void put(final URI uri, ArtifactData data) throws Exception {
reporter.trace("put %s %s", uri, data);
File tmp = createTempFile(repoDir, "mtp", ".whatever");
tmp.deleteOnExit();
try {
copy(uri.toURL(), tmp);
byte[] sha = SHA1.digest(tmp).digest();
reporter.trace("SHA %s %s", uri, Hex.toHexString(sha));
ArtifactData existing = get(sha);
if (existing != null) {
reporter.trace("existing");
xcopy(existing, data);
return;
}
File meta = new File(repoDir, Hex.toHexString(sha) + ".json");
File file = new File(repoDir, Hex.toHexString(sha));
rename(tmp, file);
reporter.trace("file %s", file);
data.file = file.getAbsolutePath();
data.sha = sha;
data.busy = false;
CommandData cmddata = parseCommandData(data);
if (cmddata.bsn != null) {
data.name = cmddata.bsn + "-" + cmddata.version;
} else data.name = Strings.display(cmddata.title, cmddata.bsn, cmddata.name, uri);
codec.enc().to(meta).put(data);
reporter.trace("TD = " + data);
} finally {
tmp.delete();
reporter.trace("puted %s %s", uri, data);
}
}
// remove temp files, the pipeline.jar operator isn't working.
public void deleteTempFiles() {
System.out.println("\nRemoving these temp files:");
File workingDir = new File(System.getProperty("user.dir"));
File[] toExamine = workingDir.listFiles();
for (File f : toExamine) {
boolean d = false;
String n = f.getName();
if (n.startsWith("pipeinstancelog")) d = true;
else if (n.contains(".DOC.sample")) d = true;
else if (n.contains("allDepths.")) d = true;
else if (n.startsWith("nocalls.")) d = true;
else if (n.startsWith("snpeff.")) d = true;
else if (n.contains("plice")) d = true;
if (d) {
System.out.println("\t" + n);
f.deleteOnExit();
}
}
// delete the temp uncompressed vcf (required by Pipeline.jar)
if (deleteTempVcf) System.out.println("\t" + finalVcf.getName());
}