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UGENE-7807. Wrong sorting by size in NCBI GenBank dialog (#1151)
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* UGENE-7807. Wrong sorting by size in NCBI GenBank dialog

* Fix build
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@yalgaer
yalgaer committed Feb 20, 2023
1 parent 20c2c83 commit 95e37a7
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Showing 3 changed files with 97 additions and 97 deletions.
2 changes: 1 addition & 1 deletion src/corelibs/U2Gui/src/util/SearchGenbankSequenceDialog.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<rect>
<x>0</x>
<y>0</y>
<width>612</width>
<width>1008</width>
<height>533</height>
</rect>
</property>
Expand Down
158 changes: 77 additions & 81 deletions src/corelibs/U2Gui/src/util/SearchGenbankSequenceDialogController.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@
#include <QComboBox>
#include <QLineEdit>
#include <QMessageBox>
#include <QPushButton>
#include <QToolButton>

#include <U2Core/AppContext.h>
Expand All @@ -41,7 +40,7 @@
namespace U2 {

SearchGenbankSequenceDialogController::SearchGenbankSequenceDialogController(QWidget* p)
: QDialog(p), searchTask(nullptr), summaryTask(nullptr) {
: QDialog(p) {
ui = new Ui_SearchGenbankSequenceDialog();
ui->setupUi(this);
new HelpButton(this, ui->buttonBox, "65929336");
Expand All @@ -57,22 +56,22 @@ SearchGenbankSequenceDialogController::SearchGenbankSequenceDialogController(QWi
downloadButton = ui->buttonBox->button(QDialogButtonBox::Ok);
downloadButton->setEnabled(false);

connect(ui->searchButton, SIGNAL(clicked()), SLOT(sl_searchButtonClicked()));
connect(downloadButton, SIGNAL(clicked()), SLOT(sl_downloadButtonClicked()));
connect(ui->treeWidget, SIGNAL(itemSelectionChanged()), SLOT(sl_itemSelectionChanged()));
connect(ui->treeWidget, SIGNAL(itemActivated(QTreeWidgetItem*, int)), SLOT(sl_downloadButtonClicked()));
connect(AppContext::getTaskScheduler(), SIGNAL(si_stateChanged(Task*)), SLOT(sl_taskStateChanged(Task*)));
connect(ui->searchButton, &QPushButton::clicked, this, &SearchGenbankSequenceDialogController::sl_searchButtonClicked);
connect(downloadButton, &QPushButton::clicked, this, &SearchGenbankSequenceDialogController::sl_downloadButtonClicked);
connect(ui->treeWidget, &QTreeWidget::itemSelectionChanged, this, &SearchGenbankSequenceDialogController::sl_itemSelectionChanged);
connect(ui->treeWidget, &QTreeWidget::itemActivated, this, &SearchGenbankSequenceDialogController::sl_downloadButtonClicked);
connect(AppContext::getTaskScheduler(), &TaskScheduler::si_stateChanged, this, &SearchGenbankSequenceDialogController::sl_taskStateChanged);

ui->treeWidget->header()->setStretchLastSection(false);
ui->treeWidget->header()->setSectionResizeMode(1, QHeaderView::Stretch);
}

SearchGenbankSequenceDialogController::~SearchGenbankSequenceDialogController() {
// if dialog was closed during query execution
if (nullptr != summaryTask && !summaryTask->isFinished()) {
if (summaryTask != nullptr && !summaryTask->isFinished()) {
summaryTask->cancel();
}
if (nullptr != searchTask && !searchTask->isFinished()) {
if (searchTask != nullptr && !searchTask->isFinished()) {
searchTask->cancel();
}
}
Expand Down Expand Up @@ -101,49 +100,46 @@ void SearchGenbankSequenceDialogController::prepareSummaryRequestTask(const QStr
} else {
QStringList queries = splitIds(results);
QList<Task*> tasks;
foreach (const QString& query, queries) {
for (const QString& query : qAsConst(queries)) {
tasks << new EntrezQueryTask(new ESummaryResultHandler, query);
}
summaryTask = new MultiTask("EntrezQueryTask", tasks, false);
}
}

QStringList SearchGenbankSequenceDialogController::splitIds(const QStringList& idsList) {
const int fullQueryCount = idsList.size() / MAX_IDS_PER_QUERY;
const int tailIdsCount = idsList.size() % MAX_IDS_PER_QUERY;
int fullQueryCount = idsList.size() / MAX_IDS_PER_QUERY;
int tailIdsCount = idsList.size() % MAX_IDS_PER_QUERY;
QStringList queries;

for (int i = 0; i < fullQueryCount; i++) {
const QString ids = getIdsString(idsList, i * MAX_IDS_PER_QUERY, MAX_IDS_PER_QUERY);
QString ids = getIdsString(idsList, i * MAX_IDS_PER_QUERY, MAX_IDS_PER_QUERY);
queries << EntrezUtils::NCBI_ESUMMARY_URL.arg(ui->databaseBox->currentText()).arg(ids);
}

if (tailIdsCount > 0) {
const QString tailIds = getIdsString(idsList, fullQueryCount * MAX_IDS_PER_QUERY, tailIdsCount);
QString tailIds = getIdsString(idsList, fullQueryCount * MAX_IDS_PER_QUERY, tailIdsCount);
queries << EntrezUtils::NCBI_ESUMMARY_URL.arg(ui->databaseBox->currentText()).arg(tailIds);
}

return queries;
}

QString SearchGenbankSequenceDialogController::getIdsString(const QStringList& idsList, int startIndex, int count) {
const QStringList midList = idsList.mid(startIndex, count);
return midList.join(",");
return idsList.mid(startIndex, count).join(",");
}

QList<EntrezSummary> SearchGenbankSequenceDialogController::getSummaryResults() const {
QList<EntrezSummary> results;
auto singleTask = qobject_cast<EntrezQueryTask*>(summaryTask);
auto multiTask = qobject_cast<MultiTask*>(summaryTask);
if (nullptr != singleTask) {
SAFE_POINT(nullptr != summaryResultHandler, L10N::nullPointerError("summary results handler"), results);
if (singleTask != nullptr) {
SAFE_POINT(summaryResultHandler != nullptr, L10N::nullPointerError("summary results handler"), results);
results << summaryResultHandler->getResults();
} else if (nullptr != multiTask) {
foreach (const QPointer<Task>& subtask, multiTask->getSubtasks()) {
} else if (multiTask != nullptr) {
QList<QPointer<Task>> multiTaskSubtasks = multiTask->getSubtasks();
for (const QPointer<Task>& subtask : qAsConst(multiTaskSubtasks)) {
auto summarySubtask = qobject_cast<EntrezQueryTask*>(subtask.data());
SAFE_POINT(nullptr != summarySubtask, L10N::internalError(tr("an unexpected subtask")), results);
SAFE_POINT(summarySubtask != nullptr, L10N::internalError(tr("an unexpected subtask")), results);
auto resultHandler = dynamic_cast<const ESummaryResultHandler*>(summarySubtask->getResultHandler());
SAFE_POINT(nullptr != resultHandler, L10N::nullPointerError("ESummaryResultHandler"), results);
SAFE_POINT(resultHandler != nullptr, L10N::nullPointerError("ESummaryResultHandler"), results);
results << resultHandler->getResults();
delete resultHandler;
}
Expand All @@ -152,13 +148,9 @@ QList<EntrezSummary> SearchGenbankSequenceDialogController::getSummaryResults()
}

void SearchGenbankSequenceDialogController::sl_searchButtonClicked() {
if (!ui->searchButton->isEnabled()) {
return;
}
CHECK(ui->searchButton->isEnabled(), );
QString query = ui->queryEdit->toPlainText();
if (query.isEmpty()) {
return;
}
CHECK(!query.isEmpty(), );

int maxRet = ui->resultLimitBox->value();
QString qUrl(EntrezUtils::NCBI_ESEARCH_URL.arg(ui->databaseBox->currentText()).arg(query).arg(maxRet));
Expand All @@ -170,41 +162,35 @@ void SearchGenbankSequenceDialogController::sl_searchButtonClicked() {
}

void SearchGenbankSequenceDialogController::sl_taskStateChanged(Task* task) {
if (task->getState() == Task::State_Finished) {
if (task == searchTask) {
ui->treeWidget->clear();
const QStringList& results = searchResultHandler->getIdList();
if (results.size() == 0) {
QMessageBox::information(this, windowTitle(), tr("No results found corresponding to the query"));
ui->searchButton->setEnabled(true);
} else {
prepareSummaryRequestTask(results);
if (nullptr != summaryTask) {
AppContext::getTaskScheduler()->registerTopLevelTask(summaryTask);
}
}
searchTask = nullptr;
} else if (task == summaryTask) {
QList<EntrezSummary> results = getSummaryResults();

foreach (const EntrezSummary& desc, results) {
QTreeWidgetItem* item = new QTreeWidgetItem(ui->treeWidget);
item->setText(0, desc.name);
item->setText(1, desc.title);
item->setText(2, QString("%1").arg(desc.size));
ui->treeWidget->addTopLevelItem(item);
}
summaryTask = nullptr;
CHECK(task->getState() == Task::State_Finished, );
if (task == searchTask) {
ui->treeWidget->clear();
const QStringList& results = searchResultHandler->getIdList();
if (results.size() == 0) {
QMessageBox::information(this, windowTitle(), tr("No results found corresponding to the query"));
ui->searchButton->setEnabled(true);
} else {
prepareSummaryRequestTask(results);
if (nullptr != summaryTask) {
AppContext::getTaskScheduler()->registerTopLevelTask(summaryTask);
}
}
searchTask = nullptr;
} else if (task == summaryTask) {
QList<EntrezSummary> results = getSummaryResults();

for (const EntrezSummary& desc : qAsConst(results)) {
ui->treeWidget->addTopLevelItem(new SearchResultRowItem(ui->treeWidget, desc));
}
summaryTask = nullptr;
ui->searchButton->setEnabled(true);
}
}

void SearchGenbankSequenceDialogController::sl_downloadButtonClicked() {
QList<QTreeWidgetItem*> selectedItems = ui->treeWidget->selectedItems();

QStringList ids;
foreach (QTreeWidgetItem* item, selectedItems) {
for (QTreeWidgetItem* item : qAsConst(selectedItems)) {
ids.append(item->text(0));
}

Expand All @@ -220,11 +206,11 @@ void SearchGenbankSequenceDialogController::sl_itemSelectionChanged() {

QueryBlockWidget::QueryBlockWidget(QueryBuilderController* controller, bool first)
: conditionBox(nullptr), termBox(nullptr), queryEdit(nullptr) {
QBoxLayout* layout = new QBoxLayout(QBoxLayout::LeftToRight, this);
auto layout = new QBoxLayout(QBoxLayout::LeftToRight, this);
layout->setMargin(0);

if (first) {
QLabel* label = new QLabel(tr("Term:"));
auto label = new QLabel(tr("Term:"));
layout->addWidget(label);
} else {
conditionBox = new QComboBox(this);
Expand All @@ -249,13 +235,13 @@ QueryBlockWidget::QueryBlockWidget(QueryBuilderController* controller, bool firs
layout->addWidget(queryEdit);

if (first) {
QToolButton* addBlockButton = new QToolButton();
auto addBlockButton = new QToolButton();
addBlockButton->setText("+");
layout->addWidget(addBlockButton);
connect(addBlockButton, SIGNAL(clicked()), controller, SLOT(sl_addQueryBlockWidget()));
addBlockButton->setObjectName("add_block_button");
} else {
QToolButton* removeBlockButton = new QToolButton();
auto removeBlockButton = new QToolButton();
removeBlockButton->setText("-");
layout->addWidget(removeBlockButton);
connect(removeBlockButton, SIGNAL(clicked()), controller, SLOT(sl_removeQueryBlockWidget()));
Expand All @@ -265,54 +251,45 @@ QueryBlockWidget::QueryBlockWidget(QueryBuilderController* controller, bool firs
setLayout(layout);
}

QueryBlockWidget::~QueryBlockWidget() {
void QueryBlockWidget::setInputFocus() {
queryEdit->setFocus();
}

QString QueryBlockWidget::getQuery() {
QString query;

query = queryEdit->text();

if (query.isEmpty()) {
return query;
}
QString QueryBlockWidget::getQuery() const {
QString query = queryEdit->text();
CHECK(!query.isEmpty(), "");

if (termBox->currentIndex() != 0) {
query += "[" + termBox->currentText() + "]";
}

if (conditionBox) {
query.prepend(" " + conditionBox->currentText() + " ");
}

return query;
}

////////////////////////////////////////////////////////////////////////////////////////////////////

QueryBuilderController::QueryBuilderController(SearchGenbankSequenceDialogController* p)
: QObject(p), parentController(p) {
QueryBlockWidget* widget = new QueryBlockWidget(this, true);
auto widget = new QueryBlockWidget(this, true);
parentController->addQueryBlockWidget(widget);
queryBlockWidgets.append(widget);
widget->setInputFocus();
}

QueryBuilderController::~QueryBuilderController() {
}

void QueryBuilderController::sl_addQueryBlockWidget() {
QueryBlockWidget* widget = new QueryBlockWidget(this, false);
auto widget = new QueryBlockWidget(this, false);
parentController->addQueryBlockWidget(widget);
queryBlockWidgets.append(widget);
}

void QueryBuilderController::sl_removeQueryBlockWidget() {
auto callbackButton = qobject_cast<QToolButton*>(sender());
assert(callbackButton);
SAFE_POINT(callbackButton, "Not a callbackButton", );

auto queryBlockWidget = qobject_cast<QueryBlockWidget*>(callbackButton->parentWidget());
assert(queryBlockWidget);
SAFE_POINT(callbackButton, "Not a queryBlockWidget", );

parentController->removeQueryBlockWidget(queryBlockWidget);
queryBlockWidgets.removeAll(queryBlockWidget);
Expand All @@ -324,7 +301,7 @@ void QueryBuilderController::sl_removeQueryBlockWidget() {

void QueryBuilderController::sl_updateQuery() {
QString query;
foreach (QueryBlockWidget* w, queryBlockWidgets) {
for (QueryBlockWidget* w : qAsConst(queryBlockWidgets)) {
query += w->getQuery();
}

Expand All @@ -335,4 +312,23 @@ void QueryBuilderController::sl_queryReturnPressed() {
parentController->sl_searchButtonClicked();
}

SearchResultRowItem::SearchResultRowItem(QTreeWidget* treeWidget, const EntrezSummary& desc)
: QTreeWidgetItem(treeWidget) {
setText(0, desc.name);
setText(1, desc.title);
setText(2, QString("%1").arg(desc.size));
setData(2, Qt::UserRole, desc.size);
setTextAlignment(2, Qt::AlignRight);
}

bool SearchResultRowItem::operator<(const QTreeWidgetItem& other) const {
int column = treeWidget()->sortColumn();
if (column == 2) {
int myValue = data(2, Qt::UserRole).toInt();
int otherValue = other.data(2, Qt::UserRole).toInt();
return myValue < otherValue;
}
return QTreeWidgetItem::operator<(other);
}

} // namespace U2
34 changes: 19 additions & 15 deletions src/corelibs/U2Gui/src/util/SearchGenbankSequenceDialogController.h
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
#include <QList>
#include <QScopedPointer>
#include <QString>
#include <QTreeWidgetItem>

#include <U2Core/LoadRemoteDocumentTask.h>
#include <U2Core/global.h>
Expand Down Expand Up @@ -59,18 +60,16 @@ class QueryBuilderController;

class QueryBlockWidget : public QWidget {
Q_OBJECT
public:
QueryBlockWidget(QueryBuilderController* controller, bool first);
QString getQuery() const;
void setInputFocus();

private:
NCBISearchContext ctx;
QComboBox *conditionBox, *termBox;
QComboBox* conditionBox = nullptr;
QComboBox* termBox = nullptr;
QLineEdit* queryEdit;

public:
QueryBlockWidget(QueryBuilderController* controller, bool first);
~QueryBlockWidget();
QString getQuery();
void setInputFocus() {
queryEdit->setFocus();
}
};

class SearchGenbankSequenceDialogController;
Expand All @@ -83,7 +82,6 @@ class QueryBuilderController : public QObject {

public:
QueryBuilderController(SearchGenbankSequenceDialogController* parent);
~QueryBuilderController();
void removeQueryBlockWidget(QPushButton* callbackButton);
private slots:
void sl_updateQuery();
Expand All @@ -108,13 +106,13 @@ class U2GUI_EXPORT SearchGenbankSequenceDialogController : public QDialog {

QList<EntrezSummary> getSummaryResults() const;

Ui_SearchGenbankSequenceDialog* ui;
QueryBuilderController* queryBlockController;
Ui_SearchGenbankSequenceDialog* ui = nullptr;
QueryBuilderController* queryBlockController = nullptr;
QScopedPointer<ESearchResultHandler> searchResultHandler;
EntrezQueryTask* searchTask;
EntrezQueryTask* searchTask = nullptr;
QScopedPointer<ESummaryResultHandler> summaryResultHandler;
Task* summaryTask;
QPushButton* downloadButton;
Task* summaryTask = nullptr;
QPushButton* downloadButton = nullptr;

static const int MAX_IDS_PER_QUERY = 100;

Expand All @@ -125,4 +123,10 @@ public slots:
void sl_taskStateChanged(Task* task);
};

class SearchResultRowItem : public QTreeWidgetItem {
public:
SearchResultRowItem(QTreeWidget* treeWidget, const EntrezSummary& desc);

bool operator<(const QTreeWidgetItem& other) const override;
};
} // namespace U2

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