@Override
public ExitCode run(final SwiftEnvironment environment) {
if (environment.getParameters().size() < 1) {
throw new MprcException(
"Missing path to configuration file.\nUsage: reformat-config <config> [<result>]");
}
final File file = new File(environment.getParameters().get(0));
final PrintWriter printWriter;
if (environment.getParameters().size() >= 2) {
String pathname = environment.getParameters().get(1);
try {
printWriter = new PrintWriter(new File(pathname));
} catch (FileNotFoundException e) {
environment.logCommandError(
"Could not open file for writing: "
+ pathname
+ "\n"
+ MprcException.getDetailedMessage(e));
return ExitCode.Error;
}
} else {
printWriter = new PrintWriter(System.out);
}
final AppConfigReader reader = new AppConfigReader(file, getFactory());
try {
reader.load(environment.getApplicationConfig());
} finally {
FileUtilities.closeQuietly(reader);
}
AppConfigWriter writer = null;
try {
writer = new AppConfigWriter(printWriter, getFactory());
writer.save(environment.getApplicationConfig());
} finally {
FileUtilities.closeQuietly(writer);
FileUtilities.closeQuietly(printWriter);
}
return ExitCode.Ok;
}
/**
* goes to the first sequence in the sequence database file so that the next call to getHeader()
* will return the first header in the file.
*/
public void beforeFirst() {
try {
FileUtilities.closeQuietly(this.reader);
reopenReader();
this.nextHeader = this.reader.readLine();
} catch (Exception e) {
throw new MprcException(
"Cannot open FASTA file [" + this.fastaFile.getAbsolutePath() + "]", e);
}
}
private static void writeWorkerAllocatorInputObject(final File file, final SgePacket object)
throws IOException {
BufferedWriter bufferedWriter = null;
try {
final XStream xStream = new XStream(new DomDriver());
bufferedWriter = new BufferedWriter(new FileWriter(file));
bufferedWriter.write(xStream.toXML(object));
} finally {
FileUtilities.closeQuietly(bufferedWriter);
}
}
/** Start reading from the beginning */
public void resetCurrentRowPointer() throws IOException {
currentRowValue = null;
FileUtilities.closeQuietly(reader);
reader = new BufferedReader(new FileReader(file), BUFFER_SIZE);
// Initialize by reading the first row
nextRow();
// Next call to nextRow will return the line we just read
previousRow();
}
/**
* @param mgf .mgf file
* @return List of all spectra titles.
*/
public static List<String> getTitles(final File mgf) {
PeakListReader sourceMgfReader = new MgfPeakListReader(mgf, false);
List<String> titles = new ArrayList<String>(1000);
try {
MascotGenericFormatPeakList peakList;
while ((peakList = sourceMgfReader.nextPeakList()) != null) {
titles.add(peakList.getTitle());
}
} finally {
FileUtilities.closeQuietly(sourceMgfReader);
}
return titles;
}
@Override
protected void doGet(final HttpServletRequest req, final HttpServletResponse resp)
throws ServletException {
PrintWriter out = null;
try {
swiftDao.begin(); // Transaction-per-request
final SearchRunFilter searchRunFilter = new SearchRunFilter();
searchRunFilter.setStart("0");
searchRunFilter.setCount("50");
out = resp.getWriter();
final StringBuilder response = new StringBuilder(TYPICAL_RESPONSE_SIZE);
response.append("[");
final List<SearchRun> searchRuns = swiftDao.getSearchRunList(searchRunFilter);
for (int i = 0; i < searchRuns.size(); i++) {
final SearchRun searchRun = searchRuns.get(i);
final int runningTasks = swiftDao.getNumberRunningTasksForSearchRun(searchRun);
JsonWriter.appendSearchRunJson(response, i, searchRun, runningTasks, null, false);
if (i + 1 < searchRuns.size()) {
response.append(",\n");
}
}
response.append("]");
out.print(response.toString());
swiftDao.commit();
} catch (Exception e) {
swiftDao.rollback();
throw new MprcException("Could not obtain list of search runs", e);
} finally {
FileUtilities.closeQuietly(out);
}
}
/**
* goes through each header in a fasta file and checks to make sure it is a valid fasta header. If
* any problems are encountered or a header does not check out then false is returned
*
* @param toCheck the file you want to see is a valid FASTA file
* @return true if the file is a valid fasta file else false
*/
public static boolean isFASTAFileValid(final File toCheck) {
DBInputStream in = null;
try {
in = new FASTAInputStream(toCheck);
int sequenceCount = 0;
in.beforeFirst();
while (in.gotoNextSequence()) {
if (isHeader(in.getHeader())) {
sequenceCount++;
} else {
return false;
}
}
return (sequenceCount != 0);
} catch (Exception e) {
// SWALLOWED: We just return false as in "not valid"
LOGGER.warn(e);
return false;
} finally {
FileUtilities.closeQuietly(in);
}
}
/** performs any cleaning up that may be necessary. */
public void close() {
FileUtilities.closeQuietly(this.out);
}
/** performs any cleaning up that may be necessary. Always call when you are done. */
public void close() {
FileUtilities.closeQuietly(this.reader);
}
@Override
public void close() throws IOException {
FileUtilities.closeQuietly(reader);
}