/**
* Creates a directory which can not be deleted completely.
*
* <p>Directory structure. The naming is important in that {@link MyFile} is used to return them
* in alphabetical order when listed.
*
* <p>del(+w) | .---------------------------------------, | | | | file1(!w) xSubDir(-rwx)
* ySubDir(+w) zlink | | | | file2(-rwx) file3 | xSubSubDir(-rwx) | file22(-rwx)
*
* @throws IOException
*/
private void setupDirsAndNonWritablePermissions() throws IOException {
Assert.assertFalse("The directory del should not have existed!", del.exists());
del.mkdirs();
new MyFile(del, file1Name).createNewFile();
// "file1" is non-deletable by default, see MyFile.delete().
xSubDir.mkdirs();
file2.createNewFile();
xSubSubDir.mkdirs();
file22.createNewFile();
revokePermissions(file22);
revokePermissions(xSubSubDir);
revokePermissions(file2);
revokePermissions(xSubDir);
ySubDir.mkdirs();
file3.createNewFile();
Assert.assertFalse("The directory tmp should not have existed!", tmp.exists());
tmp.mkdirs();
File tmpFile = new File(tmp, FILE);
tmpFile.createNewFile();
FileUtil.symLink(tmpFile.toString(), zlink.toString());
}
/**
* Creates multiple directories for testing.
*
* <p>Contents of them are dir:tmp: file: x dir:del: file: x dir: dir1 : file:x dir: dir2 : file:x
* link: y to tmp/x link: tmpDir to tmp dir:partitioned: file: part-r-00000, contents: "foo" file:
* part-r-00001, contents: "bar"
*/
private void setupDirs() throws IOException {
Assert.assertFalse(del.exists());
Assert.assertFalse(tmp.exists());
Assert.assertFalse(partitioned.exists());
del.mkdirs();
tmp.mkdirs();
partitioned.mkdirs();
new File(del, FILE).createNewFile();
File tmpFile = new File(tmp, FILE);
tmpFile.createNewFile();
// create directories
dir1.mkdirs();
dir2.mkdirs();
new File(dir1, FILE).createNewFile();
new File(dir2, FILE).createNewFile();
// create a symlink to file
File link = new File(del, LINK);
FileUtil.symLink(tmpFile.toString(), link.toString());
// create a symlink to dir
File linkDir = new File(del, "tmpDir");
FileUtil.symLink(tmp.toString(), linkDir.toString());
Assert.assertEquals(5, del.listFiles().length);
// create files in partitioned directories
createFile(partitioned, "part-r-00000", "foo");
createFile(partitioned, "part-r-00001", "bar");
// create a cycle using symlinks. Cycles should be handled
FileUtil.symLink(del.toString(), dir1.toString() + "/cycle");
}
/**
* Tests if fullyDelete deletes (a) dangling symlink to file properly (b) dangling symlink to
* directory properly
*
* @throws IOException
*/
@Test(timeout = 30000)
public void testFullyDeleteDanglingSymlinks() throws IOException {
setupDirs();
// delete the directory tmp to make tmpDir a dangling link to dir tmp and
// to make y as a dangling link to file tmp/x
boolean ret = FileUtil.fullyDelete(tmp);
Assert.assertTrue(ret);
Assert.assertFalse(tmp.exists());
// dangling symlink to file
File link = new File(del, LINK);
Assert.assertEquals(5, del.list().length);
// Even though 'y' is dangling symlink to file tmp/x, fullyDelete(y)
// should delete 'y' properly.
ret = FileUtil.fullyDelete(link);
Assert.assertTrue(ret);
Assert.assertEquals(4, del.list().length);
// dangling symlink to directory
File linkDir = new File(del, "tmpDir");
// Even though tmpDir is dangling symlink to tmp, fullyDelete(tmpDir) should
// delete tmpDir properly.
ret = FileUtil.fullyDelete(linkDir);
Assert.assertTrue(ret);
Assert.assertEquals(3, del.list().length);
}
private void doUntarAndVerify(File tarFile, File untarDir) throws IOException {
if (untarDir.exists() && !FileUtil.fullyDelete(untarDir)) {
throw new IOException("Could not delete directory '" + untarDir + "'");
}
FileUtil.unTar(tarFile, untarDir);
String parentDir = untarDir.getCanonicalPath() + Path.SEPARATOR + "name";
File testFile = new File(parentDir + Path.SEPARATOR + "version");
Assert.assertTrue(testFile.exists());
Assert.assertTrue(testFile.length() == 0);
String imageDir = parentDir + Path.SEPARATOR + "image";
testFile = new File(imageDir + Path.SEPARATOR + "fsimage");
Assert.assertTrue(testFile.exists());
Assert.assertTrue(testFile.length() == 157);
String currentDir = parentDir + Path.SEPARATOR + "current";
testFile = new File(currentDir + Path.SEPARATOR + "fsimage");
Assert.assertTrue(testFile.exists());
Assert.assertTrue(testFile.length() == 4331);
testFile = new File(currentDir + Path.SEPARATOR + "edits");
Assert.assertTrue(testFile.exists());
Assert.assertTrue(testFile.length() == 1033);
testFile = new File(currentDir + Path.SEPARATOR + "fstime");
Assert.assertTrue(testFile.exists());
Assert.assertTrue(testFile.length() == 8);
}
@Test(timeout = 30000)
public void testListAPI() throws IOException {
setupDirs();
// Test existing files case
String[] files = FileUtil.list(partitioned);
Assert.assertEquals("Unexpected number of pre-existing files", 2, files.length);
// Test existing directory with no files case
File newDir = new File(tmp.getPath(), "test");
newDir.mkdir();
Assert.assertTrue("Failed to create test dir", newDir.exists());
files = FileUtil.list(newDir);
Assert.assertEquals("New directory unexpectedly contains files", 0, files.length);
newDir.delete();
Assert.assertFalse("Failed to delete test dir", newDir.exists());
// Test non-existing directory case, this throws
// IOException
try {
files = FileUtil.list(newDir);
Assert.fail("IOException expected on list() for non-existent dir " + newDir.toString());
} catch (IOException ioe) {
// Expected an IOException
}
}
private void cleanupImpl() throws IOException {
FileUtil.fullyDelete(del, true);
Assert.assertTrue(!del.exists());
FileUtil.fullyDelete(tmp, true);
Assert.assertTrue(!tmp.exists());
FileUtil.fullyDelete(partitioned, true);
Assert.assertTrue(!partitioned.exists());
}
@Test(timeout = 30000)
/*
* Test method copy(FileSystem srcFS, Path src, File dst, boolean deleteSource, Configuration conf)
*/
public void testCopy5() throws IOException {
setupDirs();
URI uri = tmp.toURI();
Configuration conf = new Configuration();
FileSystem fs = FileSystem.newInstance(uri, conf);
final String content = "some-content";
File srcFile = createFile(tmp, "src", content);
Path srcPath = new Path(srcFile.toURI());
// copy regular file:
final File dest = new File(del, "dest");
boolean result = FileUtil.copy(fs, srcPath, dest, false, conf);
assertTrue(result);
assertTrue(dest.exists());
assertEquals(
content.getBytes().length + System.getProperty("line.separator").getBytes().length,
dest.length());
assertTrue(srcFile.exists()); // should not be deleted
// copy regular file, delete src:
dest.delete();
assertTrue(!dest.exists());
result = FileUtil.copy(fs, srcPath, dest, true, conf);
assertTrue(result);
assertTrue(dest.exists());
assertEquals(
content.getBytes().length + System.getProperty("line.separator").getBytes().length,
dest.length());
assertTrue(!srcFile.exists()); // should be deleted
// copy a dir:
dest.delete();
assertTrue(!dest.exists());
srcPath = new Path(partitioned.toURI());
result = FileUtil.copy(fs, srcPath, dest, true, conf);
assertTrue(result);
assertTrue(dest.exists() && dest.isDirectory());
File[] files = dest.listFiles();
assertTrue(files != null);
assertEquals(2, files.length);
for (File f : files) {
assertEquals(3 + System.getProperty("line.separator").getBytes().length, f.length());
}
assertTrue(!partitioned.exists()); // should be deleted
}
/**
* Test that getDU is able to handle cycles caused due to symbolic links and that directory sizes
* are not added to the final calculated size
*
* @throws IOException
*/
@Test(timeout = 30000)
public void testGetDU() throws Exception {
setupDirs();
long du = FileUtil.getDU(TEST_DIR);
// Only two files (in partitioned). Each has 3 characters + system-specific
// line separator.
final long expected = 2 * (3 + System.getProperty("line.separator").length());
Assert.assertEquals(expected, du);
// target file does not exist:
final File doesNotExist = new File(tmp, "QuickBrownFoxJumpsOverTheLazyDog");
long duDoesNotExist = FileUtil.getDU(doesNotExist);
assertEquals(0, duDoesNotExist);
// target file is not a directory:
File notADirectory = new File(partitioned, "part-r-00000");
long duNotADirectoryActual = FileUtil.getDU(notADirectory);
long duNotADirectoryExpected = 3 + System.getProperty("line.separator").length();
assertEquals(duNotADirectoryExpected, duNotADirectoryActual);
try {
// one of target files is not accessible, but the containing directory
// is accessible:
try {
FileUtil.chmod(notADirectory.getAbsolutePath(), "0000");
} catch (InterruptedException ie) {
// should never happen since that method never throws InterruptedException.
assertNull(ie);
}
assertFalse(FileUtil.canRead(notADirectory));
final long du3 = FileUtil.getDU(partitioned);
assertEquals(expected, du3);
// some target files and containing directory are not accessible:
try {
FileUtil.chmod(partitioned.getAbsolutePath(), "0000");
} catch (InterruptedException ie) {
// should never happen since that method never throws InterruptedException.
assertNull(ie);
}
assertFalse(FileUtil.canRead(partitioned));
final long du4 = FileUtil.getDU(partitioned);
assertEquals(0, du4);
} finally {
// Restore the permissions so that we can delete the folder
// in @After method:
FileUtil.chmod(partitioned.getAbsolutePath(), "0777", true /*recursive*/);
}
}
@Test(timeout = 30000)
public void testCreateLocalTempFile() throws IOException {
setupDirs();
final File baseFile = new File(tmp, "base");
File tmp1 = FileUtil.createLocalTempFile(baseFile, "foo", false);
File tmp2 = FileUtil.createLocalTempFile(baseFile, "foo", true);
assertFalse(tmp1.getAbsolutePath().equals(baseFile.getAbsolutePath()));
assertFalse(tmp2.getAbsolutePath().equals(baseFile.getAbsolutePath()));
assertTrue(tmp1.exists() && tmp2.exists());
assertTrue(tmp1.canWrite() && tmp2.canWrite());
assertTrue(tmp1.canRead() && tmp2.canRead());
tmp1.delete();
tmp2.delete();
assertTrue(!tmp1.exists() && !tmp2.exists());
}
@Test(timeout = 30000)
public void testSymlink() throws Exception {
Assert.assertFalse(del.exists());
del.mkdirs();
byte[] data = "testSymLink".getBytes();
File file = new File(del, FILE);
File link = new File(del, "_link");
// write some data to the file
FileOutputStream os = new FileOutputStream(file);
os.write(data);
os.close();
// create the symlink
FileUtil.symLink(file.getAbsolutePath(), link.getAbsolutePath());
// ensure that symlink length is correctly reported by Java
Assert.assertEquals(data.length, file.length());
Assert.assertEquals(data.length, link.length());
// ensure that we can read from link.
FileInputStream in = new FileInputStream(link);
long len = 0;
while (in.read() > 0) {
len++;
}
in.close();
Assert.assertEquals(data.length, len);
}
@Test
public void testExampleJson() throws Exception {
String json = FileUtil.readFileFromClasspath("json-examples/agreement-updated-example.json");
JsonMessage jsonMessage = new JsonMessage(json);
ServiceResult serviceResult = new ServiceResult();
serviceResult.setRawData(jsonMessage);
ServiceResult result = (ServiceResult) transformer.doTransform(serviceResult, "UTF-8");
AgreementUpdated agreementUpdated =
(AgreementUpdated) result.getIntegrationMessage().getDomainObject();
Agreement agreement = agreementUpdated.getAgreement();
collector.checkThat(agreement.getCurrencyCode().getCurrencyCode(), is("SEK"));
collector.checkThat(
agreement.getDocumentLink(), is("\\\\someserver\\somefolder\\somefile.pdf"));
collector.checkThat(agreement.getClientId(), is("Cl42824050"));
collector.checkThat(agreement.getDescription(), is("Agreement Name Example"));
collector.checkThat(agreement.getSourceSystemAgreementId(), is("1-1234567896"));
collector.checkThat(
agreement.getValidFrom().getTimestamp(), is("2012-06-25T15:30:01.999+02:00"));
collector.checkThat(agreement.getValidTo(), nullValue());
collector.checkThat(
agreement.getInvoicingRuleId().getGuid(), is("3f2504e0-4f89-11d3-9a0c-0305e82c3401"));
collector.checkThat(agreement.getMarketId().getOrganizationId(), is(51));
collector.checkThat(agreement.getProductType().getValue(), is(3));
}
@Test(timeout = 30000)
public void testFailFullyDeleteContentsGrantPermissions() throws IOException {
setupDirsAndNonWritablePermissions();
boolean ret = FileUtil.fullyDeleteContents(new MyFile(del), true);
// this time the directories with revoked permissions *should* be deleted:
validateAndSetWritablePermissions(false, ret);
}
/** Test that rename on a symlink works as expected. */
@Test(timeout = 30000)
public void testSymlinkRenameTo() throws Exception {
Assert.assertFalse(del.exists());
del.mkdirs();
File file = new File(del, FILE);
file.createNewFile();
File link = new File(del, "_link");
// create the symlink
FileUtil.symLink(file.getAbsolutePath(), link.getAbsolutePath());
Assert.assertTrue(file.exists());
Assert.assertTrue(link.exists());
File link2 = new File(del, "_link2");
// Rename the symlink
Assert.assertTrue(link.renameTo(link2));
// Make sure the file still exists
// (NOTE: this would fail on Java6 on Windows if we didn't
// copy the file in FileUtil#symlink)
Assert.assertTrue(file.exists());
Assert.assertTrue(link2.exists());
Assert.assertFalse(link.exists());
}
@Test(timeout = 30000)
public void testFullyDelete() throws IOException {
setupDirs();
boolean ret = FileUtil.fullyDelete(del);
Assert.assertTrue(ret);
Assert.assertFalse(del.exists());
validateTmpDir();
}
@Test(timeout = 30000)
public void testFullyDeleteContents() throws IOException {
setupDirs();
boolean ret = FileUtil.fullyDeleteContents(del);
Assert.assertTrue(ret);
Assert.assertTrue(del.exists());
Assert.assertEquals(0, del.listFiles().length);
validateTmpDir();
}
@Test(timeout = 30000)
public void testStat2Paths1() {
assertNull(FileUtil.stat2Paths(null));
FileStatus[] fileStatuses = new FileStatus[0];
Path[] paths = FileUtil.stat2Paths(fileStatuses);
assertEquals(0, paths.length);
Path path1 = new Path("file://foo");
Path path2 = new Path("file://moo");
fileStatuses =
new FileStatus[] {
new FileStatus(3, false, 0, 0, 0, path1), new FileStatus(3, false, 0, 0, 0, path2)
};
paths = FileUtil.stat2Paths(fileStatuses);
assertEquals(2, paths.length);
assertEquals(paths[0], path1);
assertEquals(paths[1], path2);
}
private void runImportCnaData() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
// the largest current true Entrez gene ID counts 8 digits
daoGene.addGene(new CanonicalGene(999999207, "TESTAKT1"));
daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2"));
daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3"));
daoGene.addGene(new CanonicalGene(999999369, "TESTARAF"));
daoGene.addGene(new CanonicalGene(999999472, "TESTATM"));
daoGene.addGene(new CanonicalGene(999999673, "TESTBRAF"));
daoGene.addGene(new CanonicalGene(999999672, "TESTBRCA1"));
daoGene.addGene(new CanonicalGene(999999675, "TESTBRCA2"));
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample4, 999999207);
assertEquals("-1", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999910000);
assertEquals("2", value);
value = dao.getGeneticAlteration(geneticProfileId, sample3, 999910000);
assertEquals("2", value);
int cnaStatus =
Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 999999207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList caseIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, caseIds.size());
}
@Test(timeout = 30000)
public void testFailFullyDeleteContents() throws IOException {
if (Shell.WINDOWS) {
// windows Dir.setWritable(false) does not work for directories
return;
}
LOG.info("Running test to verify failure of fullyDeleteContents()");
setupDirsAndNonWritablePermissions();
boolean ret = FileUtil.fullyDeleteContents(new MyFile(del));
validateAndSetWritablePermissions(true, ret);
}
@Test(timeout = 30000)
public void testReplaceFile() throws IOException {
setupDirs();
final File srcFile = new File(tmp, "src");
// src exists, and target does not exist:
srcFile.createNewFile();
assertTrue(srcFile.exists());
final File targetFile = new File(tmp, "target");
assertTrue(!targetFile.exists());
FileUtil.replaceFile(srcFile, targetFile);
assertTrue(!srcFile.exists());
assertTrue(targetFile.exists());
// src exists and target is a regular file:
srcFile.createNewFile();
assertTrue(srcFile.exists());
FileUtil.replaceFile(srcFile, targetFile);
assertTrue(!srcFile.exists());
assertTrue(targetFile.exists());
// src exists, and target is a non-empty directory:
srcFile.createNewFile();
assertTrue(srcFile.exists());
targetFile.delete();
targetFile.mkdirs();
File obstacle = new File(targetFile, "obstacle");
obstacle.createNewFile();
assertTrue(obstacle.exists());
assertTrue(targetFile.exists() && targetFile.isDirectory());
try {
FileUtil.replaceFile(srcFile, targetFile);
assertTrue(false);
} catch (IOException ioe) {
// okay
}
// check up the post-condition: nothing is deleted:
assertTrue(srcFile.exists());
assertTrue(targetFile.exists() && targetFile.isDirectory());
assertTrue(obstacle.exists());
}
@Test(timeout = 30000)
public void testUnZip() throws IOException {
// make sa simple zip
setupDirs();
// make a simple tar:
final File simpleZip = new File(del, FILE);
OutputStream os = new FileOutputStream(simpleZip);
ZipOutputStream tos = new ZipOutputStream(os);
try {
ZipEntry ze = new ZipEntry("foo");
byte[] data = "some-content".getBytes("UTF-8");
ze.setSize(data.length);
tos.putNextEntry(ze);
tos.write(data);
tos.closeEntry();
tos.flush();
tos.finish();
} finally {
tos.close();
}
// successfully untar it into an existing dir:
FileUtil.unZip(simpleZip, tmp);
// check result:
assertTrue(new File(tmp, "foo").exists());
assertEquals(12, new File(tmp, "foo").length());
final File regularFile = new File(tmp, "QuickBrownFoxJumpsOverTheLazyDog");
regularFile.createNewFile();
assertTrue(regularFile.exists());
try {
FileUtil.unZip(simpleZip, regularFile);
assertTrue("An IOException expected.", false);
} catch (IOException ioe) {
// okay
}
}
/**
* Tests if fullyDelete deletes (a) symlink to file only and not the file pointed to by symlink.
* (b) symlink to dir only and not the dir pointed to by symlink.
*
* @throws IOException
*/
@Test(timeout = 30000)
public void testFullyDeleteSymlinks() throws IOException {
setupDirs();
File link = new File(del, LINK);
Assert.assertEquals(5, del.list().length);
// Since tmpDir is symlink to tmp, fullyDelete(tmpDir) should not
// delete contents of tmp. See setupDirs for details.
boolean ret = FileUtil.fullyDelete(link);
Assert.assertTrue(ret);
Assert.assertFalse(link.exists());
Assert.assertEquals(4, del.list().length);
validateTmpDir();
File linkDir = new File(del, "tmpDir");
// Since tmpDir is symlink to tmp, fullyDelete(tmpDir) should not
// delete contents of tmp. See setupDirs for details.
ret = FileUtil.fullyDelete(linkDir);
Assert.assertTrue(ret);
Assert.assertFalse(linkDir.exists());
Assert.assertEquals(3, del.list().length);
validateTmpDir();
}
@Test(timeout = 30000)
public void testStat2Paths2() {
Path defaultPath = new Path("file://default");
Path[] paths = FileUtil.stat2Paths(null, defaultPath);
assertEquals(1, paths.length);
assertEquals(defaultPath, paths[0]);
paths = FileUtil.stat2Paths(null, null);
assertTrue(paths != null);
assertEquals(1, paths.length);
assertEquals(null, paths[0]);
Path path1 = new Path("file://foo");
Path path2 = new Path("file://moo");
FileStatus[] fileStatuses =
new FileStatus[] {
new FileStatus(3, false, 0, 0, 0, path1), new FileStatus(3, false, 0, 0, 0, path2)
};
paths = FileUtil.stat2Paths(fileStatuses, defaultPath);
assertEquals(2, paths.length);
assertEquals(paths[0], path1);
assertEquals(paths[1], path2);
}
/**
* Calls FileUtil.copyMerge using the specified source and destination paths. Both source and
* destination are assumed to be on the local file system. The call will not delete source on
* completion and will not add an additional string between files.
*
* @param src String non-null source path.
* @param dst String non-null destination path.
* @return boolean true if the call to FileUtil.copyMerge was successful.
* @throws IOException if an I/O error occurs.
*/
private boolean copyMerge(String src, String dst) throws IOException {
Configuration conf = new Configuration();
FileSystem fs = FileSystem.getLocal(conf);
final boolean result;
try {
Path srcPath = new Path(TEST_ROOT_DIR, src);
Path dstPath = new Path(TEST_ROOT_DIR, dst);
boolean deleteSource = false;
String addString = null;
result = FileUtil.copyMerge(fs, srcPath, fs, dstPath, deleteSource, conf, addString);
} finally {
fs.close();
}
return result;
}
private void runImportRnaData1() throws DaoException, IOException {
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
daoGene.addGene(new CanonicalGene(999999780, "A"));
daoGene.addGene(new CanonicalGene(999995982, "B"));
daoGene.addGene(new CanonicalGene(999993310, "C"));
daoGene.addGene(new CanonicalGene(999997849, "D"));
daoGene.addGene(new CanonicalGene(999992978, "E"));
daoGene.addGene(new CanonicalGene(999997067, "F"));
daoGene.addGene(new CanonicalGene(999911099, "G"));
daoGene.addGene(new CanonicalGene(999999675, "6352"));
GeneticProfile geneticProfile = new GeneticProfile();
geneticProfile.setCancerStudyId(studyId);
geneticProfile.setStableId("gbm_mrna");
geneticProfile.setGeneticAlterationType(GeneticAlterationType.MRNA_EXPRESSION);
geneticProfile.setDatatype("CONTINUOUS");
geneticProfile.setProfileName("MRNA Data");
geneticProfile.setProfileDescription("mRNA Data");
DaoGeneticProfile.addGeneticProfile(geneticProfile);
int newGeneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("gbm_mrna").getGeneticProfileId();
ProgressMonitor.setConsoleMode(true);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/mrna_test.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
ConsoleUtil.showMessages();
int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD639").getInternalId();
String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999992978);
assertEquals("2.01", value);
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD638").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997849);
assertEquals("0.55", value);
}
private void runImportCnaData2() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test2.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample4, 207);
assertEquals(value, "-1");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 10000);
assertEquals(value, "2");
value = dao.getGeneticAlteration(geneticProfileId, sample3, 10000);
assertEquals(value, "2");
int cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList sampleIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, sampleIds.size());
}
/** Test that deletion of a symlink works as expected. */
@Test(timeout = 30000)
public void testSymlinkDelete() throws Exception {
Assert.assertFalse(del.exists());
del.mkdirs();
File file = new File(del, FILE);
file.createNewFile();
File link = new File(del, "_link");
// create the symlink
FileUtil.symLink(file.getAbsolutePath(), link.getAbsolutePath());
Assert.assertTrue(file.exists());
Assert.assertTrue(link.exists());
// make sure that deleting a symlink works properly
Assert.assertTrue(link.delete());
Assert.assertFalse(link.exists());
Assert.assertTrue(file.exists());
}
/** Test that length on a symlink works as expected. */
@Test(timeout = 30000)
public void testSymlinkLength() throws Exception {
Assert.assertFalse(del.exists());
del.mkdirs();
byte[] data = "testSymLinkData".getBytes();
File file = new File(del, FILE);
File link = new File(del, "_link");
// write some data to the file
FileOutputStream os = new FileOutputStream(file);
os.write(data);
os.close();
Assert.assertEquals(0, link.length());
// create the symlink
FileUtil.symLink(file.getAbsolutePath(), link.getAbsolutePath());
// ensure that File#length returns the target file and link size
Assert.assertEquals(data.length, file.length());
Assert.assertEquals(data.length, link.length());
file.delete();
Assert.assertFalse(file.exists());
if (Shell.WINDOWS && !Shell.isJava7OrAbove()) {
// On Java6 on Windows, we copied the file
Assert.assertEquals(data.length, link.length());
} else {
// Otherwise, the target file size is zero
Assert.assertEquals(0, link.length());
}
link.delete();
Assert.assertFalse(link.exists());
}
@Test
public void testExampleJson() throws Exception {
String json =
FileUtil.readFileFromClasspath("json-examples/invoicing-rule-updated-example.json");
JsonMessage jsonMessage = new JsonMessage(json);
ServiceResult serviceResult = new ServiceResult();
serviceResult.setRawData(jsonMessage);
ServiceResult result = (ServiceResult) transformer.doTransform(serviceResult, "UTF-8");
InvoicingRuleUpdated invoicingRuleCreated =
(InvoicingRuleUpdated) result.getIntegrationMessage().getDomainObject();
MetaData metaData = invoicingRuleCreated.getMetaData();
InvoicingRule invoicingRule = invoicingRuleCreated.getInvoicingRule();
List<InvoiceRecipient> invoiceRecipients = invoicingRule.getInvoiceRecipients();
collector.checkThat(invoiceRecipients.size(), is(3));
InvoiceRecipient invoiceRecipient = invoiceRecipients.get(0);
Address registeredAddressInvoiceRecipient = invoiceRecipient.getRegisteredAddress();
List<SplittingRule> splittingRules = invoiceRecipients.get(2).getSplittingRules();
collector.checkThat(splittingRules.size(), is(3));
SplittingRule splittingRule = splittingRules.get(0);
List<PurchaseOrder> purchaseOrders = invoicingRule.getPurchaseOrders();
collector.checkThat(purchaseOrders.size(), is(3));
PurchaseOrder purchaseOrder = purchaseOrders.get(0);
List<InvoicingRuleMessageRule> invoiceMessageRules = invoicingRule.getInvoiceMessageRules();
collector.checkThat(invoiceMessageRules.size(), is(1));
InvoicingRuleMessageRule invoiceMessageRule = invoiceMessageRules.get(0);
collector.checkThat(metaData.getMessageType(), is("UpdateInvoicingRule"));
collector.checkThat(
metaData.getMessageId().getGuid(), is("28b62635-15a0-b15e-c5f4-5442b66d1059"));
collector.checkThat(
metaData.getCreationTime().getTimestamp(), is("2012-07-05T13:21:00.000+02:00"));
collector.checkThat(metaData.getVersion(), is("1.0"));
collector.checkThat(metaData.getSourceSystem(), is("CRM"));
collector.checkThat(invoicingRule.getClientId(), is("TELIA"));
collector.checkThat(invoicingRule.getMarketId().getOrganizationId(), is(51));
collector.checkThat(
invoicingRule.getInvoicingRuleId().getGuid(), is("3f2504e0-4f89-11d3-9a0c-0305e82c3405"));
collector.checkThat(invoicingRule.getInvoicingRuleName(), is("Volvo - do not edit"));
collector.checkThat(invoicingRule.getDescription(), is("Used in unit tests - do not edit"));
collector.checkThat(invoicingRule.getIssuerReference(), is("Maria Lind"));
collector.checkThat(invoicingRule.getClientReference(), is("Lasse Volvosson"));
collector.checkThat(invoicingRule.getCurrencyCode().getCurrencyCode(), is("EUR"));
collector.checkThat(invoicingRule.getDistributionMode().getValue(), is(1));
collector.checkThat(invoicingRule.getTermsOfPayment().getDays(), is(30));
collector.checkThat(invoicingRule.getPostingProfile().getValue(), is(1));
collector.checkThat(invoicingRule.isDisplayTradeDoublerCommission(), is(true));
collector.checkThat(invoicingRule.getRevenueType().getValue(), is(1));
collector.checkThat(invoicingRule.getPaymentMethod().getValue(), is(2));
collector.checkThat(invoicingRule.isDeviatingExchangeRate(), is(false));
collector.checkThat(
invoiceRecipient.getInvoiceRecipientId().getGuid(),
is("703b123f-6329-4d79-bfaa-60762a5f6cf4"));
collector.checkThat(
invoiceRecipient.getInvoicingRuleId().getGuid(),
is("3f2504e0-4f89-11d3-9a0c-0305e82c3405"));
collector.checkThat(invoiceRecipient.getAttentionRow1(), is("Attention of default recipient!"));
collector.checkThat(invoiceRecipient.getAttentionRow2(), nullValue());
collector.checkThat(invoiceRecipient.getEmailAddress(), nullValue());
collector.checkThat(invoiceRecipient.isDefaultRecipient(), is(true));
collector.checkThat(registeredAddressInvoiceRecipient.getLine1(), is("AVD. 50090 HB3S"));
collector.checkThat(registeredAddressInvoiceRecipient.getLine2(), nullValue());
collector.checkThat(registeredAddressInvoiceRecipient.getCity(), is("Göteborg"));
collector.checkThat(registeredAddressInvoiceRecipient.getCounty(), nullValue());
collector.checkThat(registeredAddressInvoiceRecipient.getPostalCode(), is("40531"));
collector.checkThat(registeredAddressInvoiceRecipient.getCountryCode().getValue(), is("SE"));
collector.checkThat(registeredAddressInvoiceRecipient.getAddressType().getValue(), is(1));
collector.checkThat(
splittingRule.getSplittingRuleId().getGuid(), is("8f756919-c9ed-e111-8b5b-005056b45da6"));
collector.checkThat(
splittingRule.getInvoiceRecipientId().getGuid(),
is("3ac9520d-c9ed-e111-8b5b-005056b45da6"));
collector.checkThat(splittingRule.getSplitter(), is("kjhh567855"));
collector.checkThat(
purchaseOrder.getInvoicingRuleId().getGuid(), is("3f2504e0-4f89-11d3-9a0c-0305e82c3405"));
collector.checkThat(purchaseOrder.getPoNumber(), is("234 - do not edit"));
collector.checkThat(
purchaseOrder.getPurchaseOrderId().getGuid(), is("00000000-0000-0000-4000-100000000001"));
collector.checkThat(
purchaseOrder.getValidFrom().getTimestamp(), is("2012-08-15T00:00:00.000+02:00"));
collector.checkThat(
purchaseOrder.getValidTo().getTimestamp(), is("2012-08-17T00:00:00.000+02:00"));
collector.checkThat(
invoiceMessageRule.getInvoiceMessageRuleId().getGuid(),
is("00000000-0000-0000-3000-100000000001"));
collector.checkThat(
invoiceMessageRule.getInvoicingRuleId().getGuid(),
is("3f2504e0-4f89-11d3-9a0c-0305e82c3405"));
collector.checkThat(
invoiceMessageRule.getMessageText(),
is("This is a text to be printed on all invoices for this invoicing rule"));
collector.checkThat(
invoiceMessageRule.getValidFrom().getTimestamp(), is("2012-08-13T00:00:00.000+02:00"));
collector.checkThat(
invoiceMessageRule.getValidTo().getTimestamp(), is("2012-08-30T00:00:00.000+02:00"));
}
/**
* Test importing of data_rppa file.
*
* @throws Exception All Errors.
*/
@Test
public void testImportRppaData() throws Exception {
MySQLbulkLoader.bulkLoadOn();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
// Genes with alias:
daoGene.addGene(makeGeneWithAlias(999999931, "TESTACACA", "TESTACC1"));
daoGene.addGene(makeGeneWithAlias(999999207, "TESTAKT1", "TESTAKT"));
daoGene.addGene(makeGeneWithAlias(999999597, "TESTSANDER", "TESTACC1"));
daoGene.addGene(makeGeneWithAlias(999997158, "TESTTP53BP1", "TEST53BP1"));
// test for NA being a special case in RPPA, and not the usual alias
daoGene.addGene(makeGeneWithAlias(999997504, "XK", "NA"));
// Other genes:
daoGene.addGene(new CanonicalGene(999999932, "TESTACACB"));
daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2"));
daoGene.addGene(new CanonicalGene(999999369, "TESTARAF"));
daoGene.addGene(new CanonicalGene(999991978, "TESTEIF4EBP1"));
daoGene.addGene(new CanonicalGene(999995562, "TESTPRKAA1"));
daoGene.addGene(new CanonicalGene(999997531, "TESTYWHAE"));
daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3"));
daoGene.addGene(new CanonicalGene(999995578, "TESTPRKCA"));
GeneticProfile geneticProfile = new GeneticProfile();
geneticProfile.setCancerStudyId(studyId);
geneticProfile.setStableId("gbm_rppa");
geneticProfile.setGeneticAlterationType(GeneticAlterationType.PROTEIN_LEVEL);
geneticProfile.setDatatype("LOG2-VALUE");
geneticProfile.setProfileName("RPPA Data");
geneticProfile.setProfileDescription("RPPA Data");
DaoGeneticProfile.addGeneticProfile(geneticProfile);
int newGeneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("gbm_rppa").getGeneticProfileId();
ProgressMonitor.setConsoleMode(true);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/tabDelimitedData/data_rppa.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
ConsoleUtil.showMessages();
int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId();
String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997531);
assertEquals("1.5", value);
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE4").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997531);
assertEquals("2", value);
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE4").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997504);
assertEquals(
"NaN",
value); // "NA" is not expected to be stored because of workaround for bug in firehose. See
// also https://github.com/cBioPortal/cbioportal/issues/839#issuecomment-203523078
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999995578);
assertEquals("1.5", value);
}
/**
* Test importing of data_expression file.
*
* @throws Exception All Errors.
*/
@Test
public void testImportmRnaData2() throws Exception {
MySQLbulkLoader.bulkLoadOn();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
// Gene with alias:
daoGene.addGene(makeGeneWithAlias(999997504, "TESTXK", "NA"));
// Other genes:
daoGene.addGene(new CanonicalGene(999999999, "TESTNAT1"));
daoGene.addGene(new CanonicalGene(999997124, "TESTTNF"));
daoGene.addGene(new CanonicalGene(999991111, "TESTCHEK1"));
daoGene.addGene(new CanonicalGene(999999919, "TESTABCA1"));
// will get generated negative id:
daoGene.addGene(new CanonicalGene(-1, "TESTphosphoprotein"));
GeneticProfile geneticProfile = new GeneticProfile();
geneticProfile.setCancerStudyId(studyId);
geneticProfile.setStableId("gbm_mrna");
geneticProfile.setGeneticAlterationType(GeneticAlterationType.MRNA_EXPRESSION);
geneticProfile.setDatatype("CONTINUOUS");
geneticProfile.setProfileName("MRNA Data");
geneticProfile.setProfileDescription("mRNA Data");
DaoGeneticProfile.addGeneticProfile(geneticProfile);
int newGeneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("gbm_mrna").getGeneticProfileId();
ProgressMonitor.setConsoleMode(true);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/tabDelimitedData/data_expression2.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
// check if expected warnings are given:
ArrayList<String> warnings = ProgressMonitor.getWarnings();
int countDuplicatedRowWarnings = 0;
int countInvalidEntrez = 0;
int countSkippedWarnings = 0;
for (String warning : warnings) {
if (warning.contains("Duplicated row")) {
countDuplicatedRowWarnings++;
}
if (warning.contains("invalid Entrez_Id")) {
// invalid Entrez
countInvalidEntrez++;
}
if (warning.contains("Record will be skipped")) {
// Entrez is a valid number, but not found
countSkippedWarnings++;
}
}
// check that we have 11 warning messages:
assertEquals(2, countDuplicatedRowWarnings);
assertEquals(3, countInvalidEntrez);
assertEquals(6, countSkippedWarnings);
Set<Long> entrezGeneIds = DaoGeneticAlteration.getGenesIdInProfile(newGeneticProfileId);
// data will be loaded for 5 of the genes
assertEquals(5, entrezGeneIds.size());
HashMap<Long, HashMap<Integer, String>> dataMap =
dao.getGeneticAlterationMap(newGeneticProfileId, entrezGeneIds);
assertEquals(5, dataMap.entrySet().size());
int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE1").getInternalId();
String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997124);
assertEquals("770", value);
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE3").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997124);
assertEquals("220", value);
// gene should also be loaded via its alias "NA" as defined above:
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "SAMPLE3").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997504);
assertEquals("9940", value);
}