/** INTERNAL: Creates a directory with some nested directories and some files. */
protected File createNestedDirectory() throws IOException {
// Structure:
//
// FILEUTILS_DIR1
// FILEUTILS_DIR2a
// FILEUTILS_DIR3
// temp_file
// FILEUTILS_DIR2b
// temp_file1
// temp_file2
// DIR1
File dir1 = new File(testdir, "FILEUTILS_DIR1");
dir1.mkdir();
// DIR1/DIR2A
File dir2a = new File(dir1, "FILEUTILS_DIR2a");
dir2a.mkdir();
// DIR1/DIR2A/DIR3
File dir3 = new File(dir2a, "FILEUTILS_DIR3");
dir3.mkdir();
File file3 = File.createTempFile("FILEUTILS", "TEST", dir3);
// DIR1/DIR2B
File dir2b = new File(dir1, "FILEUTILS_DIR2b");
dir2b.mkdir();
File file2b1 = File.createTempFile("FILEUTILS", "TEST", dir2b);
File file2b2 = File.createTempFile("FILEUTILS", "TEST", dir2b);
// Return the top level directory
return dir1;
}
/** @see java.net.URLStreamHandler#openConnection(URL) */
protected URLConnection openConnection(URL u) throws IOException {
try {
URL otherURL = new URL(u.getFile());
String host = otherURL.getHost();
String protocol = otherURL.getProtocol();
int port = otherURL.getPort();
String file = otherURL.getFile();
String query = otherURL.getQuery();
// System.out.println("Trying to load: " + u.toExternalForm());
String internalFile = null;
if (file.indexOf("!/") != -1) {
internalFile = file.substring(file.indexOf("!/") + 2);
file = file.substring(0, file.indexOf("!/"));
}
URL subURL = new URL(protocol, host, port, file);
File newFile;
if (cacheList.containsKey(subURL.toExternalForm())) {
newFile = cacheList.get(subURL.toExternalForm());
} else {
InputStream is = (InputStream) subURL.getContent();
String update = subURL.toExternalForm().replace(":", "_");
update = update.replace("/", "-");
File f = File.createTempFile("pack", update);
f.deleteOnExit();
FileOutputStream fostream = new FileOutputStream(f);
copyStream(new BufferedInputStream(is), fostream);
// Unpack
newFile = File.createTempFile("unpack", update);
newFile.deleteOnExit();
fostream = new FileOutputStream(newFile);
BufferedOutputStream bos = new BufferedOutputStream(fostream, 50 * 1024);
JarOutputStream jostream = new JarOutputStream(bos);
Unpacker unpacker = Pack200.newUnpacker();
long start = System.currentTimeMillis();
unpacker.unpack(f, jostream);
printMessage(
"Unpack of " + update + " took " + (System.currentTimeMillis() - start) + "ms");
jostream.close();
fostream.close();
cacheList.put(subURL.toExternalForm(), newFile);
}
if (internalFile != null) {
URL directoryURL = new URL("jar:" + newFile.toURL().toExternalForm() + "!/" + internalFile);
printMessage("Using DirectoryURL:" + directoryURL);
return directoryURL.openConnection();
} else return newFile.toURL().openConnection();
} catch (Exception ex) {
ex.printStackTrace();
}
printMessage("Returning null for: " + u.toExternalForm());
return null;
}
@BeforeTest
void setupBuilder() throws IOException {
tempSamFileChrM_O = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileAllChr = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileChrM_O.deleteOnExit();
tempSamFileAllChr.deleteOnExit();
final File tempSamFileUnsorted = File.createTempFile("CollectGcBias", ".bam", TEST_DIR);
tempSamFileUnsorted.deleteOnExit();
final SAMFileHeader header = new SAMFileHeader();
try {
header.setSequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(dict));
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
} catch (final SAMException e) {
e.printStackTrace();
}
// build different levels to put into the same bam file for testing multi level collection
setupTest1(
1,
readGroupId1,
readGroupRecord1,
sample1,
library1,
header,
setBuilder1); // Sample 1, Library 1, RG 1
setupTest1(
2,
readGroupId2,
readGroupRecord2,
sample1,
library2,
header,
setBuilder2); // Sample 1, Library 2, RG 2
setupTest1(
3,
readGroupId3,
readGroupRecord3,
sample2,
library3,
header,
setBuilder3); // Sample 2, Library 3, RG 3
// build one last readgroup for comparing that window count stays the same whether you use all
// contigs or not
setupTest2(1, readGroupId1, readGroupRecord1, sample1, library1, header, setBuilder4);
final List<SAMRecordSetBuilder> test1Builders = new ArrayList<SAMRecordSetBuilder>();
test1Builders.add(setBuilder1);
test1Builders.add(setBuilder2);
test1Builders.add(setBuilder3);
final List<SAMRecordSetBuilder> test2Builders = new ArrayList<SAMRecordSetBuilder>();
test2Builders.add(setBuilder4);
tempSamFileChrM_O = build(test1Builders, tempSamFileUnsorted, header);
tempSamFileAllChr = build(test2Builders, tempSamFileUnsorted, header);
}
@Before
public void setUp() throws IOException {
firstFastqFile = File.createTempFile("interleaveFastqTest", ".fq.gz");
secondFastqFile = File.createTempFile("interleaveFastqTest", ".fq.gz");
pairedFile = File.createTempFile("interleaveFastqTest", ".fq");
unpairedFile = File.createTempFile("interleaveFastqTest", ".fq");
}
/**
* testStringFunction
*
* @throws IOException
*/
public void testBackgroundProposals() throws IOException {
File bundleFile = File.createTempFile("editor_unit_tests", "rb");
bundleFile.deleteOnExit();
BundleElement bundleElement = new BundleElement(bundleFile.getAbsolutePath());
bundleElement.setDisplayName("Editor Unit Tests");
File f = File.createTempFile("snippet", "rb");
SnippetElement se =
createSnippet(f.getAbsolutePath(), "background-color-template", "background", "source.css");
bundleElement.addChild(se);
BundleManager.getInstance().addBundle(bundleElement);
// note template is interleaved into proposals
this.checkProposals(
"contentAssist/background.css",
true,
true,
"backface-visibility",
"background",
"background-attachment",
"background-clip",
"background-color",
"background-color-template",
"background-image",
"background-origin",
"background-position",
"background-position-x",
"background-position-y",
"background-repeat",
"background-size");
BundleManager.getInstance().unloadScript(f);
}
/**
* tests case when Main-Class is not in the zip launched but in another zip referenced by
* Class-Path
*
* @throws Exception in case of troubles
*/
public void test_main_class_in_another_zip() throws Exception {
File fooZip = File.createTempFile("hyts_", ".zip");
File barZip = File.createTempFile("hyts_", ".zip");
fooZip.deleteOnExit();
barZip.deleteOnExit();
// create the manifest
Manifest man = new Manifest();
Attributes att = man.getMainAttributes();
att.put(Attributes.Name.MANIFEST_VERSION, "1.0");
att.put(Attributes.Name.MAIN_CLASS, "foo.bar.execjartest.Foo");
att.put(Attributes.Name.CLASS_PATH, fooZip.getName());
File resources = Support_Resources.createTempFolder();
ZipOutputStream zoutFoo = new ZipOutputStream(new FileOutputStream(fooZip));
zoutFoo.putNextEntry(new ZipEntry("foo/bar/execjartest/Foo.class"));
zoutFoo.write(getResource(resources, "hyts_Foo.ser"));
zoutFoo.close();
ZipOutputStream zoutBar = new ZipOutputStream(new FileOutputStream(barZip));
zoutBar.putNextEntry(new ZipEntry("META-INF/MANIFEST.MF"));
man.write(zoutBar);
zoutBar.putNextEntry(new ZipEntry("foo/bar/execjartest/Bar.class"));
zoutBar.write(getResource(resources, "hyts_Bar.ser"));
zoutBar.close();
String[] args = new String[] {"-jar", barZip.getAbsolutePath()};
// execute the JAR and read the result
String res = Support_Exec.execJava(args, null, false);
assertTrue("Error executing JAR : result returned was incorrect.", res.startsWith("FOOBAR"));
}
public static File tmpdir() {
try {
File file = null;
try {
file = File.createTempFile("temp", "dir");
} catch (Throwable e) {
// Use a local tmp directory
final File tmp = new File("tmp");
if (!tmp.exists() && !tmp.mkdirs()) {
throw new IOException("Failed to create local tmp directory: " + tmp.getAbsolutePath());
}
file = File.createTempFile("temp", "dir", tmp);
}
if (!file.delete()) {
throw new IOException("Failed to create temp dir. Delete failed");
}
mkdir(file);
deleteOnExit(file);
return file;
} catch (IOException e) {
throw new FileRuntimeException(e);
}
}
/**
* Test the creation of a profile which depends on another profile. Doesn't use the {@link
* ProfileMother#createXmiDependentProfile(File, ProfileMother.DependencyCreator, File, String)}
* method, but, it serves as good executable documentation of how this is done as a whole.
*
* @throws IOException When saving the profile models fails.
* @throws UmlException When something in the model subsystem goes wrong.
*/
public void testXmiDependentProfile() throws IOException, UmlException {
Object model = mother.createSimpleProfileModel();
File file = File.createTempFile("simple-profile", ".xmi");
mother.saveProfileModel(model, file);
XmiReader xmiReader = Model.getXmiReader();
xmiReader.addSearchPath(file.getParent());
InputSource pIs = new InputSource(file.toURI().toURL().toExternalForm());
pIs.setPublicId(file.getName());
Collection simpleModelTopElements = xmiReader.parse(pIs, true);
Object model2 = mother.createSimpleProfileModel();
Object theClass = Model.getCoreFactory().buildClass("TheClass", model2);
Collection stereotypes = getFacade().getStereotypes(simpleModelTopElements.iterator().next());
Object stereotype = stereotypes.iterator().next();
Model.getCoreHelper().addStereotype(theClass, stereotype);
File dependentProfileFile = File.createTempFile("dependent-profile", ".xmi");
mother.saveProfileModel(model2, dependentProfileFile);
assertTrue(
"The file to where the file was supposed to be saved " + "doesn't exist.",
dependentProfileFile.exists());
assertStringInLineOfFile(
"The name of the file which contains the profile "
+ "from which the dependent profile depends must occur in the "
+ "file.",
file.getName(),
dependentProfileFile);
// Clean up our two models and the extent that we read profile in to
Model.getUmlFactory().delete(model);
Model.getUmlFactory().delete(model2);
Model.getUmlFactory().deleteExtent(simpleModelTopElements.iterator().next());
}
@SuppressFBWarnings(
value = "RV_RETURN_VALUE_IGNORED_BAD_PRACTICE",
justification = "createTempFile will fail anyway if there is a problem with mkdirs")
private String createLocalSocketAddress() throws IOException {
String name;
if (temp != null) {
temp.mkdirs();
}
if (OsUtils.isUNIX()) {
File socket = File.createTempFile("ssh", "", temp);
if (socket.getAbsolutePath().length() >= /*UNIX_PATH_MAX*/ 108) {
LOGGER.log(
Level.WARNING,
"Cannot use {0} due to UNIX_PATH_MAX; falling back to system temp dir",
socket);
socket = File.createTempFile("ssh", "");
}
FileUtils.deleteQuietly(socket);
name = socket.getAbsolutePath();
} else {
File socket = File.createTempFile("ssh", "", temp);
FileUtils.deleteQuietly(socket);
name = "\\\\.\\pipe\\" + socket.getName();
}
return name;
}
@Override
public void export(
MolgenisRequest request,
String fileName,
TupleTable tupleTable,
int totalPages,
int currentPage)
throws TableException, IOException {
try {
final File tempDir = new File(System.getProperty("java.io.tmpdir"));
final File spssFile = File.createTempFile("spssExport", ".sps", tempDir);
final File spssCsvFile = File.createTempFile("csvSpssExport", ".csv", tempDir);
// TODO: instruction .txt file.
final File zipExport = File.createTempFile("spssExport", ".zip", tempDir);
final FileOutputStream spssFileStream = new FileOutputStream(spssFile);
final FileOutputStream spssCsvFileStream = new FileOutputStream(spssCsvFile);
final SPSSExporter spssExporter = new SPSSExporter(tupleTable);
spssExporter.export(spssCsvFileStream, spssFileStream, spssCsvFile.getName());
spssCsvFileStream.close();
spssFileStream.close();
ZipUtils.compress(
Arrays.asList(spssFile, spssCsvFile), zipExport, DirectoryStructure.EXCLUDE_DIR);
HeaderHelper.setHeader(
request.getResponse(), "application/octet-stream", fileName + ".zip");
exportFile(zipExport, request.getResponse());
} catch (Exception e) {
throw new TableException(e);
}
}
@Test
public void testZipAndUnzipDirectory() throws IOException {
File basedir = File.createTempFile(ZipUtils.class.getSimpleName(), ".tmp");
basedir.delete();
assertTrue("Could not create temporary base directory.", basedir.mkdir());
for (int i = 0; i < 5; i++) {
createSubDirWithFiles(basedir, i);
}
File zipFile = File.createTempFile(ZipUtils.class.getSimpleName(), ".zip");
ZipArchiveOutputStream zipOutputStream =
new ZipArchiveOutputStream(new FileOutputStream(zipFile));
ZipUtils.addFilesToZipRecursively("mybase", basedir, null, zipOutputStream);
zipOutputStream.close();
final File unzipBase = File.createTempFile(ZipUtils.class.getSimpleName(), ".unzipped");
ZipUtils.unzip(zipFile, unzipBase);
IOUtils.processFiles(
unzipBase,
new FileProcessor() {
public void process(File file) {
try {
assertEquals(
IOUtils.getFileIdentifier(unzipBase, file), FileUtils.readFileToString(file));
} catch (IOException e) {
throw new RuntimeException("Could not process file.", e);
}
}
},
null);
}
@Test
public void testRun_setsErrorThrowableForParamSubstitution() {
File outputFile = null;
try {
String filename =
this.getClass().getSimpleName() + "_" + "testRun_setsErrorThrowableForParamSubstitution";
outputFile = File.createTempFile(filename, ".out");
outputFile.delete();
File scriptFile = File.createTempFile(filename, ".pig");
BufferedWriter bw = new BufferedWriter(new FileWriter(scriptFile));
bw.write("a = load '$NOEXIST';\n");
bw.write("b = group a by $0\n");
bw.write("c = foreach b generate group, COUNT(a) as cnt;\n");
bw.write("store c into 'out'\n");
bw.close();
Main.run(new String[] {"-x", "local", scriptFile.getAbsolutePath()}, null);
PigStats stats = PigStats.get();
Throwable t = stats.getErrorThrowable();
assertTrue(t instanceof IOException);
Throwable cause = t.getCause();
assertTrue(cause instanceof ParameterSubstitutionException);
ParameterSubstitutionException pse = (ParameterSubstitutionException) cause;
assertTrue(pse.getMessage().contains("NOEXIST"));
} catch (Exception e) {
log.error("Encountered exception", e);
fail("Encountered Exception");
}
}
public static Map<String, Object> createSslConfig(
boolean useClientCert, boolean trustStore, Mode mode, File trustStoreFile, String certAlias)
throws IOException, GeneralSecurityException {
Map<String, X509Certificate> certs = new HashMap<String, X509Certificate>();
File keyStoreFile;
Password password;
if (mode == Mode.SERVER) password = new Password("ServerPassword");
else password = new Password("ClientPassword");
Password trustStorePassword = new Password("TrustStorePassword");
if (useClientCert) {
keyStoreFile = File.createTempFile("clientKS", ".jks");
KeyPair cKP = generateKeyPair("RSA");
X509Certificate cCert = generateCertificate("CN=localhost, O=client", cKP, 30, "SHA1withRSA");
createKeyStore(keyStoreFile.getPath(), password, "client", cKP.getPrivate(), cCert);
certs.put(certAlias, cCert);
} else {
keyStoreFile = File.createTempFile("serverKS", ".jks");
KeyPair sKP = generateKeyPair("RSA");
X509Certificate sCert = generateCertificate("CN=localhost, O=server", sKP, 30, "SHA1withRSA");
createKeyStore(keyStoreFile.getPath(), password, password, "server", sKP.getPrivate(), sCert);
certs.put(certAlias, sCert);
}
if (trustStore) {
createTrustStore(trustStoreFile.getPath(), trustStorePassword, certs);
}
Map<String, Object> sslConfig =
createSslConfig(mode, keyStoreFile, password, password, trustStoreFile, trustStorePassword);
return sslConfig;
}
public static void openAttachment(
final Project project, String name, EntityRef parent, int size) {
try {
final File file;
boolean agmLink = name.endsWith(".agmlink");
if (agmLink) {
// for the file to open correctly, there must be no trailing extension
file = File.createTempFile("tmp", "_" + name.replaceFirst("\\.agmlink$", ""));
} else {
file = File.createTempFile("tmp", "_" + name);
}
final Runnable openFile =
new Runnable() {
@Override
public void run() {
String url =
VirtualFileManager.constructUrl(
LocalFileSystem.PROTOCOL,
FileUtil.toSystemIndependentName(file.getAbsolutePath()));
final VirtualFile virtualFile =
VirtualFileManager.getInstance().refreshAndFindFileByUrl(url);
UIUtil.invokeLaterIfNeeded(
new Runnable() {
public void run() {
if (virtualFile != null) {
FileEditor[] editors =
project
.getComponent(FileEditorManager.class)
.openFile(virtualFile, true);
if (editors.length > 0) {
return;
}
FileType type =
FileTypeManager.getInstance()
.getKnownFileTypeOrAssociate(virtualFile, project);
if (type instanceof INativeFileType
&& ((INativeFileType) type)
.openFileInAssociatedApplication(project, virtualFile)) {
return;
}
}
Messages.showWarningDialog(
"No editor seems to be associated with this file type. Try to download and open the file manually.",
"Not Supported");
}
});
}
};
if (agmLink) {
ProgressManager.getInstance()
.run(new AttachmentAgmLinkDownloadTask(project, file, name, size, parent, openFile));
} else {
ProgressManager.getInstance()
.run(new AttachmentDownloadTask(project, file, name, size, parent, openFile));
}
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public BufferedImage processUsingTemp(InputStream input, DjatokaDecodeParam params)
throws DjatokaException {
File in;
// Copy to tmp file
try {
String cacheDir = OpenURLJP2KService.getCacheDir();
if (cacheDir != null) {
in = File.createTempFile("tmp", ".pdf", new File(cacheDir));
} else {
in = File.createTempFile("tmp", ".pdf");
}
FileOutputStream fos = new FileOutputStream(in);
in.deleteOnExit();
IOUtils.copyStream(input, fos);
} catch (IOException e) {
logger.error(e, e);
throw new DjatokaException(e);
}
BufferedImage bi = process(in.getAbsolutePath(), params);
if (in != null) {
in.delete();
}
return bi;
}
@Test
public void testRedirectionCycle() throws IOException, XMLStreamException {
// source dump
File tmpSrcDump = File.createTempFile("wiki-src-dump", "xml");
File tmpTargetDump = File.createTempFile("wiki-target-dump", "xml");
// base structure - "<mediawiki><page><title></title><id><id></page></mediawiki>"
BufferedWriter bw = new BufferedWriter(new FileWriter(tmpSrcDump));
bw.write(
"<mediawiki>"
+ "<page>"
+ "<title>Test1</title>"
+ "<id>1</id>"
+ "</page>"
+ "<page>"
+ "<title>Test2</title>"
+ "<id>2</id>"
+ "</page>"
+ "<page>"
+ "<title>Test3</title>"
+ "<id>3</id>"
+ "</page>"
+ "</mediawiki>");
bw.close();
bw = new BufferedWriter(new FileWriter(tmpTargetDump));
bw.write(
"<mediawiki>"
+ "<page>"
+ "<title>Test1</title>"
+ "<id>1</id>"
+ "<redirect/>"
+ "<revision>"
+ "<id>1234556</id>"
+ "<text xml:space=\"preserve\">#REDIRECT [[Test3]] {{R from CamelCase}}</text>"
+ "</revision>"
+ "</page>"
+ "<page>"
+ "<title>NEW_Test2</title>"
+ "<id>2</id>"
+ "</page>"
+ "<page>"
+ "<title>Test3</title>"
+ "<id>3</id>"
+ "<redirect/>"
+ "<revision>"
+ "<id>1234556</id>"
+ "<text xml:space=\"preserve\">#REDIRECT [[Test1]] {{R from CamelCase}}</text>"
+ "</revision>"
+ "</page>"
+ "</mediawiki>");
bw.close();
Map<String, String> hshResults = WikipediaRevisionMapper.map(tmpSrcDump, tmpTargetDump);
assertEquals(3, hshResults.size());
// Test1 REDIRECTS TO Test3, but since it forms a cycle, Test1 is mapped to itself
assertEquals(true, !hshResults.get("Test1").equals("Test3"));
tmpSrcDump.delete();
tmpTargetDump.delete();
}
private void updateVersionFile(final Wagon wagon)
throws IOException, TransferFailedException, ResourceDoesNotExistException,
AuthorizationException {
// update the version.txt accordingly
final File versionOldFile = File.createTempFile("version-old", "txt");
final File versionNewFile = File.createTempFile("version-new", "txt");
wagon.get("version.txt", versionOldFile);
boolean updated = false;
// look for our artifactId entry
final BufferedReader reader = new BufferedReader(new FileReader(versionOldFile));
final BufferedWriter writer = new BufferedWriter(new FileWriter(versionNewFile));
for (String line = reader.readLine(); null != line; line = reader.readLine()) {
if (line.equals(project.getArtifactId())) {
updateArtifactEntry(reader, writer);
updated = true;
} else {
// line remains the same
writer.write(line);
writer.newLine();
}
}
if (!updated) {
writer.newLine();
updateArtifactEntry(reader, writer);
}
reader.close();
writer.close();
wagon.put(versionNewFile, "version.txt");
}
@SuppressWarnings("ResultOfMethodCallIgnored")
@Test
public void testUnchangedPageEntries() throws IOException, XMLStreamException {
// source dump
File tmpSrcDump = File.createTempFile("wiki-src-dump", "xml");
File tmpTargetDump = File.createTempFile("wiki-target-dump", "xml");
// base structure - "<mediawiki><page><title></title><id><id></page></mediawiki>"
BufferedWriter bw = new BufferedWriter(new FileWriter(tmpSrcDump));
bw.write(
"<mediawiki><page><title>Test1</title><id>1</id></page><page><title>Test2</title><id>2</id></page></mediawiki>");
bw.close();
bw = new BufferedWriter(new FileWriter(tmpTargetDump));
bw.write(
"<mediawiki><page><title>Test1</title><id>1</id></page><page><title>Test2</title><id>2</id></page></mediawiki>");
bw.close();
// default diff will also include all unchanged entries
Map<String, String> hshResults = WikipediaRevisionMapper.map(tmpSrcDump, tmpTargetDump);
assertEquals(2, hshResults.size());
// setting the flag to false will include unchanged entries
hshResults = WikipediaRevisionMapper.map(tmpSrcDump, tmpTargetDump, false);
assertEquals(0, hshResults.size());
// remove tmp files
tmpSrcDump.delete();
tmpTargetDump.delete();
}
@Override
public void onClick(View v) {
recorder = new MediaRecorder();
String out = new SimpleDateFormat("dd-MM-yyyy hh-mm-ss").format(new Date());
File sampleDir = new File(Environment.getExternalStorageDirectory(), "/TestData");
if (!sampleDir.exists()) {
sampleDir.mkdirs();
}
String file_name = "Record";
try {
if (spinType == "mp3") path = File.createTempFile(file_name + out, ".mp3", sampleDir);
else path = File.createTempFile(file_name + out, ".wav", sampleDir);
} catch (IOException e) {
e.printStackTrace();
}
// path=new File(Environment.getExternalStorageDirectory(),"myRecording.3gpp");
resetRecorder();
try {
recorder.start();
Toast.makeText(MainActivity.this, "Start Record", Toast.LENGTH_SHORT).show();
start.setEnabled(false);
stop.setEnabled(true);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Creates a process builder for the application, using the config, logging, and system
* properties.
*/
ProcessBuilder createProcessBuilder() throws Exception {
/* Create the application configuration file */
File configFile = File.createTempFile("SimpleApp", "config");
OutputStream configOut = new FileOutputStream(configFile);
config.store(configOut, null);
configOut.close();
/* Create the logging configuration file */
File loggingFile = File.createTempFile("SimpleApp", "logging");
OutputStream loggingOut = new FileOutputStream(loggingFile);
logging.store(loggingOut, null);
loggingOut.close();
/* Create the command line for running the Kernel */
List<String> command = new ArrayList<String>();
command.add(System.getProperty("java.home") + "/bin/java");
command.add("-cp");
command.add(System.getProperty("java.class.path"));
command.add("-Djava.util.logging.config.file=" + loggingFile);
command.add("-Djava.library.path=" + System.getProperty("java.library.path"));
Enumeration<?> names = system.propertyNames();
while (names.hasMoreElements()) {
Object name = names.nextElement();
command.add("-D" + name + "=" + system.get(name));
}
command.add("com.sun.sgs.impl.kernel.Kernel");
command.add(configFile.toURI().toURL().getPath());
/* Return the process builder */
return new ProcessBuilder(command);
}
@Test
public void testBamIntegers() throws IOException {
final List<String> errorMessages = new ArrayList<String>();
final SamReader bamReader = SamReaderFactory.makeDefault().open(BAM_INPUT);
final File bamOutput = File.createTempFile("test", ".bam");
final File samOutput = File.createTempFile("test", ".sam");
final SAMFileWriter samWriter =
new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, samOutput, null);
final SAMFileWriter bamWriter =
new SAMFileWriterFactory().makeWriter(bamReader.getFileHeader(), true, bamOutput, null);
final SAMRecordIterator iterator = bamReader.iterator();
while (iterator.hasNext()) {
try {
final SAMRecord rec = iterator.next();
samWriter.addAlignment(rec);
bamWriter.addAlignment(rec);
} catch (final Throwable e) {
System.out.println(e.getMessage());
errorMessages.add(e.getMessage());
}
}
CloserUtil.close(bamReader);
samWriter.close();
bamWriter.close();
Assert.assertEquals(errorMessages.size(), 0);
bamOutput.deleteOnExit();
samOutput.deleteOnExit();
}
/**
* Creates the script file.
*
* @return the string
* @throws Exception the exception
*/
public String createScriptFile() throws Exception {
File tempScriptFile;
if (meta.getGenerateScript()) {
tempScriptFile = File.createTempFile(FilenameUtils.getBaseName(meta.getScriptFileName()), "");
} else {
tempScriptFile =
File.createTempFile(FilenameUtils.getBaseName(meta.getExistingScriptFile()), "");
}
tempScriptFile.deleteOnExit();
try {
scriptFile = FileUtils.openOutputStream(tempScriptFile);
scriptFilePrintStream = new PrintStream(scriptFile);
} catch (IOException e) {
throw new KettleException(
BaseMessages.getString(
PKG, "TeraDataBulkLoaderMeta.Exception.OpenScriptFile", scriptFile),
e);
}
if (meta.getGenerateScript()) {
createGeneratedScriptFile();
} else {
createFromExistingScriptFile();
}
scriptFilePrintStream.close();
IOUtils.closeQuietly(scriptFile);
return tempScriptFile.getAbsolutePath();
}
public void split(File firstHalf, File lastHalf, File source, int page) throws IOException {
File temporal;
if (firstHalf == null && lastHalf == null)
throw new IllegalArgumentException("firstHalf and lastHalf are null");
temporal = null;
if (firstHalf == null)
firstHalf = temporal = File.createTempFile(this.getClass().getName() + '.', ".pdf");
if (lastHalf == null)
lastHalf = temporal = File.createTempFile(this.getClass().getName() + '.', ".pdf");
try {
int result;
result =
this.launch(
"-split",
source.getAbsolutePath(),
firstHalf.getAbsolutePath(),
lastHalf.getAbsolutePath(),
Integer.toString(page, 10));
if (result != 0)
throw new IOException(
String.format("failed on split documents" + " (process exit with %d)", result));
} finally {
if (temporal != null) temporal.delete();
}
}
/** 准备录音 */
private void initRecorder() {
try {
/* 创建一个临时文件，用来存放录音 */
File[] datafiles = SDPathDir.listFiles();
for (File file : datafiles) {
if (!file.isDirectory()) {
if (file.getName().endsWith(".mp3")) {
file.delete();
}
}
}
tempFile = File.createTempFile("tempFile", ".mp3", SDPathDir);
tempFile2 = File.createTempFile("tempFile", ".mp3", SDPathDir);
tempFile3 = File.createTempFile("tempFile", ".mp3", SDPathDir);
tempFile4 = File.createTempFile("tempFile", ".mp3", SDPathDir);
Filename_1 = tempFile.getAbsolutePath();
Filename_2 = tempFile2.getAbsolutePath();
Filename_3 = tempFile3.getAbsolutePath();
Filename_4 = tempFile4.getAbsolutePath();
soundTouchClient.setfilename(Filename_1, Filename_2, Filename_3, Filename_4);
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Prepare file for download
*
* @param response An instance of the Response object
* @throws IOException If fail to prepare file for download
* @return Prepared file for the download
*/
public File prepareDownloadFile(Response response) throws IOException {
String filename = null;
String contentDisposition = response.header("Content-Disposition");
if (contentDisposition != null && !"".equals(contentDisposition)) {
// Get filename from the Content-Disposition header.
Pattern pattern = Pattern.compile("filename=['\"]?([^'\"\\s]+)['\"]?");
Matcher matcher = pattern.matcher(contentDisposition);
if (matcher.find()) {
filename = sanitizeFilename(matcher.group(1));
}
}
String prefix = null;
String suffix = null;
if (filename == null) {
prefix = "download-";
suffix = "";
} else {
int pos = filename.lastIndexOf(".");
if (pos == -1) {
prefix = filename + "-";
} else {
prefix = filename.substring(0, pos) + "-";
suffix = filename.substring(pos);
}
// File.createTempFile requires the prefix to be at least three characters long
if (prefix.length() < 3) prefix = "download-";
}
if (tempFolderPath == null) return File.createTempFile(prefix, suffix);
else return File.createTempFile(prefix, suffix, new File(tempFolderPath));
}
@Test
public void testGetActivityAttachmentFileName() throws Exception {
RuntimeAPI runtimeAPI = AccessorUtil.getRuntimeAPI();
ManagementAPI managementAPI = AccessorUtil.getManagementAPI();
QueryRuntimeAPI queryRuntimeAPI = AccessorUtil.getQueryRuntimeAPI();
File attachmentFile = File.createTempFile("attachment-test", ".txt");
FileOutputStream fileOutputStream = new FileOutputStream(attachmentFile);
fileOutputStream.write("test".getBytes("UTF-8"));
fileOutputStream.close();
ProcessDefinition attachmentProcess =
ProcessBuilder.createProcess("attachment_process", "1.0")
.addAttachment("attachment", attachmentFile.getPath(), attachmentFile.getName())
.addHuman("john")
.addHumanTask("task1", "john")
.addHumanTask("task2", "john")
.addTransition("transition", "task1", "task2")
.done();
BusinessArchive businessArchive = BusinessArchiveFactory.getBusinessArchive(attachmentProcess);
attachmentProcess = managementAPI.deploy(businessArchive);
ProcessInstanceUUID instanceUUID = runtimeAPI.instantiateProcess(attachmentProcess.getUUID());
try {
IFormWorkflowAPI api = FormAPIFactory.getFormWorkflowAPI();
ActivityInstanceUUID activityInstanceUUID = null;
Collection<TaskInstance> tasks =
queryRuntimeAPI.getTaskList(instanceUUID, ActivityState.READY);
for (TaskInstance activityInstance : tasks) {
activityInstanceUUID = activityInstance.getUUID();
}
Assert.assertNotNull(activityInstanceUUID);
String fileName = api.getAttachmentFileName(activityInstanceUUID, "${attachment}", true);
Assert.assertEquals(attachmentFile.getName(), fileName);
runtimeAPI.executeTask(activityInstanceUUID, true);
fileName = api.getAttachmentFileName(activityInstanceUUID, "${attachment}", true);
Assert.assertEquals(attachmentFile.getName(), fileName);
File attachmentFile2 = File.createTempFile("new-attachment-test", ".txt");
tasks = queryRuntimeAPI.getTaskList(instanceUUID, ActivityState.READY);
for (TaskInstance activityInstance : tasks) {
activityInstanceUUID = activityInstance.getUUID();
}
Assert.assertNotNull(activityInstanceUUID);
runtimeAPI.addAttachment(
instanceUUID, "attachment", attachmentFile2.getName(), "test".getBytes("UTF-8"));
fileName = api.getAttachmentFileName(activityInstanceUUID, "${attachment}", true);
Assert.assertEquals(attachmentFile2.getName(), fileName);
} finally {
AccessorUtil.getCommandAPI()
.execute(new WebDeleteDocumentsOfProcessCommand(attachmentProcess.getUUID(), true));
AccessorUtil.getRuntimeAPI().deleteProcessInstance(instanceUUID);
AccessorUtil.getCommandAPI()
.execute(new WebDeleteProcessCommand(attachmentProcess.getUUID()));
}
}
@Test
public void updateImageShouldDeleteOldImage() throws IOException {
final File currentFile = File.createTempFile("avatar", "tests");
currentFile.deleteOnExit();
final Avatar currentAvatar = new Avatar();
currentAvatar.setId(1);
currentAvatar.setAvatarType(AvatarType.AVATAR_GALLERY);
currentAvatar.setFileName(currentFile.getName());
context.checking(
new Expectations() {
{
one(repository).get(1);
will(returnValue(currentAvatar));
atLeast(1).of(config).getApplicationPath();
will(returnValue(currentFile.getParent()));
atLeast(1).of(config).getValue(ConfigKeys.AVATAR_GALLERY_DIR);
will(returnValue(""));
one(config).getBoolean(ConfigKeys.AVATAR_ALLOW_GALLERY);
will(returnValue(true));
one(config).getBoolean(ConfigKeys.AVATAR_ALLOW_UPLOAD);
will(returnValue(true));
one(config).getLong(ConfigKeys.AVATAR_MAX_SIZE);
will(returnValue(10000l));
one(config).getInt(ConfigKeys.AVATAR_MAX_WIDTH);
will(returnValue(800));
one(config).getInt(ConfigKeys.AVATAR_MAX_HEIGHT);
will(returnValue(600));
one(config).getInt(ConfigKeys.AVATAR_MIN_WIDTH);
will(returnValue(1));
one(config).getInt(ConfigKeys.AVATAR_MIN_HEIGHT);
will(returnValue(1));
one(repository).update(currentAvatar);
}
});
File originalFile = new File(this.getClass().getResource("/smilies/smilie.gif").getFile());
File newFile = File.createTempFile("jforum", "tests");
TestCaseUtils.copyFile(originalFile, newFile);
UploadedFile uploadedFile =
new DefaultUploadedFile(new FileInputStream(newFile), newFile.getAbsolutePath(), "");
String oldDiskName = currentAvatar.getFileName();
Avatar newAvatar = new Avatar();
newAvatar.setId(1);
newAvatar.setAvatarType(AvatarType.AVATAR_GALLERY);
service.update(newAvatar, uploadedFile);
context.assertIsSatisfied();
Assert.assertEquals(newAvatar.getAvatarType(), currentAvatar.getAvatarType());
Assert.assertFalse(currentFile.exists());
Assert.assertFalse(currentAvatar.getFileName().equals(oldDiskName));
new File(String.format("%s/%s", currentFile.getParent(), currentAvatar.getFileName())).delete();
}
@Test
public void testSinglePageRedirection() throws IOException, XMLStreamException {
// source dump
File tmpOldDump = File.createTempFile("wiki-src-dump", "xml");
File tmpNewDump = File.createTempFile("wiki-target-dump", "xml");
// base structure - "<mediawiki><page><title></title><id><id></page></mediawiki>"
BufferedWriter bw = new BufferedWriter(new FileWriter(tmpOldDump));
bw.write(
"<mediawiki>"
+ "<page>"
+ "<title>Test1</title>"
+ "<id>1</id>"
+ "<revision>"
+ "<id>1234556</id>"
+ "<text xml:space=\"preserve\">This is entry about Test1 and it will be redirected.</text>"
+ "</revision>"
+ "</page>"
+ "<page>"
+ "<title>Test2</title>"
+ "<id>2</id>"
+ "</page>"
+ "<page>"
+ "<title>Test3</title>"
+ "<id>3</id>"
+ "</page>"
+ "</mediawiki>");
bw.close();
bw = new BufferedWriter(new FileWriter(tmpNewDump));
bw.write(
"<mediawiki>"
+ "<page>"
+ "<title>Test1</title>"
+ "<id>1</id>"
+ "<redirect/>"
+ "<revision>"
+ "<id>1234556</id>"
+ "<text xml:space=\"preserve\">#REDIRECT [[Test3]] {{R from CamelCase}}</text>"
+ "</revision>"
+ "</page>"
+ "<page>"
+ "<title>NEW_Test2</title>"
+ "<id>2</id>"
+ "</page>"
+ "<page>"
+ "<title>Test3</title>"
+ "<id>3</id>"
+ "</page>"
+ "</mediawiki>");
bw.close();
Map<String, String> hshResults = WikipediaRevisionMapper.map(tmpOldDump, tmpNewDump);
assertEquals(3, hshResults.size());
assertEquals("Test3", hshResults.get("Test1"));
tmpNewDump.delete();
tmpOldDump.delete();
}
private IWARProduct createPlainProducttWithLibraries() throws IOException {
IWARProduct product = createPlainProduct();
File testJar = File.createTempFile("test", ".jar");
Path testPath = new Path(testJar.getAbsolutePath());
product.addLibrary(testPath, false);
File bridgeJar = File.createTempFile(SERVLETBRIDGE, ".jar");
Path servletBridgePath = new Path(bridgeJar.getAbsolutePath());
product.addLibrary(servletBridgePath, false);
return product;
}
static {
try {
testSampleDeliveryFile = File.createTempFile("test-sampleDeliveryForm", ".odt");
testSampleBulkInputOdsFile = File.createTempFile("test-sampleBulkInputOds", ".ods");
testSampleBulkInputXlsFile = File.createTempFile("test-sampleBulkInputXls", ".xlsx");
} catch (IOException e) {
e.printStackTrace();
TestCase.fail();
}
}
