/**
* Executes the given workflow in the specified representation file.
*
* @param workflowFile the workflow {@link File}
* @param representationID the representation ID
* @param fileID the file ID
* @return a WorkflowExecutionOutput with the output directory and command output.
* @throws ExecutePlanException if an error occurs during the execution
*/
private WorkflowExecutionOutput executeWorkflowInFile(
final File workflowFile, final String representationID, final String fileID)
throws ExecutePlanException {
logger.info("Executing workflow in file " + representationID + "/" + fileID);
File inputValueFile = null;
try {
// Write the downloaded stream to a temporary file in the disk
final InputStream inputStream = rodaDownloader.get(representationID, fileID);
inputValueFile = File.createTempFile(representationID + "_" + fileID + "_", "");
IOUtils.copyLarge(inputStream, new FileOutputStream(inputValueFile));
final String outputDir = inputValueFile.getAbsolutePath() + "_taverna/";
final String executionOutput =
CommandUtility.execute(
taverna_bin,
"-outputdir",
outputDir,
"-inputvalue",
workflowInputPort,
inputValueFile.getAbsolutePath(),
workflowFile.getAbsolutePath());
logger.info("Workflow executed with sucess!");
logger.debug("Command output: " + executionOutput);
return new WorkflowExecutionOutput(outputDir, executionOutput);
} catch (NoSuchRODAObjectException e) {
logger.error("Error getting file - " + e.getMessage());
throw new ExecutePlanException("Error getting file " + fileID + " - " + e.getMessage(), e);
} catch (DownloaderException e) {
logger.error("Error getting file - " + e.getMessage());
throw new ExecutePlanException("Error getting file " + fileID + " - " + e.getMessage(), e);
} catch (IOException e) {
logger.error("Error getting file - " + e.getMessage());
throw new ExecutePlanException("Error getting file " + fileID + " - " + e.getMessage(), e);
} catch (CommandException e) {
logger.error("Error executing taverna workflow in file " + fileID + " - " + e.getMessage());
logger.debug("Command output: " + e.getOutput());
throw new ExecutePlanException(
"Error executing taverna workflow in file " + fileID + " - " + e.getMessage(), e);
} finally {
if (inputValueFile != null) {
if (FileUtils.deleteQuietly(inputValueFile)) {
logger.debug("Deleted temporary file " + inputValueFile);
} else {
logger.warn("Error deleting temporary file " + inputValueFile);
}
}
}
}
/**
* Create a preservation event the plan execution task.
*
* @param originalROPID the PID of the original representation.
* @param roPID the new representation PID.
* @param planExecutionDetails The plan execution details.
* @param reportItem the {@link ReportItem}.
* @return the PID of the created {@link EventPreservationObject}.
* @throws ExecutePlanException if an error occurs creating the {@link EventPreservationObject}.
*/
private String createPreservationEvent(
final String originalROPID,
final String roPID,
final String planExecutionDetails,
final ReportItem reportItem)
throws ExecutePlanException {
// Create agent
final AgentPreservationObject agentPO = new AgentPreservationObject();
agentPO.setAgentType(AgentPreservationObject.PRESERVATION_AGENT_TYPE_MIGRATOR);
agentPO.setAgentName(getName() + "/" + getVersion() + " - SCAPE plan");
try {
final EventPreservationObject eventPO = new EventPreservationObject();
eventPO.setEventType(EventPreservationObject.PRESERVATION_EVENT_TYPE_MIGRATION);
eventPO.setOutcome("success");
eventPO.setOutcomeDetailNote("Plan workflow output");
eventPO.setOutcomeDetailExtension(planExecutionDetails);
logger.debug("Event is " + eventPO);
// Register derivation event
final String epoPID =
this.rodaClient
.getIngestService()
.registerDerivationEvent(originalROPID, roPID, eventPO, agentPO, true);
logger.info("Event registration finnished. Derivation event is " + epoPID);
reportItem.addAttribute(new Attribute("Register event - event PID", epoPID));
return epoPID;
} catch (NoSuchRODAObjectException e) {
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new ExecutePlanException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
} catch (IngestException e) {
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new ExecutePlanException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
} catch (RemoteException e) {
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new ExecutePlanException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
} catch (RODAClientException e) {
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new ExecutePlanException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
}
}
private String ingestRepresentation(RepresentationObject rObject) throws IngestException {
String roPID = null;
try {
roPID = this.ingestService.createRepresentationObject(rObject);
rObject.setPid(roPID);
logger.info("RepresentationObject created with PID " + roPID);
} catch (NoSuchRODAObjectException e) {
logger.debug("Error creating representation object - " + e.getMessage(), e);
throw new IngestException("Error creating representation object - " + e.getMessage(), e);
} catch (RemoteException e) {
logger.debug("Error creating representation object - " + e.getMessage(), e);
throw new IngestException("Error creating representation object - " + e.getMessage(), e);
}
try {
// Upload root file
this.rodaUploader.uploadRepresentationFile(roPID, rObject.getRootFile());
logger.info(
"Root file "
+ rObject.getRootFile().getId()
+ " of representation "
+ roPID
+ " uploaded successfully.");
// Upload part files
if (rObject.getPartFiles() != null) {
for (RepresentationFile partFile : rObject.getPartFiles()) {
this.rodaUploader.uploadRepresentationFile(roPID, partFile);
logger.info(
"Part file "
+ partFile.getId()
+ " of representation "
+ roPID
+ " uploaded successfully.");
}
}
return roPID;
} catch (FileNotFoundException e) {
logger.debug("Error accessing representation file - " + e.getMessage(), e);
try {
logger.warn("Ingest of new representation failed. Removing created object " + roPID);
this.ingestService.removeObjects(new String[] {roPID});
} catch (RemoteException e1) {
logger.warn(
"Error removing representation " + roPID + " - " + e1.getMessage() + ". IGNORING", e1);
}
throw new IngestException("Error accessing representation file - " + e.getMessage(), e);
} catch (UploadException e) {
logger.debug("Error uploading representation file - " + e.getMessage(), e);
try {
logger.warn("Ingest of new representation failed. Removing created object " + roPID);
this.ingestService.removeObjects(new String[] {roPID});
} catch (RemoteException e1) {
logger.warn(
"Error removing representation " + roPID + " - " + e1.getMessage() + ". IGNORING", e1);
}
throw new IngestException("Error uploading representation file - " + e.getMessage(), e);
}
}
private ReportItem executeOn(String representationPID) throws PluginException {
ReportItem reportItem = new ReportItem("Convertion of representation " + representationPID);
reportItem.addAttribute(new Attribute("start datetime", DateParser.getIsoDate(new Date())));
RepresentationObject originalRObject = null;
try {
reportItem.addAttribute(
new Attribute(
"Download original representation - start datetime",
DateParser.getIsoDate(new Date())));
// Get original representation from RODA Core
originalRObject = this.browserService.getRepresentationObject(representationPID);
logger.info("Original representation is " + originalRObject);
reportItem.addAttribute(
new Attribute(
"Download original representation - finnish datetime",
DateParser.getIsoDate(new Date())));
} catch (BrowserException e) {
logger.debug(
"Error accessing representation " + representationPID + " - " + e.getMessage(), e);
throw new PluginException(
"Error accessing representation " + representationPID + " - " + e.getMessage(),
e,
reportItem);
} catch (NoSuchRODAObjectException e) {
logger.debug(
"Error accessing representation " + representationPID + " - " + e.getMessage(), e);
throw new PluginException(
"Error accessing representation " + representationPID + " - " + e.getMessage(),
e,
reportItem);
} catch (RemoteException e) {
logger.debug(
"Error accessing representation " + representationPID + " - " + e.getMessage(), e);
throw new PluginException(
"Error accessing representation " + representationPID + " - " + e.getMessage(),
e,
reportItem);
}
// Download representation files and verify if the files are already
// normalised
if (isRepresentationConverted(originalRObject)) {
// No need to call the convert plugin
try {
String normalizedROPID =
this.ingestService.setDONormalizedRepresentation(
originalRObject.getDescriptionObjectPID(), originalRObject.getPid());
logger.info(
"Marked representation "
+ normalizedROPID //$NON-NLS-1$
+ " as normalized"); //$NON-NLS-1$
reportItem.addAttributes(
new Attribute("Action", "Representation was marked as normalized"));
} catch (NoSuchRODAObjectException e) {
reportItem.addAttributes(
new Attribute(
"Error",
"Error setting representation status to normalized (" + e.getMessage() + ")"));
throw new PluginException(
"Error setting representation status to normalized - " + e.getMessage(), e, reportItem);
} catch (IngestException e) {
reportItem.addAttributes(
new Attribute(
"Error",
"Error setting representation status to normalized (" + e.getMessage() + ")"));
throw new PluginException(
"Error setting representation status to normalized - " + e.getMessage(), e, reportItem);
} catch (RemoteException e) {
RODAException exception = RODAClient.parseRemoteException(e);
reportItem.addAttributes(
new Attribute(
"Error",
"Error setting representation status to normalized (" + e.getMessage() + ")"));
throw new PluginException(
"Error setting representation status to normalized - " + exception.getMessage(),
exception,
reportItem);
}
reportItem.addAttributes(
new Attribute("finnish datetime", DateParser.getIsoDate(new Date())));
return reportItem;
} else {
// Representation is not normalized and we need to call the
// converter. Continue...
}
ConversionResult convertResult = null;
RepresentationObject convertedRObject = null;
try {
reportItem.addAttribute(
new Attribute("Conversion - start datetime", DateParser.getIsoDate(new Date())));
logger.info("Converting representation " + originalRObject.getPid());
// Calling converter
convertResult = convert(originalRObject);
convertedRObject = convertResult.getRepresentation();
logger.info("Convert " + originalRObject.getPid() + " finished");
reportItem.addAttribute(
new Attribute("Conversion - finnish datetime", DateParser.getIsoDate(new Date())));
reportItem.addAttribute(
new Attribute(
"Conversion - converted representation",
convertResult.getRepresentation().toString()));
if (convertResult.getMigrationEvent() == null) {
logger.warn("Migration event is null");
} else {
logger.info(
"Conversion outcome is "
+ convertResult.getMigrationEvent().getOutcomeDetailExtension());
logger.info("Converted representation is " + convertedRObject);
reportItem.addAttribute(
new Attribute(
"Conversion - outcome details",
convertResult.getMigrationEvent().getOutcomeDetailExtension()));
}
} catch (RepresentationConverterException e) {
logger.debug(
"Error converting representation " + representationPID + " - " + e.getMessage(), e);
e.setReportItem(reportItem);
throw e;
}
RepresentationObject writtenRO = null;
String roPID = null;
try {
// Create temporary directory
File temporaryDirectory = TempDir.createUniqueTemporaryDirectory("rep");
reportItem.addAttributes(
new Attribute(
"Download converted representation - temporary directory",
temporaryDirectory.toString()),
new Attribute(
"Download converted representation - start datetime",
DateParser.getIsoDate(new Date())));
logger.info("Writting converted representation to " + temporaryDirectory);
// Write representation to temporary directory
writtenRO =
this.migratorClient.writeRepresentationObject(convertedRObject, temporaryDirectory);
logger.info("Representation written");
reportItem.addAttribute(
new Attribute(
"Download converted representation - finnish datetime",
DateParser.getIsoDate(new Date())));
reportItem.addAttribute(
new Attribute("Ingest - start datetime", DateParser.getIsoDate(new Date())));
logger.info("Ingesting converted representation");
if (isNormalization()) {
logger.info(
"This is a normalization process. Setting representation status to "
+ RepresentationObject.STATUS_NORMALIZED);
writtenRO.setStatuses(new String[] {RepresentationObject.STATUS_NORMALIZED});
} else {
logger.info(
"This is NOT a normalization process. Setting representation status to "
+ RepresentationObject.STATUS_ALTERNATIVE);
writtenRO.setStatuses(new String[] {RepresentationObject.STATUS_ALTERNATIVE});
}
// Ingest converted representation
roPID = ingestRepresentation(writtenRO);
logger.info("Representation ingested with PID " + roPID);
reportItem.addAttribute(
new Attribute("Ingest - finnish datetime", DateParser.getIsoDate(new Date())));
reportItem.addAttribute(new Attribute("Ingest - ingested representation PID", roPID));
} catch (MigratorClientException e) {
logger.debug("Error downloading converted representation - " + e.getMessage(), e);
throw new PluginException(
"Error downloading converted representation - " + e.getMessage(), e, reportItem);
} catch (IOException e) {
logger.debug("Error downloading converted representation - " + e.getMessage(), e);
throw new PluginException(
"Error downloading converted representation - " + e.getMessage(), e, reportItem);
} catch (IngestException e) {
logger.debug("Error downloading converted representation - " + e.getMessage(), e);
throw new PluginException(
"Error downloading converted representation - " + e.getMessage(), e, reportItem);
}
AgentPreservationObject agentPO = null;
try {
logger.info("Registering derivation event");
reportItem.addAttribute(
new Attribute("Register event - start datetime", DateParser.getIsoDate(new Date())));
// Getting converter Agent
AgentPreservationObject migratorAgent = getConverter().getAgent();
reportItem.addAttribute(
new Attribute("Register event - converter agent", migratorAgent.toString()));
agentPO = new AgentPreservationObject();
agentPO.setAgentType(AgentPreservationObject.PRESERVATION_AGENT_TYPE_MIGRATOR);
agentPO.setAgentName(getName() + "/" + getVersion() + " - " + migratorAgent.getAgentName());
logger.info("Agent is " + agentPO);
reportItem.addAttribute(new Attribute("Register event - event agent", agentPO.toString()));
} catch (Exception e) {
// getConverter().getAgent();
logger.debug("Error getting converter agent - " + e.getMessage(), e);
// Delete roPID
// delete(roPID);
// try {
// logger
// .warn("Ingest of new representation failed. Removing created object "
// + roPID);
//
// this.ingestService.removeObjects(new String[] { roPID });
//
// } catch (RemoteException e1) {
// logger.warn("Error removing representation " + roPID + " - "
// + e1.getMessage() + ". IGNORING", e1);
// }
throw new PluginException("Error getting converter agent - " + e.getMessage(), e, reportItem);
}
try {
EventPreservationObject eventPO = convertResult.getMigrationEvent();
if (eventPO == null) {
eventPO = new EventPreservationObject();
}
if (isNormalization()) {
eventPO.setEventType(EventPreservationObject.PRESERVATION_EVENT_TYPE_NORMALIZATION);
} else {
eventPO.setEventType(EventPreservationObject.PRESERVATION_EVENT_TYPE_MIGRATION);
}
if (StringUtils.isBlank(eventPO.getOutcome())) {
eventPO.setOutcome("success");
}
if (StringUtils.isBlank(eventPO.getOutcomeDetailNote())) {
eventPO.setOutcomeDetailNote("Converter details");
}
if (StringUtils.isBlank(eventPO.getOutcomeDetailExtension())) {
eventPO.setOutcomeDetailExtension("no details");
}
logger.info("Event is " + eventPO);
// reportItem.addAttribute(new Attribute(
// "Register event - event outcome details", eventPO
// .getOutcomeDetailExtension()));
logger.info("Calling registerDerivationEvent(...)");
// Register derivation event
String epoPID =
this.ingestService.registerDerivationEvent(
originalRObject.getPid(), roPID, eventPO, agentPO, getParameterMakeObjectsActive());
logger.info("Event registration finnished. Derivation event is " + epoPID);
reportItem.addAttributes(
new Attribute("Register event - event PID", epoPID),
new Attribute("finnish datetime", DateParser.getIsoDate(new Date())));
return reportItem;
} catch (NoSuchRODAObjectException e) {
// registerDerivationEvent(...)
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new PluginException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
} catch (IngestException e) {
// registerDerivationEvent(...)
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new PluginException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
} catch (RemoteException e) {
// registerDerivationEvent(...)
logger.debug("Error registering convertion event - " + e.getMessage(), e);
throw new PluginException(
"Error registering convertion event - " + e.getMessage(), e, reportItem);
}
}