private void copy(File workspaceDir, InputStream in, Pattern glob, boolean overwrite)
throws Exception {
Jar jar = new Jar("dot", in);
try {
for (Entry<String, Resource> e : jar.getResources().entrySet()) {
String path = e.getKey();
bnd.trace("path %s", path);
if (glob != null && !glob.matcher(path).matches()) continue;
Resource r = e.getValue();
File dest = Processor.getFile(workspaceDir, path);
if (overwrite
|| !dest.isFile()
|| dest.lastModified() < r.lastModified()
|| r.lastModified() <= 0) {
bnd.trace("copy %s to %s", path, dest);
File dp = dest.getParentFile();
if (!dp.exists() && !dp.mkdirs()) {
throw new IOException("Could not create directory " + dp);
}
IO.copy(r.openInputStream(), dest);
}
}
} finally {
jar.close();
}
}
@Nonnull
private static File getOutputFileCreatingDirIfNeeded(
@Nonnull String outputDir, @Nonnull String sourceFilePath) {
File outputFile = getOutputFile(outputDir, sourceFilePath);
File parentDir = outputFile.getParentFile();
if (!parentDir.exists()) {
boolean outputDirCreated = parentDir.mkdirs();
assert outputDirCreated : "Failed to create output dir: " + outputDir;
}
return outputFile;
}
/**
* Constructor
*
* @throws IOException
*/
public JustAnotherPackageManager(Reporter reporter, Platform platform, File homeDir, File binDir)
throws IOException {
this.platform = platform;
this.reporter = reporter;
this.homeDir = homeDir;
if (!homeDir.exists() && !homeDir.mkdirs())
throw new IllegalArgumentException("Could not create directory " + homeDir);
repoDir = IO.getFile(homeDir, "repo");
if (!repoDir.exists() && !repoDir.mkdirs())
throw new IllegalArgumentException("Could not create directory " + repoDir);
commandDir = new File(homeDir, COMMANDS);
serviceDir = new File(homeDir, SERVICE);
commandDir.mkdir();
serviceDir.mkdir();
service = new File(repoDir, SERVICE_JAR_FILE);
if (!service.isFile()) init();
this.binDir = binDir;
if (!binDir.exists() && !binDir.mkdirs())
throw new IllegalArgumentException("Could not create bin directory " + binDir);
}
public static void storeImage(BufferedImage image, String s) {
String ext;
File f;
try {
ext = s.substring(s.lastIndexOf(".") + 1);
f = new File(s);
f.mkdirs();
} catch (Exception e) {
System.out.println(e);
return;
}
if (!ext.equals("gif") && !ext.equals("jpg") && !ext.equals("png")) {
System.out.println("Cannot write to file: Illegal extension " + ext);
return;
}
try {
ImageIO.write(image, ext, f);
} catch (Exception e) {
System.out.println(e);
}
}
/**
* @param data
* @param target
* @throws Exception
* @throws IOException
*/
public String createService(ServiceData data) throws Exception, IOException {
File sdir = new File(serviceDir, data.name);
if (!sdir.exists() && !sdir.mkdirs()) {
throw new IOException("Could not create directory " + data.sdir);
}
data.sdir = sdir.getAbsolutePath();
File lock = new File(data.sdir, LOCK);
data.lock = lock.getAbsolutePath();
if (data.work == null) data.work = new File(data.sdir, "work").getAbsolutePath();
if (data.user == null) data.user = platform.user();
if (data.user == null) data.user = "******";
new File(data.work).mkdir();
if (data.log == null) data.log = new File(data.sdir, "log").getAbsolutePath();
// TODO
// if (Data.validate(data) != null)
// return "Invalid service data: " + Data.validate(data);
if (service == null)
throw new RuntimeException(
"Missing biz.aQute.jpm.service in repo, should have been installed by init, try reiniting");
data.serviceLib = service.getAbsolutePath();
platform.chown(data.user, true, new File(data.sdir));
String s = platform.createService(data, null, false);
if (s == null) storeData(new File(data.sdir, "data"), data);
return s;
}
public void _workspace(WorkspaceOptions opts) throws Exception {
File base = bnd.getBase();
String name = opts._arguments().get(0);
File workspaceDir = Processor.getFile(base, name);
name = workspaceDir.getName();
base = workspaceDir.getParentFile();
if (base == null) {
bnd.error(
"You cannot create a workspace in the root (%s). The parent of a workspace %n"
+ "must be a valid directory. Recommended is to dedicate a directory to %n"
+ "all (or related) workspaces.",
workspaceDir);
return;
}
if (!opts.anyname() && !Verifier.isBsn(name)) {
bnd.error(
"You specified a workspace name that does not follow the recommended pattern "
+ "(it should be like a Bundle Symbolic name). It is a bit pedantic but it "
+ "really helps hwne you get many workspaces. If you insist on this name, use the -a/--anyname option.");
return;
}
Workspace ws = bnd.getWorkspace((File) null);
if (ws != null && ws.isValid()) {
bnd.error(
"You are currently in a workspace already (%s) in %s. You can only create a new workspace outside an existing workspace",
ws, base);
return;
}
File eclipseDir = workspaceDir;
workspaceDir.mkdirs();
if (!opts.single()) workspaceDir = new File(workspaceDir, "scm");
workspaceDir.mkdirs();
if (!base.isDirectory()) {
bnd.error("Could not create directory for the bnd workspace %s", base);
} else if (!eclipseDir.isDirectory()) {
bnd.error("Could not create directory for the Eclipse workspace %s", eclipseDir);
}
if (!workspaceDir.isDirectory()) {
bnd.error("Could not create the workspace directory %s", workspaceDir);
return;
}
if (!opts.update() && !opts.force() && workspaceDir.list().length > 0) {
bnd.error(
"The workspace directory %s is not empty, specify -u/--update to update or -f/--force to replace",
workspaceDir);
}
InputStream in = getClass().getResourceAsStream("/templates/enroute.zip");
if (in == null) {
bnd.error("Cannot find template in this jar %s", "/templates/enroute.zip");
return;
}
Pattern glob = Pattern.compile("[^/]+|cnf/.*|\\...+/.*");
copy(workspaceDir, in, glob, opts.force());
File readme = new File(workspaceDir, "README.md");
if (readme.isFile()) IO.copy(readme, bnd.out);
bnd.out.printf(
"%nWorkspace %s created.%n%n" //
+ " Start Eclipse:%n" //
+ " 1) Select the Eclipse workspace %s%n" //
+ " 2) Package Explorer context menu: Import/General/Existing Projects from %s%n"
+ "%n"
+ "", //
workspaceDir.getName(), eclipseDir, workspaceDir);
}
/** This method will process each argument and assign new variables */
public void processArgs(String[] args) {
Pattern pat = Pattern.compile("-[a-z]");
System.out.println(
"\n" + IO.fetchUSeqVersion() + " Arguments: " + Misc.stringArrayToString(args, " ") + "\n");
for (int i = 0; i < args.length; i++) {
String lcArg = args[i].toLowerCase();
Matcher mat = pat.matcher(lcArg);
if (mat.matches()) {
char test = args[i].charAt(1);
try {
switch (test) {
case 'o':
jobId = args[++i];
break;
case 's':
sampleId = args[++i];
break;
case 'm':
submitter = args[++i];
break;
case 'y':
analysisType = args[++i];
break;
case 'w':
webRootForLinks = new File(args[++i]);
break;
case 'e':
snpEffGenome = args[++i];
break;
case 'i':
minimumReadDepth = args[++i];
break;
case 't':
threads = args[++i];
break;
case 'l':
uploadVarsToNGSWeb = true;
break;
case 'j':
pJar = new File(args[++i]);
break;
case 'p':
truncPipePropFile = new File(args[++i]);
break;
case 'q':
bedForCoverageQC = new File(args[++i]);
break;
case 'b':
bedForVarCalling = new File(args[++i]);
break;
case 'r':
fastaReference = new File(args[++i]);
break;
case 'u':
unfilteredBam = new File(args[++i]);
break;
case 'f':
finalBam = new File(args[++i]);
break;
case 'v':
finalVcf = new File(args[++i]);
break;
case 'd':
outputDirectory = new File(args[++i]);
break;
case 'c':
referenceDir = new File(args[++i]);
break;
case 'h':
printDocs();
System.exit(0);
default:
Misc.printErrAndExit("\nProblem, unknown option! " + mat.group());
}
} catch (Exception e) {
Misc.printErrAndExit(
"\nSorry, something doesn't look right with this parameter: -" + test + "\n");
}
}
}
// check output dir and if needed set sampleId
if (outputDirectory != null) {
outputDirectory.mkdirs();
if (sampleId.length() == 0) sampleId = outputDirectory.getName();
}
// check root directory if needed
if (webRootForLinks != null) {
if (webRootForLinks.exists() == false) webRootForLinks.mkdirs();
// links dir?
File links = new File(webRootForLinks, "links");
if (links.exists() == false) links.mkdirs();
}
// look for required fields and files
checkPrintFields();
checkPrintFiles();
checkForGzippedVcf();
}