String[] sargs = args.toArray(new String[args.size()]);
log.info("Running " + StringUtil.join(sargs, "\n "));
- return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ // don't set the working dir, leave it the same as the working dir of the invocation
+ //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+ return Runtime.getRuntime().exec(sargs, envp);
}
/**
} else {
if (processingEntry.hasRetrievalUrl())
{
- String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+ String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8").replace("%","__");
// retrieve from URL to new local tmpfile
File tmpFile = File.createTempFile(safePDBId,