public String fetchCleanupReviewDirLinkGenXml() {
String s = null;
try {
s = // Organize and Clean Up Section
"<ReviewDirGenerator class='operator.ReviewDirGenerator' destination.dir='"
+ outputDirectory.getCanonicalPath()
+ "' sample='"
+ outputDirectory.getName()
+ "' submitter='"
+ submitter
+ "' analysis.type='"
+ analysisType
+ "'> \n"
+ " <finalVariants /> \n"
+ " <ViewerCSV /> \n"
+ " <InstanceLog class='buffer.InstanceLogFile' /> \n"
+ " <finalBAM /> \n"
+ " <QCOutputFile /> \n"
+ " <bedForVars /> \n"
+ "</ReviewDirGenerator> \n\n";
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nError fetching clean up and review dir links.\n");
}
return s;
}
private String listFiles(final File cache, List<File> toDelete) throws Exception {
boolean stopServices = false;
if (toDelete == null) {
toDelete = new ArrayList<File>();
} else {
stopServices = true;
}
int count = 0;
Formatter f = new Formatter();
f.format(" - Cache:%n * %s%n", cache.getCanonicalPath());
f.format(" - Commands:%n");
for (CommandData cdata : getCommands(new File(cache, COMMANDS))) {
f.format(" * %s \t0 handle for \"%s\"%n", cdata.bin, cdata.name);
toDelete.add(new File(cdata.bin));
count++;
}
f.format(" - Services:%n");
for (ServiceData sdata : getServices(new File(cache, SERVICE))) {
if (sdata != null) {
f.format(" * %s \t0 service directory for \"%s\"%n", sdata.sdir, sdata.name);
toDelete.add(new File(sdata.sdir));
File initd = platform.getInitd(sdata);
if (initd != null && initd.exists()) {
f.format(" * %s \t0 init.d file for \"%s\"%n", initd.getCanonicalPath(), sdata.name);
toDelete.add(initd);
}
if (stopServices) {
Service s = getService(sdata);
try {
s.stop();
} catch (Exception e) {
}
}
count++;
}
}
f.format("%n");
String result = (count > 0) ? f.toString() : null;
f.close();
return result;
}
/**
* Get the canonical path of a file.
*
* @param f The file.
* @return The canonical path.
*/
private String canonize(File f) {
String path = null;
try {
path = f.getCanonicalPath();
} catch (IOException e) {
App.exit(e);
}
return path;
}
private void executePipelineJob() {
String[] cmd = null;
try {
// write out tempTemplate
File template = new File(outputDirectory, "pipelineTemplate.xml");
if (IO.writeString(xmlTemplate, template) == false)
Misc.printErrAndExit("Problem writing -> " + template);
// build and execute cmd
cmd =
new String[] {
"java",
"-jar",
"-Xmx2G",
pJar.getCanonicalPath(),
"-props",
completePipelinePropFile.getCanonicalPath(),
template.getCanonicalPath()
};
String stringCmd = Misc.stringArrayToString(cmd, " ");
System.out.println("\nExecuting:\n" + stringCmd);
System.out.println("\nPipelineOutput:");
String[] out = IO.executeViaProcessBuilder(cmd, true);
// check output for possible errors
for (String line : out) {
String lcLine = line.toLowerCase();
// watch out for cases where error is mentioned in a warning output line.
if (lcLine.contains("error") && lcLine.startsWith("warning") == false)
Misc.printErrAndExit(
"\n\nERROR found in Pipeline.jar output, see above. Aborting!\n" + line);
}
} catch (Exception e) {
e.printStackTrace();
Misc.printErrAndExit("ERROR: executing " + Misc.stringArrayToString(cmd, " "));
}
}
public String what(String key, boolean oneliner) throws Exception {
byte[] sha;
Matcher m = SHA_P.matcher(key);
if (m.matches()) {
sha = Hex.toByteArray(key);
} else {
m = URL_P.matcher(key);
if (m.matches()) {
URL url = new URL(key);
sha = SHA1.digest(url.openStream()).digest();
} else {
File jarfile = new File(key);
if (!jarfile.exists()) {
reporter.error("File does not exist: %s", jarfile.getCanonicalPath());
}
sha = SHA1.digest(jarfile).digest();
}
}
reporter.trace("sha %s", Hex.toHexString(sha));
Revision revision = library.getRevision(sha);
if (revision == null) {
return null;
}
StringBuilder sb = new StringBuilder();
Formatter f = new Formatter(sb);
Justif justif = new Justif(120, 20, 70, 20, 75);
DateFormat dateFormat = DateFormat.getDateInstance();
try {
if (oneliner) {
f.format("%20s %s%n", Hex.toHexString(revision._id), createCoord(revision));
} else {
f.format("Artifact: %s%n", revision.artifactId);
if (revision.organization != null && revision.organization.name != null) {
f.format(" (%s)", revision.organization.name);
}
f.format("%n");
f.format("Coordinates\t0: %s%n", createCoord(revision));
f.format("Created\t0: %s%n", dateFormat.format(new Date(revision.created)));
f.format("Size\t0: %d%n", revision.size);
f.format("Sha\t0: %s%n", Hex.toHexString(revision._id));
f.format("URL\t0: %s%n", createJpmLink(revision));
f.format("%n");
f.format("%s%n", revision.description);
f.format("%n");
f.format("Dependencies\t0:%n");
boolean flag = false;
Iterable<RevisionRef> closure = library.getClosure(revision._id, true);
for (RevisionRef dep : closure) {
f.format(
" - %s \t2- %s \t3- %s%n",
dep.name, createCoord(dep), dateFormat.format(new Date(dep.created)));
flag = true;
}
if (!flag) {
f.format(" None%n");
}
f.format("%n");
}
f.flush();
justif.wrap(sb);
return sb.toString();
} finally {
f.close();
}
}
public CommandData parseCommandData(ArtifactData artifact) throws Exception {
File source = new File(artifact.file);
if (!source.isFile()) throw new FileNotFoundException();
CommandData data = new CommandData();
data.sha = artifact.sha;
data.jpmRepoDir = repoDir.getCanonicalPath();
JarFile jar = new JarFile(source);
try {
reporter.trace("Parsing %s", source);
Manifest m = jar.getManifest();
Attributes main = m.getMainAttributes();
data.name = data.bsn = main.getValue("Bundle-SymbolicName");
String version = main.getValue("Bundle-Version");
if (version == null) data.version = Version.LOWEST;
else data.version = new Version(version);
data.main = main.getValue("Main-Class");
data.description = main.getValue("Bundle-Description");
data.title = main.getValue("JPM-Name");
reporter.trace("name " + data.name + " " + data.main + " " + data.title);
DependencyCollector path = new DependencyCollector(this);
path.add(artifact);
DependencyCollector bundles = new DependencyCollector(this);
if (main.getValue("JPM-Classpath") != null) {
Parameters requires = OSGiHeader.parseHeader(main.getValue("JPM-Classpath"));
for (Map.Entry<String, Attrs> e : requires.entrySet()) {
path.add(e.getKey(), e.getValue().get("name")); // coordinate
}
} else if (!artifact.local) { // No JPM-Classpath, falling back to
// server's revision
// Iterable<RevisionRef> closure =
// library.getClosure(artifact.sha,
// false);
// System.out.println("getting closure " + artifact.url + " " +
// Strings.join("\n",closure));
// if (closure != null) {
// for (RevisionRef ref : closure) {
// path.add(Hex.toHexString(ref.revision));
// }
// }
}
if (main.getValue("JPM-Runbundles") != null) {
Parameters jpmrunbundles = OSGiHeader.parseHeader(main.getValue("JPM-Runbundles"));
for (Map.Entry<String, Attrs> e : jpmrunbundles.entrySet()) {
bundles.add(e.getKey(), e.getValue().get("name"));
}
}
reporter.trace("collect digests runpath");
data.dependencies.addAll(path.getDigests());
reporter.trace("collect digests bundles");
data.runbundles.addAll(bundles.getDigests());
Parameters command = OSGiHeader.parseHeader(main.getValue("JPM-Command"));
if (command.size() > 1) reporter.error("Only one command can be specified");
for (Map.Entry<String, Attrs> e : command.entrySet()) {
data.name = e.getKey();
Attrs attrs = e.getValue();
if (attrs.containsKey("jvmargs")) data.jvmArgs = attrs.get("jvmargs");
if (attrs.containsKey("title")) data.title = attrs.get("title");
if (data.title != null) data.title = data.name;
}
return data;
} finally {
jar.close();
}
}