void NGSD::executeQueriesFromFile(QString filename)
{
QStringList lines = Helper::loadTextFile(filename, true);
QString query = "";
for(const QString& line : lines)
{
if (line.isEmpty()) continue;
if (line.startsWith("--")) continue;
query.append(' ');
query.append(line);
if (query.endsWith(';'))
{
//qDebug() << query;
getQuery().exec(query);
query.clear();
}
}
if (query.endsWith(';'))
{
//qDebug() << query;
getQuery().exec(query);
query.clear();
}
}
TEST_F(DocumentSourceMatchTest, MultipleMatchStagesShouldCombineIntoOne) {
auto match1 = DocumentSourceMatch::create(BSON("a" << 1), getExpCtx());
auto match2 = DocumentSourceMatch::create(BSON("b" << 1), getExpCtx());
auto match3 = DocumentSourceMatch::create(BSON("c" << 1), getExpCtx());
Pipeline::SourceContainer container;
// Check initial state
ASSERT_BSONOBJ_EQ(match1->getQuery(), BSON("a" << 1));
ASSERT_BSONOBJ_EQ(match2->getQuery(), BSON("b" << 1));
ASSERT_BSONOBJ_EQ(match3->getQuery(), BSON("c" << 1));
container.push_back(match1);
container.push_back(match2);
match1->optimizeAt(container.begin(), &container);
ASSERT_EQUALS(container.size(), 1U);
ASSERT_BSONOBJ_EQ(match1->getQuery(), fromjson("{'$and': [{a:1}, {b:1}]}"));
container.push_back(match3);
match1->optimizeAt(container.begin(), &container);
ASSERT_EQUALS(container.size(), 1U);
ASSERT_BSONOBJ_EQ(match1->getQuery(),
fromjson("{'$and': [{'$and': [{a:1}, {b:1}]},"
"{c:1}]}"));
}
static void manual() {
if (smatch(getQuery(), "send")) {
setHeader("X-SendCache", "true");
finalize();
} else if (!espRenderCached(getConn())) {
render("{ when: %Ld, uri: '%s', query: '%s' }\r\n", mprGetTicks(), getUri(), getQuery());
}
}
int NGSD::geneToApprovedID(const QByteArray& gene)
{
//init
static SqlQuery q_gene = getQuery(true);
static SqlQuery q_prev = getQuery(true);
static SqlQuery q_syn = getQuery(true);
static bool init = false;
if (!init)
{
q_gene.prepare("SELECT id FROM gene WHERE symbol=:1");
q_prev.prepare("SELECT g.id FROM gene g, gene_alias ga WHERE g.id=ga.gene_id AND ga.symbol=:1 AND ga.type='previous'");
q_syn.prepare("SELECT g.id FROM gene g, gene_alias ga WHERE g.id=ga.gene_id AND ga.symbol=:1 AND ga.type='synonym'");
init = true;
}
//approved
q_gene.bindValue(0, gene);
q_gene.exec();
if (q_gene.size()==1)
{
q_gene.next();
return q_gene.value(0).toInt();
}
//previous
q_prev.bindValue(0, gene);
q_prev.exec();
if (q_prev.size()==1)
{
q_prev.next();
return q_prev.value(0).toInt();
}
else if(q_prev.size()>1)
{
return -1;
}
//synonymous
q_syn.bindValue(0, gene);
q_syn.exec();
if (q_syn.size()==1)
{
q_syn.next();
return q_syn.value(0).toInt();
}
return -1;
}
bool NGSD::tableEmpty(QString table)
{
SqlQuery query = getQuery();
query.exec("SELECT COUNT(*) FROM " + table);
query.next();
return query.value(0).toInt()==0;
}
QStringList NGSD::getEnum(QString table, QString column)
{
//check cache
static QMap<QString, QStringList> cache;
QString hash = table+"."+column;
if (cache.contains(hash))
{
return cache.value(hash);
}
//DB query
SqlQuery q = getQuery();
q.exec("DESCRIBE "+table+" "+column);
while (q.next())
{
QString type = q.value(1).toString();
type.replace("'", "");
type.replace("enum(", "");
type.replace(")", "");
cache[hash] = type.split(",");
return cache[hash];
}
THROW(ProgrammingException, "Could not determine enum values of column '"+column+"' in table '"+table+"'!");
}
void NGSD::init(QString password)
{
//remove existing tables
SqlQuery query = getQuery();
query.exec("SHOW TABLES");
if (query.size()>0)
{
//check password for re-init of production DB
if (!test_db_ && password!=Settings::string("ngsd_pass"))
{
THROW(DatabaseException, "Password provided for re-initialization of procution database is incorrect!");
}
//get table list
QStringList tables;
while(query.next())
{
tables << query.value(0).toString();
}
//remove old tables
if (!tables.isEmpty())
{
query.exec("SET FOREIGN_KEY_CHECKS = 0;");
query.exec("DROP TABLE " + tables.join(","));
query.exec("SET FOREIGN_KEY_CHECKS = 1;");
}
}
//initilize
executeQueriesFromFile(":/resources/NGSD_schema.sql");
}
string OAuthClient::getSignedUrl(string url, bool post, bool remove, bool put){
// cout << "Get URL signed" << endl;
string urlSigned="";
string parameter;
size_t pos = url.find(questionMark);
string query;
if(remove)
query = deleteQuery(url, true);
else
if(post)
query = postQuery(url, true);
else
if(put)
query = putQuery(url, true);
else
query = getQuery(url, true);
if(pos!=string::npos){ // if '?' found
parameter = url.substr(pos+1, url.size()-1);
url = url.substr(0,pos);
}
urlSigned = url + questionMark + query;
return urlSigned;
}
CPLErr RasdamanRasterBand::IReadBlock( int nBlockXOff, int nBlockYOff,
void * pImage )
{
//cerr << "Read block " << nBlockXOff << " " << nBlockYOff << endl;
RasdamanDataset *poGDS = (RasdamanDataset *) poDS;
r_Database database;
r_Transaction transaction;
memset(pImage, 0, nRecordSize);
try {
database.set_servername(poGDS->host, poGDS->port);
database.set_useridentification(poGDS->username, poGDS->userpassword);
database.open(poGDS->databasename);
transaction.begin();
char x_lo[11], x_hi[11], y_lo[11], y_hi[11];
int xPos = poGDS->xPos;
int yPos = poGDS->yPos;
sprintf(x_lo, "%d", nBlockXOff * nBlockXSize);
sprintf(x_hi, "%d", (nBlockXOff+1) * nBlockXSize-1);
sprintf(y_lo, "%d", nBlockYOff * nBlockYSize);
sprintf(y_hi, "%d", (nBlockYOff+1) * nBlockYSize-1);
CPLString queryString = getQuery(poGDS->queryParam, x_lo, x_hi, y_lo, y_hi);
r_Set<r_Ref_Any> result_set;
r_OQL_Query query (queryString);
r_oql_execute (query, result_set);
if (result_set.get_element_type_schema()->type_id() == r_Type::MARRAYTYPE) {
r_Iterator<r_Ref_Any> iter = result_set.create_iterator();
r_Ref<r_GMarray> gmdd = r_Ref<r_GMarray>(*iter);
r_Minterval sp = gmdd->spatial_domain();
r_Point extent = sp.get_extent();
r_Point base = sp.get_origin();
int tileX = extent[xPos];
int tileY = extent[yPos];
r_Point access = base;
char *resultPtr;
for (int j=0; j<tileY; ++j) {
for (int i=0; i<tileX; ++i) {
resultPtr = (char*)pImage + (j*nBlockYSize+i)*typeSize;
access[xPos] = base[xPos]+i;
access[yPos] = base[yPos]+j;
const char *data = (*gmdd)[access] + typeOffset;
memcpy(resultPtr, data, typeSize);
}
}
}
transaction.commit();
database.close();
} catch (r_Error error) {
CPLError(CE_Failure, CPLE_AppDefined, "%s", error.what());
return CPLGetLastErrorType();
}
return CE_None;
}
void init(){
// Read the first line containing number of patients
int tmp ;
scanf("%d",&tmp);
// Read into binary tree
struct node * tree ;
int i = 0 ;
for ( i = 0 ; i < tmp ; i++){
if ( i == 0 ) tree = makeNode(readPatient());
else{
insert(&tree,readPatient());
}
}
// Read line containing number of queries.
scanf("%d",&tmp);
// Loop tmp number of times, reading the two queries, finding the query, and printing the value
for ( i = 0 ; i < tmp ; i++ ){
char * organQ = (char *)malloc(sizeof(char)*20);
char * bloodtypeQ = (char *)malloc(sizeof(char)*20);
organT * rtn = NULL ;
scanf("%s %s",organQ,bloodtypeQ);
getQuery(&rtn, tree,organQ,bloodtypeQ);
printPatient((rtn));
free(organQ);
free(bloodtypeQ);
free(rtn);
}
recursiveFree(tree);
}
int TestUndelete::getPINIndex(PID lPID)
{
assert(lPID.pid != STORE_INVALID_PID);
IPIN *lPIN = mSession->getPIN(lPID);
if(!lPIN)
{
int i = 0;
for( i = 0; i < (int)mPIDs.size(); i++) if(lPID.pid == mPIDs[i].pid && lPID.ident == mPIDs[i].ident) break;
Value lV[1]; lV[0].set(i);
IStmt *lQ = getQuery(4, mPropIDs[1], lV);
ICursor *lR = NULL;
TVERIFYRC(lQ->execute(&lR, 0,0,~0,0,MODE_DELETED));
if(lR) { lPIN = lR->next(); lR->destroy(); } else assert(lPIN!=NULL && "Failed to get PIN");
lQ->destroy();
}
int lRetVal = 0;
if(lPIN->defined(&mPropIDs[1], 1))
{
Value const *lV = lPIN->getValue(mPropIDs[1]);
lRetVal = lV->i;
TVERIFY(lV!=NULL && "NULL Value returned");
}
lPIN->destroy();
return lRetVal;
}
/**
* @brief Entry point for docker_volumes table.
*/
QueryData genVolumes(QueryContext& context) {
std::string query;
std::set<std::string> names;
getQuery(context, "name", query, names, false);
QueryData results;
pt::ptree tree;
Status s = dockerApi("/volumes" + query, tree);
if (!s.ok()) {
VLOG(1) << "Error getting docker volumes: " << s.what();
return results;
}
for (const auto& entry : tree.get_child("Volumes")) {
try {
const pt::ptree& node = entry.second;
Row r;
r["name"] = getValue(node, names, "Name");
r["driver"] = node.get<std::string>("Driver", "");
r["mount_point"] = node.get<std::string>("Mountpoint", "");
r["type"] = node.get<std::string>("Options.type", "");
results.push_back(r);
} catch (const pt::ptree_error& e) {
VLOG(1) << "Error getting docker volume details: " << e.what();
}
}
return results;
}
std::string Uri::toString()
{
std::ostringstream oss;
oss << proto_ << "://";
if ( !user_.empty() )
{
oss << user_;
if ( !pwd_.empty() )
{
oss << ":" << pwd_;
}
oss << "@";
}
oss << host_;
if ( port_ != 80 && port_ != 443 && port_ != 22 )
{
oss << ":" << port_;
}
oss << path_;
oss << getQuery();
if ( anchor_.size() > 0 )
oss << "#" << anchor_;
return oss.str();
}
SongListView::SongListView(DataStore *dataStore, QWidget *parent):
QTableView(parent),
dataStore(dataStore),
currentSongListId(-1)
{
setEditTriggers(QAbstractItemView::NoEditTriggers);
createActions();
songListEntryModel =
new MusicModel(getQuery(currentSongListId), dataStore, this);
proxyModel = new QSortFilterProxyModel(this);
proxyModel->setSourceModel(songListEntryModel);
setModel(proxyModel);
setSortingEnabled(true);
horizontalHeader()->setStretchLastSection(true);
verticalHeader()->hide();
setSelectionBehavior(QAbstractItemView::SelectRows);
setContextMenuPolicy(Qt::CustomContextMenu);
connect(this, SIGNAL(customContextMenuRequested(const QPoint&)),
this, SLOT(handleContextMenuRequest(const QPoint&)));
connect(dataStore, SIGNAL(songListModified(song_list_id_t)),
this, SLOT(onSongListEntriesChanged(song_list_id_t)));
connect(dataStore, SIGNAL(songListDeleted(song_list_id_t)),
this, SLOT(onSongListDelete(song_list_id_t)));
songListEntryModel->refresh();
configHeaders();
}
static void sml() {
int i;
for (i = 0; i < 1; i++) {
render("Line: %05d %s", i, "aaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbccccccccccccccccccddddddd<br/>\r\n");
}
render("{ when: %Ld, uri: '%s', query: '%s' }\r\n", mprGetTicks(), getUri(), getQuery());
}
void QueryExpression::setQueryContext(QueryContext& inCtx)
{
if(_ss == NULL){
MessageLoaderParms parms("Query.QueryExpression.SS_IS_NULL",
"Trying to process a query with a NULL SelectStatement.");
throw QueryException(parms);
}
// SelectStatement only allows this to be called once.
_ss->setQueryContext(inCtx);
#ifndef PEGASUS_DISABLE_CQL
String cql("CIM:CQL");
if (_queryLang == cql)
{
// Now that we have a QueryContext, we can finish compiling
// the CQL statement.
CQLSelectStatement* tempSS = dynamic_cast<CQLSelectStatement*>(_ss);
if (tempSS != NULL)
{
CQLParser::parse(getQuery(), *tempSS);
tempSS->applyContext();
}
}
#endif
}
bool run(OperationContext* txn, const string& dbname, BSONObj& jsobj, int, string& errmsg, BSONObjBuilder& result, bool fromRepl ) {
if ( !globalScriptEngine ) {
errmsg = "server-side JavaScript execution is disabled";
return false;
}
/* db.$cmd.findOne( { group : <p> } ) */
const BSONObj& p = jsobj.firstElement().embeddedObjectUserCheck();
BSONObj q;
if ( p["cond"].type() == Object )
q = p["cond"].embeddedObject();
else if ( p["condition"].type() == Object )
q = p["condition"].embeddedObject();
else
q = getQuery( p );
BSONObj key;
string keyf;
if ( p["key"].type() == Object ) {
key = p["key"].embeddedObjectUserCheck();
if ( ! p["$keyf"].eoo() ) {
errmsg = "can't have key and $keyf";
return false;
}
}
else if ( p["$keyf"].type() ) {
keyf = p["$keyf"]._asCode();
}
else {
// no key specified, will use entire object as key
}
BSONElement reduce = p["$reduce"];
if ( reduce.eoo() ) {
errmsg = "$reduce has to be set";
return false;
}
BSONElement initial = p["initial"];
if ( initial.type() != Object ) {
errmsg = "initial has to be an object";
return false;
}
string finalize;
if (p["finalize"].type())
finalize = p["finalize"]._asCode();
const string ns = parseNs(dbname, jsobj);
Client::ReadContext ctx(txn, ns);
return group( txn, ctx.ctx().db() , ns , q ,
key , keyf , reduce._asCode() , reduce.type() != CodeWScope ? 0 : reduce.codeWScopeScopeDataUnsafe() ,
initial.embeddedObject() , finalize ,
errmsg , result );
}
static void huge() {
int i;
// This will emit ~762K (over the item limit)
for (i = 0; i < 10000; i++) {
render("Line: %05d %s", i, "aaaaaaaaaaaaaaaaaabbbbbbbbbbbbbbbbccccccccccccccccccddddddd<br/>\r\n");
}
render("{ when: %Ld, uri: '%s', query: '%s' }\r\n", mprGetTicks(), getUri(), getQuery());
}
enum ePrivilegeLevel cUser::privilegeLevel() const
{
if (_privilegeLevel == ENUM_INVALID) {
QSqlQuery q = getQuery();
return const_cast<cUser *>(this)->getRights(q);
}
return (ePrivilegeLevel)_privilegeLevel;
}
bool run(const string& dbname, BSONObj& jsobj, string& errmsg, BSONObjBuilder& result, bool fromRepl ) {
/* db.$cmd.findOne( { group : <p> } ) */
const BSONObj& p = jsobj.firstElement().embeddedObjectUserCheck();
BSONObj q;
if ( p["cond"].type() == Object )
q = p["cond"].embeddedObject();
else if ( p["condition"].type() == Object )
q = p["condition"].embeddedObject();
else
q = getQuery( p );
if ( p["ns"].type() != String ) {
errmsg = "ns has to be set";
return false;
}
string ns = dbname + "." + p["ns"].String();
BSONObj key;
string keyf;
if ( p["key"].type() == Object ) {
key = p["key"].embeddedObjectUserCheck();
if ( ! p["$keyf"].eoo() ) {
errmsg = "can't have key and $keyf";
return false;
}
}
else if ( p["$keyf"].type() ) {
keyf = p["$keyf"]._asCode();
}
else {
// no key specified, will use entire object as key
}
BSONElement reduce = p["$reduce"];
if ( reduce.eoo() ) {
errmsg = "$reduce has to be set";
return false;
}
BSONElement initial = p["initial"];
if ( initial.type() != Object ) {
errmsg = "initial has to be an object";
return false;
}
string finalize;
if (p["finalize"].type())
finalize = p["finalize"]._asCode();
return group( dbname , ns , q ,
key , keyf , reduce._asCode() , reduce.type() != CodeWScope ? 0 : reduce.codeWScopeScopeData() ,
initial.embeddedObject() , finalize ,
errmsg , result );
}
const std::string Uri::getFullPath() const
{
std::ostringstream oss;
oss << path_;
oss << getQuery();
if ( anchor_.size() > 0 )
oss << "#" << anchor_;
return oss.str();
}
void FindSequenceDialog::aaSearch ()
{
int a , b ;
TVector *v = c->vec ;
if ( v->getType() != TYPE_VECTOR &&
v->getType() != TYPE_SEQUENCE &&
v->getType() != TYPE_PRIMER )
return ;
wxString s = getQuery() ;
for ( a = 0 ; a < v->items.size() ; a++ )
{
wxString ls = v->items[a].getAminoAcidSequence() ;
if ( ls.IsEmpty() ) continue ;
int dir = v->items[a].getDirection() ;
int off = v->items[a].getOffset() ;
vector <Tdna2aa> dna2aa ;
p = 0 ;
b = subsearch ( ls , s , p ) ;
while ( b != -1 )
{
if ( lb->GetCount() > FIND_MAX ) return ;
if ( dna2aa.size() == 0 )
v->items[a].translate ( v , NULL , dna2aa ) ;
int from = dir==1?b:last ;
int to = dir==1?last:b ;
wxString msg ;
if ( off != -1 )
msg = wxString::Format ( _T(" [%d-%d]") , from+off , to+off ) ;
from = dna2aa[from].dna[0] + 1 ;
to = dna2aa[to].dna[2] + 1 ;
if ( from > to ) { int x = from ; from = to ; to = x ; }
lb->Append ( wxString::Format ( _T("%s: %s (%d-%d)%s") ,
txt("amino_acid").c_str() ,
v->items[a].name.c_str() ,
from , to , msg.c_str() ) ) ;
vi.Add ( -1 ) ;
p = b + 1 ;
b = subsearch ( ls , s , p ) ;
}
}
// Fixed reading frames
wxString ss ;
ss = v->getSequence() ;
if ( v->isCircular() ) ss += ss.Left ( 2 ) ;
else ss += _T(" ") ;
aaSubSearch ( ss , 0 , 1 , txt("m_aa_1") ) ; // Reading frame +1
aaSubSearch ( ss , 1 , 1 , txt("m_aa_2") ) ; // Reading frame +2
aaSubSearch ( ss , 2 , 1 , txt("m_aa_3") ) ; // Reading frame +3
ss = v->transformSequence ( true , false ) ;
if ( v->isCircular() ) ss = ss.Right ( 2 ) + ss ;
else ss = _T(" ") + ss ;
aaSubSearch ( ss , -1 , -1 , txt("m_aa_m1") ) ; // Reading frame -1
aaSubSearch ( ss , -2 , -1 , txt("m_aa_m2") ) ; // Reading frame -2
aaSubSearch ( ss , -3 , -1 , txt("m_aa_m3") ) ; // Reading frame -3
}
void TestUndelete::testClass()
{
IStmt *lQ = getQuery(2);
long const lStartTime = getTimeInMs();
test(lQ);
long const lEndTime = getTimeInMs();
mLogger.out() << "Time taken for testClass() :: " << (lEndTime - lStartTime) << " ms" << std::endl;
lQ->destroy();
}
void NGSD::tableExists(QString table)
{
SqlQuery query = getQuery();
query.exec("SHOW TABLES LIKE '" + table + "'");
if (query.size()==0)
{
THROW(DatabaseException, "Table '" + table + "' does not exist!")
}
}
void NGSD::setReportVariants(const QString& filename, const VariantList& variants, QSet<int> selected_indices)
{
QString ps_id = processedSampleId(filename);
//get variant ID
for(int i=0; i<variants.count(); ++i)
{
getQuery().exec("UPDATE detected_variant SET report=" + QString(selected_indices.contains(i) ? "1" : "0" ) + " WHERE processed_sample_id='" + ps_id + "' AND variant_id='" + variantId(variants[i]) + "'");
}
}
void TestUndelete::testFullScan()
{
Value lV[1]; lV[0].set(mQueryStr.c_str());
IStmt *lQ = getQuery(1, mPropIDs[2], lV);
long const lStartTime = getTimeInMs();
test(lQ);
long const lEndTime = getTimeInMs();
mLogger.out() << "Time taken for testFullScan() :: " << (lEndTime - lStartTime) << " ms" << std::endl;
lQ->destroy();
}
int main(int argc, char *argv[])
{
cLv2QApp app(argc, argv);
SETAPP();
lanView::snmpNeeded = true;
lanView::sqlNeeded = SN_SQL_NEED;
lv2test mo;
if (mo.lastError != NULL) {
_DBGFNL() << mo.lastError->mErrorCode << endl;
return mo.lastError->mErrorCode; // a mo destruktora majd kiírja a hibaüzenetet.
}
if (mo.lastError) { // Ha hiba volt, vagy vége
return mo.lastError->mErrorCode; // a mo destruktora majd kiírja a hibaüzenetet.
}
try {
/* cRecordAny a1;
cRecordAny a2;
cNode n;
cSnmpDevice s;
a1 = n;
a2 = s;
n.clone(a1);
s.clone(a2);
n.clone(a2);
n.clone(n);
n.clone(s);
s.clone(a1);*/
QString exp;
QSqlQuery q = getQuery();
/* cUser u;
if (u.fetch(*mo.pq, false, QBitArray(1))) {
do {
exp = u.objectExport(q, 1);
PDEB(INFO) << exp << endl;
} while (u.next(*mo.pq));
}
cEnumVal oev;
if (oev.fetch(*mo.pq, false, QBitArray(1))) {
do {
exp = oev.objectExport(q, 1);
PDEB(INFO) << exp << endl;
} while (oev.next(*mo.pq));
}*/
cTableShape ts;
ts.setByName(q, "nodes");
exp = ts.objectExport(q);
PDEB(INFO) << exp << endl;
} CATCHS(mo.lastError)
return mo.lastError == NULL ? 0 : mo.lastError->mErrorCode;
}
bool DnsLayer::removeQuery(const std::string& queryNameToRemove, bool exactMatch)
{
DnsQuery* queryToRemove = getQuery(queryNameToRemove, exactMatch);
if (queryToRemove == NULL)
{
LOG_DEBUG("Query not found");
return false;
}
return removeQuery(queryToRemove);
}
/**
* @brief Utility method to get containers tree.
*/
Status getContainers(QueryContext& context,
std::set<std::string>& ids,
pt::ptree& containers) {
std::string query;
getQuery(context, "id", query, ids, true);
Status s = dockerApi("/containers/json" + query, containers);
if (!s.ok()) {
VLOG(1) << "Error getting docker containers: " << s.what();
return s;
}
return Status(0);
}
bool MultiPlanRunner::forceYield() {
saveState();
ClientCursor::registerRunner(this);
ClientCursor::staticYield(ClientCursor::suggestYieldMicros(),
getQuery().getParsed().ns(),
NULL);
// During the yield, the database we're operating over or any collection we're relying on
// may be dropped. When this happens all cursors and runners on that database and
// collection are killed or deleted in some fashion. (This is how the _killed gets set.)
ClientCursor::deregisterRunner(this);
if (!_killed) { restoreState(); }
return !_killed;
}