/**
* Computes and results the line count for a file revision using its storage. Uses a line number
* reader to compute the line count.
*
* @param fr file revision
* @param monitor progress monitor for storage access
* @return line count or zero, exceptions caught and reported to log
*/
protected int getLineCount(IFileRevision fr, IProgressMonitor monitor) {
int lineCount = 0;
try {
IStorage storage = fr.getStorage(monitor);
InputStream is = storage.getContents();
LineNumberReader lineNumberReader = new LineNumberReader(new InputStreamReader(is));
while (lineNumberReader.ready()) {
lineNumberReader.readLine();
lineCount++;
}
lineNumberReader.close();
is.close();
} catch (Exception e) {
CertWareLog.logError(
String.format("%s %s", "Gathering line count for revision", fr.getName()), e);
}
return lineCount;
}
/**
* Computes and results the byte count for a file revision using its storage. Uses an input stream
* reader to count bytes read.
*
* @param fr file revision
* @param monitor progress monitor for storage access
* @return line count or zero, exceptions caught and reported to log
*/
protected int getByteCount(IFileRevision fr, IProgressMonitor monitor) {
int byteCount = 0;
try {
IStorage storage = fr.getStorage(monitor);
InputStream is = storage.getContents();
InputStreamReader isr = new InputStreamReader(is);
while (isr.read() != -1) {
byteCount++;
}
isr.close();
is.close();
} catch (Exception e) {
CertWareLog.logError(
String.format("%s %s", "Gathering byte count for revision", fr.getName()), e);
}
return byteCount;
}
/**
* Process file revision
*
* @param fr file revision
* @param ch commit history, already populated with artifact history records
* @param monitor progress monitor
*/
private void processFileRevision(IFileRevision fr, CommitHistory ch, IProgressMonitor monitor) {
String commitId = fr.getContentIdentifier();
String name = fr.getName();
int lineCount = getLineCount(fr, monitor);
// create artifact identifier and add it to the existing commit
ArtifactIdentifier ai = ScoFactory.eINSTANCE.createArtifactIdentifier();
ai.setCurrentLineCount(lineCount);
ai.setResourceName(name);
// add the resource revision identifier to the corresponding commit record
ArtifactCommit ac = findCommit(ch, commitId);
if (ac != null) {
ac.getArtifactIdentifiers().add(ai);
} else {
CertWareLog.logWarning(
String.format("%s %s", "Could not find commit for file", fr.getName()));
}
}
/**
* Process the EGit history associated with a given project.
*
* @param selectedProject selected project, presumably an object contribution selection
* @throws CoreException
* @throws IOException
*/
public void processHistory(IProject selectedProject, IProgressMonitor monitor)
throws CoreException, IOException {
// find the repository mapping for the project
// if none found, return
RepositoryMapping repositoryMapping = RepositoryMapping.getMapping((IResource) selectedProject);
if (repositoryMapping == null) {
CertWareLog.logWarning(
String.format("%s %s", "Missing repository for project", selectedProject.getName()));
return;
}
// build the commit history model, load it from the tree walk
final CommitHistory commitHistory = ScoFactory.eINSTANCE.createCommitHistory();
Repository repo = repositoryMapping.getRepository();
RevWalk revWalk = new RevWalk(repo);
ObjectId headObject = repo.resolve("HEAD");
revWalk.markStart(revWalk.parseCommit(headObject));
final Set<String> repositoryPaths =
Collections.singleton(repositoryMapping.getRepoRelativePath(selectedProject));
revWalk.setTreeFilter(PathFilterGroup.createFromStrings(repositoryPaths));
for (RevCommit commit : revWalk) {
String commitName = commit.getName();
ArtifactCommit artifactCommit = ScoFactory.eINSTANCE.createArtifactCommit();
artifactCommit.setCommitIdentifier(commitName);
commitHistory.getCommitRecord().add(artifactCommit);
}
revWalk.dispose();
// use the Git provider to find the file history, then converge into the model
GitProvider provider = (GitProvider) RepositoryProvider.getProvider(selectedProject);
IFileHistoryProvider fileHistoryProvider = provider.getFileHistoryProvider();
IResource[] projectMembers = selectedProject.members();
monitor.beginTask("Processing project resources", projectMembers.length);
for (IResource resource : projectMembers) {
processResource(resource, fileHistoryProvider, commitHistory, monitor);
monitor.worked(1);
if (monitor.isCanceled()) {
return;
}
}
// model complete with commit history and associated file sizes
// write the resulting model to an SCO file
// expecting preference to have no extension, so add it if necessary
IPreferenceStore store = Activator.getDefault().getPreferenceStore();
String fileName = store.getString(PreferenceConstants.P_FILENAME_SCO);
if (fileName.endsWith(ICertWareConstants.SCO_EXTENSION) == false) {
fileName = fileName + '.' + ICertWareConstants.SCO_EXTENSION;
}
// fully specify the path to the new file given the container project
final String modelFile =
selectedProject.getFullPath().toPortableString() + IPath.SEPARATOR + fileName;
// create the resource in a workspace modify operation
WorkspaceModifyOperation operation =
new WorkspaceModifyOperation() {
@Override
protected void execute(IProgressMonitor progressMonitor) {
try {
// create a resource set and resource for a new file
ResourceSet resourceSet = new ResourceSetImpl();
URI fileURI = URI.createPlatformResourceURI(modelFile, true);
Resource resource = resourceSet.createResource(fileURI);
resource.getContents().add(commitHistory);
// save the contents of the resource to the file system
Map<Object, Object> options = new HashMap<Object, Object>();
options.put(XMLResource.OPTION_ENCODING, FILE_ENCODING);
resource.save(options);
} catch (Exception e) {
CertWareLog.logError(String.format("%s %s", "Saving SCO file", modelFile), e);
}
}
};
// modify the workspace
try {
operation.run(monitor);
} catch (Exception e) {
CertWareLog.logError(
String.format("%s %s", "Modifying workspace for", selectedProject.getName()), e);
}
monitor.done();
}
/**
* Production method for computations.
*
* @param monitor progress monitor
* @return CANCEL or OK
*/
@SuppressWarnings({"unchecked", "rawtypes"})
public IStatus produce(IProgressMonitor monitor) {
/** network name for messages */
String networkName = "undefined"; // $NON-NLS-1$
try {
if (initialNetwork == null) {
cancel();
CertWareLog.logWarning("Network not defined for calculation");
view.setWarningMessage(CANCEL_MSG);
return Status.CANCEL_STATUS;
}
if (nodes.isEmpty()) {
cancel();
CertWareLog.logWarning("No variable selections available for Pr(e) calculation");
view.setWarningMessage(CANCEL_MSG);
return Status.CANCEL_STATUS;
}
// network name from loaded file
networkName = view.getSelectedFile().getName();
// initialize variables from selections
Set setPreVariables = new HashSet();
for (VariableNode v : nodes) {
if (v.isSelected()) {
setPreVariables.add(v.getNode());
}
}
// initialize evidence from selections
HashMap evidence = new HashMap();
for (VariableNode vn : nodes) {
for (VariableNodeState vns : vn.states) {
if (vns.isSelected()) {
FiniteVariable fv = vn.getNode();
evidence.put(fv, fv.instance(vns.getStateName()));
}
}
}
// instantiation formatter
VariableImpl.setStringifier(AbstractStringifier.VARIABLE_ID);
monitor.worked(1);
if (monitor.isCanceled()) {
CertWareLog.logWarning(CANCEL_MSG);
view.setWarningMessage(CANCEL_MSG);
return Status.CANCEL_STATUS;
}
/*
// create a new set of variables and remove those whose evidence have set keys
Set allVarsMinusEvidence = new HashSet( initialNetwork );
allVarsMinusEvidence.removeAll( evidence.keySet() );
// initialize a MapEngine and perform the MPE computation
MapEngine mpe = new MapEngine( initialNetwork, allVarsMinusEvidence, evidence );
VariableImpl.setStringifier( AbstractStringifier.VARIABLE_ID );
*/
// create the dynamator
JEngineGenerator dynamator = new JEngineGenerator();
// edit settings
JoinTreeSettings settings =
dynamator.getSettings((PropertySuperintendent) initialNetwork, true);
// define the elimination order heuristic used to create the join tree
settings.setEliminationHeuristic(EliminationHeuristic.MIN_FILL);
// create the inference engine
InferenceEngine engine = dynamator.manufactureInferenceEngine(initialNetwork);
// set the observations
try {
initialNetwork.getEvidenceController().setObservations(evidence);
} catch (StateNotFoundException e) {
CertWareLog.logError("Performing Pr(e) query", e);
view.setErrorMessage(e.getMessage());
return null;
}
;
// results
double score = engine.probability();
// Map instantiation = engine.getInstance();
monitor.worked(2);
if (monitor.isCanceled()) {
CertWareLog.logWarning(CANCEL_MSG);
return Status.CANCEL_STATUS;
}
// reset marginals
// clearMarginals();
setMarginals(engine);
// update results in view
LinkedHashMap<String, String> rows = new LinkedHashMap<String, String>();
rows.put("Pr(e)", getProbability(score));
view.addResult(rows);
monitor.worked(1);
} catch (Exception e) {
CertWareLog.logError(String.format("%s %s", "Pr(e) query for", networkName), e);
return Status.CANCEL_STATUS;
}
String doneMessage = String.format("%s %s %s", "Pr(e) query for", networkName, "complete.");
CertWareLog.logInfo(doneMessage);
return Status.OK_STATUS;
}
