@Before
public void before() throws Exception {
File test = new File("dir");
test.mkdir();
File testFile = new File(test, "test.txt");
FileUtils.writeLines(testFile, Arrays.asList("Hello", "My", "Name"));
File multiDir = new File("multidir");
for (int i = 0; i < 2; i++) {
File newTestFile = new File(multiDir, "testfile-" + i);
FileUtils.writeLines(newTestFile, Arrays.asList("Sentence 1.", "Sentence 2.", "Sentence 3."));
}
}
@Before
public void createTestFiles() throws IOException {
SOME_FILE = test_folder.newFile();
FileUtils.writeLines(SOME_FILE, Arrays.asList(SOME_FILE_LINE1, SOME_FILE_LINE2));
OTHER_FILE = test_folder.newFile();
FileUtils.writeLines(
OTHER_FILE, Arrays.asList(OTHER_FILE_LINE1, OTHER_FILE_LINE2, OTHER_FILE_LINE3));
DIRECTORY_DOES_NOT_EXIST = new File("");
VALID_DIRECTORY_INPUT = new DirectoryInput(test_folder.getRoot());
NON_READABLE_DIRECTORY = test_folder.newFolder();
NON_READABLE_DIRECTORY.setReadable(false);
}
private List<String> loadAllApkIds() throws Exception {
File allFile = getAllApkIdsFile();
if (allFile.exists()) return FileUtils.readLines(allFile);
List<String> apkIds =
(List<String>)
executeSql(
new ConnectionHandler() {
@Override
public Object handle(Connection conn) throws Exception {
ArrayList<String> l = new ArrayList<String>();
Statement stmt = conn.createStatement();
ResultSet rs =
stmt.executeQuery("select package, version_code, architecture from qapk");
while (rs.next()) {
l.add(
ApkId.of(
rs.getString("package"),
rs.getInt("version_code"),
rs.getInt("architecture"))
.toString());
}
stmt.close();
return l;
}
});
FileUtils.writeLines(allFile, apkIds);
return apkIds;
}
private File checkUrlrewriteConf(String basePath) throws IOException {
// create and register config file
String urlrewritePath = basePath + "/urlwrewrite.xml";
File urlrewriteFile = new File(urlrewritePath);
// Create structr.conf if not existing
if (!urlrewriteFile.exists()) {
// synthesize a urlrewrite.xml file
List<String> config = new LinkedList<String>();
config.add("<?xml version=\"1.0\" encoding=\"utf-8\"?>");
config.add(
"<!DOCTYPE urlrewrite\n"
+ " PUBLIC \"-//tuckey.org//DTD UrlRewrite 3.2//EN\"\n"
+ " \"http://www.tuckey.org/res/dtds/urlrewrite3.2.dtd\">");
config.add("<urlrewrite>");
config.add(" <rule match-type=\"regex\">");
config.add(" <name>RedirectToHtmlServlet</name>");
config.add(
" <condition type=\"request-uri\" operator=\"notequal\">^/structr/</condition>");
config.add(" <from>^/(.*)$</from>");
config.add(" <to type=\"forward\" last=\"true\">/structr/html/$1</to>");
config.add(" </rule>");
config.add("</urlrewrite>");
urlrewriteFile.createNewFile();
FileUtils.writeLines(urlrewriteFile, "UTF-8", config);
}
return urlrewriteFile;
}
private synchronized void addFailedRecord(
PollTableEntry pollTableEntry, FileObject failedObject, String timeString) {
try {
String record =
failedObject.getName().getBaseName() + VFSConstants.FAILED_RECORD_DELIMITER + timeString;
String recordFile =
pollTableEntry.getFailedRecordFileDestination()
+ pollTableEntry.getFailedRecordFileName();
File failedRecordFile = new File(recordFile);
if (!failedRecordFile.exists()) {
FileUtils.writeStringToFile(failedRecordFile, record);
if (log.isDebugEnabled()) {
log.debug("Added fail record '" + record + "' into the record file '" + recordFile + "'");
}
} else {
List<String> content = FileUtils.readLines(failedRecordFile);
if (!content.contains(record)) {
content.add(record);
}
FileUtils.writeLines(failedRecordFile, content);
}
} catch (IOException e) {
log.fatal("Failure while writing the failed records!", e);
}
}
public static void writeLines(File file, String encoding, Collection lines) {
try {
FileUtils.writeLines(file, encoding, lines);
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
public static void writeLines(File file, Collection lines, String lineEnding) {
try {
FileUtils.writeLines(file, lines, lineEnding);
} catch (IOException e) {
throw new UncheckedIOException(e);
}
}
@Override
public String analyze(Iterable<Mutation> mutations, HtmlReport report) {
List<String> lines = new ArrayList<String>();
for (Mutation mutation : mutations) {
if (mutation.isKilled()) {
MutationTestResult result = mutation.getMutationResult();
Set<TestMessage> detecting = new HashSet<TestMessage>();
Collection<TestMessage> failures = result.getFailures();
detecting.addAll(failures);
Collection<TestMessage> errors = result.getErrors();
detecting.addAll(errors);
String tests = getIds(detecting);
String line = mutation.getId() + "," + tests;
lines.add(line);
}
}
Set<Entry<String, Integer>> entrySet = testsIds.entrySet();
lines.add("Ids");
for (Entry<String, Integer> entry : entrySet) {
lines.add(entry.getKey() + "," + entry.getValue());
}
try {
FileUtils.writeLines(new File("detectedByTest.csv"), lines);
} catch (IOException e) {
e.printStackTrace();
}
return Joiner.on("\n").join(lines);
}
public static void generatePageLinks() throws Exception {
List<String> pageLinks = new ArrayList<String>();
for (int i = 1; i <= 100; i++) {
String url = "http://esf.sh.fang.com/house-a026/i3" + i + "/";
pageLinks.add(url);
}
FileUtils.writeLines(new File("./output/soufang/pagelink.txt"), pageLinks, true);
}
public void createAnnotationFile(List<String> sentences) {
try {
final String file = FrameNetOptions.ABS_PATH_FNDATA + FrameNetOptions.FN_FILE_NAME;
FileUtils.writeLines(new File(file), sentences);
} catch (IOException e) {
e.printStackTrace();
}
}
private void writeItems() {
File filesDir = getFilesDir();
File todoFile = new File(filesDir, "todo.txt");
try {
FileUtils.writeLines(todoFile, items);
} catch (IOException e) {
e.printStackTrace();
}
}
private static void output_result(String outPath, Map<String, List<String>> result_map) {
for (String s : result_map.keySet()) {
try {
FileUtils.writeLines(new File(outPath + s), result_map.get(s));
} catch (IOException e) {
e.printStackTrace();
}
}
}
@Test
public void verify_readFileSource() throws IOException {
File file = writer.getSourceFile(COMPONENT_REF);
FileUtils.writeLines(file, of("1", "2", "3"));
CloseableIterator<String> res = underTest.readFileSource(COMPONENT_REF).get();
assertThat(res).containsExactly("1", "2", "3");
res.close();
}
public static void writeLines(final File file, final List<String> lines) {
try {
if (!file.exists()) {
file.createNewFile();
}
FileUtils.writeLines(file, lines);
} catch (IOException e) {
logger.warn("I/O error while writing lines to file " + file.getPath(), e);
}
}
private void createReadMeFile(final File binaryRepoFolder) throws IOException {
// add a "README.md" file and commit
final File readmeFile = new File(binaryRepoFolder, "README.md");
final List<String> readmeContent = new ArrayList<String>();
readmeContent.add("Binary Repository For " + getSourceRemoteUrl());
readmeContent.add("=======================================================");
readmeContent.add("");
readmeContent.add("Stores the class files for the above source repository");
org.apache.commons.io.FileUtils.writeLines(readmeFile, readmeContent, "\n");
}
/**
* Modifies public getters to return {@code Object} so inheriting classes could override them with
* different signature.
*
* @param distPath the top level directory of the source code
* @param accessors a map where keys are class names and values are the list of properties (and
* thus getters) to be modified
*/
public static void modifyGetters(String distPath, Map<String, List<String>> accessors)
throws IOException {
String templateOriginal = " public $accessor$ get$accessor$() {";
String templateReplace = " public Object get$accessor$() {";
String placeHolder = "$accessor$";
boolean isInAccessor = false;
// change shadowed getters
File entitiesDir = new File(distPath, ENTITIES_PACKAGE.replace('.', File.separatorChar));
for (File file : entitiesDir.listFiles()) {
List<String> finalLines = new ArrayList<>(COPYRIGHT_LINES);
List<String> tempLines = new ArrayList<>();
List<String> accessorsToCheck = accessors.get(file.getName().replace(".java", ""));
if (accessorsToCheck == null) {
injectCopyrightHeader(file);
continue;
}
for (String line : FileUtils.readLines(file)) {
if (line.isEmpty()) {
isInAccessor = false;
finalLines.addAll(tempLines);
finalLines.add(line);
tempLines.clear();
} else if (line.equals("}")) {
isInAccessor = false;
finalLines.add("}");
} else {
if (!isInAccessor) {
for (String accessor : accessorsToCheck) {
if (line.toLowerCase()
.equals(templateOriginal.replace(placeHolder, accessor).toLowerCase())) {
isInAccessor = true;
tempLines.add(templateReplace.replace(placeHolder, accessor));
break;
}
}
if (!isInAccessor) {
tempLines.add(line);
} else {
isInAccessor = false;
}
}
}
}
// Save the new content:
finalLines = StringUtils.removeTrailingWhitespace(finalLines);
FileUtils.writeLines(file, finalLines);
}
}
// "hermitfang";
// "https://abs.twimg.com/sticky/default_profile_images/default_profile_5_bigger.png";
private void writeItems() {
myProfile.add("hermitfang");
myProfile.add(
"https://abs.twimg.com/sticky/default_profile_images/default_profile_5_bigger.png");
File filesDir = getFilesDir();
File todoFile = new File(filesDir, "myProfile.txt");
try {
FileUtils.writeLines(todoFile, myProfile);
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Write manifest in the install jar.
*
* @throws IOException for any I/O error
*/
protected void writeManifest() throws IOException {
// Add splash screen configuration
List<String> lines = IOUtils.readLines(getClass().getResourceAsStream("MANIFEST.MF"));
if (splashScreenImage != null) {
String destination = String.format("META-INF/%s", splashScreenImage.getName());
mergeManager.addResourceToMerge(splashScreenImage.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");
}
public void output(int start, int end)
throws MalformedURLException, IOException, XPatherException {
ArrayList<InstitutionDataItem> data = new ArrayList<InstitutionDataItem>();
for (int i = start; i <= end; i++) {
data.addAll(this.getData(i));
}
File outputFile = new File("complete-institutions-" + start + "-" + end + ".csv");
String headings = data.get(0).getHeadings() + "\n";
FileUtils.write(outputFile, headings);
FileUtils.writeLines(outputFile, data, true);
}
/**
* 将日志写入文件
*
* @param logs
* @param destFile
*/
private static void writeLogToFile(Collection<SVNLog> logs, File destFile) throws Exception {
if (logs == null || logs.isEmpty()) {
return;
}
if (!destFile.exists()) {
destFile.createNewFile();
}
List<String> contents = new LinkedList<String>();
for (SVNLog e : logs) {
contents.add(e.toSimpleString());
}
FileUtils.writeLines(destFile, contents, false);
}
/**
* Generate the new config spec
*
* @return The generated {@link ConfigSpec}
* @throws net.praqma.clearcase.exceptions.CleartoolException Thrown when ClearCase reports errors
* @throws java.io.IOException Thrown if we're not able to create the temporary config spec file
*/
public ConfigSpec generate() throws CleartoolException, IOException {
List<String> csLines = catcs();
/* Remove custom load rules */
removeLoadRules(csLines);
/* Add new custom load rules */
logger.fine("Add new custom load rules");
logger.fine("Load rules: " + loadRules);
csLines.addAll(addLoad(loadRules));
temporaryCSFile = File.createTempFile("ClearCase", "configspec");
FileUtils.writeLines(temporaryCSFile, csLines);
return this;
}
private static void cleanFile(final InputStream is, final File file) throws IOException {
try {
final List<String> updatedLines = new LinkedList<>();
final List<String> lines = FileUtils.readLines(file);
for (String line : lines) {
if (line.contains("DOCTYPE")) {
break;
}
updatedLines.add(line);
}
FileUtils.writeLines(file, updatedLines, false);
} catch (IOException e) {
throw e;
}
}
@RequestMapping(value = "export-list", method = RequestMethod.GET)
public String exportTaskList() {
Collection<Task> tasks = this.taskService.getAllTasks();
try {
String filePath = this.localSettingsProperties.getProperty(Constants.TASKS_FILE);
FileUtils.writeLines(new File(filePath), tasks);
} catch (IOException ex) {
LOGGER.error(ExceptionUtils.getFullStackTrace(ex));
}
return "redirect:/";
}
public static void main(String[] args) throws Throwable {
final InputStream is = ServerLogsService.class.getResourceAsStream("/access.log");
final File log = new File("teste.txt");
FileUtils.copyInputStreamToFile(is, log);
final List<String> updatedLines = new LinkedList<>();
final List<String> lines = FileUtils.readLines(log);
for (String line : lines) {
if (line.contains("DOCTYPE")) {
break;
}
updatedLines.add(line);
}
final File file = new File("teste_resul.log");
FileUtils.writeLines(file, updatedLines, false);
}
/**
* 得到图片地址路径
*
* @param path
* @return
*/
public static boolean listDir(String path) {
File picPath = new File("/home/lifeix/temp/uploadpicPath.txt");
// File picPath = new File("/home/lifeix/temp/picPath.txt");
if (picPath.exists()) {
try {
imgsArr = FileUtils.readLines(picPath);
return true;
} catch (IOException e) {
e.printStackTrace();
}
}
File dir = new File(path);
File[] files = dir.listFiles();
for (File file : files) {
if (file.isDirectory()) {
listDir(file.getAbsolutePath());
} else {
try {
ImageInputStream is = ImageIO.createImageInputStream(file);
if (is != null && file.getAbsolutePath().endsWith(".jpg")) {
imgsArr.add(file.getAbsolutePath());
System.out.println(file.getAbsolutePath());
}
is.close();
} catch (IOException e) {
e.printStackTrace();
}
// System.out.println(file.getAbsolutePath());
// System.out.println(file.getParent() + "-->" + file.getName());
}
}
if (picPath.exists()) {
try {
FileUtils.writeLines(picPath, imgsArr);
} catch (IOException e) {
e.printStackTrace();
}
}
return true;
}
private static void execPrintTypesDoeCorpus(String[] args) {
boolean ascending = true;
// Ascending or descending?
if (args.length > 1)
if ("asc".equalsIgnoreCase(args[1])) ascending = true;
else if ("desc".equalsIgnoreCase(args[1])) ascending = false;
else throw new IllegalArgumentException("Second parameter must be either 'asc' or 'desc'");
// Save to file?
String path = "";
List<String> lines = null;
boolean writeToFile = false;
if (args.length > 2) {
path = args[2];
lines = new ArrayList<>();
writeToFile = true;
}
// Load corpus first
execParseDoeCorpus(false /* doSave */);
HashMap<String, Integer> types = corpus.getVocabulary();
Map<String, Integer> sortedTypes = ListAndMapUtil.sortByComparator(types, ascending);
for (String key : sortedTypes.keySet()) {
String line = key + ";" + sortedTypes.get(key);
System.out.println(line);
if (writeToFile) lines.add(line);
}
// Save to file
if (writeToFile)
try {
FileUtils.writeLines(new File(path), lines);
} catch (IOException e) {
System.out.println("Error while trying to write to file " + path);
e.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");
}
public static void saveAgentLinks(String pageLink) throws Exception {
String html = HttpUtil.HttpGet(pageLink);
// System.out.println(html);
Document doc = Jsoup.parse(html);
// Document doc = Jsoup.parse(new File("./input/html.txt"), "utf-8");
List<String> agentLinks = new ArrayList<String>();
Elements elements = doc.select("A[target=_blank]");
for (Element element : elements) {
String href = element.attr("href");
if (href.startsWith("/a/")) {
String url = "http://esf.sh.fang.com" + href;
System.out.println(url);
agentLinks.add(url);
}
}
FileUtils.writeLines(new File("./output/soufang/agentlink.txt"), agentLinks, true);
}
public ModuleRunner(String sdkHome) throws Exception {
if (sdkHome == null) {
sdkHome = System.getenv(ModuleBuilder.GLOBAL_SDK_HOME_ENV_VAR);
if (sdkHome == null)
throw new IllegalStateException(
"Path to kb-sdk home folder should be set either"
+ " in command line (-h) or in "
+ ModuleBuilder.GLOBAL_SDK_HOME_ENV_VAR
+ " system environment variable");
}
File sdkHomeDir = new File(sdkHome);
if (!sdkHomeDir.exists()) sdkHomeDir.mkdirs();
File sdkCfgFile = new File(sdkHomeDir, "sdk.cfg");
String sdkCfgPath = sdkCfgFile.getCanonicalPath();
if (!sdkCfgFile.exists()) {
System.out.println(
"Warning: file "
+ sdkCfgFile.getAbsolutePath()
+ " will be "
+ "initialized (with 'kbase_endpoint'/'catalog_url' pointing to AppDev "
+ "environment, user and password will be prompted every time if not set)");
FileUtils.writeLines(
sdkCfgFile,
Arrays.asList(
"kbase_endpoint=https://appdev.kbase.us/services",
"catalog_url=https://appdev.kbase.us/services/catalog",
"user="******"password="******"### Please use next parameter to specify custom list of network",
"### interfaces used for callback IP address lookup:",
"#callback_networks=docker0,vboxnet0,vboxnet1,en0,en1,en2,en3"));
}
Properties sdkConfig = new Properties();
try (InputStream is = new FileInputStream(sdkCfgFile)) {
sdkConfig.load(is);
}
kbaseEndpoint = sdkConfig.getProperty("kbase_endpoint");
if (kbaseEndpoint == null) {
throw new IllegalStateException("Couldn't find 'kbase_endpoint' parameter in " + sdkCfgFile);
}
String catalogUrlText = sdkConfig.getProperty("catalog_url");
if (catalogUrlText == null) {
throw new IllegalStateException("Couldn't find 'catalog_url' parameter in " + sdkCfgFile);
}
catalogUrl = new URL(catalogUrlText);
runDir = new File(sdkHomeDir, "run_local");
user = sdkConfig.getProperty("user");
password = sdkConfig.getProperty("password");
if (user == null || user.trim().isEmpty()) {
System.out.println(
"You haven't preset your user/password in " + sdkCfgPath + ". " + "Please enter it now.");
user = new String(System.console().readLine("User: "******"Password: "******"You haven't preset your password in " + sdkCfgPath + ". " + "Please enter it now.");
password = new String(System.console().readPassword("Password: "******"callback_networks");
if (callbackNetworksText != null) {
callbackNetworks = callbackNetworksText.trim().split("\\s*,\\s*");
}
}
public int run(
String methodName,
File inputFile,
boolean stdin,
String inputJson,
File output,
String tagVer,
boolean verbose,
boolean keepTempFiles,
String provRefs,
String mountPoints)
throws Exception {
AuthToken auth = AuthService.login(user, password).getToken();
////////////////////////////////// Loading image name /////////////////////////////////////
CatalogClient client = new CatalogClient(catalogUrl);
String moduleName = methodName.split(Pattern.quote("."))[0];
ModuleVersion mv =
client.getModuleVersion(
new SelectModuleVersion()
.withModuleName(moduleName)
.withVersion(tagVer)
.withIncludeCompilationReport(1L));
if (mv.getDataVersion() != null)
throw new IllegalStateException(
"Reference data is required for module "
+ moduleName
+ ". This feature is not supported for local calls.");
String dockerImage = mv.getDockerImgName();
System.out.println("Docker image name recieved from Catalog: " + dockerImage);
////////////////////////////////// Standard files in run_local ////////////////////////////
if (!runDir.exists()) runDir.mkdir();
File runLocalSh = new File(runDir, "run_local.sh");
File runDockerSh = new File(runDir, "run_docker.sh");
if (!runLocalSh.exists()) {
FileUtils.writeLines(
runLocalSh,
Arrays.asList(
"#!/bin/bash",
"sdir=\"$(cd \"$(dirname \"$(readlink -f \"$0\")\")\" && pwd)\"",
"callback_url=$1",
"cnt_id=$2",
"docker_image=$3",
"mount_points=$4",
"$sdir/run_docker.sh run -v $sdir/workdir:/kb/module/work $mount_points "
+ "-e \"SDK_CALLBACK_URL=$callback_url\" --name $cnt_id $docker_image async"));
ProcessHelper.cmd("chmod", "+x", runLocalSh.getCanonicalPath()).exec(runDir);
}
if (!runDockerSh.exists()) {
FileUtils.writeLines(runDockerSh, Arrays.asList("#!/bin/bash", "docker \"$@\""));
ProcessHelper.cmd("chmod", "+x", runDockerSh.getCanonicalPath()).exec(runDir);
}
////////////////////////////////// Temporary files ////////////////////////////////////////
StringBuilder mountPointsDocker = new StringBuilder();
if (mountPoints != null) {
for (String part : mountPoints.split(Pattern.quote(","))) {
String[] fromTo = part.split(Pattern.quote(":"));
String to;
if (fromTo.length != 2) {
if (fromTo.length == 1) {
to = "tmp";
} else {
throw new IllegalStateException("Unexpected mount point format: " + part);
}
} else {
to = fromTo[1];
}
File fromDir = new File(fromTo[0]);
if ((!fromDir.exists()) || (!fromDir.isDirectory()))
throw new IllegalStateException("Mount point directory doesn't exist: " + fromDir);
String from = fromDir.getCanonicalPath();
if (!to.startsWith("/")) to = "/kb/module/work/" + to;
if (mountPointsDocker.length() > 0) mountPointsDocker.append(" ");
mountPointsDocker.append("-v ").append(from).append(":").append(to);
}
}
File workDir = new File(runDir, "workdir");
if (workDir.exists()) FileUtils.deleteDirectory(workDir);
workDir.mkdir();
File subjobsDir = new File(runDir, "subjobs");
if (subjobsDir.exists()) FileUtils.deleteDirectory(subjobsDir);
File tokenFile = new File(workDir, "token");
try (FileWriter fw = new FileWriter(tokenFile)) {
fw.write(auth.getToken());
}
String jobSrvUrl = kbaseEndpoint + "/userandjobstate";
String wsUrl = kbaseEndpoint + "/ws";
String shockUrl = kbaseEndpoint + "/shock-api";
File configPropsFile = new File(workDir, "config.properties");
PrintWriter pw = new PrintWriter(configPropsFile);
try {
pw.println("[global]");
pw.println("job_service_url = " + jobSrvUrl);
pw.println("workspace_url = " + wsUrl);
pw.println("shock_url = " + shockUrl);
pw.println("kbase_endpoint = " + kbaseEndpoint);
} finally {
pw.close();
}
////////////////////////////////// Preparing input.json ///////////////////////////////////
String jsonString;
if (inputFile != null) {
jsonString = FileUtils.readFileToString(inputFile);
} else if (inputJson != null) {
jsonString = inputJson;
} else if (stdin) {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
IOUtils.copy(System.in, baos);
jsonString = new String(baos.toByteArray(), Charset.forName("utf-8"));
} else {
throw new IllegalStateException("No one input method is used");
}
jsonString = jsonString.trim();
if (!jsonString.startsWith("["))
jsonString = "[" + jsonString + "]"; // Wrapping one argument by array
if (verbose) System.out.println("Input parameters: " + jsonString);
Map<String, Object> rpc = new LinkedHashMap<String, Object>();
rpc.put("version", "1.1");
rpc.put("method", methodName);
List<UObject> params =
UObject.getMapper().readValue(jsonString, new TypeReference<List<UObject>>() {});
rpc.put("params", params);
rpc.put("context", new LinkedHashMap<String, Object>());
UObject.getMapper().writeValue(new File(workDir, "input.json"), rpc);
////////////////////////////////// Starting callback service //////////////////////////////
int callbackPort = NetUtils.findFreePort();
URL callbackUrl = CallbackServer.getCallbackUrl(callbackPort, callbackNetworks);
Server jettyServer = null;
if (callbackUrl != null) {
if (System.getProperty("os.name").startsWith("Windows")) {
JsonServerSyslog.setStaticUseSyslog(false);
JsonServerSyslog.setStaticMlogFile(new File(workDir, "callback.log").getCanonicalPath());
}
CallbackServerConfig cfg =
new CallbackServerConfigBuilder(
new URL(kbaseEndpoint),
callbackUrl,
runDir.toPath(),
new LineLogger() {
@Override
public void logNextLine(String line, boolean isError) {
if (isError) {
System.err.println(line);
} else {
System.out.println(line);
}
}
})
.build();
Set<String> releaseTags = new TreeSet<String>();
if (mv.getReleaseTags() != null) releaseTags.addAll(mv.getReleaseTags());
String requestedRelease =
releaseTags.contains("release")
? "release"
: (releaseTags.contains("beta") ? "beta" : "dev");
final ModuleRunVersion runver =
new ModuleRunVersion(
new URL(mv.getGitUrl()),
new ModuleMethod(methodName),
mv.getGitCommitHash(),
mv.getVersion(),
requestedRelease);
List<String> inputWsObjects = new ArrayList<String>();
if (provRefs != null) {
inputWsObjects.addAll(Arrays.asList(provRefs.split(Pattern.quote(","))));
}
JsonServerServlet catalogSrv =
new SDKCallbackServer(auth, cfg, runver, params, inputWsObjects);
jettyServer = new Server(callbackPort);
ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
context.setContextPath("/");
jettyServer.setHandler(context);
context.addServlet(new ServletHolder(catalogSrv), "/*");
jettyServer.start();
} else {
if (callbackNetworks != null && callbackNetworks.length > 0) {
throw new IllegalStateException(
"No proper callback IP was found, "
+ "please check callback_networks parameter in configuration");
}
System.out.println(
"WARNING: No callback URL was recieved "
+ "by the job runner. Local callbacks are disabled.");
}
////////////////////////////////// Running Docker /////////////////////////////////////////
final String containerName =
"local_" + moduleName.toLowerCase() + "_" + System.currentTimeMillis();
try {
System.out.println();
int exitCode =
ProcessHelper.cmd(
"bash",
DirUtils.getFilePath(runLocalSh),
callbackUrl.toExternalForm(),
containerName,
dockerImage,
mountPointsDocker.toString())
.exec(runDir)
.getExitCode();
File outputTmpFile = new File(workDir, "output.json");
if (!outputTmpFile.exists())
throw new IllegalStateException("Output JSON file was not found");
FinishJobParams outObj = UObject.getMapper().readValue(outputTmpFile, FinishJobParams.class);
if (outObj.getError() != null || outObj.getResult() == null) {
System.out.println();
if (outObj.getError() == null) {
System.err.println("Unknown error (no information)");
} else {
System.err.println("Error: " + outObj.getError().getMessage());
if (verbose && outObj.getError().getError() != null) {
System.err.println("Error details: \n" + outObj.getError().getError());
}
}
System.out.println();
} else {
String outputJson = UObject.getMapper().writeValueAsString(outObj.getResult());
if (output != null) {
FileUtils.writeStringToFile(output, outputJson);
System.out.println("Output is saved to file: " + output.getCanonicalPath());
} else {
System.out.println();
System.out.println("Output returned by the method:");
System.out.println(outputJson);
System.out.println();
}
}
return exitCode;
} finally {
try {
System.out.println("Deleteing docker container...");
ProcessHelper.cmd(
"bash", DirUtils.getFilePath(runDockerSh), "rm", "-v", "-f", containerName)
.exec(runDir);
} catch (Exception ex) {
System.out.println("Error deleting container [" + containerName + "]: " + ex.getMessage());
}
if (jettyServer != null) {
System.out.println("Shutting down callback server...");
jettyServer.stop();
}
if (!keepTempFiles) {
System.out.println("Deleting temporary files...");
FileUtils.deleteDirectory(workDir);
FileUtils.deleteDirectory(subjobsDir);
}
}
}