QgsGeometryCheckerSetupTab::QgsGeometryCheckerSetupTab( QgisInterface* iface , QWidget *parent )
: QWidget( parent ), mIface( iface )
{
ui.setupUi( this );
ui.progressBar->hide();
ui.labelStatus->hide();
ui.comboBoxInputLayer->setFilters( QgsMapLayerProxyModel::HasGeometry );
mRunButton = ui.buttonBox->addButton( tr( "Run" ), QDialogButtonBox::ActionRole );
mAbortButton = new QPushButton( tr( "Abort" ) );
mRunButton->setEnabled( false );
connect( mRunButton, SIGNAL( clicked() ), this, SLOT( runChecks() ) );
connect( ui.comboBoxInputLayer, SIGNAL( currentIndexChanged( int ) ), this, SLOT( validateInput() ) );
connect( QgsMapLayerRegistry::instance(), SIGNAL( layersAdded( QList<QgsMapLayer*> ) ), this, SLOT( updateLayers() ) );
connect( QgsMapLayerRegistry::instance(), SIGNAL( layersWillBeRemoved( QStringList ) ), this, SLOT( updateLayers() ) );
connect( ui.radioButtonOutputNew, SIGNAL( toggled( bool ) ), ui.lineEditOutput, SLOT( setEnabled( bool ) ) );
connect( ui.radioButtonOutputNew, SIGNAL( toggled( bool ) ), ui.pushButtonOutputBrowse, SLOT( setEnabled( bool ) ) );
connect( ui.buttonGroupOutput, SIGNAL( buttonClicked( int ) ), this, SLOT( validateInput() ) );
connect( ui.pushButtonOutputBrowse, SIGNAL( clicked() ), this, SLOT( selectOutputFile() ) );
connect( ui.lineEditOutput, SIGNAL( textChanged( QString ) ), this, SLOT( validateInput() ) );
connect( ui.checkBoxSliverPolygons, SIGNAL( toggled( bool ) ), ui.widgetSliverThreshold, SLOT( setEnabled( bool ) ) );
connect( ui.checkBoxSliverArea, SIGNAL( toggled( bool ) ), ui.doubleSpinBoxSliverArea, SLOT( setEnabled( bool ) ) );
updateLayers();
Q_FOREACH ( const QgsGeometryCheckFactory* factory, QgsGeometryCheckFactoryRegistry::getCheckFactories() )
{
factory->restorePrevious( ui );
}
void cStream::runBenchmarkTuned()
{
initializeVariables();
runChecks();
runTunedTests();
checkSTREAMresults();
calculateBandwidthResults();
outputSummary();
}; // void cStream::runBenchmarkTuned()
void suppressionsSettings()
{
runChecks(&TestSuppressions::checkSuppression);
if (ThreadExecutor::isEnabled())
runChecks(&TestSuppressions::checkSuppressionThreads);
}
rc_t run(const TestCase& test_case)
{
rc_t rc;
KDirectory * cur_dir;
const VDBManager * manager;
const VDatabase * database;
const VTable * table;
const VCursor * cursor;
uint32_t name_idx;
uint32_t name_range_idx;
rc = KDirectoryNativeDir( &cur_dir );
if ( rc != 0 )
LOGERR( klogInt, rc, "KDirectoryNativeDir() failed" );
else
{
rc = VDBManagerMakeRead ( &manager, cur_dir );
if ( rc != 0 )
LOGERR( klogInt, rc, "VDBManagerMakeRead() failed" );
else
{
rc = VDBManagerOpenDBRead( manager, &database, NULL, "%s", test_case.path );
if (rc != 0)
LOGERR( klogInt, rc, "VDBManagerOpenDBRead() failed" );
else
{
rc = VDatabaseOpenTableRead( database, &table, "%s", TABLE_NAME );
if ( rc != 0 )
LOGERR( klogInt, rc, "VDatabaseOpenTableRead() failed" );
else
{
rc = VTableCreateCursorRead( table, &cursor );
if ( rc != 0 )
LOGERR( klogInt, rc, "VTableCreateCursorRead() failed" );
else
{
/* add columns to cursor */
rc = VCursorAddColumn( cursor, &name_idx, "(utf8)NAME" );
if ( rc != 0 )
LOGERR( klogInt, rc, "VCursorAddColumn() failed" );
else
{
rc = VCursorAddColumn( cursor, &name_range_idx, "NAME_RANGE" );
if ( rc != 0 )
LOGERR( klogInt, rc, "VCursorAddColumn() failed" );
else
{
rc = VCursorOpen( cursor );
if (rc != 0)
LOGERR( klogInt, rc, "VCursorOpen() failed" );
else
rc = runChecks( test_case, cursor, name_idx, name_range_idx );
}
}
VCursorRelease( cursor );
}
VTableRelease( table );
}
VDatabaseRelease( database );
}
VDBManagerRelease( manager );
}
KDirectoryRelease( cur_dir );
}
return rc;
}
/**
* returns true if accession is good
*/
bool checkAccession ( const char * accession, const CheckCorruptConfig * config )
{
rc_t rc;
KDirectory * cur_dir;
const VDBManager * manager;
const VDatabase * database;
const VTable * pa_table;
const VTable * sa_table;
const VTable * seq_table;
const VCursor * pa_cursor;
const VCursor * sa_cursor;
const VCursor * seq_cursor;
rc = KDirectoryNativeDir( &cur_dir );
if ( rc != 0 )
PLOGERR( klogInt, (klogInt, rc, "$(ACC) KDirectoryNativeDir() failed", "ACC=%s", accession));
else
{
rc = VDBManagerMakeRead ( &manager, cur_dir );
if ( rc != 0 )
PLOGERR( klogInt, (klogInt, rc, "$(ACC) VDBManagerMakeRead() failed", "ACC=%s", accession));
else
{
int type = VDBManagerPathType ( manager, "%s", accession );
if ( ( type & ~ kptAlias ) != kptDatabase )
PLOGMSG (klogInfo, (klogInfo, "$(ACC) SKIPPING - can't be opened as a database", "ACC=%s", accession));
else
{
rc = VDBManagerOpenDBRead( manager, &database, NULL, "%s", accession );
if (rc != 0)
PLOGERR( klogInt, (klogInt, rc, "$(ACC) VDBManagerOpenDBRead() failed", "ACC=%s", accession));
else
{
rc = VDatabaseOpenTableRead( database, &pa_table, "%s", "PRIMARY_ALIGNMENT" );
if ( rc != 0 )
{
PLOGMSG (klogInfo, (klogInfo, "$(ACC) SKIPPING - failed to open PRIMARY_ALIGNMENT table", "ACC=%s", accession));
rc = 0;
}
else
{
rc = VTableCreateCursorRead( pa_table, &pa_cursor );
if ( rc != 0 )
PLOGERR( klogInt, (klogInt, rc, "$(ACC) VTableCreateCursorRead() failed for PRIMARY_ALIGNMENT cursor", "ACC=%s", accession));
else
{
rc = VDatabaseOpenTableRead( database, &sa_table, "%s", "SECONDARY_ALIGNMENT" );
if ( rc != 0 )
{
PLOGMSG (klogInfo, (klogInfo, "$(ACC) SKIPPING - failed to open SECONDARY_ALIGNMENT table", "ACC=%s", accession));
rc = 0;
}
else
{
rc = VTableCreateCursorRead( sa_table, &sa_cursor );
if ( rc != 0 )
PLOGERR( klogInt, (klogInt, rc, "$(ACC) VTableCreateCursorRead() failed for SECONDARY_ALIGNMENT cursor", "ACC=%s", accession));
else
{
rc = VDatabaseOpenTableRead( database, &seq_table, "%s", "SEQUENCE" );
if ( rc != 0 )
{
PLOGMSG (klogInfo, (klogInfo, "$(ACC) SKIPPING - failed to open SEQUENCE table", "ACC=%s", accession));
rc = 0;
}
else
{
rc = VTableCreateCursorRead( seq_table, &seq_cursor );
if ( rc != 0 )
PLOGERR( klogInt, (klogInt, rc, "VTableCreateCursorRead() failed for SEQUENCE cursor", "ACC=%s", accession));
else
{
try {
runChecks( accession, config, pa_cursor, sa_cursor, seq_cursor );
} catch ( VDB_ERROR & x ) {
PLOGERR (klogErr, (klogInfo, x.rc, "$(ACC) VDB error: $(MSG)", "ACC=%s,MSG=%s", accession, x.msg));
rc = 1;
} catch ( VDB_ROW_ERROR & x ) {
PLOGERR (klogErr, (klogInfo, x.rc, "$(ACC) VDB error: $(MSG) row_id: $(ROW_ID)", "ACC=%s,MSG=%s,ROW_ID=%ld", accession, x.msg, x.row_id));
rc = 1;
} catch ( DATA_ERROR & x ) {
KOutMsg("%s\n", accession);
PLOGMSG (klogInfo, (klogInfo, "$(ACC) Invalid data: $(MSG) ", "ACC=%s,MSG=%s", accession, x.msg.c_str()));
rc = 1;
}
VCursorRelease( seq_cursor );
}
VTableRelease( seq_table );
}
VCursorRelease( sa_cursor );
}
VTableRelease( sa_table );
}
VCursorRelease( pa_cursor );
}
VTableRelease( pa_table );
}
VDatabaseRelease( database );
}
}
VDBManagerRelease( manager );
}
KDirectoryRelease( cur_dir );
}
return rc == 0;
}
