void handleRESTQuery( string ns , string action , map<string,string> & params , int & responseCode , stringstream & out ) {
Timer t;
int skip = _getOption( params["skip"] , 0 );
int num = _getOption( params["limit"] , _getOption( params["count" ] , 1000 ) ); // count is old, limit is new
int one = 0;
if ( params["one"].size() > 0 && tolower( params["one"][0] ) == 't' ) {
num = 1;
one = 1;
}
BSONObjBuilder queryBuilder;
for ( map<string,string>::iterator i = params.begin(); i != params.end(); i++ ) {
if ( ! i->first.find( "filter_" ) == 0 )
continue;
const char * field = i->first.substr( 7 ).c_str();
const char * val = i->second.c_str();
char * temp;
// TODO: this is how i guess if something is a number. pretty lame right now
double number = strtod( val , &temp );
if ( temp != val )
queryBuilder.append( field , number );
else
queryBuilder.append( field , val );
}
BSONObj query = queryBuilder.obj();
auto_ptr<DBClientCursor> cursor = db.query( ns.c_str() , query, num , skip );
if ( one ) {
if ( cursor->more() ) {
BSONObj obj = cursor->next();
out << obj.jsonString() << "\n";
}
else {
responseCode = 404;
}
return;
}
out << "{\n";
out << " \"offset\" : " << skip << ",\n";
out << " \"rows\": [\n";
int howMany = 0;
while ( cursor->more() ) {
if ( howMany++ )
out << " ,\n";
BSONObj obj = cursor->next();
out << " " << obj.jsonString();
}
out << "\n ],\n\n";
out << " \"total_rows\" : " << howMany << " ,\n";
out << " \"query\" : " << query.jsonString() << " ,\n";
out << " \"millis\" : " << t.millis() << "\n";
out << "}\n";
}
/**
* Parses the command line setting the global parameters of the program
*
* @param begin address of the first command line argument
* @param end address of the last command line argument
*/
int Config::parseCmdLine(int argc, char* argv[]){
if(_optionExists(argv, argv + argc, "--version")){
printVersion();
exit(0);
}
if(_optionExists(argv, argv + argc, "--help")){
printHelp();
exit(0);
}
bamFileName = _getOption(argv, argv + argc, "-f");
if(bamFileName==NULL){
fprintf(stderr, "-f<ChIP.bam> is required. in.bam is a sorted bam file\n");
exit(EXIT_FAILURE);
}
outputPrefix = _getOption(argv, argv + argc, "-o");
if(outputPrefix ==NULL){
outputPrefix = bamFileName;
} else {
fprintf(stderr, "Output prefix set to [%s]\n", outputPrefix);
}
/** deprecated
char * MAX_FRAGMENT_LENGTH_STR = _getOption(argv, argv + argc, "-m");
if(MAX_FRAGMENT_LENGTH_STR){
setMaxFragmentLength(atoi(MAX_FRAGMENT_LENGTH_STR));
}
*/
debugFolder = _getOption(argv, argv + argc, "--debug-folder");
if(debugFolder!=NULL){
fprintf(stderr, "Debug folder set to [%s]\n", debugFolder);
}
filterFile = _getOption(argv, argv + argc, "--filter-file");
if(filterFile!=NULL){
fprintf(stderr, "Reading filter from file [%s]\n", filterFile);
}
FLDFile = _getOption(argv, argv + argc, "--FLD-file");
if(FLDFile!=NULL){
fprintf(stderr, "Reading FLD from file [%s]\n", FLDFile);
}
TRAINFile = _getOption(argv, argv + argc, "--TRAIN-file");
if(TRAINFile!=NULL){
fprintf(stderr, "Reading training peaks from from file [%s]\n", TRAINFile);
}
char* NUM_THREADS_STR = _getOption(argv, argv + argc, "-p");
if(NUM_THREADS_STR){
numThreads = atoi(NUM_THREADS_STR);
fprintf(stderr, "Set number to threads to [%d]\n", numThreads);
}
char* LQVAL_SIGNIF_STR = _getOption(argv, argv + argc, "-q");
if(LQVAL_SIGNIF_STR){
logQValSignifThreshold = atof(LQVAL_SIGNIF_STR);
fprintf(stderr, "Setting the log q-Value significance threshold to [%f]\n", logQValSignifThreshold);
}
char* SIG_VAL_STR = _getOption(argv, argv + argc, "-s");
if(SIG_VAL_STR){
signalValueThreshold = atof(SIG_VAL_STR);
fprintf(stderr, "Setting the signal value threshold to [%f]\n", signalValueThreshold);
}
char* MIN_READ_STR = _getOption(argv, argv + argc, "-n");
if(MIN_READ_STR){
minReadThreshold = atof(MIN_READ_STR);
fprintf(stderr, "Setting the minimum read and matched filter threshold to [%f]\n", minReadThreshold);
}
if(_optionExists(argv, argv + argc, "--OCE")){
modelOpenChromatinEffect=true;
fprintf(stderr, "Adding open chromatin effect to the model\n");
}
if(_optionExists(argv, argv + argc, "--Correct-PCR")){
correctPCR=true;
fprintf(stderr, "PCR correction preprocessing on\n");
}
if(_optionExists(argv, argv + argc, "--no-artifact-handling")){
handleArtifacts=false;
fprintf(stderr, "Turning off artifact handling\n");
}
return 0;
}