/**
* Copy the checkstyle configuration of a check configuration into another configuration.
*
* @param source the source check configuration
* @param target the target check configuartion
* @throws CheckstylePluginException Error copying the configuration
*/
public static void copyConfiguration(ICheckConfiguration source, ICheckConfiguration target)
throws CheckstylePluginException {
// use the export function ;-)
File targetFile = FileUtils.toFile(target.getResolvedConfigurationFileURL());
File sourceFile = FileUtils.toFile(source.getResolvedConfigurationFileURL());
// copying from a file to the same file will destroy it.
if (ObjectUtils.equals(targetFile, sourceFile)) {
return;
}
exportConfiguration(targetFile, source);
}
public Map<String, Map<GM_Position, Double>> readMatResultsFile(final String pStrFilter) {
MatFileReader lMatFileReader = null;
final MatFileFilter lMatFilter = new MatFileFilter();
Map<String, Map<GM_Position, Double>> lRes = null;
try {
if (pStrFilter != null) {
lMatFilter.addArrayName(STR_XP_NAME);
lMatFilter.addArrayName(STR_YP_NAME);
lMatFilter.addArrayName(pStrFilter);
}
if (m_strResultsFile == null) {
lMatFileReader = new MatFileReader(FileUtils.toFile(m_resultsFile.getURL()), lMatFilter);
} else {
lMatFileReader = new MatFileReader(m_strResultsFile, lMatFilter);
}
} catch (final Exception e) {
// throw new MatlabIOException( "Cannot open or read SWAN result matlab file." );
}
if (lMatFileReader != null) {
try {
final GM_Position lShiftPosition =
SWANDataConverterHelper.readCoordinateShiftValues(m_resultsFile);
m_doubleShiftX = lShiftPosition.getX();
m_doubleShiftY = lShiftPosition.getY();
final Map<String, MLArray> lMapData = lMatFileReader.getContent();
// printDebugParsedSWANRawData( lMatFileReader, null );
lRes = getValuesFormatedNameDatePosition(lMapData);
// printDebugResultData( lRes, null );
} catch (final Exception e) {
e.printStackTrace();
}
}
return lRes;
}
private boolean OpenFile() throws Exception {
data.oneFileOpened = true;
String realFilename = environmentSubstitute(meta.getFilename());
if (log.isBasic()) {
logBasic(BaseMessages.getString(PKG, "AccessOutput.log.WritingToFile", realFilename));
}
FileObject fileObject = KettleVFS.getFileObject(realFilename, getTransMeta());
File file = FileUtils.toFile(fileObject.getURL());
// First open or create the access file
if (!file.exists()) {
if (meta.isFileCreated()) {
data.db = Database.create(file);
} else {
logError(
BaseMessages.getString(PKG, "AccessOutput.InitError.FileDoesNotExist", realFilename));
return false;
}
} else {
data.db = Database.open(file);
}
// Add the filename to the result object...
//
if (meta.isAddToResultFiles()) {
ResultFile resultFile =
new ResultFile(
ResultFile.FILE_TYPE_GENERAL, fileObject, getTransMeta().getName(), toString());
resultFile.setComment("This file was created with an access output step");
addResultFile(resultFile);
}
return true;
}
static {
File testResources = FileUtils.toFile(TestUtils.class.getResource("/TestUtils.txt"));
HOME =
testResources // home/tests/src/tests/resources
.getParentFile() // home/tests/src/tests
.getParentFile() // home/tests/src
.getParentFile() // home/tests
.getParentFile(); // home
}
@BeforeClass
public static void beforeClass() throws Exception {
simpleSchema =
AvroUtils.inputStreamToString(
AvroDaoTest.class.getResourceAsStream("/SchemaTool/SimpleHBaseRecord.avsc"));
simpleSchemaFile =
FileUtils.toFile(AvroDaoTest.class.getResource("/SchemaTool/SimpleHBaseRecord.avsc"));
HBaseTestUtils.getMiniCluster();
}
private void generateAdministrationData() throws IOException {
File file = FileUtils.toFile(getClass().getClassLoader().getResource("data/cpr34200.csv"));
boolean first = true;
List<String> lines = FileUtils.readLines(file);
for (String line : lines) {
if (first) {
// first row is column metadata
first = false;
continue;
}
String[] splits = line.split(";");
String recnum = splits[0];
String sygehus = splits[1];
String afdeling = splits[2];
String type = splits[3];
String cpr = splits[4];
String idate = splits[5];
String udate = splits[6];
String itime = splits[7];
if (itime.length() == 0) {
itime = "0";
}
String utime = splits[8];
if (utime.length() == 0) {
utime = "0";
}
StringBuffer sql = new StringBuffer();
sql.append(
"INSERT INTO T_ADM (V_RECNUM, C_SGH, C_AFD, V_CPR, D_INDDTO,D_UDDTO,V_INDTIME,V_UDTIME, C_PATTYPE) VALUES (");
sql.append(recnum);
sql.append(", '");
sql.append(sygehus);
sql.append("', '");
sql.append(afdeling);
sql.append("', '");
sql.append(cpr);
sql.append("', '");
sql.append(idate);
sql.append("', '");
sql.append(udate);
sql.append("', ");
sql.append(itime);
sql.append(", ");
sql.append(utime);
sql.append(", ");
sql.append(type);
sql.append(");");
System.out.println(sql.toString());
}
}
/**
* Search for a test resource in the classpath. For example
* getResource("org/sonar/MyClass/foo.txt");
*
* @param path the starting slash is optional
* @return the resource. Null if resource not found
*/
public static File getResource(String path) {
String resourcePath = path;
if (!resourcePath.startsWith("/")) {
resourcePath = "/" + resourcePath;
}
URL url = TestUtils.class.getResource(resourcePath);
if (url != null) {
return FileUtils.toFile(url);
}
return null;
}
@Test
public void exceptionHandlingRequiredFilesMissing() throws Exception {
TakstParser takstParser = new TakstParser();
File dir = FileUtils.toFile(getClass().getClassLoader().getResource("data/incomplete/"));
try {
takstParser.parseFiles(dir.listFiles());
fail("expected the parser to complain about missing file");
} catch (ParserException e) {
assertTrue(e.getMessage().contains("lms28.txt")); // the missing file
}
}
public String getClasspath() {
// this assumes we run in Maven
StringBuilder buf = new StringBuilder();
URLClassLoader ucl = (URLClassLoader) getClass().getClassLoader();
for (URL url : ucl.getURLs()) {
if (buf.length() > 0) {
buf.append(File.pathSeparatorChar);
}
buf.append(FileUtils.toFile(url)); // assume all of them are file URLs
}
return buf.toString();
}
@Test
public void exceptionHandlingUnparsable() throws Exception {
TakstParser takstParser = new TakstParser();
File dir = FileUtils.toFile(getClass().getClassLoader().getResource("data/unparsable/"));
try {
takstParser.parseFiles(dir.listFiles());
fail("expected the parser to complain about missing file");
} catch (ParserException e) {
assertTrue(e.getMessage().contains("8100009555S")); // the offending value
assertTrue(e.getMessage().contains("Laegemiddel")); // the name of the entity involved
}
}
/**
* @return <code>true</code> if given {@link URL} represents {@link File} with non-canonical
* path, such as using incorrect case on Windows. JDT compiler tried to detect if given name
* "test" is name of package or not, by searching for "test.class" resource. But on Windows
* file system is not case sensitive, so "Test.class" resource returned, so it is considered
* not as package, but as type.
*/
private boolean isWrongURL(URL url) {
if (EnvironmentUtils.IS_WINDOWS) {
File file = FileUtils.toFile(url);
if (file != null && file.exists()) {
try {
String absolutePath = file.getAbsolutePath();
String canonicalPath = file.getCanonicalPath();
return !absolutePath.equals(canonicalPath);
} catch (Throwable e) {
}
}
}
return false;
}
public class AutorisationParserIntegrationTest {
private static final File valid =
FileUtils.toFile(
AutorisationParserIntegrationTest.class
.getClassLoader()
.getResource("data/aut/valid/20090915AutDK.csv"));
private AutorisationImporter importer = new AutorisationImporter();
private Connection connection;
@Before
public void setUp() throws Exception {
connection = new ConnectionManager().getConnection();
Statement statement = connection.createStatement();
statement.execute("truncate table Autorisation");
}
@After
public void tearDown() throws Exception {
connection.rollback();
connection.close();
}
@Test
public void should_return_true_if_expected_files_are_present() {
File[] files = new File[] {valid};
assertTrue(importer.validateInputStructure(files));
}
@Test
public void should_return_false_if_no_file_are_present() {
File[] file = new File[] {};
assertFalse(importer.validateInputStructure(file));
}
@SuppressWarnings("unchecked")
@Test
public void should_successfully_import_a_file() throws Exception {
AuditingPersister persister = Mockito.spy(new AuditingPersister(connection));
File[] files = new File[] {valid};
importer.parse(files, persister, null);
verify(persister).persistCompleteDataset(Mockito.any(CompleteDataset.class));
}
}
protected Provider<SmtpAgentConfig> createCompatConfigProvider(URL configURL) {
Provider<SmtpAgentConfig> provider;
if (configURL.getProtocol().equalsIgnoreCase("HTTP")
|| configURL.getProtocol().equalsIgnoreCase("HTTPS")) {
// web services based
provider = new WSSmtpAgentConfigProvider(configURL, null);
} else {
// use the default XML configuration
// convert URL to file location
File fl = FileUtils.toFile(configURL);
provider = new XMLSmtpAgentConfigProvider(fl.getAbsolutePath(), null);
}
return provider;
}
private static String createConfig(String rootDir) throws IOException {
URL configURL = TestDbService.class.getResource("db-test.yaml");
if (configURL == null) {
throw new IllegalStateException("Could not find cassandra.yaml");
}
File path = FileUtils.toFile(configURL);
String data = FileUtils.readFileToString(path, "UTF-8");
StrSubstitutor substitutor = new StrSubstitutor(Collections.singletonMap("rootDir", rootDir));
String contents = substitutor.replace(data);
File configFile = File.createTempFile("db-test", ".yaml");
configFile.deleteOnExit();
FileUtils.writeStringToFile(configFile, contents, "UTF-8");
return "file:" + configFile.getAbsolutePath();
}
@Test
public void renderJavaFile() throws IOException {
File java =
FileUtils.toFile(
getClass().getResource("/org/sonar/colorizer/HtmlRendererTest/Sample.java"));
String html =
new HtmlRenderer()
.render(
new FileReader(java),
Arrays.<Channel<HtmlCodeBuilder>>asList(javaKeywordTokenizer));
assertThat(html, containsString("<html>"));
assertThat(html, containsString("<style"));
assertThat(html, containsString("<table class=\"code\""));
assertThat(html, containsString("public"));
assertThat(html, containsString("class"));
assertThat(html, containsString("Sample"));
assertThat(html, containsString("</html>"));
}
public void readLsat7Data() {
lsat7 = new byte[1000][5];
try {
File f = FileUtils.toFile(this.getClass().getResource("/testdata/lsat7-expanded.txt"));
BufferedReader br = new BufferedReader(new FileReader(f));
String line = "";
String[] s = null;
int row = 0;
br.readLine(); // eliminate column names by skipping first row
while ((line = br.readLine()) != null) {
s = line.split(",");
for (int j = 0; j < s.length; j++) {
lsat7[row][j] = Byte.parseByte(s[j]);
}
row++;
}
br.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
/** Write manifest in the install jar. */
@Override
public void writeManifest() throws IOException {
IXMLElement data = resourceFinder.getXMLTree();
IXMLElement guiPrefsElement = data.getFirstChildNamed("guiprefs");
// Add splash screen configuration
List<String> lines = IOUtils.readLines(getClass().getResourceAsStream("MANIFEST.MF"));
IXMLElement splashNode = guiPrefsElement.getFirstChildNamed("splash");
if (splashNode != null) {
// Add splash image to installer jar
File splashImage =
FileUtils.toFile(
resourceFinder.findProjectResource(splashNode.getContent(), "Resource", splashNode));
String destination = String.format("META-INF/%s", splashImage.getName());
mergeManager.addResourceToMerge(splashImage.getAbsolutePath(), destination);
lines.add(String.format("SplashScreen-Image: %s", destination));
}
lines.add("");
File tempManifest = com.izforge.izpack.util.file.FileUtils.createTempFile("MANIFEST", ".MF");
FileUtils.writeLines(tempManifest, lines);
mergeManager.addResourceToMerge(tempManifest.getAbsolutePath(), "META-INF/MANIFEST.MF");
}
/** {@inheritDoc} */
public boolean isConfigurable(ICheckConfiguration checkConfiguration) {
boolean isConfigurable = true;
boolean isProtected =
Boolean.valueOf(checkConfiguration.getAdditionalData().get(KEY_PROTECT_CONFIG))
.booleanValue();
isConfigurable = !isProtected;
if (!isProtected) {
// The configuration can be changed when the external configuration
// file can is writable
try {
isConfigurable =
FileUtils.toFile(checkConfiguration.getResolvedConfigurationFileURL()).canWrite();
} catch (CheckstylePluginException e) {
CheckstyleLog.log(e);
isConfigurable = false;
}
}
return isConfigurable;
}
public static File toFile(URL url) {
return FileUtils.toFile(url);
}
@Test
public void testAllInOneFile() {
parser.parse(FileUtils.toFile(getClass().getResource("/parser/cSharpSyntaxAllInOneFile.cs")));
}
@Test
public void testLinqFile() {
parser.parse(FileUtils.toFile(getClass().getResource("/parser/LinqBridge-1.2.cs")));
}
@Test
public void testParsingRealLifeSourceFile() {
parser.parse(FileUtils.toFile(getClass().getResource("/parser/NUnitFramework.cs")));
}
@Test
public void testParsingSimpleSourceFile() {
parser.parse(FileUtils.toFile(getClass().getResource("/parser/simpleFile.cs")));
}
@Before
public void setUp() throws ConfigurationException {
File configFile = FileUtils.toFile(this.getClass().getResource("/phresco-unit.xml"));
configmanagerImpl = new ConfigManagerImpl(configFile);
}
protected File readFile(String path) {
return FileUtils.toFile(getClass().getResource(path));
}
private static File getDriverRootDirectory() {
File resourcesDirectory =
FileUtils.toFile(DriverConfigurationFileHelper.class.getResource("/"));
File targetDirectory = resourcesDirectory.getParentFile();
return targetDirectory.getParentFile();
}
/** User: maplesod Date: 06/08/13 Time: 14:15 */
public class CegmaV24Test {
@Rule public TemporaryFolder temp = new TemporaryFolder();
private String pwd;
private static String testDir;
private static String correctCommand;
private static String correctFullCommand;
@Before
public void setup() {
String pwdFull = new File(".").getAbsolutePath();
this.pwd = pwdFull.substring(0, pwdFull.length() - 2);
this.testDir = temp.getRoot().getAbsolutePath();
correctCommand =
"cegma --genome "
+ pwd
+ "/assembly.fa --output "
+ testDir
+ "/cegma-output --threads 16 2>&1";
correctFullCommand =
"cd "
+ testDir
+ "; CEGMATMP="
+ testDir
+ "/temp; "
+ "sed 's/>/>seq_/g' "
+ pwd
+ "/assembly.fa > "
+ testDir
+ "/assembly.fa.mod.fa; "
+ "cegma --genome "
+ testDir
+ "/assembly.fa.mod.fa --output "
+ testDir
+ "/cegma-output --threads 16 2>&1"
+ "; cd "
+ pwd;
}
private CegmaV24 createProcess() {
CegmaV24.Args args = new CegmaV24.Args();
args.setGenomeFile(new File("assembly.fa"));
args.setOutputPrefix(new File(testDir, "cegma-output"));
args.setThreads(16);
return new CegmaV24(null, args);
}
@Test
public void testCommand() {
CegmaV24 process = createProcess();
String command = process.getCommand();
assertTrue(command.equals(correctCommand));
}
@Test
public void testFullCommand() throws IOException, ConanParameterException {
CegmaV24 process = createProcess();
process.initialise();
String fullCommand = process.getFullCommand();
assertTrue(fullCommand.equals(correctFullCommand));
}
private File cegmaReportFile =
FileUtils.toFile(this.getClass().getResource("/stats/cegma-report.txt"));
@Test
public void testQuastReport() throws IOException {
CegmaV24.Report report = new CegmaV24.Report(cegmaReportFile);
assertTrue(report.getPcComplete() == 93.55);
assertTrue(report.getPcPartial() == 93.95);
}
}
