bool StrainHMObject::setGraph(std::string title, std::string patientName, int patientid, int taxid, osg::Vec4 color)
{
std::stringstream queryss;
queryss << "select value, unix_timestamp(timestamp) as timestamp from EcoliShigella_Measurement where patient_id = " << patientid << " and taxonomy_id = " << taxid << " order by timestamp;";
struct StrainData
{
float value;
time_t timestamp;
};
StrainData * sdata = NULL;
int dataSize = 0;
if(ComController::instance()->isMaster())
{
if(_dbm)
{
DBMQueryResult result;
_dbm->runQuery(queryss.str(),result);
dataSize = result.numRows();
if(dataSize)
{
sdata = new struct StrainData[dataSize];
for(int i = 0; i < dataSize; ++i)
{
sdata[i].value = atof(result(i,"value").c_str());
sdata[i].timestamp = atol(result(i,"timestamp").c_str());
}
}
}
else
{
std::cerr << "No Database connection." << std::endl;
}
ComController::instance()->sendSlaves(&dataSize,sizeof(int));
if(dataSize)
{
ComController::instance()->sendSlaves(sdata,dataSize*sizeof(struct StrainData));
}
}
else
{
ComController::instance()->readMaster(&dataSize,sizeof(int));
if(dataSize)
{
sdata = new struct StrainData[dataSize];
ComController::instance()->readMaster(sdata,dataSize*sizeof(struct StrainData));
}
}
bool graphValid = false;
if(dataSize)
{
std::vector<std::string> labels;
std::vector<float> values;
std::vector<osg::Vec4> colors;
float minValue = FLT_MAX;
float maxValue = FLT_MIN;
for(int i = 0; i < dataSize; ++i)
{
char temp[1024];
strftime(temp,1023,"%F",localtime(&sdata[i].timestamp));
labels.push_back(temp);
values.push_back(sdata[i].value);
colors.push_back(color);
if(sdata[i].value > maxValue)
{
maxValue = sdata[i].value;
}
if(sdata[i].value < minValue)
{
minValue = sdata[i].value;
}
}
if(minValue < 0.00003)
{
std::cerr << "Graph discarded for low range." << std::endl;
if(sdata)
{
delete[] sdata;
}
return false;
}
std::stringstream titless;
titless << patientName << " : " << title;
graphValid = _graph->setGraph(titless.str(),labels,values,minValue,maxValue,0.1,1.0,colors);
}
PluginHelper::registerSceneObject(this,"FuturePatient");
attachToScene();
if(sdata)
{
delete[] sdata;
}
return graphValid;
}
bool MicrobePointLineObject::setGraph(std::string microbeTableSuffix, std::string measureTableSuffix, bool expandAxis)
{
std::vector<std::string> phylumOrder;
// larry order
/*phylumOrder.push_back("Bacteroidetes");
phylumOrder.push_back("Firmicutes");
phylumOrder.push_back("Verrucomicrobia");
phylumOrder.push_back("Proteobacteria");
phylumOrder.push_back("Actinobacteria");
phylumOrder.push_back("Fusobacteria");
phylumOrder.push_back("Euryarchaeota");*/
phylumOrder.push_back("Bacteroidetes");
phylumOrder.push_back("Firmicutes");
phylumOrder.push_back("Actinobacteria");
phylumOrder.push_back("Proteobacteria");
phylumOrder.push_back("Verrucomicrobia");
phylumOrder.push_back("Euryarchaeota");
phylumOrder.push_back("Fusobacteria");
int numPatients = 0;
std::vector<patientData> data;
std::string measurementTable = "Microbe_Measurement";
measurementTable += measureTableSuffix;
std::string microbesTable = "Microbes";
microbesTable += microbeTableSuffix;
std::stringstream queryss;
queryss << "SELECT Patient.p_condition, Patient.last_name, unix_timestamp(" << measurementTable << ".timestamp) as timestamp, " << microbesTable << ".phylum, sum(" << measurementTable << ".value) as value from " << measurementTable << " inner join " << microbesTable << " on " << measurementTable << ".taxonomy_id = " << microbesTable << ".taxonomy_id inner join Patient on Patient.patient_id = " << measurementTable << ".patient_id where Patient.region = \"US\" group by Patient.last_name, " << measurementTable << ".timestamp, " << microbesTable << ".phylum;";
std::string querystr = queryss.str();
//std::cerr << querystr << std::endl;
if(ComController::instance()->isMaster())
{
if(_dbm)
{
DBMQueryResult result;
_dbm->runQuery(querystr,result);
std::map<patType,std::map<std::string,std::map<time_t,std::map<std::string,float> > > > sortMap;
for(int i = 0; i < result.numRows(); ++i)
{
std::string condition = result(i,"p_condition").c_str();
patType type;
if(condition == "CD" || condition == "crohn's disease")
{
type = CROHNS;
}
else if(condition == "healthy")
{
type = HEALTHY;
}
else if(condition == "Larry")
{
type = SMARR;
}
else if(condition == "UC" || condition == "ulcerous colitis")
{
type = UC;
}
else
{
continue;
}
sortMap[type][result(i,"last_name").c_str()][atol(result(i,"timestamp").c_str())][result(i,"phylum").c_str()] = atof(result(i,"value").c_str());
}
for(std::map<patType,std::map<std::string,std::map<time_t,std::map<std::string,float> > > >::iterator git = sortMap.begin(); git != sortMap.end(); ++git)
{
for(std::map<std::string,std::map<time_t,std::map<std::string,float> > >::iterator pit = git->second.begin(); pit != git->second.end(); ++pit)
{
for(std::map<time_t,std::map<std::string,float> >::iterator tsit = pit->second.begin(); tsit != pit->second.end(); ++tsit)
{
patientData pd;
pd.type = git->first;
strncpy(pd.name,pit->first.c_str(),511);
pd.timestamp = tsit->first;
for(int i = 0; i < phylumOrder.size(); ++i)
{
pd.data[i] = tsit->second[phylumOrder[i]];
}
data.push_back(pd);
}
}
}
numPatients = data.size();
}
ComController::instance()->sendSlaves(&numPatients,sizeof(int));
if(numPatients)
{
ComController::instance()->sendSlaves(data.data(),numPatients*sizeof(struct patientData));
}
}
else
{
ComController::instance()->readMaster(&numPatients,sizeof(int));
if(numPatients)
{
data.resize(numPatients);
ComController::instance()->readMaster(data.data(),numPatients*sizeof(struct patientData));
}
}
std::cerr << "Got " << numPatients << " patients." << std::endl;
if(!numPatients)
{
return false;
}
std::vector<std::string> groupNames;
groupNames.push_back("LS");
groupNames.push_back("Crohns");
groupNames.push_back("UC");
groupNames.push_back("Healthy");
std::vector<std::vector<std::string> > patientNames;
patientNames.push_back(std::vector<std::string>());
patientNames.push_back(std::vector<std::string>());
patientNames.push_back(std::vector<std::string>());
patientNames.push_back(std::vector<std::string>());
std::vector<std::vector<std::vector<float> > > values;
values.push_back(std::vector<std::vector<float> >());
values.push_back(std::vector<std::vector<float> >());
values.push_back(std::vector<std::vector<float> >());
values.push_back(std::vector<std::vector<float> >());
for(int i = 0; i < data.size(); ++i)
{
int index = (int)data[i].type;
char timestamp[512];
std::string name = data[i].name;
if(name == "Smarr")
{
name = "LS";
}
name += " - ";
strftime(timestamp,511,"%F",localtime(&data[i].timestamp));
name += timestamp;
patientNames[index].push_back(name);
values[index].push_back(std::vector<float>());
for(int j = 0; j < 7; ++j)
{
values[index].back().push_back(data[i].data[j]);
}
}
bool tret = _graph->setGraph("Phylum Line Chart",groupNames,phylumOrder,patientNames,values,expandAxis);
if(tret)
{
addChild(_graph->getRootNode());
}
return tret;
}
bool StrainGraphObject::setGraph(std::string title, int taxId, bool larryOnly)
{
std::stringstream ss;
if(!larryOnly)
{
ss << "select Patient.last_name, Patient.p_condition, EcoliShigella_Measurement.value, unix_timestamp(EcoliShigella_Measurement.timestamp) as timestamp from EcoliShigella_Measurement inner join Patient on Patient.patient_id = EcoliShigella_Measurement.patient_id where EcoliShigella_Measurement.taxonomy_id = " << taxId << " order by Patient.p_condition, EcoliShigella_Measurement.value desc;";
}
else
{
ss << "select \"Smarr\" as last_name, \"Larry\" as p_condition, value, unix_timestamp(timestamp) as timestamp from EcoliShigella_Measurement where patient_id = 1 and taxonomy_id = " << taxId << " order by timestamp;";
}
struct StrainData
{
char name[1024];
char group[1024];
float value;
time_t timestamp;
};
StrainData * sdata = NULL;
int dataSize = 0;
if(ComController::instance()->isMaster())
{
if(_dbm)
{
DBMQueryResult result;
_dbm->runQuery(ss.str(),result);
dataSize = result.numRows();
if(dataSize)
{
sdata = new struct StrainData[dataSize];
for(int i = 0; i < dataSize; ++i)
{
strncpy(sdata[i].name,result(i,"last_name").c_str(),1023);
strncpy(sdata[i].group,result(i,"p_condition").c_str(),1023);
sdata[i].value = atof(result(i,"value").c_str());
sdata[i].timestamp = atol(result(i,"timestamp").c_str());
}
}
}
/*if(_conn)
{
mysqlpp::Query strainQuery = _conn->query(ss.str().c_str());
mysqlpp::StoreQueryResult strainResult = strainQuery.store();
dataSize = strainResult.num_rows();
if(dataSize)
{
sdata = new struct StrainData[dataSize];
for(int i = 0; i < dataSize; ++i)
{
strncpy(sdata[i].name,strainResult[i]["last_name"].c_str(),1023);
strncpy(sdata[i].group,strainResult[i]["p_condition"].c_str(),1023);
sdata[i].value = atof(strainResult[i]["value"].c_str());
sdata[i].timestamp = atol(strainResult[i]["timestamp"].c_str());
}
}
}
else
{
std::cerr << "No Database connection." << std::endl;
}*/
ComController::instance()->sendSlaves(&dataSize,sizeof(int));
if(dataSize)
{
ComController::instance()->sendSlaves(sdata,dataSize*sizeof(struct StrainData));
}
}
else
{
ComController::instance()->readMaster(&dataSize,sizeof(int));
if(dataSize)
{
sdata = new struct StrainData[dataSize];
ComController::instance()->readMaster(sdata,dataSize*sizeof(struct StrainData));
}
}
std::map<std::string,std::string> condition2Group;
condition2Group["crohn's disease"] = "Crohns";
condition2Group["healthy"] = "Healthy";
condition2Group["Larry"] = "LS";
condition2Group["ulcerous colitis"] = "UC";
std::map<std::string, std::vector<std::pair<std::string, float> > > dataMap;
std::vector<std::string> orderVec;
for(int i = 0; i < dataSize; ++i)
{
char timestamp[512];
std::string name = sdata[i].name;
name += " - ";
strftime(timestamp,511,"%F",localtime(&sdata[i].timestamp));
name += timestamp;
if(!larryOnly)
{
if(sdata[i].value > 0.0)
{
dataMap[condition2Group[sdata[i].group]].push_back(std::pair<std::string,float>(name,sdata[i].value));
}
}
else
{
std::stringstream ss;
ss << "LS" << (i+1);
if(sdata[i].value > 0.0)
{
dataMap[ss.str()].push_back(std::pair<std::string,float>(name,sdata[i].value));
}
}
}
for(std::map<std::string, std::vector<std::pair<std::string, float> > >::iterator it = dataMap.begin(); it != dataMap.end(); ++it)
{
orderVec.push_back(it->first);
}
bool graphValid = false;
if(orderVec.size())
{
graphValid = _graph->setGraph(title, dataMap, orderVec, BGAT_LOG, "Relative Abundance", "", "condition / patient", osg::Vec4());
}
if(graphValid)
{
addChild(_graph->getRootNode());
std::vector<std::pair<std::string,int> > customOrder;
if(!larryOnly)
{
int totalEntries = 0;
for(std::map<std::string, std::vector<std::pair<std::string, float> > >::iterator it = dataMap.begin(); it != dataMap.end(); ++it)
{
totalEntries += it->second.size();
}
std::map<std::string,int> groupIndexMap;
while(customOrder.size() < totalEntries)
{
float maxVal = FLT_MIN;
std::string group;
for(std::map<std::string, std::vector<std::pair<std::string, float> > >::iterator it = dataMap.begin(); it != dataMap.end(); ++it)
{
if(groupIndexMap[it->first] >= it->second.size())
{
continue;
}
if(it->second[groupIndexMap[it->first]].second > maxVal)
{
group = it->first;
maxVal = it->second[groupIndexMap[it->first]].second;
}
}
customOrder.push_back(std::pair<std::string,int>(group,groupIndexMap[group]));
groupIndexMap[group]++;
}
}
else
{
for(std::map<std::string, std::vector<std::pair<std::string, float> > >::iterator it = dataMap.begin(); it != dataMap.end(); ++it)
{
for(int i = 0; i < it->second.size(); ++i)
{
customOrder.push_back(std::pair<std::string,int>(it->first,i));
}
}
std::map<std::string,osg::Vec4> larryColors;
float step = 0.75 / ((float)customOrder.size());
for(int i = 0; i < customOrder.size(); ++i)
{
std::stringstream ss;
ss << "LS" << (i+1);
larryColors[ss.str()] = osg::Vec4(1.0-((float)i)*step,0.0,0.0,1.0);
}
_graph->setColorMapping(osg::Vec4(0.0,0.0,0.0,1.0),larryColors);
}
_graph->setCustomOrder(customOrder);
_graph->setDisplayMode(BGDM_CUSTOM);
_graph->setShowLabels(false);
}
if(sdata)
{
delete[] sdata;
}
return graphValid;
}