7 +414,8 @@ public class InputsManager {
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return structure.toString();
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}
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public void addInputServiceParameters(List<StatisticalType> agentInputs, InfrastructureDialoguer infrastructureDialoguer) throws Exception {
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public void addInputServiceParameters(List<StatisticalType> agentInputs,
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InfrastructureDialoguer infrastructureDialoguer) throws Exception {
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// check and fullfil additional parameters
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DatabaseInfo dbinfo = null;
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@ -384,10 +423,10 @@ public class InputsManager {
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for (StatisticalType type : agentInputs) {
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if (type instanceof PrimitiveType) {
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if (((PrimitiveType) type).getType()==PrimitiveTypes.CONSTANT){
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String constant = ""+((PrimitiveType) type).getDefaultValue();
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if (((PrimitiveType) type).getType() == PrimitiveTypes.CONSTANT) {
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String constant = "" + ((PrimitiveType) type).getDefaultValue();
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config.setParam(type.getName(), constant);
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LOGGER.debug("Constant parameter: "+constant);
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LOGGER.debug("Constant parameter: " + constant);
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}
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}
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if (type instanceof ServiceType) {
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@ -400,10 +439,10 @@ public class InputsManager {
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String value = "";
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if (sp == ServiceParameters.RANDOMSTRING)
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value = "stat" + UUID.randomUUID().toString().replace("-", "");
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else if (sp == ServiceParameters.USERNAME){
|
||||
else if (sp == ServiceParameters.USERNAME) {
|
||||
value = (String) inputs.get(ConfigurationManager.usernameParameter);
|
||||
|
||||
LOGGER.debug("User name used by the client: "+value);
|
||||
LOGGER.debug("User name used by the client: " + value);
|
||||
}
|
||||
LOGGER.debug("ServiceType Adding: (" + name + "," + value + ")");
|
||||
config.setParam(name, value);
|
||||
|
|
@ -444,8 +483,7 @@ public class InputsManager {
|
|||
|
||||
}
|
||||
|
||||
|
||||
private void saveInputData(String name, String description, String payload){
|
||||
private void saveInputData(String name, String description, String payload) {
|
||||
String id = name;
|
||||
DataProvenance provenance = DataProvenance.IMPORTED;
|
||||
String creationDate = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
|
||||
|
|
@ -453,18 +491,17 @@ public class InputsManager {
|
|||
|
||||
String type = "text/plain";
|
||||
|
||||
if (payload != null && (new File (payload).exists())) {
|
||||
if (payload != null && (new File(payload).exists())) {
|
||||
if (payload.toLowerCase().endsWith(".csv") || payload.toLowerCase().endsWith(".txt")) {
|
||||
type = "text/csv";
|
||||
} else
|
||||
type = "application/d4science";
|
||||
}
|
||||
|
||||
StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope());
|
||||
StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,
|
||||
payload, config.getGcubeScope());
|
||||
|
||||
provenanceData.add(data);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -140,7 +140,7 @@ public class OutputsManager {
|
|||
outputs.put(pkey, "");
|
||||
}
|
||||
}
|
||||
|
||||
LOGGER.debug("OutputsManager outputs "+outputs);
|
||||
return outputs;
|
||||
}
|
||||
|
||||
|
|
@ -256,10 +256,7 @@ public class OutputsManager {
|
|||
String mimetype = info.getMimetype();
|
||||
String abstractStr = info.getAbstractStr();
|
||||
|
||||
LOGGER.debug("IOWPS Information: " + "name "+info.getName()+","
|
||||
+"abstr "+info.getAbstractStr()+","
|
||||
+"content "+info.getContent()+","
|
||||
+"def "+info.getDefaultVal()+",");
|
||||
LOGGER.debug("IOWPS Information [name="+info.getName()+", abstr="+info.getAbstractStr()+", content="+info.getContent()+", def="+info.getDefaultVal()+"]");
|
||||
|
||||
if ((abstractStr==null || abstractStr.trim().length()==0) && (payload!= null && payload.trim().length()>0))
|
||||
abstractStr = info.getName();
|
||||
|
|
|
|||
|
|
@ -62,12 +62,15 @@ public class DataspaceManager implements Runnable {
|
|||
public static String operator = "operator_name";
|
||||
public static String payload = "payload";
|
||||
|
||||
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, List<File> generatedFiles) {
|
||||
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
|
||||
List<StoredData> outputData, List<File> generatedFiles) {
|
||||
this.config = config;
|
||||
this.computation = computation;
|
||||
this.inputData = inputData;
|
||||
this.outputData = outputData;
|
||||
this.generatedFiles = generatedFiles;
|
||||
LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
|
||||
+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
|
||||
}
|
||||
|
||||
public void run() {
|
||||
|
|
@ -92,20 +95,23 @@ public class DataspaceManager implements Runnable {
|
|||
|
||||
StorageHubClient shc = new StorageHubClient();
|
||||
|
||||
FolderContainer root =shc.getWSRoot();
|
||||
FolderContainer root = shc.getWSRoot();
|
||||
|
||||
List<ItemContainer<? extends Item>> dataminerItems = root.findByName(dataminerFolder).getContainers();
|
||||
|
||||
FolderContainer dataminerFolderContainer;
|
||||
FolderContainer dataminerFolderContainer;
|
||||
|
||||
// manage folders: create the folders network
|
||||
if (dataminerItems.isEmpty()) {
|
||||
LOGGER.debug("Dataspace->Creating DataMiner main folder");
|
||||
dataminerFolderContainer = root.newFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
|
||||
//((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
|
||||
} else if (dataminerItems.size()>1) throw new Exception("found more than one dataminer folder (impossible!!!)");
|
||||
else dataminerFolderContainer = (FolderContainer) dataminerItems.get(0);
|
||||
|
||||
dataminerFolderContainer = root.newFolder(dataminerFolder,
|
||||
"A folder collecting DataMiner experiments data and computation information");
|
||||
// ((WorkspaceFolder)
|
||||
// root.find(dataminerFolder)).setSystemFolder(true);
|
||||
} else if (dataminerItems.size() > 1)
|
||||
throw new Exception("found more than one dataminer folder (impossible!!!)");
|
||||
else
|
||||
dataminerFolderContainer = (FolderContainer) dataminerItems.get(0);
|
||||
|
||||
if (dataminerFolderContainer.findByName(importedDataFolder).getContainers().isEmpty()) {
|
||||
LOGGER.debug("Dataspace->Creating DataMiner imported data folder");
|
||||
|
|
@ -118,37 +124,41 @@ public class DataspaceManager implements Runnable {
|
|||
}
|
||||
if (dataminerFolderContainer.findByName(computationsFolder).getContainers().isEmpty()) {
|
||||
LOGGER.debug("Dataspace->Creating DataMiner computations folder");
|
||||
dataminerFolderContainer.newFolder(computationsFolder, "A folder collecting DataMiner computations information");
|
||||
dataminerFolderContainer.newFolder(computationsFolder,
|
||||
"A folder collecting DataMiner computations information");
|
||||
}
|
||||
|
||||
return dataminerFolderContainer;
|
||||
}
|
||||
|
||||
public String uploadData(StoredData data, FolderContainer destinationFolder) throws Exception {
|
||||
public String uploadData(StoredData data, FolderContainer destinationFolder) throws Exception {
|
||||
return uploadData(data, destinationFolder, true);
|
||||
}
|
||||
|
||||
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
|
||||
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
|
||||
LOGGER.debug("Dataspace->Analysing " + data);
|
||||
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder);
|
||||
String filenameonwsString = data.name ;
|
||||
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
|
||||
// wsFolder);
|
||||
String filenameonwsString = data.name;
|
||||
if (changename)
|
||||
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload, data.type));
|
||||
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
|
||||
getExtension(data.payload));
|
||||
|
||||
InputStream in = null;
|
||||
String url = "";
|
||||
try {
|
||||
long size = 0;
|
||||
if (data.type.equals("text/csv")||data.type.equals("application/d4science")||data.type.equals("image/png")) {
|
||||
//long size = 0;
|
||||
if (data.type.equals("text/csv") || data.type.equals("application/d4science")
|
||||
|| data.type.equals("image/png")) {
|
||||
|
||||
if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
|
||||
LOGGER.debug("Dataspace->Uploading file {}", data.payload);
|
||||
in = new FileInputStream(new File(data.payload));
|
||||
size = new File(data.payload).length();
|
||||
//size = new File(data.payload).length();
|
||||
} else {
|
||||
LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
|
||||
int tries = 10;
|
||||
for (int i=0;i<tries;i++){
|
||||
for (int i = 0; i < tries; i++) {
|
||||
try {
|
||||
URL urlc = new URL(data.payload);
|
||||
url = urlc.toString();
|
||||
|
|
@ -156,21 +166,22 @@ public class DataspaceManager implements Runnable {
|
|||
urlConnection.setConnectTimeout(10000);
|
||||
urlConnection.setReadTimeout(10000);
|
||||
in = new BufferedInputStream(urlConnection.getInputStream());
|
||||
}catch(Exception ee){
|
||||
LOGGER.warn("Dataspace->Retrying connection to {} number {} ",data.payload,(i+1),ee);
|
||||
in =null;
|
||||
} catch (Exception ee) {
|
||||
LOGGER.warn("Dataspace->Retrying connection to {} number {} ", data.payload, (i + 1), ee);
|
||||
in = null;
|
||||
}
|
||||
if (in!=null)
|
||||
if (in != null)
|
||||
break;
|
||||
else
|
||||
Thread.sleep(10000);
|
||||
}
|
||||
|
||||
}
|
||||
if (in==null)
|
||||
throw new Exception("Impossible to open stream from "+data.payload);
|
||||
if (in == null)
|
||||
throw new Exception("Impossible to open stream from " + data.payload);
|
||||
|
||||
// LOGGER.debug("Dataspace->final file name on ws " + data.name+" description "+data.description);
|
||||
// LOGGER.debug("Dataspace->final file name on ws " +
|
||||
// data.name+" description "+data.description);
|
||||
LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
|
||||
Map<String, Object> properties = new LinkedHashMap<String, Object>();
|
||||
|
||||
|
|
@ -198,7 +209,7 @@ public class DataspaceManager implements Runnable {
|
|||
in.close();
|
||||
} catch (Exception e) {
|
||||
LOGGER.debug("Dataspace->Error creating file {}", e.getMessage());
|
||||
//LOGGER.debug(e);
|
||||
// LOGGER.debug(e);
|
||||
}
|
||||
LOGGER.debug("Dataspace->File created {}", filenameonwsString);
|
||||
} else {
|
||||
|
|
@ -206,8 +217,8 @@ public class DataspaceManager implements Runnable {
|
|||
url = data.payload;
|
||||
}
|
||||
} catch (Throwable e) {
|
||||
LOGGER.error("Dataspace->Could not retrieve input payload {} ",data.payload,e);
|
||||
//LOGGER.debug(e);
|
||||
LOGGER.error("Dataspace->Could not retrieve input payload {} ", data.payload, e);
|
||||
// LOGGER.debug(e);
|
||||
url = "payload was not made available for this dataset";
|
||||
data.payload = url;
|
||||
}
|
||||
|
|
@ -216,24 +227,25 @@ public class DataspaceManager implements Runnable {
|
|||
|
||||
public List<String> uploadInputData(List<StoredData> inputData, FolderContainer dataminerFolder) throws Exception {
|
||||
LOGGER.debug("Dataspace->uploading input data; Number of data: {}", inputData.size());
|
||||
FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder).getContainers().get(0);
|
||||
FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder)
|
||||
.getContainers().get(0);
|
||||
List<String> urls = new ArrayList<String>();
|
||||
for (StoredData input : inputData) {
|
||||
List<ItemContainer<? extends Item>> items = null;
|
||||
|
||||
if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png"))
|
||||
if (input.type.equals("text/csv") || input.type.equals("application/d4science")
|
||||
|| input.type.equals("image/png"))
|
||||
items = destinationFolder.findByName(input.name).getContainers();
|
||||
|
||||
if (items==null || items.isEmpty()){
|
||||
String url = uploadData(input, destinationFolder,false);
|
||||
LOGGER.debug("Dataspace->returning property {}",url);
|
||||
if (items == null || items.isEmpty()) {
|
||||
String url = uploadData(input, destinationFolder, false);
|
||||
LOGGER.debug("Dataspace->returning property {}", url);
|
||||
urls.add(url);
|
||||
}
|
||||
else{
|
||||
} else {
|
||||
FileContainer item = (FileContainer) items.get(0);
|
||||
LOGGER.debug("Dataspace->Input item {} is already available in the input folder",input.name);
|
||||
LOGGER.debug("Dataspace->Input item {} is already available in the input folder", input.name);
|
||||
String url = item.getPublicLink().toString();
|
||||
LOGGER.debug("Dataspace->returning WS url {}",url);
|
||||
LOGGER.debug("Dataspace->returning WS url {}", url);
|
||||
urls.add(url);
|
||||
}
|
||||
}
|
||||
|
|
@ -242,9 +254,11 @@ public class DataspaceManager implements Runnable {
|
|||
return urls;
|
||||
}
|
||||
|
||||
public List<String> uploadOutputData(List<StoredData> outputData,FolderContainer dataminerFolder) throws Exception {
|
||||
public List<String> uploadOutputData(List<StoredData> outputData, FolderContainer dataminerFolder)
|
||||
throws Exception {
|
||||
LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size());
|
||||
FolderContainer destinationFolder = (FolderContainer)dataminerFolder.findByName(computedDataFolder).getContainers().get(0);
|
||||
FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(computedDataFolder)
|
||||
.getContainers().get(0);
|
||||
List<String> urls = new ArrayList<String>();
|
||||
for (StoredData output : outputData) {
|
||||
String url = uploadData(output, destinationFolder);
|
||||
|
|
@ -254,21 +268,23 @@ public class DataspaceManager implements Runnable {
|
|||
return urls;
|
||||
}
|
||||
|
||||
public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, FolderContainer dataminerFolder) throws Exception {
|
||||
public void uploadComputationData(ComputationData computation, List<StoredData> inputData,
|
||||
List<StoredData> outputData, FolderContainer dataminerFolder) throws Exception {
|
||||
LOGGER.debug("Dataspace->uploading computation data");
|
||||
FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder).getContainers().get(0);
|
||||
FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder)
|
||||
.getContainers().get(0);
|
||||
// create a folder in here
|
||||
LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
|
||||
String cfoldername = computation.id;
|
||||
FolderContainer newcomputationFolder = null;
|
||||
try{
|
||||
try {
|
||||
newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
|
||||
}catch(java.lang.ClassCastException e){
|
||||
} catch (java.lang.ClassCastException e) {
|
||||
LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
|
||||
deleteRunningComputationData();
|
||||
newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
|
||||
}
|
||||
//String itemType = "COMPUTATION";
|
||||
// String itemType = "COMPUTATION";
|
||||
|
||||
// create IO folders
|
||||
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
|
||||
|
|
@ -313,86 +329,88 @@ public class DataspaceManager implements Runnable {
|
|||
LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
|
||||
for (int i = 1; i <= ninput; i++) {
|
||||
StoredData input = inputData.get(i - 1);
|
||||
if (input.payload.contains("|")){
|
||||
String payload = input .payload;
|
||||
LOGGER.debug("Dataspace->Managing complex input {} : {}",input.name, payload);
|
||||
//delete the names that are not useful
|
||||
if (input.payload.contains("|")) {
|
||||
String payload = input.payload;
|
||||
LOGGER.debug("Dataspace->Managing complex input {} : {}", input.name, payload);
|
||||
// delete the names that are not useful
|
||||
|
||||
for (StoredData subinput:inputData){
|
||||
if (input.description.equals(subinput.description)){
|
||||
payload = payload.replace(subinput.name,subinput.payload);
|
||||
subinput.name=null;
|
||||
for (StoredData subinput : inputData) {
|
||||
if (input.description.equals(subinput.description)) {
|
||||
payload = payload.replace(subinput.name, subinput.payload);
|
||||
subinput.name = null;
|
||||
}
|
||||
}
|
||||
|
||||
input.name = null;
|
||||
|
||||
//delete last pipe character
|
||||
// delete last pipe character
|
||||
if (payload.endsWith("|"))
|
||||
payload = payload.substring(0,payload.length()-1);
|
||||
LOGGER.debug("Dataspace->Complex input after processing "+payload);
|
||||
payload = payload.substring(0, payload.length() - 1);
|
||||
LOGGER.debug("Dataspace->Complex input after processing " + payload);
|
||||
properties.put("input" + i + "_" + input.description, payload);
|
||||
input.payload=payload;
|
||||
input.payload = payload;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 1; i <= ninput; i++) {
|
||||
StoredData input = inputData.get(i - 1);
|
||||
if (input.name!=null){
|
||||
properties.put(String.format("input%d_%s",i, input.name), inputurls.get(i - 1));
|
||||
if (input.name != null) {
|
||||
properties.put(String.format("input%d_%s", i, input.name), inputurls.get(i - 1));
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
|
||||
for (int i = 1; i <= noutput; i++) {
|
||||
properties.put(String.format("output%d_%s",i,outputData.get(i - 1).name), outputurls.get(i - 1));
|
||||
properties.put(String.format("output%d_%s", i, outputData.get(i - 1).name), outputurls.get(i - 1));
|
||||
|
||||
}
|
||||
|
||||
LOGGER.debug("Dataspace->Properties of the folder: {} ", properties );
|
||||
LOGGER.debug("Dataspace->Properties of the folder: {} ", properties);
|
||||
|
||||
LOGGER.debug("Dataspace->Saving properties to ProvO XML file {} outputs",noutput);
|
||||
LOGGER.debug("Dataspace->Saving properties to ProvO XML file {} outputs", noutput);
|
||||
|
||||
/*
|
||||
* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
|
||||
* XStream xstream = new XStream(); String xmlproperties =
|
||||
* xstream.toXML(properties);
|
||||
*/
|
||||
try {
|
||||
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
|
||||
|
||||
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
|
||||
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
|
||||
try(InputStream sis = new FileInputStream(xmltosave)){
|
||||
newcomputationFolder.uploadFile(sis,computation.id + ".xml", computation.operatorDescription);
|
||||
try (InputStream sis = new FileInputStream(xmltosave)) {
|
||||
newcomputationFolder.uploadFile(sis, computation.id + ".xml", computation.operatorDescription);
|
||||
}
|
||||
xmltosave.delete();
|
||||
} catch (Exception e) {
|
||||
LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
|
||||
LOGGER.error("Dataspace->Failed creating ProvO XML file ", e);
|
||||
}
|
||||
/*
|
||||
List<String> scopes = new ArrayList<String>();
|
||||
scopes.add(config.getGcubeScope());
|
||||
ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
|
||||
* List<String> scopes = new ArrayList<String>();
|
||||
* scopes.add(config.getGcubeScope());
|
||||
* ws.createGcubeItem(computation.id, computation.operatorDescription,
|
||||
* scopes, computation.user, itemType, properties,
|
||||
* newcomputationFolder.getId());
|
||||
*/
|
||||
newcomputationFolder.setMetadata(new Metadata(properties));
|
||||
|
||||
|
||||
LOGGER.debug("Dataspace->finished uploading computation data");
|
||||
}
|
||||
|
||||
public String buildCompositePayload(List<StoredData> inputData,String payload, String inputName){
|
||||
public String buildCompositePayload(List<StoredData> inputData, String payload, String inputName) {
|
||||
|
||||
for (StoredData input:inputData){
|
||||
if (inputName.equals(input.description)){
|
||||
payload = payload.replace(input.name,input.payload);
|
||||
for (StoredData input : inputData) {
|
||||
if (inputName.equals(input.description)) {
|
||||
payload = payload.replace(input.name, input.payload);
|
||||
}
|
||||
}
|
||||
return payload;
|
||||
}
|
||||
|
||||
|
||||
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception {
|
||||
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData)
|
||||
throws Exception {
|
||||
LOGGER.debug("Dataspace->connecting to Workspace");
|
||||
LOGGER.debug("Dataspace->create folders network");
|
||||
FolderContainer dataminerFolder = createFoldersNetwork();
|
||||
|
|
@ -412,19 +430,18 @@ public class DataspaceManager implements Runnable {
|
|||
try {
|
||||
deleteRunningComputationData();
|
||||
} catch (Exception e) {
|
||||
LOGGER.debug("Dataspace->impossible to delete running computation : {} ",e.getMessage());
|
||||
LOGGER.debug("Dataspace->impossible to delete running computation : {} ", e.getMessage());
|
||||
}
|
||||
StorageHubClient shc = new StorageHubClient();
|
||||
|
||||
|
||||
// LOGGER.debug("Dataspace->create folders network");
|
||||
FolderContainer folderContainer = createFoldersNetwork();
|
||||
FolderContainer folderContainer = createFoldersNetwork();
|
||||
|
||||
FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder).getContainers().get(0);
|
||||
// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status);
|
||||
FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder)
|
||||
.getContainers().get(0);
|
||||
// LOGGER.debug("Dataspace->Creating computation item " +
|
||||
// computation.id+" with status"+computation.status);
|
||||
String itemType = "COMPUTATION";
|
||||
|
||||
|
||||
|
||||
// write a computation item for the computation
|
||||
Map<String, Object> properties = new LinkedHashMap<String, Object>();
|
||||
properties.put(computation_id, computation.id);
|
||||
|
|
@ -452,23 +469,22 @@ public class DataspaceManager implements Runnable {
|
|||
|
||||
computationsContainer.newGcubeItem(gcubeItem);
|
||||
|
||||
|
||||
LOGGER.debug("Dataspace->finished uploading computation data");
|
||||
}
|
||||
|
||||
public String getStatus(String status){
|
||||
public String getStatus(String status) {
|
||||
double statusD = 0;
|
||||
try{
|
||||
try {
|
||||
statusD = Double.parseDouble(status);
|
||||
}catch(Exception e){
|
||||
} catch (Exception e) {
|
||||
return status;
|
||||
}
|
||||
|
||||
if (statusD==100)
|
||||
if (statusD == 100)
|
||||
return "completed";
|
||||
else if (statusD==-2)
|
||||
else if (statusD == -2)
|
||||
return "error";
|
||||
else if (statusD==-1)
|
||||
else if (statusD == -1)
|
||||
return "cancelled";
|
||||
else
|
||||
return status;
|
||||
|
|
@ -479,65 +495,69 @@ public class DataspaceManager implements Runnable {
|
|||
LOGGER.debug("Dataspace->deleting computation item");
|
||||
LOGGER.debug("Dataspace->connecting to Workspace");
|
||||
StorageHubClient shc = new StorageHubClient();
|
||||
FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder).getContainers().get(0);
|
||||
FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder).getContainers().get(0);
|
||||
FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder)
|
||||
.getContainers().get(0);
|
||||
FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder)
|
||||
.getContainers().get(0);
|
||||
LOGGER.debug("Dataspace->removing computation data");
|
||||
|
||||
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(computation.id).getContainers();
|
||||
if (wi.isEmpty()){
|
||||
for (ItemContainer<? extends Item> container : wi)
|
||||
if (wi.isEmpty()) {
|
||||
for (ItemContainer<? extends Item> container : wi)
|
||||
container.delete();
|
||||
}
|
||||
else
|
||||
LOGGER.debug("Dataspace->Warning Could not find {} under {}",computation.id, computationContainer.get().getName());
|
||||
} else
|
||||
LOGGER.debug("Dataspace->Warning Could not find {} under {}", computation.id,
|
||||
computationContainer.get().getName());
|
||||
|
||||
List<ItemContainer<? extends Item>> fileComputations = computationContainer.findByName(computation.id)
|
||||
.getContainers();
|
||||
|
||||
List<ItemContainer<? extends Item>> fileComputations = computationContainer.findByName(computation.id).getContainers();
|
||||
|
||||
if (fileComputations.size()>0)
|
||||
if (fileComputations.size() > 0)
|
||||
fileComputations.get(0).delete();
|
||||
|
||||
/*TODO: ASK GIANPAOLO
|
||||
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++;
|
||||
}*/
|
||||
/*
|
||||
* TODO: ASK GIANPAOLO 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 ");
|
||||
}
|
||||
|
||||
public static String getExtension(String payload, String type){
|
||||
String extension = "";
|
||||
if (type.toLowerCase().equals("text/plain")){}
|
||||
else if (payload.toLowerCase().startsWith("http")){
|
||||
// TODO
|
||||
public static String getExtension(String payload) {
|
||||
LOGGER.debug("DataSpace->Get Extension from: " + payload);
|
||||
String extension="";
|
||||
if (payload.toLowerCase().startsWith("http")) {
|
||||
try {
|
||||
URL obj= new URL(payload);
|
||||
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=")){
|
||||
LOGGER.debug("DataSpace->Searching in http header: found "+value);
|
||||
extension = value.substring(value.lastIndexOf("."),value.lastIndexOf("\""));
|
||||
LOGGER.debug("Header value: " + value);
|
||||
if (value.toLowerCase().contains("filename")) {
|
||||
LOGGER.debug("DataSpace->Searching in http header: found " + value);
|
||||
extension = value.substring(value.lastIndexOf("."), value.lastIndexOf("\""));
|
||||
break;
|
||||
}
|
||||
}
|
||||
conn.getInputStream().close();
|
||||
} catch (Exception e) {
|
||||
LOGGER.warn("DataSpace->Error in the payload http link ",e);
|
||||
LOGGER.warn("DataSpace->Error in the payload http link ", e);
|
||||
}
|
||||
}
|
||||
else {
|
||||
} else {
|
||||
File paylFile = new File(payload);
|
||||
if (paylFile.exists()){
|
||||
if (paylFile.exists()) {
|
||||
String paylname = paylFile.getName();
|
||||
extension = paylname.substring(paylname.lastIndexOf("."));
|
||||
}
|
||||
}
|
||||
LOGGER.debug("DataSpace->Extension retrieved: " + extension);
|
||||
return extension;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@ package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.datasp
|
|||
|
||||
import java.io.StringReader;
|
||||
import java.io.StringWriter;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
|
|
|
|||
Loading…
Reference in New Issue