@NotNull
private Map<String, Ref> getRemoteRefs(@NotNull Repository db, @NotNull GitVcsRoot gitRoot)
throws Exception {
long retryInterval = myConfig.getConnectionRetryIntervalMillis();
int attemptsLeft = myConfig.getConnectionRetryAttempts();
while (true) {
final long start = System.currentTimeMillis();
Transport transport = null;
FetchConnection connection = null;
try {
transport =
myTransportFactory.createTransport(
db, gitRoot.getRepositoryFetchURL(), gitRoot.getAuthSettings());
connection = transport.openFetch();
return connection.getRefsMap();
} catch (NotSupportedException nse) {
throw friendlyNotSupportedException(gitRoot, nse);
} catch (TransportException te) {
attemptsLeft--;
if (isRecoverable(te) && attemptsLeft > 0) {
LOG.warn(
"List remote refs failed: "
+ te.getMessage()
+ ", "
+ attemptsLeft
+ " attempt(s) left");
} else {
throw friendlyTransportException(te, gitRoot);
}
} catch (WrongPassphraseException e) {
throw new VcsException(e.getMessage(), e);
} finally {
if (connection != null) connection.close();
if (transport != null) transport.close();
final long finish = System.currentTimeMillis();
PERFORMANCE_LOG.debug(
"[getRemoteRefs] repository: "
+ LogUtil.describe(gitRoot)
+ ", took "
+ (finish - start)
+ "ms");
}
Thread.sleep(retryInterval);
retryInterval *= 2;
}
}
/**
* Expected fullPath format:
*
* <p>"<git revision hash>|<repository url>|<file relative path>"
*
* @param rootEntry indicates the association between VCS root and build configuration
* @param fullPath change path from IDE patch
* @return the mapped path
*/
@NotNull
public Collection<String> mapFullPath(
@NotNull final VcsRootEntry rootEntry, @NotNull final String fullPath) {
OperationContext context = createContext(rootEntry.getVcsRoot(), "map full path");
try {
return myMapFullPath.mapFullPath(context, rootEntry, fullPath);
} catch (VcsException e) {
LOG.warnAndDebugDetails(
"Error while mapping path for root " + LogUtil.describe(rootEntry.getVcsRoot()), e);
return Collections.emptySet();
} catch (Throwable t) {
LOG.error("Error while mapping path for root " + LogUtil.describe(rootEntry.getVcsRoot()), t);
return Collections.emptySet();
} finally {
context.close();
}
}
private void logBuildPatch(
@NotNull VcsRoot root, @Nullable String fromRevision, @NotNull String toRevision) {
StringBuilder msg = new StringBuilder();
msg.append("Build");
if (fromRevision != null) msg.append(" incremental");
msg.append(" patch in VCS root ").append(LogUtil.describe(root));
if (fromRevision != null) msg.append(" from revision ").append(fromRevision);
msg.append(" to revision ").append(toRevision);
LOG.info(msg.toString());
}
@NotNull
public Map<String, Ref> getRemoteRefs(@NotNull final VcsRoot root) throws VcsException {
OperationContext context = createContext(root, "list remote refs");
GitVcsRoot gitRoot = context.getGitRoot();
try {
Repository db = context.getRepository();
Map<String, Ref> remoteRefs = getRemoteRefs(db, gitRoot);
if (LOG.isDebugEnabled())
LOG.debug("Remote refs for VCS root " + LogUtil.describe(root) + ": " + remoteRefs);
return remoteRefs;
} catch (Exception e) {
throw context.wrapException(e);
} finally {
context.close();
}
}
@NotNull
public RepositoryStateData getCurrentState(@NotNull GitVcsRoot gitRoot) throws VcsException {
String refInRoot = gitRoot.getRef();
String fullRef = GitUtils.expandRef(refInRoot);
Map<String, String> branchRevisions = new HashMap<String, String>();
for (Ref ref : getRemoteRefs(gitRoot.getOriginalRoot()).values()) {
if (!ref.getName().startsWith("ref")) continue;
if (!gitRoot.isReportTags() && isTag(ref) && !fullRef.equals(ref.getName())) continue;
branchRevisions.put(ref.getName(), getRevision(ref));
}
if (branchRevisions.get(fullRef) == null && !gitRoot.isIgnoreMissingDefaultBranch()) {
throw new VcsException(
"Cannot find revision of the default branch '"
+ refInRoot
+ "' of vcs root "
+ LogUtil.describe(gitRoot));
}
return RepositoryStateData.createVersionState(fullRef, branchRevisions);
}
/** Handles XEP-0337 "log" extensions. */
private void handleLogRequest(LogPacketExtension log, String jid) {
JitsiMeetConference conference = getConferenceForMucJid(jid);
if (conference == null) {
logger.debug("Room not found for JID: " + jid);
return;
}
Participant participant = conference.findParticipantForRoomJid(jid);
if (participant == null) {
logger.info("Ignoring log request from an unknown JID: " + jid);
return;
}
EventAdmin eventAdmin = FocusBundleActivator.getEventAdmin();
if (eventAdmin == null) return;
if (LogUtil.LOG_ID_PC_STATS.equals(log.getID())) {
String content = LogUtil.getContent(log);
if (content != null) {
ColibriConference colibriConference = conference.getColibriConference();
if (colibriConference != null) {
Event event =
EventFactory.peerConnectionStats(
colibriConference.getConferenceId(), participant.getEndpointId(), content);
if (event != null) eventAdmin.sendEvent(event);
} else {
logger.warn("Unhandled log request" + " - no valid Colibri conference");
}
}
} else if (logger.isInfoEnabled()) {
logger.info("Ignoring log request with an unknown ID:" + log.getID());
}
}
/**
* Make a dataset with the file
*
* @return dataset
*/
private RaobDataSet doMakeRaobDataSet() {
SoundingAdapter adapter = null;
try {
adapter = new NetcdfSoundingAdapter(file);
} catch (Exception ill) {
}
if (adapter == null) {
try {
adapter = new CMASoundingAdapter(file);
} catch (Exception exc) {
LogUtil.logException("Reading sounding:" + file, exc);
return null;
}
}
if (adapter == null) {
throw new IllegalArgumentException("Could not open sounding file:" + file);
}
SoundingOb[] obs = adapter.getSoundingObs();
return new RaobDataSet(adapter, Misc.toList(obs));
}
public void persist() {
DataElementConcept dec = DomainObjectFactory.newDataElementConcept();
List<DataElementConcept> decs = elements.getElements(dec);
logger.debug("***** Inside DEC Persist ");
int count = 0;
sendProgressEvent(count++, decs.size(), "DECs");
logger.debug("decs... ");
if (decs != null) {
for (ListIterator<DataElementConcept> it = decs.listIterator(); it.hasNext(); ) {
DataElementConcept newDec = DomainObjectFactory.newDataElementConcept();
dec = it.next();
sendProgressEvent(count++, decs.size(), "DEC : " + dec.getLongName());
List<AlternateName> passedAltNames = new ArrayList<AlternateName>();
for (AlternateName _an : dec.getAlternateNames()) passedAltNames.add(_an);
List<Definition> modelDefinitions = new ArrayList<Definition>();
for (Definition _def : dec.getDefinitions()) modelDefinitions.add(_def);
List<AdminComponentClassSchemeClassSchemeItem> passedACCSCSI = dec.getAcCsCsis();
dec.removeDefinitions();
dec.removeAlternateNames();
if (!StringUtil.isEmpty(dec.getPublicId()) && dec.getVersion() != null) {
newDec = existingMapping(dec);
dec.setId(newDec.getId());
for (AlternateName _an : passedAltNames) {
persisterUtil.addAlternateName(dec, _an);
}
it.set(newDec);
persisterUtil.addPackageClassification(dec);
logger.info(PropertyAccessor.getProperty("mapped.to.existing.dec"));
continue;
}
// update object class with persisted one
if (dec.getObjectClass().getPublicId() == null)
dec.setObjectClass(LookupUtil.lookupObjectClass(dec.getObjectClass().getPreferredName()));
else
dec.setObjectClass(
LookupUtil.lookupObjectClass(
dec.getObjectClass().getPublicId(), dec.getObjectClass().getVersion()));
newDec.setObjectClass(dec.getObjectClass());
// update property with persisted one
if (dec.getProperty().getPublicId() == null)
dec.setProperty(LookupUtil.lookupProperty(dec.getProperty().getPreferredName()));
else
dec.setProperty(
LookupUtil.lookupProperty(
dec.getProperty().getPublicId(), dec.getProperty().getVersion()));
newDec.setProperty(dec.getProperty());
logger.debug("dec name: " + dec.getLongName());
// logger.debug("alt Name: " + ne);
List<String> eager = new ArrayList<String>();
eager.add("definitions");
// does this dec exist?
List l = dataElementConceptDAO.find(newDec, eager);
logger.debug("***** decs size : " + l.size());
if (l.size() == 0) {
logger.debug("***** one or more decs ");
if (dec.getConceptualDomain() == null)
dec.setConceptualDomain(defaults.getConceptualDomain());
dec.setContext(defaults.getContext());
dec.setLongName(
dec.getObjectClass().getLongName() + " " + dec.getProperty().getLongName());
dec.setPreferredDefinition(
dec.getObjectClass().getPreferredDefinition()
+ DEC_PREFERRED_DEF_CONCAT_CHAR
+ dec.getProperty().getPreferredDefinition());
dec.setPreferredName(
ConventionUtil.publicIdVersion(dec.getObjectClass())
+ DEC_PREFERRED_NAME_CONCAT_CHAR
+ ConventionUtil.publicIdVersion(dec.getProperty()));
dec.setVersion(new Float(1.0f));
dec.setWorkflowStatus(defaults.getWorkflowStatus());
dec.setProperty(LookupUtil.lookupProperty(dec.getProperty().getPreferredName()));
dec.setAudit(defaults.getAudit());
dec.setLifecycle(defaults.getLifecycle());
StringBuilder builder = new StringBuilder();
for (char currentChar : dec.getPreferredDefinition().toCharArray()) {
Character replacementChar = charReplacementMap.get(currentChar);
builder.append(replacementChar != null ? replacementChar : currentChar);
}
dec.setPreferredDefinition(builder.toString());
logger.debug(
"***** preferred name " + dec.getPreferredName() + " public ID " + dec.getPublicId());
newDec = dataElementConceptDAO.create(dec);
logger.info(PropertyAccessor.getProperty("created.dec"));
} else {
newDec = (DataElementConcept) l.get(0);
logger.info(PropertyAccessor.getProperty("existed.dec"));
/* if DEC alreay exists, check context
* If context is different, add Used_by alt_name
*/
dec.setId(newDec.getId());
if (!newDec.getContext().getId().equals(defaults.getContext().getId())) {
AlternateName _an = DomainObjectFactory.newAlternateName();
_an.setName(defaults.getContext().getName());
_an.setType(AlternateName.TYPE_USED_BY);
persisterUtil.addAlternateName(dec, _an);
}
}
dec.setId(newDec.getId());
for (AlternateName _an : passedAltNames) {
persisterUtil.addAlternateName(dec, _an);
}
for (Definition def : modelDefinitions) {
persisterUtil.addAlternateDefinition(dec, def);
}
LogUtil.logAc(newDec, logger);
logger.info("-- Public ID: " + newDec.getPublicId());
logger.info(
PropertyAccessor.getProperty("oc.longName", newDec.getObjectClass().getLongName()));
logger.info(
PropertyAccessor.getProperty("prop.longName", newDec.getProperty().getLongName()));
dec.setAcCsCsis(passedACCSCSI);
persisterUtil.addPackageClassification(dec);
it.set(newDec);
// dec still referenced in DE. Need ID to retrieve it in DEPersister.
dec.setId(newDec.getId());
}
}
logger.debug("***** End DEC persist");
}
/**
* Get the data for the given DataChoice and selection criteria.
*
* @param dataChoice DataChoice for selection
* @param category DataCategory for the DataChoice (not used)
* @param subset subsetting criteria
* @param requestProperties extra request properties
* @return the Data object for the request
* @throws RemoteException couldn't create a remote data object
* @throws VisADException couldn't create the data
*/
protected Data getDataInner(
final DataChoice dataChoice,
DataCategory category,
final DataSelection subset,
final Hashtable requestProperties)
throws VisADException, RemoteException {
try {
List times = null;
if (subset != null) {
times = getTimesFromDataSelection(subset, dataChoice);
}
if (times == null) {
times = dataChoice.getSelectedDateTimes();
}
List dtimes = subset.getTimeDriverTimes();
if (dtimes != null && useDriverTime == false) {
useDriverTime = true;
}
List<RadarAdapter> adapters = getAdapters();
DateTime[] realDateTimes = new DateTime[adapters.size()];
for (int i = 0; i < adapters.size(); i++) {
realDateTimes[i] = ((RadarAdapter) adapters.get(i)).getBaseTime();
}
Arrays.sort(realDateTimes);
// Flip it to get youngest date first
boolean isRealTime = isRealTime();
if (isRealTime) {
realDateTimes =
(DateTime[]) Misc.reverseArray(realDateTimes, new DateTime[realDateTimes.length]);
}
// if use time driver
if (useDriverTime) {
List tests = resetTimesList(realDateTimes, times);
if (!compareTimeLists(times, tests)) {
reloadData();
adapters = getAdapters();
realDateTimes = new DateTime[adapters.size()];
for (int i = 0; i < adapters.size(); i++) {
realDateTimes[i] = ((RadarAdapter) adapters.get(i)).getBaseTime();
}
Arrays.sort(realDateTimes);
// Flip it to get youngest date first
isRealTime = isRealTime();
if (isRealTime) {
realDateTimes =
(DateTime[]) Misc.reverseArray(realDateTimes, new DateTime[realDateTimes.length]);
}
tests = resetTimesList(realDateTimes, times);
}
times = tests;
}
// if times are null, then that means all times
DateTime[] dateTimes = null;
if ((times == null) || (times.size() == 0)) {
dateTimes = realDateTimes;
} else {
dateTimes = new DateTime[times.size()];
for (int i = 0; i < times.size(); i++) {
Object time = times.get(i);
if (time instanceof TwoFacedObject) {
int index = ((Integer) ((TwoFacedObject) time).getId()).intValue();
dateTimes[i] = realDateTimes[index];
} else if (time instanceof DateTime) {
dateTimes[i] = (DateTime) time;
}
}
}
Arrays.sort(dateTimes);
final Data[] datas = new Data[dateTimes.length];
int timeIndex = 0;
final MathType[] mt = {null};
// create a new field of (Time -> (radar data)).
// fill in the times array and data array with dates/data
// only from those adapters which match the selected times.
// if a data object is null, stick it in the list.
// if all are null, then the MathType (mt) will never get set,
// so return null.
// System.err.println ("Reading " + adapters.size() + " radar files");
int cnt = 0;
ThreadManager threadManager = new visad.util.ThreadManager("radar data reading");
for (Iterator iter = adapters.iterator(); iter.hasNext(); ) {
final RadarAdapter adapter = (RadarAdapter) iter.next();
timeIndex = Arrays.binarySearch(dateTimes, adapter.getBaseTime());
// System.err.println ("timeIndex:" + timeIndex);
if (timeIndex < 0) {
continue;
}
cnt++;
LogUtil.message("Time: " + (cnt) + "/" + dateTimes.length + " From:" + toString());
final int theTimeIndex = timeIndex;
threadManager.addRunnable(
new visad.util.ThreadManager.MyRunnable() {
public void run() throws Exception {
Trace.call1("RDS.getData");
Data d = adapter.getData(dataChoice, subset, requestProperties);
Trace.call2("RDS.getData");
datas[theTimeIndex] = d;
if (d != null) {
mt[0] = d.getType();
} else {
}
}
});
}
try {
// threadManager.debug = true;
threadManager.runInParallel(getDataContext().getIdv().getMaxDataThreadCount());
} catch (VisADException ve) {
LogUtil.printMessage(ve.toString());
}
if (mt[0] == null) {
return null;
}
FunctionType ft = new FunctionType(RealType.Time, mt[0]);
SampledSet domainSet =
(dateTimes.length == 1)
? (SampledSet) new SingletonSet(new RealTuple(dateTimes))
: (SampledSet) DateTime.makeTimeSet(dateTimes);
FieldImpl fi = new FieldImpl(ft, domainSet);
fi.setSamples(datas, false);
return fi;
} catch (Exception exc) {
logException("Creating obs", exc);
}
return null;
}
/**
* Make the adapters for the given list of files
*
* @param files Data files
* @throws Exception When bad things happen
*/
private void makeAdapters(List files) throws Exception {
adapters = new ArrayList<RadarAdapter>();
Hashtable<String, RadarAdapter> oldAdapterMap = fileToAdapter;
fileToAdapter = new Hashtable<String, RadarAdapter>();
int cnt = 0;
final List<String> badFiles = new ArrayList<String>();
final List<Exception> badExceptions = new ArrayList<Exception>();
final List<RadarAdapter> goodAdapters = new ArrayList<RadarAdapter>();
final List<String> goodFiles = new ArrayList<String>();
visad.util.ThreadManager threadManager =
new visad.util.ThreadManager("radar data initialization");
LogUtil.message("Initializing radar files");
for (Iterator iter = files.iterator(); iter.hasNext(); ) {
final String filename = iter.next().toString();
RadarAdapter adapter = (RadarAdapter) oldAdapterMap.get(filename);
cnt++;
if (adapter == null) {
threadManager.addRunnable(
new visad.util.ThreadManager.MyRunnable() {
public void run() throws Exception {
try {
RadarAdapter myAdapter = makeRadarAdapter(filename);
synchronized (goodAdapters) {
goodAdapters.add(myAdapter);
goodFiles.add(filename);
}
} catch (Exception e) {
synchronized (badExceptions) {
badExceptions.add(e);
badFiles.add(filename);
}
}
}
});
} else {
goodAdapters.add(adapter);
goodFiles.add(filename);
}
}
// threadManager.debug = true;
threadManager.runInParallel(getDataContext().getIdv().getMaxDataThreadCount());
LogUtil.message("");
for (int i = 0; i < goodAdapters.size(); i++) {
adapters.add(goodAdapters.get(i));
fileToAdapter.put(goodFiles.get(i), goodAdapters.get(i));
}
if (!badFiles.isEmpty()) {
StringBuffer buf = new StringBuffer();
if (badFiles.size() < files.size()) {
buf.append("<html>");
buf.append("There were problems reading these files:");
buf.append("<ul>");
for (Iterator iterator = badFiles.iterator(); iterator.hasNext(); ) {
buf.append("<li>");
buf.append((String) iterator.next());
buf.append("</li>");
}
buf.append("</ul>");
buf.append("<p>Continue loading good data?<p></html>");
boolean ok = ucar.unidata.util.GuiUtils.askYesNo("Error reading data", buf.toString());
badExceptions.get(0).printStackTrace();
if (ok) {
files.removeAll(badFiles);
} else {
throw new VisADException("error reading files");
}
} else {
throw badExceptions.get(0);
}
}
// clean up any old adapters
for (String source : oldAdapterMap.keySet()) {
if (fileToAdapter.get(source) == null) {
((RadarAdapter) oldAdapterMap.get(source)).doRemove();
}
}
oldAdapterMap = null;
}