/**
* Removes a previously uploaded result file.
*
* @param alternative Alternative the file was uploaded for.
* @param sampleObject Sample the file was uploaded for.
*/
public void removeResultFile(Alternative alternative, SampleObject sampleObject) {
DigitalObject resultFile =
alternative.getExperiment().getResults().put(sampleObject, new DigitalObject());
bytestreamsToRemove.add(resultFile.getPid());
alternative.getExperiment().getResults().put(sampleObject, new DigitalObject());
}
/** Characterises results for all alternatives. */
public void characteriseResults() {
List<Alternative> runnableAlternatives = getRunnableAlternatives();
List<SampleObject> allRecords = plan.getSampleRecordsDefinition().getRecords();
for (Alternative alternative : runnableAlternatives) {
Experiment exp = alternative.getExperiment();
for (SampleObject record : allRecords) {
DigitalObject u = exp.getResults().get(record);
if (u.isDataExistent() && (u.getFitsXMLString() == null)) {
characteriseFits(u);
}
}
}
}
/**
* Method responsible for uploading a result file.
*
* @param resultFile File to upload.
* @param alternative Alternative the file was uploaded for.
* @param sampleObject Sample the file was uploaded for.
* @throws StorageException is thrown if any error occurs at uploading the result file.
*/
public void uploadResultFile(
DigitalObject resultFile, Alternative alternative, SampleObject sampleObject)
throws StorageException {
digitalObjectManager.moveDataToStorage(resultFile);
addedBytestreams.add(resultFile.getPid());
characteriseFits(resultFile);
alternative.getExperiment().getResults().put(sampleObject, resultFile);
}
/**
* Adds an executable plan t2flow to the parent.
*
* @param t2flow the t2flow to add
* @param parent the parent element of the element to create
* @return the newly created element or null if none was created
* @throws TavernaParserException if the workflow could not be parsed
* @throws StorageException if the data could not be loaded
*/
private Element addPreservationActionPlanT2flow(DigitalObject t2flow, Element parent)
throws TavernaParserException, StorageException {
Element executablePlan = null;
if (t2flow != null && t2flow.isDataExistent()) {
executablePlan = parent.addElement("executablePlan").addAttribute("type", "t2flow");
if (!addDigitalObjectData) {
// Add only DigitalObject ID, it can be replaced later
executablePlan.setText(String.valueOf(t2flow.getId()));
} else {
DigitalObject t2flowObject = t2flow;
try {
if (t2flowObject.getData().getData() == null
|| t2flowObject.getData().getData().length == 0) {
t2flowObject = digitalObjectManager.getCopyOfDataFilledDigitalObject(t2flowObject);
}
T2FlowParser parser =
T2FlowParser.createParser(new ByteArrayInputStream(t2flowObject.getData().getData()));
Document doc = parser.getDoc();
executablePlan.add(doc.getRootElement());
} finally {
t2flowObject = null;
}
}
}
return executablePlan;
}
/**
* Adds data for the preservation action plan to the parent element.
*
* @param collectionProfile source of the data
* @param parent the parent element of the element to create
* @return the newly created element or null if none was created
* @throws ParserException if the collection profile could not be parsed
* @throws StorageException if the data could not be loaded
*/
private Element addPreservationActionPlanData(CollectionProfile collectionProfile, Element parent)
throws ParserException, StorageException {
Element collection = null;
if (collectionProfile != null) {
collection = parent.addElement("collection");
collection.addAttribute("uid", collectionProfile.getCollectionID());
// TODO: Collection has no name
// collection.addAttribute("name",
// p.getSampleRecordsDefinition().getCollectionProfile().getCollectionID());
// Objects
Element objects = parent.addElement("objects");
DigitalObject profileObject = collectionProfile.getProfile();
try {
if (profileObject != null && profileObject.isDataExistent()) {
if (!addDigitalObjectData) {
objects.setText(String.valueOf(profileObject.getId()));
} else {
if (profileObject.getData().getData() == null
|| profileObject.getData().getData().length == 0) {
profileObject = digitalObjectManager.getCopyOfDataFilledDigitalObject(profileObject);
}
C3POProfileParser parser = new C3POProfileParser();
parser.read(new ByteArrayInputStream(profileObject.getData().getData()), false);
List<String> objectIdentifiers = parser.getObjectIdentifiers();
for (String objectIdentifier : objectIdentifiers) {
objects.addElement("object").addAttribute("uid", objectIdentifier);
}
}
}
} finally {
profileObject = null;
}
}
return collection;
}
/**
* Generates an executable plan.
*
* @param planName the plan name
* @param alternative the alternative to base the workflow on
* @param measures the measures to include in the workflow
* @param sourceMimetype the source mimetype of the workflow
* @param targetMimetype the target mimetype of the workflow
* @return an executable plan
* @throws PlanningException if an error occurred during generation
*/
@Asynchronous
public Future<DigitalObject> generateExecutablePlan(
final String planName,
final Alternative alternative,
final List<String> measures,
final String sourceMimetype,
final String targetMimetype)
throws PlanningException {
DigitalObject workflow = new DigitalObject();
String name = planName + " - " + alternative.getName();
T2FlowExecutablePlanGenerator generator =
new T2FlowExecutablePlanGenerator(name, user.getFullName());
// Add ports
generator.addSourcePort();
generator.addTargetPort();
// Migration action
PreservationActionDefinition action = alternative.getAction();
if (action != null) {
try {
WorkflowDescription wf = MyExperimentRESTClient.getWorkflow(action.getDescriptor());
if (wf != null) {
HashMap<String, String> parameters = new HashMap<String, String>();
for (Parameter p : action.getParams()) {
parameters.put(p.getName(), p.getValue());
}
wf.readMetadata();
String workflowContent = MyExperimentRESTClient.getWorkflowContent(wf);
generator.setMigrationComponent(wf, workflowContent, parameters);
} else {
log.warn(String.format("The workflow [%s] could not be found.", action.getDescriptor()));
}
} catch (Exception e) {
throw new PlanningException(
"An error occured querying myExperiment migration component", e);
}
}
// Add QA components
addQaComponents(generator, measures, sourceMimetype, targetMimetype);
// Create digital object
ByteArrayOutputStream out = new ByteArrayOutputStream();
OutputStreamWriter writer = new OutputStreamWriter(out);
try {
generator.generate(writer);
} catch (IOException e) {
log.warn("An error occured generating the executable plan.", e.getMessage());
throw new PlanningException("An error occured generating the executable plan.", e);
} finally {
if (writer != null) {
try {
writer.close();
} catch (IOException e) {
log.warn(
"An error occured closing the executable plan generator writer.", e.getMessage());
throw new PlanningException(
"An error occured closing the executable plan generator writer.", e);
}
}
}
byte[] data = out.toByteArray();
ByteStream bsData = new ByteStream();
bsData.setData(data);
workflow.setContentType("application/vnd.taverna.t2flow+xml");
workflow.setData(bsData);
workflow.setFullname(FileUtils.makeFilename(name + ".t2flow"));
return new AsyncResult<DigitalObject>(workflow);
}