int SampleActionsManager::getValidClickedActionId(U2OpStatus &os) const {
QAction *a = qobject_cast<QAction*>(sender());
CHECK_EXT(NULL != a, os.setError(L10N::internalError("Unexpected method call")), -1);
bool ok = false;
int id = a->property(ID_PROPERTY).toInt(&ok);
CHECK_EXT(ok, os.setError(L10N::internalError("Wrong action ID")), -1);
CHECK_EXT(id >=0 && id < actions.size(), os.setError(L10N::internalError("Out of range action ID")), -1);
return id;
}
U2VariantTrack MysqlVariantDbi::getVariantTrack(const U2DataId& variantTrackId, U2OpStatus& os) {
U2VariantTrack res;
DBI_TYPE_CHECK(variantTrackId, U2Type::VariantTrack, os, res);
MysqlTransaction t(db, os);
Q_UNUSED(t);
dbi->getMysqlObjectDbi()->getObject(res, variantTrackId, os);
CHECK_OP(os, res);
static const QString queryString = "SELECT sequence, sequenceName, trackType, fileHeader FROM VariantTrack WHERE object = :object";
U2SqlQuery q(queryString, db, os);
q.bindDataId(":object", variantTrackId);
if (q.step()) {
res.sequence = q.getDataId(0, U2Type::Sequence);
res.sequenceName = q.getString(1);
int trackType = q.getInt32(2);
CHECK_EXT(TrackType_FIRST <= trackType && trackType <= TrackType_LAST,
os.setError(U2DbiL10n::tr("Invalid variant track type: %1").arg(trackType)), res);
res.trackType = static_cast<VariantTrackType>(trackType);
res.fileHeader = q.getString(3);
q.ensureDone();
}
return res;
}
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;
}
QList<long> CmdlineTaskRunner::getChildrenProcesses(qint64 processId, bool fullTree) {
QList<long> children;
#if defined(Q_OS_LINUX) || defined(Q_OS_MAC)
char *buff = NULL;
size_t len = 255;
char command[256] = {0};
sprintf(command,"ps -ef|awk '$3==%u {print $2}'", (unsigned)processId);
FILE *fp = (FILE*) popen(command, "r");
while (getline(&buff, &len, fp) >= 0) {
int child_process_id = QString(buff).toInt();
if (child_process_id != 0) {
children << child_process_id;
}
}
free(buff);
fclose(fp);
#elif defined(Q_OS_WIN)
HANDLE hProcessSnap;
HANDLE hProcess;
PROCESSENTRY32 pe32;
// Take a snapshot of all processes in the system.
hProcessSnap = CreateToolhelp32Snapshot(TH32CS_SNAPPROCESS, 0);
CHECK(hProcessSnap != INVALID_HANDLE_VALUE, children);
// Set the size of the structure before using it.
pe32.dwSize = sizeof(PROCESSENTRY32);
// Retrieve information about the first process,
// and exit if unsuccessful
CHECK_EXT(Process32First(hProcessSnap, &pe32), CloseHandle(hProcessSnap), children);
// Now walk the snapshot of processes, and
// display information about each process in turn
do {
if (pe32.th32ParentProcessID == processId) {
hProcess = OpenProcess(PROCESS_ALL_ACCESS, FALSE, pe32.th32ProcessID);
if (hProcess != NULL) {
CloseHandle(hProcess);
children << pe32.th32ProcessID;
}
}
} while (Process32Next(hProcessSnap, &pe32));
CloseHandle(hProcessSnap);
#endif
if (fullTree && children.length() > 0) {
foreach(long child, children) {
QList<long> children2 = getChildrenProcesses(child, fullTree);
children << children2;
}
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;
}
int readLongLine (QString &buffer, IOAdapter* io, QScopedArrayPointer<char> &charbuff, int readBufferSize, U2OpStatus& os) {
int len;
buffer.clear();
do {
len = io->readLine(charbuff.data(), readBufferSize - 1);
CHECK_EXT(!io->hasError(), os.setError(io->errorString()), -1);
charbuff.data()[len] = '\0';
buffer.append(QString(charbuff.data()));
} while (readBufferSize - 1 == len);
return buffer.length();
}
int ImageWrite( struct ImageLibrary *im, File *rootDev, gdImagePtr img, const char *path )
{
FHandler *fh = rootDev->f_FSys;
File *rfp = (File *)fh->FileOpen( rootDev, path, "wb" );
if( rfp != NULL )
{
char *buffer = NULL;
int length = 0;
int psize = strlen( path );
if( psize > 3 ) //we are checking if file have extension
{
char ext[ 4 ];
strcpy( ext, &(path[ psize-4 ]) );
ext[ 0 ] = toupper( ext[ 0 ] );
ext[ 1 ] = toupper( ext[ 1 ] );
ext[ 2 ] = toupper( ext[ 2 ] );
if( CHECK_EXT( ext, 'P','N','G' ) )
{
buffer = gdImagePngPtr( img, &length );
}else if( CHECK_EXT( ext, 'J','P','G' ) ){
buffer = gdImageJpegPtr( img, &length, 100 );
}else if( CHECK_EXT( ext, 'G','I','F' ) ){
buffer = gdImageGifPtr( img, &length );
}else if( CHECK_EXT( ext, 'W','E','B' ) ){
buffer = gdImageWebpPtr( img, &length );
}else if( CHECK_EXT( ext, 'I','I','F' ) ){
buffer = gdImageTiffPtr( img, &length );
}else if( CHECK_EXT( ext, 'B','M','P' ) ){
buffer = gdImageBmpPtr( img, &length, 100 );
}
if( buffer == NULL )
{
fh->FileClose( rootDev, rfp );
ERROR("Cannot save picture, GD couldnt create buffer from image\n");
return 2;
}
else
{
fh->FileWrite( rfp, buffer, length );
}
}
else
{
ERROR("Extension name is too short, file format not recognized\n");
}
fh->FileClose( rootDev, rfp );
}
else
{
ERROR("Cannot open file: %s to write\n", path );
return 1;
}
return 0;
}
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;
}
Task::ReportResult GTest_CompareTwoMsa::report() {
Document *doc1 = getContext<Document>(this, docContextName);
CHECK_EXT(NULL != doc1, setError(QString("document not found: %1").arg(docContextName)), ReportResult_Finished);
const QList<GObject *> objs1 = doc1->getObjects();
CHECK_EXT(1 == objs1.size(), setError(QString("document '%1' contains several objects: the comparison not implemented").arg(docContextName)), ReportResult_Finished);
MultipleSequenceAlignmentObject *msa1 = qobject_cast<MultipleSequenceAlignmentObject *>(objs1.first());
CHECK_EXT(NULL != msa1, setError(QString("document '%1' contains an incorrect object: expected '%2', got '%3'")
.arg(docContextName)
.arg(GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT)
.arg(objs1.first()->getGObjectType())), ReportResult_Finished);
Document *doc2 = getContext<Document>(this, secondDocContextName);
CHECK_EXT(NULL != doc2, setError(QString("document not found: %1").arg(secondDocContextName)), ReportResult_Finished);
const QList<GObject *> objs2 = doc2->getObjects();
CHECK_EXT(1 == objs2.size(), setError(QString("document '%1' contains several objects: the comparison not implemented").arg(secondDocContextName)), ReportResult_Finished);
MultipleSequenceAlignmentObject *msa2 = qobject_cast<MultipleSequenceAlignmentObject *>(objs2.first());
CHECK_EXT(NULL != msa2, setError(QString("document '%1' contains an incorrect object: expected '%2', got '%3'")
.arg(secondDocContextName)
.arg(GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT)
.arg(objs2.first()->getGObjectType())), ReportResult_Finished);
const qint64 rowsNumber1 = msa1->getNumRows();
const qint64 rowsNumber2 = msa2->getNumRows();
CHECK_EXT(rowsNumber1 == rowsNumber2,
setError(QString("The rows numbers differ: the object '%1' from the document '%2' contains %3 rows, the object '%4' from the document '%5' contains %6 rows")
.arg(msa1->getGObjectName())
.arg(docContextName)
.arg(rowsNumber1)
.arg(msa2->getGObjectName())
.arg(secondDocContextName)
.arg(rowsNumber2)), ReportResult_Finished);
for (int i = 0; i < rowsNumber1; i++) {
const MultipleSequenceAlignmentRow row1 = msa1->getMsaRow(i);
const MultipleSequenceAlignmentRow row2 = msa2->getMsaRow(i);
const bool areEqual = row1->isRowContentEqual(row2);
CHECK_EXT(areEqual, setError(QString("The rows with number %1 differ from each other").arg(i)), ReportResult_Finished);
}
return ReportResult_Finished;
}
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;
}
bool WevoteValidator::validateTaxonomy(const Actor *actor, NotificationsList ¬ificationList) const {
bool isValid = true;
U2DataPathRegistry *dataPathRegistry = AppContext::getDataPathRegistry();
SAFE_POINT_EXT(NULL != dataPathRegistry, notificationList.append(WorkflowNotification("U2DataPathRegistry is NULL", actor->getId())), false);
U2DataPath *taxonomyDataPath = dataPathRegistry->getDataPathByName(NgsReadsClassificationPlugin::TAXONOMY_DATA_ID);
CHECK_EXT(NULL != taxonomyDataPath && taxonomyDataPath->isValid(),
notificationList << WorkflowNotification(tr("Taxonomy classification data from NCBI are not available."), actor->getId()), false);
const QString missingFileMessage = tr("Taxonomy classification data from NCBI are not full: file '%1' is missing.");
if (taxonomyDataPath->getPathByName(NgsReadsClassificationPlugin::TAXON_NODES_ITEM_ID).isEmpty()) {
notificationList << WorkflowNotification(missingFileMessage.arg(NgsReadsClassificationPlugin::TAXON_NODES_ITEM_ID), actor->getId());
isValid = false;
}
if (taxonomyDataPath->getPathByName(NgsReadsClassificationPlugin::TAXON_NAMES_ITEM_ID).isEmpty()) {
notificationList << WorkflowNotification(missingFileMessage.arg(NgsReadsClassificationPlugin::TAXON_NAMES_ITEM_ID), actor->getId());
isValid = false;
}
return isValid;
}
QList<Task*> AddExportedDocumentAndOpenViewTask::onSubTaskFinished( Task* subTask ) {
QList<Task*> subTasks;
if (subTask == exportTask && !subTask->hasError() && !subTask->isCanceled()) {
Document* doc = exportTask->getDocument();
const GUrl& fullPath = doc->getURL();
Project* prj = AppContext::getProject();
if (prj) {
Document* sameURLdoc = prj->findDocumentByURL(fullPath);
if (sameURLdoc) {
taskLog.trace(tr("Document is already added to the project %1").arg(doc->getURL().getURLString()));
subTasks << new LoadUnloadedDocumentAndOpenViewTask(sameURLdoc);
return subTasks;
}
}
loadTask = LoadDocumentTask::getDefaultLoadDocTask(doc->getURL());
CHECK_EXT(NULL != loadTask, setError(tr("Can't create load task")), subTasks);
subTasks << loadTask;
}
if (subTask == loadTask) {
subTasks << new AddDocumentAndOpenViewTask(loadTask->takeDocument());
}
//TODO: provide a report if subtask fails
return subTasks;
}
UdrRecordId getRecordId(UdrDbi *dbi, const U2DataId &objId, U2OpStatus &os) {
const QList<UdrRecord> records = dbi->getObjectRecords(RawDataUdrSchema::ID, objId, os);
CHECK_OP(os, UdrRecordId("", ""));
CHECK_EXT(1 == records.size(), os.setError("Unexpected records count"), UdrRecordId("", ""));
return records.first().getId();
}
Primer PrimerLibraryModel::getPrimer(const QModelIndex &index, U2OpStatus &os) const {
CHECK_EXT(index.row() >= 0 && index.row() < primers.size(), os.setError(L10N::internalError("Incorrect primer number")), Primer());
return primers.at(index.row());
}
