QList<U2MsaRow> MAlignmentExporter::exportRows( const U2DataId &msaId, const QList<qint64> rowIds,
U2OpStatus &os ) const
{
U2MsaDbi* msaDbi = con.dbi->getMsaDbi( );
SAFE_POINT( NULL != msaDbi, NULL_MSA_DBI_ERROR, QList<U2MsaRow>( ) );
QList<U2MsaRow> result;
foreach ( qint64 rowId, rowIds ) {
result.append( msaDbi->getRow( msaId, rowId, os) );
SAFE_POINT_OP( os, QList<U2MsaRow>( ) );
}
Task::ReportResult SimpleAddToAlignmentTask::report() {
CHECK(!hasError() && !isCanceled(), ReportResult_Finished);
U2UseCommonUserModStep modStep(settings.msaRef, stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
U2MsaDbi *dbi = modStep.getDbi()->getMsaDbi();
int posInMsa = inputMsa->getNumRows();
dbi->updateMsaAlphabet(settings.msaRef.entityId, settings.alphabet, stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
QListIterator<QString> namesIterator(settings.addedSequencesNames);
const QList<qint64> rowsIds = inputMsa->getRowsIds();
const U2MsaListGapModel msaGapModel = inputMsa->getGapModel();
for (int i = 0; i < inputMsa->getNumRows(); i++) {
MaDbiUtils::updateRowGapModel(settings.msaRef, rowsIds[i], msaGapModel[i], stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
}
foreach(const U2EntityRef& sequence, settings.addedSequencesRefs) {
QString seqName = namesIterator.peekNext();
U2SequenceObject seqObject(seqName, sequence);
U2MsaRow row = MSAUtils::copyRowFromSequence(&seqObject, settings.msaRef.dbiRef, stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
dbi->addRow(settings.msaRef.entityId, posInMsa, row, stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
posInMsa++;
if(sequencePositions.contains(seqName) && sequencePositions[seqName] > 0) {
QList<U2MsaGap> gapModel;
gapModel << U2MsaGap(0, sequencePositions[seqName]);
dbi->updateGapModel(settings.msaRef.entityId, row.rowId, gapModel, stateInfo);
}
namesIterator.next();
}
MsaDbiUtils::trim(settings.msaRef, stateInfo);
CHECK_OP(stateInfo, ReportResult_Finished);
return ReportResult_Finished;
}
IMPLEMENT_TEST(SQLiteObjectDbiUnitTests, setTrackModType) {
U2OpStatusImpl os;
U2MsaDbi *msaDbi = SQLiteObjectDbiTestData::getMsaDbi();
SQLiteObjectDbi *objectDbi = SQLiteObjectDbiTestData::getSQLiteObjectDbi();
// Create alignment 1
U2DataId msaId1 = msaDbi->createMsaObject("", "Test name 1", BaseDNAAlphabetIds::NUCL_DNA_DEFAULT(), os);
CHECK_NO_ERROR(os);
Utils::addRow(msaDbi->getRootDbi(), msaId1, "1", "ACGTACGT", QList<U2MsaGap>(), os);
CHECK_NO_ERROR(os);
QList<U2MsaRow> rows1 = msaDbi->getRows(msaId1, os);
CHECK_NO_ERROR(os);
// Create alignment 2
U2DataId msaId2 = msaDbi->createMsaObject("", "Test name 2", BaseDNAAlphabetIds::NUCL_DNA_DEFAULT(), os);
CHECK_NO_ERROR(os);
Utils::addRow(msaDbi->getRootDbi(), msaId2, "2", "CCCCCCC", QList<U2MsaGap>(), os);
CHECK_NO_ERROR(os);
QList<U2MsaRow> rows2 = msaDbi->getRows(msaId2, os);
CHECK_NO_ERROR(os);
// Change mod track 1
objectDbi->setTrackModType(msaId1, TrackOnUpdate, os);
CHECK_NO_ERROR(os);
U2TrackModType newType1_1 = objectDbi->getTrackModType(rows1[0].sequenceId, os);
CHECK_EQUAL(TrackOnUpdate, newType1_1, "new mod track type 1_1");
U2TrackModType newType1_2 = objectDbi->getTrackModType(rows2[0].sequenceId, os);
CHECK_EQUAL(NoTrack, newType1_2, "new mod track type 1_2");
// Change mod track 2
objectDbi->setTrackModType(msaId1, NoTrack, os);
CHECK_NO_ERROR(os);
objectDbi->setTrackModType(msaId2, TrackOnUpdate, os);
CHECK_NO_ERROR(os);
U2TrackModType newType2_1 = objectDbi->getTrackModType(rows1[0].sequenceId, os);
CHECK_EQUAL(NoTrack, newType2_1, "new mod track type 2_1");
U2TrackModType newType2_2 = objectDbi->getTrackModType(rows2[0].sequenceId, os);
CHECK_EQUAL(TrackOnUpdate, newType2_2, "new mod track type 2_2");
}
QList<U2MsaRow> MAlignmentExporter::exportRows(const U2DataId& msaId, U2OpStatus& os) const {
U2MsaDbi* msaDbi = con.dbi->getMsaDbi();
SAFE_POINT(NULL != msaDbi, NULL_MSA_DBI_ERROR, QList<U2MsaRow>());
return msaDbi->getRows(msaId, os);
}
IMPLEMENT_TEST(SQLiteObjectDbiUnitTests, removeMsaObject) {
U2OpStatusImpl os;
U2MsaDbi* msaDbi = SQLiteObjectDbiTestData::getMsaDbi();
// FIRST ALIGNMENT
// Create an alignment
U2DataId msaId = msaDbi->createMsaObject("", "Test name", BaseDNAAlphabetIds::NUCL_DNA_DEFAULT(), os);
CHECK_NO_ERROR(os);
// Add alignment info
U2StringAttribute attr(msaId, "MSA1 info key", "MSA1 info value");
U2AttributeDbi* attrDbi = SQLiteObjectDbiTestData::getAttributeDbi();
attrDbi->createStringAttribute(attr, os);
CHECK_NO_ERROR(os);
// Create sequences
U2SequenceDbi* sequenceDbi = SQLiteObjectDbiTestData::getSequenceDbi();
U2Sequence seq1;
U2Sequence seq2;
sequenceDbi->createSequenceObject(seq1, "", os);
CHECK_NO_ERROR(os);
sequenceDbi->createSequenceObject(seq2, "", os);
CHECK_NO_ERROR(os);
// Add rows
U2MsaRow row1;
row1.rowId = 0;
row1.sequenceId = seq1.id;
row1.gstart = 0;
row1.gend = 5;
U2MsaGap row1gap1(0, 2);
U2MsaGap row1gap2(3, 1);
QList<U2MsaGap> row1gaps;
row1gaps << row1gap1 << row1gap2;
row1.gaps = row1gaps;
U2MsaRow row2;
row2.rowId = 1;
row2.sequenceId = seq2.id;
row2.gstart = 2;
row2.gend = 4;
U2MsaGap row2gap(1, 2);
QList<U2MsaGap> row2gaps;
row2gaps << row2gap;
row2.gaps = row2gaps;
QList<U2MsaRow> rows;
rows << row1 << row2;
msaDbi->addRows(msaId, rows, os);
CHECK_NO_ERROR(os);
// SECOND ALIGNMENT
// Create an alignment
U2DataId msaId2 = msaDbi->createMsaObject("", "Test name 2", BaseDNAAlphabetIds::AMINO_DEFAULT(), os);
CHECK_NO_ERROR(os);
// Add alignment info
U2StringAttribute attr2(msaId2, "MSA2 info key", "MSA2 info value");
attrDbi->createStringAttribute(attr2, os);
CHECK_NO_ERROR(os);
// Create sequences
U2Sequence al2Seq;
sequenceDbi->createSequenceObject(al2Seq, "", os);
CHECK_NO_ERROR(os);
// Add rows
U2MsaRow al2Row;
al2Row.rowId = 0;
al2Row.sequenceId = al2Seq.id;
al2Row.gstart = 0;
al2Row.gend = 15;
U2MsaGap al2RowGap(1, 12);
QList<U2MsaGap> al2RowGaps;
al2RowGaps << al2RowGap;
al2Row.gaps = al2RowGaps;
QList<U2MsaRow> al2Rows;
al2Rows << al2Row;
msaDbi->addRows(msaId2, al2Rows, os);
CHECK_NO_ERROR(os);
// REMOVE THE FIRST ALIGNMENT OBJECT
SQLiteObjectDbi* sqliteObjectDbi = SQLiteObjectDbiTestData::getSQLiteObjectDbi();
sqliteObjectDbi->removeObject(msaId, os);
// VERIFY THAT THERE IS ONLY THE SECOND ALIGNMENT'S RECORDS LEFT IN TABLES
SQLiteDbi* sqliteDbi = SQLiteObjectDbiTestData::getSQLiteDbi();
// "Attribute"
SQLiteReadQuery qAttr("SELECT COUNT(*) FROM Attribute WHERE name = ?1", sqliteDbi->getDbRef(), os);
qAttr.bindString(1, "MSA1 info key");
qint64 msa1AttrNum = qAttr.selectInt64();
CHECK_EQUAL(0, msa1AttrNum, "MSA1 attributes number");
qAttr.reset(true);
qAttr.bindString(1, "MSA2 info key");
qint64 msa2AttrNum = qAttr.selectInt64();
CHECK_EQUAL(1, msa2AttrNum, "MSA2 attributes number");
// "StringAttribute"
SQLiteReadQuery qStringAttr("SELECT COUNT(*) FROM StringAttribute WHERE value = ?1", sqliteDbi->getDbRef(), os);
qStringAttr.bindString(1, "MSA1 info value");
qint64 msa1StrAttrNum = qStringAttr.selectInt64();
CHECK_EQUAL(0, msa1StrAttrNum, "MSA1 string attributes number");
qStringAttr.reset(true);
qStringAttr.bindString(1, "MSA2 info value");
qint64 msa2StrAttrNum = qStringAttr.selectInt64();
CHECK_EQUAL(1, msa2StrAttrNum, "MSA2 string attributes number");
// "MsaRow"
SQLiteReadQuery qMsaRow("SELECT COUNT(*) FROM MsaRow WHERE msa = ?1", sqliteDbi->getDbRef(), os);
qMsaRow.bindDataId(1, msaId);
qint64 msa1Rows = qMsaRow.selectInt64();
CHECK_EQUAL(0, msa1Rows, "number of rows in MSA1");
qMsaRow.reset(true);
qMsaRow.bindDataId(1, msaId2);
qint64 msa2Rows = qMsaRow.selectInt64();
CHECK_EQUAL(1, msa2Rows, "number of rows in MSA2");
// "MsaRowGap"
SQLiteReadQuery qMsaRowGap("SELECT COUNT(*) FROM MsaRowGap WHERE msa = ?1", sqliteDbi->getDbRef(), os);
qMsaRowGap.bindDataId(1, msaId);
qint64 msa1Gaps = qMsaRowGap.selectInt64();
CHECK_EQUAL(0, msa1Gaps, "number of gaps in MSA1 rows");
qMsaRowGap.reset(true);
qMsaRowGap.bindDataId(1, msaId2);
qint64 msa2Gaps = qMsaRowGap.selectInt64();
CHECK_EQUAL(1, msa2Gaps, "number of gaps in MSA2 rows");
// "Sequence"
SQLiteReadQuery qSeq("SELECT COUNT(*) FROM Sequence WHERE object = ?1", sqliteDbi->getDbRef(), os);
qSeq.bindDataId(1, seq1.id);
qint64 msa1seq1 = qSeq.selectInt64();
CHECK_EQUAL(0, msa1seq1, "seq1 of msa1");
qSeq.reset(true);
qSeq.bindDataId(1, seq2.id);
qint64 msa1seq2 = qSeq.selectInt64();
CHECK_EQUAL(0, msa1seq2, "seq2 of msa1");
qSeq.reset(true);
qSeq.bindDataId(1, al2Seq.id);
qint64 msa2seq = qSeq.selectInt64();
CHECK_EQUAL(1, msa2seq, "seq of msa2");
// "Msa"
SQLiteReadQuery qMsa("SELECT COUNT(*) FROM Msa WHERE object = ?1", sqliteDbi->getDbRef(), os);
qMsa.bindDataId(1, msaId);
qint64 msa1records = qMsa.selectInt64();
CHECK_EQUAL(0, msa1records, "number of MSA1 records");
qMsa.reset(true);
qMsa.bindDataId(1, msaId2);
qint64 msa2records = qMsa.selectInt64();
CHECK_EQUAL(1, msa2records, "number of MSA2 records");
// "Object"
SQLiteReadQuery qObj("SELECT COUNT(*) FROM Object WHERE id = ?1", sqliteDbi->getDbRef(), os);
qObj.bindDataId(1, msaId);
qint64 msa1objects = qObj.selectInt64();
CHECK_EQUAL(0, msa1objects, "number of MSA1 objects");
qObj.reset(true);
qObj.bindDataId(1, msaId2);
qint64 msa2objects = qObj.selectInt64();
CHECK_EQUAL(1, msa2objects, "number of MSA2 objects");
// Remove the second alignment
sqliteObjectDbi->removeObject(msaId2, os);
}
