/** Creates a new document server */
public DocServer() {
super();
/* really should try and get the companion service name from the env
* here, but not worth the effort
*/
JsonServerSyslog templogger =
new JsonServerSyslog(
DEFAULT_COMPANION_SERVICE_NAME,
JsonServerServlet.KB_DEP,
JsonServerSyslog.LOG_LEVEL_INFO,
false);
if (sysLogOut != null) {
templogger.changeOutput(sysLogOut);
}
// getConfig() gets the service name from the env if it exists
config = JsonServerServlet.getConfig(DEFAULT_COMPANION_SERVICE_NAME, templogger);
String serverName = config.get(CFG_SERVICE_NAME);
if (serverName == null || serverName.isEmpty()) {
serverName = DEFAULT_SERVICE_NAME;
}
final String dlog = config.get(CFG_DOCS_LOC);
if (dlog == null || dlog.isEmpty()) {
docsLoc = defaultDocsLoc;
} else {
if (!dlog.startsWith("/")) {
docsLoc = "/" + dlog;
} else {
docsLoc = dlog;
}
}
logger =
new JsonServerSyslog(
serverName, JsonServerServlet.KB_DEP, JsonServerSyslog.LOG_LEVEL_INFO, false);
if (sysLogOut != null) {
logger.changeOutput(sysLogOut);
}
}
@Override
protected void doGet(final HttpServletRequest request, final HttpServletResponse response)
throws ServletException, IOException {
final RpcInfo rpc = JsonServerSyslog.getCurrentRpcInfo();
rpc.setId(("" + Math.random()).substring(2));
rpc.setIp(JsonServerServlet.getIpAddress(request, config));
rpc.setMethod("GET");
logHeaders(request);
String path = request.getPathInfo();
if (path == null) { // e.g. /docs
handle404(request, response);
return;
}
if (path.endsWith("/")) { // e.g. /docs/
path = path + "index.html";
}
// the path is already normalized by the framework, so no need to
// normalize here
path = docsLoc + path;
final InputStream is = getClass().getResourceAsStream(path);
if (is == null) {
handle404(request, response);
return;
}
try {
final byte[] page = IOUtils.toByteArray(is);
response.getOutputStream().write(page);
} catch (IOException ioe) {
logger.logErr(request.getRequestURI() + " 500 " + request.getHeader(USER_AGENT));
logger.logErr(ioe);
response.sendError(500);
return;
}
logger.logInfo(request.getRequestURI() + " 200 " + request.getHeader(USER_AGENT));
}
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);
}
}
}
private void logHeaders(final HttpServletRequest req) {
final String xFF = req.getHeader(X_FORWARDED_FOR);
if (xFF != null && !xFF.isEmpty()) {
logger.logInfo(X_FORWARDED_FOR + ": " + xFF);
}
}
private void handle404(final HttpServletRequest request, final HttpServletResponse response)
throws IOException {
logger.logErr(request.getRequestURI() + " 404 " + request.getHeader(USER_AGENT));
response.sendError(404);
}
