/**
* Downloads the given file specified via url to the given canonicalDestination.
*
* @param urlSource String
* @param urlDestination String
* @throws Exception
*/
@Override
public void downloadFile(String urlSource, String urlDestination) throws Exception {
// sanity check
if (urlSource == null
|| urlSource.length() == 0
|| urlDestination == null
|| urlDestination.length() == 0) {
throw new IllegalArgumentException(
"downloadFile(): urlSource or urlDestination argument is null...");
}
// URLs for given parameters
URL source = new URL(urlSource);
URL destination = new URL(urlDestination);
// we have a compressed file
if (GzipUtils.isCompressedFilename(urlSource)) {
// downlod to temp destination
File tempDestinationFile =
org.apache.commons.io.FileUtils.getFile(
org.apache.commons.io.FileUtils.getTempDirectory(),
new File(source.getFile()).getName());
if (LOG.isInfoEnabled()) {
LOG.info("downloadFile(), " + urlSource + ", this may take a while...");
}
org.apache.commons.io.FileUtils.copyURLToFile(source, tempDestinationFile);
if (LOG.isInfoEnabled()) {
LOG.info("downloadFile(), gunzip: we have compressed file, decompressing...");
}
// decompress the file
gunzip(tempDestinationFile.getCanonicalPath());
if (LOG.isInfoEnabled()) {
LOG.info("downloadFile(), gunzip complete...");
}
// move temp/decompressed file to final destination
File destinationFile = new File(destination.getFile());
if (destinationFile.exists()) {
org.apache.commons.io.FileUtils.forceDelete(destinationFile);
}
org.apache.commons.io.FileUtils.moveFile(
org.apache.commons.io.FileUtils.getFile(
GzipUtils.getUncompressedFilename(tempDestinationFile.getCanonicalPath())),
destinationFile);
// lets cleanup after ourselves - remove compressed file
tempDestinationFile.delete();
}
// uncompressed file, download directry to urlDestination
else {
if (LOG.isInfoEnabled()) {
LOG.info("downloadFile(), " + urlSource + ", this may take a while...");
}
org.apache.commons.io.FileUtils.copyURLToFile(
source, org.apache.commons.io.FileUtils.getFile(destination.getFile()));
}
}
public static void init() {
if (initialize) {
logger.warn("配置文件已经加载，不需要在调用init()方法！");
return;
}
final Properties p = new Properties();
ResourceKit.loadFileInProperties(APPLICATION_PROP, p);
if (checkNullOrEmpty(p)) {
throw new IllegalArgumentException("Properties file can not be empty. " + APPLICATION_PROP);
}
final String configFolder = p.getProperty(GojaPropConst.APPCONFIGFOLDER);
if (!Strings.isNullOrEmpty(configFolder)) {
configFolderFile = new File(configFolder);
if (!configFolderFile.exists()) {
throw new RuntimeException(
"The application config folder " + configFolder + " is not found!");
}
configProps =
PropKit.use(FileUtils.getFile(configFolderFile, "application.conf")).getProperties();
} else {
configProps = p;
}
applicationMode = getApplicationModel();
security = getPropertyToBoolean(GojaPropConst.APPSECURITY, true);
appSecurityConfig = getProperty(GojaPropConst.APPSECURITYCONFIG, "security.conf");
if (security) {
// 如果启用了身份验证，如果配置文件不存在，系统无法启动
if (!Strings.isNullOrEmpty(configFolder)) {
final File securityFile = FileUtils.getFile(configFolderFile, appSecurityConfig);
if (!securityFile.exists()) {
throw new RuntimeException(
"The app security config file [ "
+ appSecurityConfig
+ "] not found in ["
+ configFolder
+ "]!");
}
}
}
version = getProperty(GojaPropConst.APPVERSION, "V0.0.1");
appName = getProperty(GojaPropConst.APPNAME, "application");
appDomain = getProperty(GojaPropConst.APPDOMAIN, "http://127.0.0.1:8080/" + appName);
defaultDBUrl = getProperty(GojaPropConst.DBURL);
defaultDBUsername = getProperty(GojaPropConst.DBUSERNAME, "root");
defaultDBPassword = getProperty(GojaPropConst.DBPASSWORD, "123456");
defaultViewPath =
GojaConfig.getProperty(
GojaPropConst.APP_VIEWPATH, File.separator + "WEB-INF" + File.separator + "views");
String appScan = GojaConfig.getProperty(GojaPropConst.APP_SCAN, "app");
appScans = Func.COMMA_SPLITTER.splitToList(appScan);
jsonMode = GojaConfig.getProperty(GojaPropConst.APP_JSON_MODE);
api = GojaConfig.getPropertyToBoolean(GojaPropConst.APP_API, false);
initialize = true;
}
@AfterClass
public static void tearDownAfterClass() throws Exception {
System.out.println("Resetting fits.xml");
// Set the backup to the original fits.xml
FileUtils.copyFile(FileUtils.getFile("xml/fits_back.xml"), FileUtils.getFile("xml/fits.xml"));
// Remove the temp file
FileUtils.deleteQuietly(FileUtils.getFile("xml/fits_back.xml"));
}
@BeforeClass
public static void setUpBeforeClass() throws Exception {
System.out.println("Moving test fits.xml in");
// Copy fits.xml to fits_back.xml
FileUtils.copyFile(FileUtils.getFile("xml/fits.xml"), FileUtils.getFile("xml/fits_back.xml"));
// Copy in test fits.xml
FileUtils.copyFile(
FileUtils.getFile("testfiles/properties/fits_no_md5_audio.xml"),
FileUtils.getFile("xml/fits.xml"));
}
/**
* Creates a staging file with contents from the given DataMatrix.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeStagingFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
// staging file
String stagingFilename = datatypeMetadata.getStagingFilename();
stagingFilename =
stagingFilename.replaceAll(
DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
File stagingFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
stagingFilename);
if (LOG.isInfoEnabled()) {
LOG.info("writingStagingFile(), staging file: " + stagingFile);
}
FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(stagingFile, false);
dataMatrix.write(out);
IOUtils.closeQuietly(out);
// meta file
if (datatypeMetadata.requiresMetafile()) {
if (LOG.isInfoEnabled()) {
LOG.info("writingStagingFile(), creating metadata file for staging file: " + stagingFile);
}
writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix);
}
}
@Override
public void write(String path) throws IOException {
File dir = FileUtils.getFile(path, "ensemble", getName());
if (!dir.isDirectory()) {
dir.mkdirs();
}
ObjectOutputStream oop =
new ObjectOutputStream(new FileOutputStream(new File(dir, "similarityCoefficients")));
oop.writeObject(simlarityCoefficients);
oop.flush();
oop.close();
oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "mostSimilarCoefficients")));
oop.writeObject(mostSimilarCoefficients);
oop.flush();
oop.close();
oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "similarityInterpolator")));
oop.writeObject(similarityInterpolator);
oop.flush();
oop.close();
oop = new ObjectOutputStream(new FileOutputStream(new File(dir, "mostSimilarInterpolator")));
oop.writeObject(mostSimilarInterpolator);
oop.flush();
oop.close();
}
/**
* Creates a staging file for mutation data (and meta file) with contents from the given
* DataMatrix. This is called when the mutation file needs to be run through the Oncotator and
* Mutation Assessor Tools.
*
* @param portalMetadata PortalMetadata
* @param cancerStudy CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeMutationStagingFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
// we only have data matrix at this point, we need to create a temp with its contents
File oncotatorInputFile =
org.apache.commons.io.FileUtils.getFile(
org.apache.commons.io.FileUtils.getTempDirectory(), "oncotatorInputFile");
FileOutputStream out = org.apache.commons.io.FileUtils.openOutputStream(oncotatorInputFile);
dataMatrix.write(out);
IOUtils.closeQuietly(out);
// output should be the path/name of staging file
String stagingFilename = datatypeMetadata.getStagingFilename();
stagingFilename =
stagingFilename.replaceAll(
DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
File stagingFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
stagingFilename);
// call oncotateAF
oncotateMAF(
FileUtils.FILE_URL_PREFIX + oncotatorInputFile.getCanonicalPath(),
FileUtils.FILE_URL_PREFIX + stagingFile.getCanonicalPath());
// clean up
if (oncotatorInputFile.exists()) {
org.apache.commons.io.FileUtils.forceDelete(oncotatorInputFile);
}
// meta file
if (datatypeMetadata.requiresMetafile()) {
if (LOG.isInfoEnabled()) {
LOG.info(
"writingMutationStagingFile(), creating metadata file for staging file: "
+ stagingFile);
}
writeMetadataFile(portalMetadata, cancerStudyMetadata, datatypeMetadata, dataMatrix);
}
}
/**
* Unpacks file into temporary directory
*
* @param inputStream InputStream representing archive file
* @param originalFileName Name of the archive
* @return Directory to which the archive was unpacked
* @throws IOException
* @throws ZipException
*/
private File unpackArchive(InputStream inputStream, String originalFileName)
throws IOException, ZipException {
String randomDirectoryName = RandomStringUtils.randomAlphanumeric(8);
File directoryForUnpacking =
FileUtils.getFile(FileUtils.getTempDirectoryPath(), randomDirectoryName);
FileUtils.forceMkdir(directoryForUnpacking);
File zipFileDownloaded = FileUtils.getFile(FileUtils.getTempDirectoryPath(), originalFileName);
try (OutputStream os = new FileOutputStream(zipFileDownloaded)) {
IOUtils.copy(inputStream, os);
}
ZipFile zipFile = new ZipFile(zipFileDownloaded);
zipFile.extractAll(directoryForUnpacking.toString());
FileUtils.forceDelete(zipFileDownloaded);
return directoryForUnpacking;
}
public File createInfile(int fileId) {
if (infile != null) {
cleanUp();
}
infile = FileUtils.getFile(Integer.toString(fileId) + ".txt");
return infile;
}
/**
* Creates (or overwrites) the given file with the given contents. Filename is canonical
* path/filename.
*
* @param filename String
* @param fileContent String
* @return File
* @throws Exception
*/
@Override
public File createFileWithContents(String filename, String fileContent) throws Exception {
File file = org.apache.commons.io.FileUtils.getFile(filename);
org.apache.commons.io.FileUtils.writeStringToFile(file, fileContent, false);
// outta here
return file;
}
/**
* Load an MEI file.
*
* @param filename A path to an MEI file to load
* @return an {@link MeiDocument} representing the MEI file.
*/
public static MeiDocument loadFile(String filename) {
try {
File fp = FileUtils.getFile(filename);
MeiXmlReader loader = new MeiXmlReader(fp);
return loader.readDocument();
} catch (FileNotFoundException e) {
throw new MeiXmlReadException("Cannot find file " + filename);
}
}
public File getInfile(int fileId) {
if (infile == null) {
infile = FileUtils.getFile(Integer.toString(fileId) + ".txt");
if (!infile.exists()) {
infile = null;
}
}
return infile;
}
/**
* This method takes care to not load the metric itself, and just deal in names. Once the metric
* is loaded, it has already accessed its data files.
*
* @throws ConfigurationException
*/
public void deleteDataDirectories() throws ConfigurationException {
for (String name : getSubmetrics(metricName)) {
File dir = FileUtils.getFile(srDir, name, language.getLangCode());
if (dir.exists()) {
LOG.info("deleting metric directory " + dir);
FileUtils.deleteQuietly(dir);
}
}
}
/**
* Creates a temporary file with the given contents.
*
* @param filename String
* @param fileContent String
* @return File
* @throws Exception
*/
@Override
public File createTmpFileWithContents(String filename, String fileContent) throws Exception {
File tmpFile =
org.apache.commons.io.FileUtils.getFile(
org.apache.commons.io.FileUtils.getTempDirectoryPath(), filename);
org.apache.commons.io.FileUtils.writeStringToFile(tmpFile, fileContent, false);
return tmpFile;
}
/**
* Returns an override file (if it exists) for the given portal & cancer study. The override in
* this case is the override file that a DataMatrix is created from.
*
* <p>Null is returned if an override file is not found.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param filename String
* @return File
* @throws Exception
*/
@Override
public File getOverrideFile(
PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, String filename)
throws Exception {
File overrideFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getOverrideDirectory(), cancerStudyMetadata.getStudyPath(), filename);
return (overrideFile.exists()) ? overrideFile : null;
}
public static URI createNeoGraphURI(URI uri) {
if (NeoURI.FILE_SCHEME.equals(uri.scheme())) {
return createNeoGraphURI(FileUtils.getFile(uri.toFileString()));
} else if (NEO_GRAPH_SCHEME.equals(uri.scheme())) {
return NeoURI.createNeoURI(uri);
} else {
throw new IllegalArgumentException(
MessageFormat.format("Can not create NeoGraphURI from the URI scheme {0}", uri.scheme()));
}
}
public LoadButtonAndSheetHandler() {
File sheet =
FileUtils.getFile(
ConfigurationSettings.getPreviewDir(),
"companions",
"compact_companion.htm"); //$NON-NLS-1$ //$NON-NLS-2$
this.sheetSupport = new HtmlSheetSupport(infoPane, sheet.getAbsolutePath());
this.selectedRow = -1;
this.selectionModel = companionsTable.getSelectionModel();
this.frame = (PCGenFrame) JOptionPane.getFrameForComponent(CompanionInfoTab.this);
}
private static File getXMLTemplate(CharacterFacade character) {
File template =
FileUtils.getFile(
ConfigurationSettings.getSystemsDir(),
"gameModes",
character.getDataSet().getGameMode().getName(),
"base.xml.ftl");
if (!template.exists()) {
template = new File(ConfigurationSettings.getOutputSheetsDir(), "base.xml.ftl");
}
return template;
}
@Test
// SONAR-6184
public void testDuplicationFix() throws IOException {
analyzeProject(projectDir, PROJECT_KEY, true);
verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 45);
verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 75);
// remove File1 from module1
File f1 = FileUtils.getFile(projectDir, "module1", "src", "main", "xoo", "sample", "File1.xoo");
File f1m =
FileUtils.getFile(
projectDir, "module2", "src", "main", "xoo", "sample", "File1.xoo.measures");
f1.delete();
f1m.delete();
// duplication should be 0
analyzeProject(projectDir, PROJECT_KEY, false);
verifyDuplicationMeasures(PROJECT_KEY + ":module1", 0, 0, 0, 0);
verifyDuplicationMeasures(PROJECT_KEY + ":module2", 0, 0, 0, 0);
}
public static void main(String[] args) throws IOException {
String workDir = "E:/dev_workspace/tmp/workspace/duc2007";
String idfFilename = "duc2007.idf";
final double TOTAL_PAGE_COUNT = 30000000000.0D;
Map<String, Double> idfValues = new HashMap<String, Double>();
File idfFIle = FileUtils.getFile(workDir + "/" + DIR_IDF_FILE, idfFilename);
log.info("Loading idf value file[" + idfFIle.getAbsolutePath() + "]");
LineIterator lineIterator = null;
try {
lineIterator = FileUtils.lineIterator(idfFIle, DEFAULT_CHARSET.toString());
while (lineIterator.hasNext()) {
String line = lineIterator.nextLine();
String[] strs = line.split("###");
if (strs.length != 2) {
log.warn("Line[" + line + "] format is illegal, ignore it!");
continue;
}
idfValues.put(strs[0].trim(), Long.parseLong(strs[1]) / TOTAL_PAGE_COUNT);
}
log.info("Load idf value file[" + idfFIle.getAbsolutePath() + "] finished!");
} catch (IOException e) {
log.error("Load idf value file[" + idfFIle.getAbsolutePath() + "] error!", e);
throw e;
} finally {
if (lineIterator != null) {
lineIterator.close();
}
}
String question =
"Describe the legal battle between various recording artists and members of the record industry and the Internet music site Napster. What support, or lack thereof, have the litigants received?";
EhCacheUtil ehCacheUtil = new EhCacheUtil("db_cache_vec", "lab");
SummaryBuilderByVector summaryBuilder =
new SummaryBuilderByVector(
workDir, "0", "D0714D.txt", 10, idfValues, question, ehCacheUtil, 1.0f, 1.6f);
ExecutorService es = Executors.newSingleThreadExecutor();
Future<Boolean> future = es.submit(summaryBuilder);
try {
future.get();
} catch (InterruptedException | ExecutionException e) {
e.printStackTrace();
}
es.shutdown();
EhCacheUtil.close();
}
/**
* If it exists, moves an override file into the proper location in the given portals staging area
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param overrideFilename String
* @param stagingFilename String
* @throws Exception
*/
@Override
public void applyOverride(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
String overrideFilename,
String stagingFilename)
throws Exception {
// check for override file
File overrideFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getOverrideDirectory(),
cancerStudyMetadata.getStudyPath(),
overrideFilename);
if (overrideFile.exists()) {
File stagingFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
stagingFilename);
if (LOG.isInfoEnabled()) {
LOG.info(
"applyOverride(), override file exists for "
+ stagingFile.getCanonicalPath()
+ ": "
+ overrideFile.getCanonicalPath());
}
// copy override file to staging area
if (overrideFile.isFile()) {
org.apache.commons.io.FileUtils.copyFile(overrideFile, stagingFile);
} else {
org.apache.commons.io.FileUtils.copyDirectory(overrideFile, stagingFile);
}
}
}
@Test
// SONAR-6184
public void testGhostDuplication() throws IOException {
analyzeProject(projectDir, PROJECT_KEY, true);
verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 45);
verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 75);
// move File2 from module1 to module2
File src =
FileUtils.getFile(projectDir, "module1", "src", "main", "xoo", "sample", "File2.xoo");
File dst =
FileUtils.getFile(projectDir, "module2", "src", "main", "xoo", "sample", "File2.xoo");
FileUtils.moveFile(src, dst);
src = new File(src.getParentFile(), "File2.xoo.measures");
dst = new File(dst.getParentFile(), "File2.xoo.measures");
FileUtils.moveFile(src, dst);
// duplication should remain unchanged (except for % of duplication)
analyzeProject(projectDir, PROJECT_KEY, false);
verifyDuplicationMeasures(PROJECT_KEY + ":module1", 1, 27, 1, 75);
verifyDuplicationMeasures(PROJECT_KEY + ":module2", 1, 27, 1, 45);
}
/**
* Method which writes the cancer study metadata file.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param numCases int
* @throws Exception
*/
@Override
public void writeCancerStudyMetadataFile(
PortalMetadata portalMetadata, CancerStudyMetadata cancerStudyMetadata, int numCases)
throws Exception {
File metaFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
cancerStudyMetadata.getCancerStudyMetadataFilename());
if (LOG.isInfoEnabled()) {
LOG.info("writeMetadataFile(), meta file: " + metaFile);
}
PrintWriter writer =
new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false));
writer.print("type_of_cancer: " + cancerStudyMetadata.getTumorType() + "\n");
writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n");
String name =
(cancerStudyMetadata.getName().length() > 0)
? cancerStudyMetadata.getName()
: cancerStudyMetadata.getTumorTypeMetadata().getName();
name =
name.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_NAME_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getName());
writer.print("name: " + name + "\n");
String description = cancerStudyMetadata.getDescription();
description =
description.replaceAll(CancerStudyMetadata.NUM_CASES_TAG, Integer.toString(numCases));
description =
description.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getType());
description =
description.replaceAll(
CancerStudyMetadata.TUMOR_TYPE_NAME_TAG,
cancerStudyMetadata.getTumorTypeMetadata().getName());
writer.print("description: " + description + "\n");
if (cancerStudyMetadata.getCitation().length() > 0) {
writer.print("citation: " + cancerStudyMetadata.getCitation() + "\n");
}
if (cancerStudyMetadata.getPMID().length() > 0) {
writer.print("pmid: " + cancerStudyMetadata.getPMID() + "\n");
}
writer.flush();
writer.close();
}
/**
* Method which writes a metadata file for the given DatatypeMetadata. DataMatrix may be null.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param datatypeMetadata DatatypeMetadata
* @param dataMatrix DataMatrix
* @throws Exception
*/
@Override
public void writeMetadataFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
DatatypeMetadata datatypeMetadata,
DataMatrix dataMatrix)
throws Exception {
File metaFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
datatypeMetadata.getMetaFilename());
if (LOG.isInfoEnabled()) {
LOG.info("writeMetadataFile(), meta file: " + metaFile);
}
PrintWriter writer =
new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(metaFile, false));
writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n");
writer.print(
"genetic_alteration_type: " + datatypeMetadata.getMetaGeneticAlterationType() + "\n");
String stableID = datatypeMetadata.getMetaStableID();
stableID =
stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
writer.print("stable_id: " + stableID + "\n");
writer.print(
"show_profile_in_analysis_tab: "
+ datatypeMetadata.getMetaShowProfileInAnalysisTab()
+ "\n");
String profileDescription = datatypeMetadata.getMetaProfileDescription();
if (dataMatrix != null) {
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.NUM_GENES_TAG, Integer.toString(dataMatrix.getGeneIDs().size()));
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.NUM_CASES_TAG, Integer.toString(dataMatrix.getCaseIDs().size()));
}
profileDescription =
profileDescription.replaceAll(
DatatypeMetadata.TUMOR_TYPE_TAG, cancerStudyMetadata.getTumorType());
writer.print("profile_description: " + profileDescription + "\n");
writer.print("profile_name: " + datatypeMetadata.getMetaProfileName() + "\n");
writer.flush();
writer.close();
}
private Optional<Consumer<String>> getOutputMethod(final String fileName) {
Consumer<String> out;
if (outputFile != null) {
final String outputName = fileName.replace(".xml", ".java");
final File outFile = FileUtils.getFile(this.outputFile, outputName);
out =
(sourceCode) -> {
try (FileWriter fw = new FileWriter(outFile)) {
System.out.println("gm.compiler :: writing " + fileName + " to " + outFile.getPath());
fw.write(sourceCode);
} catch (Exception ex) {
Logger.getAnonymousLogger().log(Level.SEVERE, null, ex);
}
};
} else {
out = this.outputMethod;
}
return Optional.ofNullable(out);
}
/**
* Runs all MAFs for the given dataaSourcesMetadata through the Oncotator and OMA tools.
*
* @param dataSourcesMetadata DataSourcesMetadata
* @throws Exception
*/
@Override
public void oncotateAllMAFs(DataSourcesMetadata dataSourcesMetadata) throws Exception {
// iterate over datasource download directory and process all MAFs
String[] extensions = new String[] {DatatypeMetadata.MAF_FILE_EXT};
for (File maf :
listFiles(new File(dataSourcesMetadata.getDownloadDirectory()), extensions, true)) {
// create temp for given maf
File oncotatorInputFile =
org.apache.commons.io.FileUtils.getFile(
org.apache.commons.io.FileUtils.getTempDirectory(), "oncotatorInputFile");
org.apache.commons.io.FileUtils.copyFile(maf, oncotatorInputFile);
// input is tmp file we just created, we want output to go into the original maf
oncotateMAF(
FileUtils.FILE_URL_PREFIX + oncotatorInputFile.getCanonicalPath(),
FileUtils.FILE_URL_PREFIX + maf.getCanonicalPath());
// clean up
org.apache.commons.io.FileUtils.forceDelete(oncotatorInputFile);
}
}
public static void main(String args[]) throws IOException {
String outputDir = DEFAULT_DIR;
String resources[] = DEFAULT_RESOURCES;
if (args.length == 0) {
// use default settings
} else if (args.length == 1) {
usage();
return;
} else {
resources = ArrayUtils.subarray(args, 1, args.length);
}
if (!new File(outputDir).isDirectory()) {
System.err.println("Output directory '" + outputDir + "' does not exist");
usage();
return;
}
for (String resource : resources) {
File dest = FileUtils.getFile(outputDir, resource);
InputStream is = ResourceInstaller.class.getResourceAsStream(resource);
if (is == null) {
System.err.println("Couldn't find resource " + resource);
usage();
return;
}
if (dest.isFile()) {
File backup = new File(dest + ".backup");
System.err.println("backing up " + dest + " to " + backup);
FileUtils.deleteQuietly(backup);
FileUtils.moveFile(dest, backup);
}
FileUtils.copyInputStreamToFile(is, dest);
System.err.println("creating file " + dest.getAbsolutePath() + " from resources");
is.close();
if (dest.getName().toLowerCase().endsWith(".sh")) {
dest.setExecutable(true);
}
}
}
/**
* Create a case list file from the given case list metadata file.
*
* @param portalMetadata PortalMetadata
* @param cancerStudyMetadata CancerStudyMetadata
* @param caseListMetadata CaseListMetadata
* @param caseList String[]
* @throws Exception
*/
@Override
public void writeCaseListFile(
PortalMetadata portalMetadata,
CancerStudyMetadata cancerStudyMetadata,
CaseListMetadata caseListMetadata,
String[] caseList)
throws Exception {
File caseListFile =
org.apache.commons.io.FileUtils.getFile(
portalMetadata.getStagingDirectory(),
cancerStudyMetadata.getStudyPath(),
"case_lists",
caseListMetadata.getCaseListFilename());
if (LOG.isInfoEnabled()) {
LOG.info("writeCaseListFile(), case list file: " + caseListFile.getCanonicalPath());
}
PrintWriter writer =
new PrintWriter(org.apache.commons.io.FileUtils.openOutputStream(caseListFile, false));
writer.print("cancer_study_identifier: " + cancerStudyMetadata + "\n");
String stableID = caseListMetadata.getMetaStableID();
stableID =
stableID.replaceAll(DatatypeMetadata.CANCER_STUDY_TAG, cancerStudyMetadata.toString());
writer.print("stable_id: " + stableID + "\n");
writer.print("case_list_name: " + caseListMetadata.getMetaCaseListName() + "\n");
String caseListDescription = caseListMetadata.getMetaCaseListDescription();
caseListDescription =
caseListDescription.replaceAll(
DatatypeMetadata.NUM_CASES_TAG, Integer.toString(caseList.length));
writer.print("case_list_description: " + caseListDescription + "\n");
writer.print("case_list_category: " + caseListMetadata.getMetaCaseListCategory() + "\n");
writer.print("case_list_ids: ");
for (String caseID : caseList) {
writer.print(caseID + Converter.VALUE_DELIMITER);
}
writer.println();
writer.flush();
writer.close();
}
@Override
public ConnectionState execute(Connection connection, ApplicationConfiguration configuration) {
if (connection.getInputQueue().hasAny()) {
String path = connection.getInputQueue().pop();
if (path.isEmpty()) {
return connectionStateProvider.get(AdministrationMenu.class);
}
File file = FileUtils.getFile(path);
if (file.exists()) {
ImportConfiguration importConfiguration = new ImportConfiguration();
importConfiguration.setFile(file);
databaseImportLauncher.launchWith(importConfiguration);
return connectionStateProvider.get(AdministrationMenu.class);
} else {
String text =
textMaker.getText(
TextName.FileNotFound, connection.getLocale(), ImmutableMap.of("file path", path));
connection.getOutputQueue().push(text);
return connectionStateProvider.get(ImportPathPrompt.class);
}
}
return this;
}
@Override
public void read(String path) throws IOException {
File dir = FileUtils.getFile(path, "ensemble", getName());
if (!dir.isDirectory()) {
return;
}
try {
ObjectInputStream oip =
new ObjectInputStream(new FileInputStream(new File(dir, "similarityCoefficients")));
this.simlarityCoefficients = (TDoubleArrayList) oip.readObject();
oip.close();
oip = new ObjectInputStream(new FileInputStream(new File(dir, "mostSimilarCoefficients")));
this.mostSimilarCoefficients = (TDoubleArrayList) oip.readObject();
oip.close();
oip = new ObjectInputStream(new FileInputStream(new File(dir, "similarityInterpolator")));
this.similarityInterpolator = (Interpolator) oip.readObject();
oip.close();
oip = new ObjectInputStream(new FileInputStream(new File(dir, "mostSimilarInterpolator")));
this.mostSimilarInterpolator = (Interpolator) oip.readObject();
oip.close();
} catch (ClassNotFoundException e) {
throw new IOException("Malformed coefficient file(s)", e);
}
}