void ExternalToolsDialog::Apply()
{
// If a tool doesn't have a name, give it one since this prevents
// us from putting it in the menu.
int selectedItem = m_listBox->GetSelection();
for (unsigned int i = 0; i < m_workingTools.size(); ++i)
{
ExternalTool* tool = m_workingTools[i];
if (tool->GetTitle().IsEmpty())
{
tool->SetTitle("Unnamed Tool");
m_listBox->Delete(i);
m_listBox->Insert(tool->GetTitle(), i);
}
}
m_listBox->SetSelection(selectedItem);
UpdateControlsForSelection(selectedItem);
// Apply the changes.
CopyVector(*m_appliedTools, m_workingTools);
}
void ExternalToolsDialog::OnEventHook(wxCommandEvent& event)
{
ExternalTool* tool = GetSelectedTool();
if (tool != NULL)
{
tool->SetEvent(m_externalEvents[m_eventHookList->GetSelection()]);
}
}
void ExternalToolsDialog::OnInitialDirectoryTextBoxChanged(wxCommandEvent& event)
{
ExternalTool* tool = GetSelectedTool();
if (tool != NULL)
{
tool->SetInitialDirectory(m_initialDirectoryTextBox->GetValue());
}
}
void ExternalToolsDialog::OnArgumentsTextBoxChanged(wxCommandEvent& event)
{
ExternalTool* tool = GetSelectedTool();
if (tool != NULL)
{
tool->SetArguments(m_argumentsTextBox->GetValue());
}
}
void ExternalToolsDialog::OnAdd(wxCommandEvent& event)
{
ExternalTool* tool = new ExternalTool;
m_workingTools.push_back(tool);
m_listBox->Append(tool->GetTitle());
int newItem = m_listBox->GetCount() - 1;
m_listBox->SetSelection(newItem);
UpdateControlsForSelection(newItem);
m_titleTextBox->SetFocus();
}
void ExternalToolsDialog::OnTitleTextBoxChanged(wxCommandEvent& event)
{
ExternalTool* tool = GetSelectedTool();
if (tool != NULL)
{
tool->SetTitle(m_titleTextBox->GetValue());
int selectedItem = m_listBox->GetSelection();
m_listBox->Delete(selectedItem);
m_listBox->Insert(tool->GetTitle(), selectedItem);
m_listBox->SetSelection(selectedItem);
}
}
void ExternalToolsFilter::prepareSearch(const QString &entry)
{
m_results.clear();
Qt::CaseSensitivity useCaseSensitivity = caseSensitivity(entry);
const QMap<QString, ExternalTool *> externalToolsById = ExternalToolManager::toolsById();
auto end = externalToolsById.cend();
for (auto it = externalToolsById.cbegin(); it != end; ++it) {
ExternalTool *tool = *it;
if (tool->description().contains(entry, useCaseSensitivity) ||
tool->displayName().contains(entry, useCaseSensitivity)) {
LocatorFilterEntry filterEntry(this, tool->displayName(), QVariant::fromValue(tool));
filterEntry.extraInfo = tool->description();
m_results.append(filterEntry);
}
}
}
QList<Task *> SpideyAlignmentTask::onSubTaskFinished(Task *subTask) {
QList<Task *> res;
propagateSubtaskError();
if (hasError() || isCanceled()) {
return res;
}
if (subTask == prepareDataForSpideyTask) {
SAFE_POINT(!prepareDataForSpideyTask->getResultPath().isEmpty(), "Invalid result path!",
res);
tmpOutputUrl = prepareDataForSpideyTask->getResultPath();
const QStringList &arguments = prepareDataForSpideyTask->getArgumentsList();
spideyTask = new ExternalToolRunTask(ET_SPIDEY, arguments, new SpideyLogParser());
spideyTask->setSubtaskProgressWeight(95);
res.append(spideyTask);
} else if (subTask == spideyTask) {
if (!QFile::exists(tmpOutputUrl)) {
if (AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY)->isValid()) {
stateInfo.setError(tr("Output file not found"));
} else {
ExternalTool *spideyTool = AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY);
SAFE_POINT(NULL != spideyTool, "Invalid Spidey tool!", res);
stateInfo.setError(
tr("Output file not found. May be %1 tool path '%2' not valid?")
.arg(spideyTool->getName()).arg(spideyTool->getPath()));
}
return res;
}
// parse result
QFile resultFile(tmpOutputUrl);
if (!resultFile.open(QFile::ReadOnly)) {
setError(tr("Failed to open result file %1").arg(tmpOutputUrl));
return res;
}
QTextStream inStream(&resultFile);
bool strandDirect = true;
U2Location location;
location->op = U2LocationOperator_Join;
while (!inStream.atEnd()) {
QByteArray buf = inStream.readLine().toLatin1();
if (buf.startsWith("Strand")) {
strandDirect = buf.contains("plus");
}
if (buf.startsWith("Exon")) {
// TODO: better to use reg exp here
int startPos = buf.indexOf(":") + 1;
int endPos = buf.indexOf("(gen)");
if (startPos == -1 || endPos == -1) {
continue;
}
QByteArray loc = buf.mid(startPos, endPos - startPos).trimmed();
QList<QByteArray> loci = loc.split('-');
if (loci.size() < 2) {
continue;
}
int start = QString(loci.at(0)).toInt();
int finish = QString(loci.at(1)).toInt();
if (start == finish) {
continue;
}
location->regions.append(U2Region(start - 1, finish - start + 1));
}
}
if (!location->isEmpty()) {
SharedAnnotationData data(new AnnotationData);
data->location = location;
data->setStrand(U2Strand(strandDirect ? U2Strand::Direct : U2Strand::Complementary));
data->type = U2FeatureTypes::Exon;
data->name = "exon";
U1AnnotationUtils::addDescriptionQualifier(data, annDescription);
resultAnnotations.append(data);
}
}
return res;
}
ExternalTool::ExternalTool(const ExternalTool& other) : ExternalTool(other.executable(), other.parameters()) {}
void ExternaltoolTest::testReadLocale()
{
QString error;
ExternalTool *tool;
tool = ExternalTool::createFromXml(QByteArray(TEST_XML_LANG), &error);
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->description(), QString::fromLatin1("Hi"));
QCOMPARE(tool->displayName(), QString::fromLatin1("Hi"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Hi"));
delete tool;
tool = ExternalTool::createFromXml(QByteArray(TEST_XML_LANG), &error, QLatin1String("uk"));
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->description(), QString::fromLatin1("Hi"));
QCOMPARE(tool->displayName(), QString::fromLatin1("Hi"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Hi"));
delete tool;
tool = ExternalTool::createFromXml(QByteArray(TEST_XML_LANG), &error, QLatin1String("de_DE.UTF-8"));
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->description(), QString::fromLatin1("Hallo"));
QCOMPARE(tool->displayName(), QString::fromLatin1("Hallo"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Hallo"));
delete tool;
tool = ExternalTool::createFromXml(QByteArray(TEST_XML_LANG), &error, QLatin1String("de_CH"));
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->description(), QString::fromLatin1("Grüezi"));
QCOMPARE(tool->displayName(), QString::fromLatin1("Grüezi"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Grüezi"));
delete tool;
}
void ExternaltoolTest::testRead3()
{
QString error;
ExternalTool *tool = ExternalTool::createFromXml(QByteArray(TEST_XML3), &error);
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->id(), QString::fromLatin1("vi"));
QVERIFY(tool->description().startsWith(QLatin1String("Opens the")));
QCOMPARE(tool->displayName(), QString::fromLatin1("Edit with vi"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Text"));
QCOMPARE(tool->order(), -1);
QCOMPARE(tool->executables().size(), 1);
QCOMPARE(tool->executables().at(0), QString::fromLatin1("xterm"));
QVERIFY(tool->arguments().startsWith(QLatin1String("-geom %{")));
QCOMPARE(tool->input(), QString());
QCOMPARE(tool->workingDirectory(), QString::fromLatin1("%{CurrentPath}"));
QCOMPARE(tool->outputHandling(), ExternalTool::ShowInPane);
QCOMPARE(tool->modifiesCurrentDocument(), true);
QCOMPARE(tool->errorHandling(), ExternalTool::ShowInPane);
delete tool;
}
void ExternaltoolTest::testRead2()
{
QString error;
ExternalTool *tool = ExternalTool::createFromXml(QByteArray(TEST_XML2), &error);
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->id(), QString::fromLatin1("sort"));
QVERIFY(tool->description().startsWith(QLatin1String("Sorts the")));
QCOMPARE(tool->displayName(), QString::fromLatin1("Sort"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Text"));
QCOMPARE(tool->order(), -1);
QCOMPARE(tool->executables().size(), 1);
QCOMPARE(tool->executables().at(0), QString::fromLatin1("sort"));
QCOMPARE(tool->arguments(), QString());
QCOMPARE(tool->input(), QString::fromLatin1("%{CurrentSelection}"));
QCOMPARE(tool->workingDirectory(), QString::fromLatin1("%{CurrentPath}"));
QCOMPARE(tool->outputHandling(), ExternalTool::ReplaceSelection);
QCOMPARE(tool->errorHandling(), ExternalTool::ShowInPane);
delete tool;
}
void ExternaltoolTest::testRead1()
{
QString error;
ExternalTool *tool = ExternalTool::createFromXml(QByteArray(TEST_XML1), &error);
QVERIFY(tool != 0);
QVERIFY(error.isEmpty());
QCOMPARE(tool->id(), QString::fromLatin1("lupdate"));
QVERIFY(tool->description().startsWith(QLatin1String("Synchronizes tran")));
QCOMPARE(tool->displayName(), QString::fromLatin1("Update translations (lupdate)"));
QCOMPARE(tool->displayCategory(), QString::fromLatin1("Linguist"));
QCOMPARE(tool->order(), 1);
QCOMPARE(tool->executables().size(), 2);
QCOMPARE(tool->executables().at(0), QString::fromLatin1("%{QT_INSTALL_BINS}/lupdate"));
QCOMPARE(tool->executables().at(1), QString::fromLatin1("lupdate"));
QCOMPARE(tool->arguments(), QString::fromLatin1("%{CurrentProjectFilePath}"));
QCOMPARE(tool->input(), QString());
QCOMPARE(tool->workingDirectory(), QString::fromLatin1("%{CurrentProjectPath}"));
QCOMPARE(tool->outputHandling(), ExternalTool::ShowInPane);
QCOMPARE(tool->errorHandling(), ExternalTool::Ignore);
delete tool;
}
