/**
* 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);
}
}
}
}
protected String getVersion() throws ConverterException {
try {
String version = getClass().getName() + "/" + VERSION + " - ";
String executableVersion = CommandUtility.execute(this.office2pdfExecutable, "--version");
return version + executableVersion;
} catch (CommandException e) {
logger.warn("Exception getting Doc2Pdf version - " + e.getMessage(), e);
throw new ConverterException("Exception getting Doc2Pdf version - " + e.getMessage(), e);
}
}
protected RepresentationFile convertRootFile(
RepresentationFile originalRootFile, File tempDirectory, StringBuffer report)
throws IOException, CommandException {
// /tmp/original.../F0
File originalFile = new File(URI.create(originalRootFile.getAccessURL()));
// Detect extension by DROID
String origNameWithExt = originalRootFile.getOriginalName();
FileFormat detectedFileFormat = FormatUtility.getFileFormat(originalFile, origNameWithExt);
if ((detectedFileFormat != null)
&& (detectedFileFormat.getExtensions() != null)
&& (detectedFileFormat.getExtensions().length > 0)) {
origNameWithExt = origNameWithExt + "." + detectedFileFormat.getExtensions()[0];
}
// /tmp/original.../originalName.doc
File originalFileWithExtension = new File(originalFile.getParentFile(), origNameWithExt);
// mv /tmp/original.../F0 /tmp/original.../originalName.doc
FileUtils.moveFile(originalFile, originalFileWithExtension);
// /tmp/converted.../F0
File convertedFile = new File(tempDirectory, originalFile.getName());
// /tmp/converted.../originalName.doc.pdf
File convertedFileWithExtension =
new File(tempDirectory, originalRootFile.getOriginalName() + this.formatExtension);
// Execute the command
List<String> commandArgs = new ArrayList<String>();
commandArgs.add(this.office2pdfExecutable);
commandArgs.add(originalFileWithExtension.getAbsolutePath());
commandArgs.add(convertedFileWithExtension.getAbsolutePath());
String convertOutput = CommandUtility.execute(commandArgs);
String commandline = StringUtility.join(commandArgs, " "); // $NON-NLS-1$
String message;
if (StringUtils.isBlank(convertOutput)) {
message =
String.format(
"%s: %s => %s%n(Command: %s)%n%n", //$NON-NLS-1$
originalRootFile.getId(),
originalRootFile.getOriginalName(),
convertedFileWithExtension.getName(),
commandline);
} else {
message =
String.format(
"%s: %s => %s (%s)%n(Command: %s)%n%n",
originalRootFile //$NON-NLS-1$
.getId(),
originalRootFile.getOriginalName(),
convertedFileWithExtension.getName(),
convertOutput,
commandline);
}
logger.trace(message);
report.append(message);
// mv /tmp/converted.../originalName.doc.pdf /tmp/converted.../F0
FileUtils.moveFile(convertedFileWithExtension, convertedFile);
RepresentationFile convertedRootFile = new RepresentationFile(originalRootFile);
// convertedRootFile.setMimetype(format);
convertedRootFile.importFileFormat(
FormatUtility.getFileFormat(convertedFile, convertedFileWithExtension.getName()));
convertedRootFile.setSize(convertedFile.length());
convertedRootFile.setAccessURL(convertedFile.getAbsolutePath());
convertedRootFile.setOriginalName(convertedRootFile.getOriginalName() + this.formatExtension);
return convertedRootFile;
}