Document* ClustalWAlnFormat::loadDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& fs, U2OpStatus& os) {
QList<GObject*> objects;
load(io, dbiRef, objects, fs, os);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
assert(objects.size() == 1);
return new Document(this, io->getFactory(), io->getURL(), dbiRef, objects, fs);
}
Document* FastqFormat::loadTextDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& _hints, U2OpStatus& os) {
CHECK_EXT(io != NULL && io->isOpen(), os.setError(L10N::badArgument("IO adapter")), NULL);
QVariantMap hints = _hints;
QList<GObject*> objects;
QMap<QString, QString> skippedLines;
int gapSize = qBound(-1, DocumentFormatUtils::getMergeGap(_hints), 1000*1000);
int predictedSize = qMax(100*1000, DocumentFormatUtils::getMergedSize(hints, gapSize==-1 ? 0 : io->left()));
QString lockReason;
load(io, dbiRef, _hints, objects, os, gapSize, predictedSize, lockReason, skippedLines);
if (skippedLines.size() > 0){
QMapIterator<QString, QString> i(skippedLines);
QStringList errors;
while (i.hasNext()) {
i.next();
QString msg = i.key() + ": " + i.value();
if (objects.length() > 0){
os.addWarning(msg);
}else{
errors.append(msg);
}
}
if (errors.length() > 0){
os.setError(errors.join("\n"));
}
}
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
DocumentFormatUtils::updateFormatHints(objects, hints);
Document* doc = new Document(this, io->getFactory(), io->getURL(), dbiRef, objects, hints, lockReason);
return doc;
}
Document* FpkmTrackingFormat::loadDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& hints, U2OpStatus& os)
{
CHECK_EXT(io != NULL && io->isOpen(), os.setError(L10N::badArgument("IO adapter")), NULL);
QList<GObject*> objects;
load(io, objects, dbiRef, hints, os);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
Document* doc = new Document(this, io->getFactory(), io->getURL(), dbiRef, objects);
return doc;
}
Task* CallVariantsWorker::tick() {
U2OpStatus2Log os;
//put variant tracks
while (!cache.isEmpty()) {
output->put(cache.takeFirst());
}
checkState(os);
CHECK_OP_EXT(os, setDone(), NULL);
//take assemblies from one dataset
if (assemblyPort->hasMessage() && settings.assemblyUrls.isEmpty()) {
takeAssembly(os);
CHECK_OP_EXT(os, processError(os), NULL);
} else if (settings.assemblyUrls.isEmpty() && !assemblyUrls.isEmpty()) {
settings.assemblyUrls = assemblyUrls;
assemblyUrls.clear();
}
//take reference sequence
if (refSeqPort->hasMessage() && settings.refSeqUrl.isEmpty()) {
takeReference(os);
CHECK_OP_EXT(os, processError(os), NULL);
}
//do
if (cache.isEmpty() && !settings.refSeqUrl.isEmpty() && !settings.assemblyUrls.isEmpty()) {
settings.variationsUrl = GUrlUtils::rollFileName(getValue<QString>(OUT_URL), "_", QSet<QString>());
CallVariantsTask* t = new CallVariantsTask(settings, context->getDataStorage());
t->addListeners(createLogListeners(3));
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
settings.assemblyUrls.clear();
settings.refSeqUrl.clear();
return t;
}
return NULL;
}
Document* FastaFormat::loadTextDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& fs, U2OpStatus& os) {
CHECK_EXT(io!=NULL && io->isOpen(), os.setError(L10N::badArgument("IO adapter")), NULL);
QList<GObject*> objects;
int gapSize = qBound(-1, DocumentFormatUtils::getMergeGap(fs), 1000 * 1000);
QString lockReason;
load(io, dbiRef, fs, objects, gapSize, lockReason, os);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
Document* doc = new Document(this, io->getFactory(), io->getURL(), dbiRef, objects, fs, lockReason);
return doc;
}
Document* DatabaseConnectionFormat::loadDocument(IOAdapter* io, const U2DbiRef&, const QVariantMap& hints, U2OpStatus& os) {
DatabaseConnectionAdapter* databaseConnectionAdapter = qobject_cast<DatabaseConnectionAdapter*>(io);
SAFE_POINT(NULL != databaseConnectionAdapter, QString("Can't use current IOAdapter: %1").arg(io->getAdapterName()), NULL);
U2Dbi* dbi = databaseConnectionAdapter->getConnection().dbi;
SAFE_POINT(NULL != dbi, "NULL dbi", NULL);
QList<GObject*> objects = getObjects(dbi, os);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
const QString modLockDesc = dbi->getFeatures().contains(U2DbiFeature_GlobalReadOnly)
? DocumentFormat::tr("You have no permissions to modify the content of this database")
: QString();
Document* resultDocument = new Document(this, io->getFactory(), io->getURL(), dbi->getDbiRef(), objects, hints, modLockDesc);
resultDocument->setDocumentOwnsDbiResources(false);
return resultDocument;
}
Document* FastqFormat::loadDocument(IOAdapter* io, const U2DbiRef& dbiRef, const QVariantMap& _hints, U2OpStatus& os) {
CHECK_EXT(io != NULL && io->isOpen(), os.setError(L10N::badArgument("IO adapter")), NULL);
QVariantMap hints = _hints;
QList<GObject*> objects;
int gapSize = qBound(-1, DocumentFormatUtils::getMergeGap(_hints), 1000*1000);
int predictedSize = qMax(100*1000, DocumentFormatUtils::getMergedSize(hints, gapSize==-1 ? 0 : io->left()));
QString lockReason;
load(io, dbiRef, _hints, io->getURL(), objects, os, gapSize, predictedSize, lockReason);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
DocumentFormatUtils::updateFormatHints(objects, hints);
Document* doc = new Document(this, io->getFactory(), io->getURL(), dbiRef, objects, hints, lockReason );
return doc;
}
Document* DbiDocumentFormat::loadDocument(IOAdapter* io, const U2DbiRef& dstDbiRef, const QVariantMap& fs, U2OpStatus& os){
//1. open db
//2. read all objects
//3. if there is a DEEP_COPY_OBJECT hint, all objects are cloned to the db defined by dstDbiRef
//3. close db
QString url = io->getURL().getURLString();
U2DbiRef srcDbiRef(id, url);
DbiConnection handle(srcDbiRef, true, os);
CHECK_OP(os, NULL);
U2ObjectDbi* odbi = handle.dbi->getObjectDbi();
QList<U2DataId> objectIds = odbi->getObjects(U2ObjectDbi::ROOT_FOLDER, 0, U2DbiOptions::U2_DBI_NO_LIMIT, os);
CHECK_OP(os, NULL);
QList<GObject*> objects;
U2EntityRef ref;
ref.dbiRef = srcDbiRef;
objects << prepareObjects(handle, objectIds);
if (fs.value(DEEP_COPY_OBJECT, false).toBool()) {
QList<GObject *> clonedObjects = cloneObjects(objects, dstDbiRef, fs, os);
qDeleteAll(objects);
CHECK_OP_EXT(os, qDeleteAll(clonedObjects), NULL);
objects = clonedObjects;
} else {
renameObjectsIfNamesEqual(objects);
}
QString lockReason = handle.dbi->isReadOnly() ? "The database is read-only" : "";
Document* d = new Document(this, io->getFactory(), io->getURL(), dstDbiRef, objects, fs, lockReason);
d->setDocumentOwnsDbiResources(false);
d->setModificationTrack(false);
return d;
}
