public void testGeneratedSources() throws Exception { // #187595
TestFileUtils.writeFile(
d,
"pom.xml",
"<project xmlns='http://maven.apache.org/POM/4.0.0'>"
+ "<modelVersion>4.0.0</modelVersion>"
+ "<groupId>grp</groupId>"
+ "<artifactId>art</artifactId>"
+ "<packaging>jar</packaging>"
+ "<version>0</version>"
+ "</project>");
FileObject src = FileUtil.createFolder(d, "src/main/java");
FileObject gsrc = FileUtil.createFolder(d, "target/generated-sources/xjc");
gsrc.createData("Whatever.class");
FileObject tsrc = FileUtil.createFolder(d, "src/test/java");
FileObject gtsrc = FileUtil.createFolder(d, "target/generated-test-sources/jaxb");
gtsrc.createData("Whatever.class");
assertEquals(
Arrays.asList(src, gsrc),
Arrays.asList(
SourceForBinaryQuery.findSourceRoots(new URL(d.toURL(), "target/classes/"))
.getRoots()));
assertEquals(
Arrays.asList(tsrc, gtsrc),
Arrays.asList(
SourceForBinaryQuery.findSourceRoots(new URL(d.toURL(), "target/test-classes/"))
.getRoots()));
}
protected @Override void setUp() throws Exception {
MockLookup.setLayersAndInstances(TestUtil.testProjectFactory());
ProjectManager.getDefault().reset();
FileOwnerQuery.reset();
scratch = TestUtil.makeScratchDir(this);
projdir = scratch.createFolder("my-project");
projdir.createFolder("testproject");
randomfile = scratch.createData("randomfile");
projfile = projdir.createData("projfile");
FileObject projsubdir = projdir.createFolder("projsubdir");
projfile2 = projsubdir.createData("projfile2");
subprojdir = projdir.createFolder("subproject");
subprojdir.createFolder("testproject");
subprojfile = subprojdir.createData("subprojfile");
scratch.createFolder("external1").createFolder("subdir").createData("file");
scratch.createFolder("external2").createFolder("subdir").createData("file");
scratch.createFolder("external3").createFolder("subproject").createFolder("testproject");
p = ProjectManager.getDefault().findProject(projdir);
assertNotNull("found a project successfully", p);
// make jar:file:/.../projdir/foo.jar!/zipfile/zippedfile
FileObject foojar = TestFileUtils.writeZipFile(projdir, "foo.jar", "zipdir/zippedfile:");
FileObject foojarRoot = FileUtil.getArchiveRoot(foojar);
assertNotNull("have an archive in " + foojar, foojarRoot);
zippedfile = foojarRoot.getFileObject("zipdir/zippedfile");
assertNotNull("zippedfile found in it", zippedfile);
hashedFile = TestFileUtils.writeZipFile(projdir, ".#webapp.jar.1.45", "zipdir/zippedfile:");
foojarRoot = FileUtil.getArchiveRoot(hashedFile);
assertNotNull("have an archive in " + hashedFile, foojarRoot);
hashedFile = foojarRoot.getFileObject("zipdir/zippedfile");
}
public void testGetSourceLevelWithBrokenPlatform() throws Exception {
this.prepareProject("BrokenPlatform");
FileObject file = scratch.createData("some.java");
String sl = SourceLevelQuery.getSourceLevel(file);
assertEquals("Non-project Java file does not have any source level", null, sl);
file = sources.createData("a.java");
sl = SourceLevelQuery.getSourceLevel(file);
assertEquals("Project's Java file must have project's source", "4.3", sl);
}
private void writeResultsXml(GtaResult resultsObject) throws IOException {
String newAnResFileName =
FileUtil.findFreeFileName(
resultsfolder,
resultsfolder.getName() + "_" + modelReference.getFilename() + "_results",
"xml");
FileObject newAnResFile = resultsfolder.createData(newAnResFileName, "xml");
resultsObject.setSummary(new Summary());
resultsObject.getSummary().setFitModelCall(fitModelCall);
// TODO resolve problem with multiple modelcalls
resultsObject.getSummary().setInitModelCall(modelCalls.get(0));
for (int i = 0; i < relationsList.size(); i++) {
resultsObject.getDatasetRelations().add(new DatasetRelation());
resultsObject
.getDatasetRelations()
.get(i)
.setTo(String.valueOf((int) floor(relationsList.get(i)[0])));
resultsObject
.getDatasetRelations()
.get(i)
.setFrom(String.valueOf((int) floor(relationsList.get(i)[1])));
// TODO do this in a different way
// resultsObject.getDatasetRelations().get(i).getValues().add(relationsList.get(i)[2]);
String cmd =
timpcontroller.NAME_OF_RESULT_OBJECT
+ "$currTheta[["
+ (int) floor(relationsList.get(i)[0])
+ "]]@drel";
resultsObject.getDatasetRelations().get(i).getValues().add(timpcontroller.getDouble(cmd));
}
createAnalysisResultsFile(resultsObject, FileUtil.toFile(newAnResFile));
}
public void savePreset(String name, Layout layout) {
Preset preset = addPreset(new Preset(name, layout));
try {
// Create file if dont exist
FileObject folder = FileUtil.getConfigFile("layoutpresets");
if (folder == null) {
folder = FileUtil.getConfigRoot().createFolder("layoutpresets");
}
FileObject presetFile = folder.getFileObject(name, "xml");
if (presetFile == null) {
presetFile = folder.createData(name, "xml");
}
// Create doc
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = factory.newDocumentBuilder();
final Document document = documentBuilder.newDocument();
document.setXmlVersion("1.0");
document.setXmlStandalone(true);
// Write doc
preset.writeXML(document);
// Write XML file
Source source = new DOMSource(document);
Result result = new StreamResult(FileUtil.toFile(presetFile));
Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
transformer.transform(source, result);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Test of validateDirectory method, of class YiiCustomizerValidator.
*
* @throws java.io.IOException
*/
@Test
public void testValidateDirectory() throws IOException {
FileSystem fileSystem = FileUtil.createMemoryFileSystem();
FileObject sourceDirectory = fileSystem.getRoot();
sourceDirectory.createFolder("myfolder");
sourceDirectory.createData("test.php");
// existing directory
YiiCustomizerValidator validator =
new YiiCustomizerValidator().validateDirectory(sourceDirectory, "myfolder");
ValidationResult result = validator.getResult();
assertFalse(result.hasErrors());
assertFalse(result.hasWarnings());
// not existing directory
validator = new YiiCustomizerValidator().validateDirectory(sourceDirectory, "dummy");
result = validator.getResult();
assertFalse(result.hasErrors());
assertTrue(result.hasWarnings());
// file
validator = new YiiCustomizerValidator().validateDirectory(sourceDirectory, "test.php");
result = validator.getResult();
assertFalse(result.hasErrors());
assertTrue(result.hasWarnings());
}
@BeforeClass
public static void setUpClass() throws Exception {
MockServices.setServices();
DalvikPlatformManager.getDefault().setSdkLocation(SDK_DIR);
tempFolder = File.createTempFile("junit", "");
tempFolder.delete();
tempFolder.mkdir();
FileObject scratch = FileUtil.toFileObject(tempFolder);
FileObject cacheDir = scratch.createFolder("cache");
CacheFolder.setCacheFolder(cacheDir);
FileObject sdkDirFo = FileUtil.toFileObject(new File(SDK_DIR));
projdir = scratch.createFolder("Snake");
FileUtilities.recursiveCopy(sdkDirFo.getFileObject("samples/android-8/Snake"), projdir);
FileObject dir = projdir;
for (String dirName : Splitter.on('/').split("gen/com/example/android/snake")) {
dir = dir.createFolder(dirName);
}
OutputStream os = dir.createData("R.java").getOutputStream();
FileUtil.copy(ProjectRefResolverTest.class.getResourceAsStream("Snake_R_java.txt"), os);
os.close();
pp = ProjectManager.getDefault().findProject(projdir);
}
public void testUnowned() throws Exception {
FileObject subdir = projdir.createFolder("subUnowned");
FileObject subfile = subdir.createData("subfile");
assertEquals(p, FileOwnerQuery.getOwner(subfile));
FileOwnerQuery.markExternalOwner(
subdir, FileOwnerQuery.UNOWNED, FileOwnerQuery.EXTERNAL_ALGORITHM_TRANSIENT);
assertEquals(null, FileOwnerQuery.getOwner(subfile));
FileOwnerQuery.markExternalOwner(subdir, null, FileOwnerQuery.EXTERNAL_ALGORITHM_TRANSIENT);
assertEquals(p, FileOwnerQuery.getOwner(subfile));
}
public FileObject createEmptyClickFO() {
LOGGER.log(Level.ALL, "enter @createModel");
try {
FileObject clickFO = fsRoot.createData("click", "xml");
return clickFO;
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
return null;
}
private static void setModules(final FileObject dir, final WizardDescriptor wiz) {
final Properties properties =
(Properties) wiz.getProperty(ModuleSelectionWizardPanel1.MODULE_SELECTION_PROPS);
if (properties != null) {
final FileObject jinferProjectDir = dir.getFileObject("jinferproject");
try {
final FileObject projectProperties = jinferProjectDir.createData("project", "properties");
properties.store(new FileOutputStream(FileUtil.toFile(projectProperties)), null);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
}
private File getStorageFile() {
File storage = null;
if (dbFolder != null) {
FileObject storageFO = dbFolder.getFileObject(STORAGE, STORAGE_EXT);
try {
if (storageFO == null) {
storageFO = dbFolder.createData(STORAGE, STORAGE_EXT);
}
} catch (IOException e) {
}
if (storageFO != null) {
storage = NbClassPath.toFile(storageFO);
}
}
return storage;
}
/**
* Create a new application manifest file with minimal initial contents.
*
* @param dir the directory to create it in
* @param path the relative path of the file
* @throws IOException in case of problems
*/
private static void createManifest(FileObject dir, String path) throws IOException {
FileObject manifest = dir.createData(MANIFEST_FILE);
FileLock lock = manifest.lock();
try {
OutputStream os = manifest.getOutputStream(lock);
try {
PrintWriter pw = new PrintWriter(os);
pw.println("Manifest-Version: 1.0"); // NOI18N
pw.println("X-COMMENT: Main-Class will be added automatically by build"); // NOI18N
pw.println(); // safest to end in \n\n due to JRE parsing bug
pw.flush();
} finally {
os.close();
}
} finally {
lock.releaseLock();
}
}
public static void registerXMLKit() {
String[] path = new String[] {"Editors", "text", "x-xml"};
FileObject target = FileUtil.getConfigRoot();
try {
for (int i = 0; i < path.length; i++) {
FileObject f = target.getFileObject(path[i]);
if (f == null) {
f = target.createFolder(path[i]);
}
target = f;
}
String name = "EditorKit.instance";
if (target.getFileObject(name) == null) {
FileObject f = target.createData(name);
f.setAttribute("instanceClass", "org.netbeans.modules.xml.text.syntax.XMLKit");
}
} catch (IOException ioe) {
ioe.printStackTrace();
}
}
private void writeResults(
TimpResultDataset[] results, GtaModelReference modelReference, String[] nlsprogressResult) {
Tgm model = getModel(modelReference);
GtaResult newResultsObject = new GtaResult();
String freeResultsFilename =
FileUtil.findFreeFileName(resultsfolder, resultsfolder.getName(), "summary");
try {
writeSummary(resultsfolder, freeResultsFilename);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
if (nlsprogressResult != null) {
for (int i = 0; i < nlsprogressResult.length; i++) {
NlsProgress progress = new NlsProgress();
progress.setRss(nlsprogressResult[i]);
newResultsObject.getNlsprogress().add(progress);
}
}
for (int i = 0; i < results.length; i++) {
TimpResultDataset timpResultDataset = results[i];
timpResultDataset.setType(datasets[i].getType());
newResultsObject.getDatasets().add(new Dataset());
newResultsObject.getDatasets().get(i).setDatasetFile(new OutputFile());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setFilename(datasetContainer.getDatasets().get(i).getFilename());
newResultsObject
.getDatasets()
.get(i)
.getDatasetFile()
.setPath(datasetContainer.getDatasets().get(i).getPath());
newResultsObject.getDatasets().get(i).getDatasetFile().setFiletype(datasets[i].getType());
newResultsObject.getDatasets().get(i).setId(String.valueOf(i + 1));
if (model.getDat().getIrfparPanel().getLamda() != null) {
timpResultDataset.setLamdac(model.getDat().getIrfparPanel().getLamda());
}
if (datasets[i].getType().equalsIgnoreCase("flim")) {
timpResultDataset.setOrheigh(datasets[i].getOriginalHeight());
timpResultDataset.setOrwidth(datasets[i].getOriginalWidth());
timpResultDataset.setIntenceIm(datasets[i].getIntenceIm().clone());
timpResultDataset.setMaxInt(datasets[i].getMaxInt());
timpResultDataset.setMinInt(datasets[i].getMinInt());
timpResultDataset.setX(datasets[i].getX().clone());
timpResultDataset.setX2(datasets[i].getX2().clone());
}
try {
String freeFilename =
FileUtil.findFreeFileName(
resultsfolder,
resultsfolder.getName() + "_d" + (i + 1) + "_" + timpResultDataset.getDatasetName(),
"timpres");
timpResultDataset.setDatasetName(freeFilename);
writeTo = resultsfolder.createData(freeFilename, "timpres");
ObjectOutputStream stream = new ObjectOutputStream(writeTo.getOutputStream());
stream.writeObject(timpResultDataset);
stream.close();
newResultsObject.getDatasets().get(i).setResultFile(new OutputFile());
newResultsObject.getDatasets().get(i).getResultFile().setFilename(freeFilename);
newResultsObject
.getDatasets()
.get(i)
.getResultFile()
.setPath(FileUtil.getRelativePath(project.getProjectDirectory(), resultsfolder));
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
try {
writeResultsXml(newResultsObject);
} catch (IOException ex) {
Exceptions.printStackTrace(ex);
}
}
private void writeSummary(FileObject resultsfolder, String freeFilename) throws IOException {
writeTo = resultsfolder.createData(freeFilename, "summary");
BufferedWriter outputWriter = new BufferedWriter(new FileWriter(FileUtil.toFile(writeTo)));
// TODO: Complete the summary here:
outputWriter.append("Summary");
outputWriter.newLine();
// outputWriter.append("Used dataset(s): ");
// for (int j = 0; j < datasets.length; j++) {
// DatasetTimp dataset = datasets[j];
// if (j > 0) {
// outputWriter.append(", ");
// }
// outputWriter.append(dataset.getDatasetName());
// }
// outputWriter.newLine();
// outputWriter.newLine();
// outputWriter.append("Used model(s): ");
// for (int j = 0; j < models.length; j++) {
// if (j > 0) {
// outputWriter.append(", ");
// }
// outputWriter.append(models[j].getDat().getModelName());
// }
// outputWriter.newLine();
// outputWriter.newLine();
outputWriter.append("Number of iterations: ");
outputWriter.append(String.valueOf(numIterations));
outputWriter.newLine();
outputWriter.newLine();
outputWriter.append("R Call for the TIMP function \"initModel\": ");
outputWriter.newLine();
ArrayList<String> list = modelCalls;
for (String string : list) {
outputWriter.append(string);
outputWriter.newLine();
}
outputWriter.newLine();
outputWriter.append("R Call for the TIMP function \"fitModel\": ");
outputWriter.newLine();
outputWriter.write(fitModelCall);
outputWriter.newLine();
outputWriter.newLine();
if (results != null) {
outputWriter.append("Final residual standard error: ");
outputWriter.append((new Formatter().format("%g", results[0].getRms())).toString());
outputWriter.newLine();
outputWriter.newLine();
String[] slots = {
"getKineticParameters",
"getSpectralParameters",
"getIrfpar",
"getSpecdisppar",
"getParmu",
"getPartau",
"getKinscal",
"getPrel",
"getJvec"
};
String[] slotsName = {
"Kinetic parameters",
"Spectral parameters",
"Irf parameters",
"Specdisppar",
"Parmu",
"Partau",
"Kinscal",
"Prel",
"J vector"
};
double[] params = null;
for (int k = 0; k < slots.length; k++) {
try {
try {
for (int i = 0; i < results.length; i++) {
// TODO: verify the next line
// params = (double[]) results[i].getClass().getMethod(slots[k], new
// Class[]{results[i].getClass().getClass()}).invoke(results[i], new
// Object[]{results});
params =
(double[])
results[i].getClass().getMethod(slots[k], null).invoke(results[i], null);
if (params != null) {
if (i == 0) {
outputWriter.newLine();
outputWriter.append("Estimated " + slotsName[k] + ": ");
}
outputWriter.append("Dataset" + (i + 1) + ": ");
for (int j = 0; j < params.length / 2; j++) {
if (j > 0) {
outputWriter.append(", ");
}
outputWriter.append((new Formatter().format("%g", params[j])).toString());
}
outputWriter.newLine();
outputWriter.append("Standard errors: ");
for (int j = 0; j < params.length / 2; j++) {
if (j > 0) {
outputWriter.append(", ");
}
outputWriter.append(
(new Formatter().format("%g", params[j + params.length / 2])).toString());
}
outputWriter.newLine();
}
}
} catch (IllegalAccessException ex) {
Exceptions.printStackTrace(ex);
} catch (IllegalArgumentException ex) {
Exceptions.printStackTrace(ex);
} catch (InvocationTargetException ex) {
Exceptions.printStackTrace(ex);
}
} catch (NoSuchMethodException ex) {
Exceptions.printStackTrace(ex);
} catch (SecurityException ex) {
Exceptions.printStackTrace(ex);
}
}
} else {
outputWriter.newLine();
outputWriter.append("Error: The analysis did not return valid results.");
outputWriter.newLine();
outputWriter.append("Try again with different parameters.");
}
outputWriter.close();
}
public boolean generateTarget(ProgressHandle ph, String target) {
if (mapping.getServiceMapping(target) != null) {
String msg = NbBundle.getMessage(ClientJavonTemplate.class, "MSG_Client"); // NOI18N
ph.progress(msg);
OutputLogger.getInstance().log(msg);
mapping.setProperty("target", "client");
JavonMapping.Service service = mapping.getServiceMapping(target);
FileObject outputDir =
FileUtil.toFileObject(
FileUtil.normalizeFile(new File(mapping.getClientMapping().getOutputDirectory())));
outputDir =
outputDir.getFileObject(mapping.getClientMapping().getPackageName().replace('.', '/'));
FileObject outputFile =
outputDir.getFileObject(mapping.getClientMapping().getClassName(), "java");
if (outputFile == null) {
OutputLogger.getInstance()
.log(
MessageFormat.format(
NbBundle.getMessage(ClientJavonTemplate.class, "MSG_ClientJavonCreation"),
mapping.getClientMapping().getClassName())); // NOI18N
try {
outputFile = outputDir.createData(mapping.getClientMapping().getClassName(), "java");
} catch (IOException e) {
OutputLogger.getInstance()
.log(
LogLevel.ERROR,
MessageFormat.format(
NbBundle.getMessage(ClientJavonTemplate.class, "MSG_FailClientJavonCreation"),
mapping.getClientMapping().getClassName())); // NOI18N
}
}
OutputFileFormatter off = null;
try {
off = new OutputFileFormatter(outputFile);
} catch (DataObjectNotFoundException e) {
generationFailed(e, outputFile);
return false;
} catch (IOException e) {
generationFailed(e, outputFile);
return false;
}
ScriptEngineManager mgr = new ScriptEngineManager();
ScriptEngine eng = mgr.getEngineByName("freemarker");
Bindings bind = eng.getContext().getBindings(ScriptContext.ENGINE_SCOPE);
FileObject template = FileUtil.getConfigFile("Templates/Client/Client.java");
OutputLogger.getInstance()
.log(NbBundle.getMessage(ClientJavonTemplate.class, "MSG_ConfigureBindings")); // NOI18N
Set<ClassData> returnTypes = service.getReturnTypes();
Set<ClassData> parameterTypes = service.getParameterTypes();
bind.put("mapping", mapping);
bind.put("registry", mapping.getRegistry());
bind.put("returnTypes", returnTypes);
bind.put("parameterTypes", parameterTypes);
bind.put("service", service);
bind.put("utils", new Utils(mapping.getRegistry()));
// Compute imports for JavaBeans
Set<String> imports = new HashSet<String>();
for (ClassData cd : parameterTypes) {
while (cd.isArray()) {
cd = cd.getComponentType();
}
if (cd.isPrimitive()) continue;
if (cd.getPackage().equals("java.lang")) continue;
if (cd.getFullyQualifiedName().equals("java.util.List")) continue;
imports.add(cd.getFullyQualifiedName());
}
for (ClassData cd : returnTypes) {
while (cd.isArray()) {
cd = cd.getComponentType();
}
if (cd.isPrimitive()) continue;
if (cd.getPackage().equals("java.lang")) continue;
if (cd.getFullyQualifiedName().equals("java.util.List")) continue;
imports.add(cd.getFullyQualifiedName());
}
bind.put("imports", imports);
OutputLogger.getInstance()
.log(
MessageFormat.format(
NbBundle.getMessage(ClientBeanGeneratorTemplate.class, "MSG_GenerateJavonClient"),
FileUtil.toFile(outputFile))); // NOI18N
Writer w = null;
Reader is = null;
try {
try {
w = new StringWriter();
is = new InputStreamReader(template.getInputStream());
eng.getContext().setWriter(w);
eng.getContext()
.setAttribute(FileObject.class.getName(), template, ScriptContext.ENGINE_SCOPE);
eng.getContext()
.setAttribute(
ScriptEngine.FILENAME, template.getNameExt(), ScriptContext.ENGINE_SCOPE);
eng.eval(is);
} catch (FileNotFoundException e) {
OutputLogger.getInstance().log(e);
ErrorManager.getDefault().notify(e);
return false;
} catch (ScriptException e) {
OutputLogger.getInstance().log(e);
ErrorManager.getDefault().notify(e);
return false;
} finally {
if (w != null) {
off.write(w.toString());
// System.err.println( "" + w.toString());
w.close();
}
if (is != null) is.close();
off.close();
}
} catch (IOException e) {
generationFailed(e, FileUtil.toFile(outputFile));
return false;
}
OutputLogger.getInstance()
.log(
MessageFormat.format(
NbBundle.getMessage(ClientJavonTemplate.class, "MSG_ClientGenerated"),
FileUtil.toFile(outputFile)));
}
return true;
}