int
makeDirs(const char *path) {
char dir[MAX_NAME_LEN];
char file[MAX_NAME_LEN];
int status;
rodsLog (LOG_DEBUG, "makeDirs: %s", path);
if (path == NULL) {
rodsLog (LOG_ERROR, "makeDirs: input path is NULL");
return (SYS_INTERNAL_NULL_INPUT_ERR);
}
splitPathByKey ((char *) path, dir, file, '/');
if(isDirectory(dir) < 0) {
// parent not exist
// call recursively
status = makeDirs(dir);
if(status < 0) {
return (status);
}
}
// parent now exist
status = mkdir(path, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
if(status == -EEXIST) {
return (0);
}
return status;
}
static int
_preparePreloadCacheDir(const char *path) {
int status;
status = makeDirs(path);
return status;
}
bool AmeJobMan::makeDirs(wxFileName f){
wxFileName p = f.GetPath();
if(f.DirExists())
return true;
if(!p.DirExists() && !makeDirs(p))
return false;
return f.Mkdir();
}
static int
_prepareBufferDir(const char *path) {
int status;
status = makeDirs(path);
return status;
}
void makeDirOnlyOnce(char *dir, struct hash *hash)
/* Check if dir is already in hash. If so we're done. If not make dir and add it to hash. */
{
if (!hashLookup(hash, dir))
{
verbose(2, "make dir %s\n", dir);
hashAdd(hash, dir, NULL);
makeDirs(dir);
}
}
int
prepareDir(const char *path) {
int status;
char dir[MAX_NAME_LEN], file[MAX_NAME_LEN];
if (path == NULL) {
rodsLog (LOG_ERROR, "prepareDir: input path is NULL");
return (SYS_INTERNAL_NULL_INPUT_ERR);
}
splitPathByKey ((char *) path, dir, file, '/');
// make dirs
status = makeDirs(dir);
return status;
}
void CreateDatacards(float XMIN, float XMAX, int CAT_MIN,int CAT_MAX,int BRN_ORDER_NOM, int BRN_ORDER_VBF, TString TR, TString OUTPATH, TString CATVETO="", int MASS, float XMAXDIFF=0.)
{
TString PATH(TString::Format("%s/output/",OUTPATH.Data()).Data());
const int NCAT = 7;
const int NF = 6;
const int NMASS = 5;
//---- uncertainties -------------------------------------
const float UNC_BR[NMASS] = {1.024,1.028,1.032,1.037,1.043};
const float UNC_UEPS_VBF[NCAT] = {1.04,1.02,0.97,0.93,1.02,1.03,1.04};
const float UNC_JES_VBF[NCAT] = {1.06,1.08,1.09,1.10,1.06,1.08,1.10};
const float UNC_JER_VBF[NCAT] = {0.97,0.96,0.97,0.98,0.99,0.98,0.99};
const float UNC_TRIG_VBF[NCAT] = {1.03,1.04,1.05,1.06,1.01,1.01,1.02};
const float UNC_CSV_VBF[NCAT] = {1.03,0.99,0.97,0.94,1.01,0.94,0.91};
const float UNC_QGL_VBF[NCAT] = {1.03,1.01,1.00,0.98,1.03,1.01,0.98};
const float UNC_SCALE_VBF[NCAT] = {1.00,1.00,1.01,1.02,1.03,1.03,1.05};
const float UNC_PDF_VBF[NCAT] = {1.02,1.02,1.02,1.02,1.03,1.03,1.03};
const float UNC_PDFGlobal_VBF[NMASS] = {1.028,1.028,1.028,1.027,1.027};
const float UNC_SCALEGlobal_VBF[NMASS] = {1.002,1.002,1.002,1.002,1.002};
const float UNC_UEPS_GF[NCAT] = {1.25,1.10,0.80,0.90,0.65,1.65,1.45};
const float UNC_JES_GF[NCAT] = {1.08,1.10,1.12,1.12,1.04,1.09,1.10};
const float UNC_JER_GF[NCAT] = {0.99,0.99,0.95,0.96,0.91,0.99,0.95};
const float UNC_TRIG_GF[NCAT] = {1.05,1.05,1.10,1.15,1.09,1.09,1.19};
const float UNC_CSV_GF[NCAT] = {0.99,0.97,0.93,0.93,0.93,0.97,0.90};
const float UNC_QGL_GF[NCAT] = {1.03,1.01,1.00,0.98,1.03,1.01,0.98};
const float UNC_SCALE_GF[NCAT] = {1.00,1.00,1.01,1.02,1.03,1.03,1.05};
const float UNC_PDF_GF[NCAT] = {1.04,1.04,1.04,1.04,1.05,1.04,1.04};
const float UNC_PDFGlobal_GF[NMASS] = {1.076,1.075,1.075,1.075,1.074};
const float UNC_SCALEGlobal_GF[NMASS] = {1.081,1.079,1.078,1.077,1.077};
vector<int> vCATVETO = tokenize(CATVETO);
TString tCATVETO = tag(CATVETO);
bool FreeTF=false, TF=false;
if (TR!="" && TR!="BRN") TF=true;
if (TF && (TR(0,5)!="Fixed"&&TR!="EXPO")) FreeTF=true;
TString sTRF="";
if (TR(0,5)=="Fixed") sTRF = TR(5,4);
else sTRF = TR;
if (XMAXDIFF==0) TFile *fData = TFile::Open(PATH+"data_shapes_workspace_"+TString::Format("BRN%dp%d_B%.f-%.f",BRN_ORDER_NOM,BRN_ORDER_VBF,XMIN,XMAX)+"_Fit"+TR+".root");
else TFile *fData = TFile::Open(PATH+"data_shapes_workspace_"+TString::Format("BRN%dp%d_B%.f-%.f%.f",BRN_ORDER_NOM,BRN_ORDER_VBF,XMIN,XMAX,XMAX+XMAXDIFF)+"_Fit"+TR+".root");
if (XMAXDIFF==0) TFile *fSig = TFile::Open(PATH+"signal_shapes_workspace_"+TString::Format("B%.f-%.f.root",XMIN,XMAX));
else TFile *fSig = TFile::Open(PATH+"signal_shapes_workspace_"+TString::Format("B%.f-%.f%.f.root",XMIN,XMAX,XMAX+XMAXDIFF));
RooWorkspace *wData = (RooWorkspace*)fData->Get("w");
RooWorkspace *wSig = (RooWorkspace*)fSig->Get("w");
TString nameData = fData->GetName();
TString nameDataShort = nameData(nameData.Last('/')+1,nameData.Length());
TString nameSig = fSig->GetName();
TString nameSigShort = nameSig(nameSig.Last('/')+1,nameSig.Length());
char name[1000];
int H_MASS[5] = {115,120,125,130,135};
float nData[NCAT],nZ[NCAT],nTop[NCAT],nSigVBF[5][NCAT],nSigGF[5][NCAT];
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
sprintf(name,"yield_data_CAT%d",i);
nData[i] = float((RooRealVar*)wData->var(name)->getValV());
sprintf(name,"yield_ZJets_CAT%d",i);
nZ[i] = ((RooRealVar*)wData->var(name))->getValV();
sprintf(name,"yield_Top_CAT%d",i);
nTop[i] = ((RooRealVar*)wData->var(name))->getValV();
for(int m=0;m<5;m++) {
if (H_MASS[m]!=MASS) continue;
sprintf(name,"yield_signalVBF_mass%d_CAT%d",H_MASS[m],i);
nSigVBF[m][i] = ((RooRealVar*)wSig->var(name))->getValV();
sprintf(name,"yield_signalGF_mass%d_CAT%d",H_MASS[m],i);
nSigGF[m][i] = ((RooRealVar*)wSig->var(name))->getValV();
}
}
makeDirs(OUTPATH);
makeDirs(OUTPATH+"/output/");
makeDirs(OUTPATH+"/output/datacards");
for(int m=0;m<5;m++) {
if (H_MASS[m]!=MASS) continue;
cout << m << endl;
ofstream datacard;
if (XMAXDIFF==0) sprintf(name,"%s/output/datacards/datacard_m%d_BRN%dp%d_B%.f-%.f_CAT%d-CAT%d%s_Fit%s.txt",OUTPATH.Data(),H_MASS[m],BRN_ORDER_NOM,BRN_ORDER_VBF,XMIN,XMAX,CAT_MIN,CAT_MAX,tCATVETO.Data(),TR.Data());
else sprintf(name,"%s/output/datacards/datacard_m%d_BRN%dp%d_B%.f-%.f%.f_CAT%d-CAT%d%s_Fit%s.txt",OUTPATH.Data(),H_MASS[m],BRN_ORDER_NOM,BRN_ORDER_VBF,XMIN,XMAX,XMAX+XMAXDIFF,CAT_MIN,CAT_MAX,tCATVETO.Data(),TR.Data());
cout<<"======================================="<<endl;
cout<<"Creating datacard: "<<name<<endl;
cout<<"======================================="<<endl;
datacard.open(name);
datacard.setf(ios::right);
datacard<<"imax "<<CAT_MAX-CAT_MIN+1-vCATVETO.size()<<"\n";
datacard<<"jmax *"<<"\n";
datacard<<"kmax *"<<"\n";
datacard<<"----------------"<<"\n";
datacard<<"shapes data_obs * "<<nameDataShort<<" w:data_hist_$CHANNEL"<<"\n";
datacard<<"shapes qcd * "<<nameDataShort<<" w:qcd_model_Fit"<<TR.Data()<<"_$CHANNEL"<<"\n";
datacard<<"shapes top * "<<nameDataShort<<" w:Top_model_$CHANNEL"<<"\n";
datacard<<"shapes zjets * "<<nameDataShort<<" w:Z_model_$CHANNEL"<<"\n";
datacard<<"shapes qqH * "<<nameSigShort<<" w:signal_model_m"<<H_MASS[m]<<"_$CHANNEL \n";
datacard<<"shapes ggH * "<<nameSigShort<<" w:signal_model_m"<<H_MASS[m]<<"_$CHANNEL \n";
datacard<<"----------------"<<"\n";
datacard<<"bin ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
sprintf(name,"CAT%d ",i);
datacard<<name;
}
datacard<<"\n";
datacard<<"observation ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<"-1 ";
}
datacard<<"\n";
datacard<<"----------------"<<"\n";
datacard<<"bin ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
sprintf(name,"CAT%d CAT%d CAT%d CAT%d CAT%d ",i,i,i,i,i);
datacard<<name;
}
datacard<<"\n";
datacard<<"process ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<"qqH ggH qcd top zjets ";
}
datacard<<"\n";
datacard<<"process ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<"0 -1 1 1 1 ";
}
datacard<<"\n";
datacard<<"rate ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
cout<<"cat#"<<i<<setw(8)<<nData[i]<<setw(8)<<nSigVBF[m][i]<<setw(8)<<nSigGF[m][i]<<setw(8)<<nTop[i]<<setw(8)<<nZ[i]<<setw(8)<<", S/B = "<<(nSigVBF[m][i]+nSigGF[m][i])/nData[i]<<endl;
datacard<<nSigVBF[m][i]<<" "<<nSigGF[m][i]<<" "<<nData[i]<<" "<<nTop[i]<<" "<<nZ[i]<<" ";
}
datacard<<"\n";
datacard<<"----------------"<<"\n";
datacard<<"BR lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_BR[m]<<setw(NF)<<UNC_BR[m]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"QCDscale_qqh lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_SCALEGlobal_VBF[m]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"QCDscale_ggh lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"-"<<setw(NF)<<UNC_SCALEGlobal_GF[m]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"pdf_qqbar lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_PDFGlobal_VBF[m]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"pdf_gg lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"-"<<setw(NF)<<UNC_PDFGlobal_GF[m]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"lumi lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"1.026"<<setw(NF)<<"1.026"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_scale_j_ACCEPT lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_JES_VBF[i]<<setw(NF)<<UNC_JES_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"pdf_ACCEPT lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"1.05"<<setw(NF)<<"1.05"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_res_j_ACCEPT lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_JER_VBF[i]<<setw(NF)<<UNC_JER_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_qqH_hbb_trigger lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_TRIG_VBF[i]<<setw(NF)<<UNC_TRIG_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_qqH_hbb_btag lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_CSV_VBF[i]<<setw(NF)<<UNC_CSV_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_qqH_hbb_qgl lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_QGL_VBF[i]<<setw(NF)<<UNC_QGL_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"UEPS lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_UEPS_VBF[i]<<setw(NF)<<UNC_UEPS_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_qqH_hbb_QCDscale lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_SCALE_VBF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_ggH_hbb_QCDscale lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"-"<<setw(NF)<<UNC_SCALE_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_qqH_hbb_pdf lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<UNC_PDF_VBF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
datacard<<"CMS_ggH_hbb_pdf lnN ";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
datacard<<setw(NF)<<"-"<<setw(NF)<<UNC_PDF_GF[i]<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
datacard<<"\n";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
sprintf(name,"CMS_vbfbb_qcd_norm_CAT%d lnU ",i);
datacard<<name<<setw(NF);
for(int j=CAT_MIN;j<=CAT_MAX;j++) {
if (veto(vCATVETO, j)) continue;
if (j == i) {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<1.5<<setw(NF)<<"-"<<setw(NF)<<"-";
}
else {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
}
datacard<<"\n";
}
datacard<<"\n";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
sprintf(name,"CMS_vbfbb_zjets_norm_CAT%d lnN ",i);
datacard<<name<<setw(NF);
for(int j=CAT_MIN;j<=CAT_MAX;j++) {
if (veto(vCATVETO, j)) continue;
if (j == i) {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"1.3";
}
else {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
}
datacard<<"\n";
}
datacard<<"\n";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
sprintf(name,"CMS_vbfbb_top_norm_CAT%d lnN ",i);
datacard<<name<<setw(NF);
for(int j=CAT_MIN;j<=CAT_MAX;j++) {
if (veto(vCATVETO, j)) continue;
if (j == i) {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"1.3"<<setw(NF)<<"-";
}
else {
datacard<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-"<<setw(NF)<<"-";
}
}
datacard<<"\n";
}
datacard<<"\n";
datacard<<"#--- signal and Z shape parameters ------ \n";
datacard<<"\n";
datacard<<"CMS_vbfbb_scale_mbb_selNOM param 1.0 0.02"<<"\n";
datacard<<"CMS_vbfbb_scale_mbb_selVBF param 1.0 0.02"<<"\n";
datacard<<"CMS_vbfbb_res_mbb_selNOM param 1.0 0.1"<<"\n";
datacard<<"CMS_vbfbb_res_mbb_selVBF param 1.0 0.1"<<"\n";
for(int i=CAT_MIN;i<=CAT_MAX;i++) {
if (veto(vCATVETO, i)) continue;
//cout << "CAT" << i << endl;
/*
sprintf(name,"CMS_vbfbb_scale_mbb_CAT%d",i);
datacard<<name<<" param 1.0 0.02"<<"\n";
sprintf(name,"CMS_vbfbb_res_mbb_CAT%d",i);
datacard<<name<<" param 1.0 0.1"<<"\n";
*/
sprintf(name,"mean_m%d_CAT%d",H_MASS[m],i);
RooRealVar *vmass = (RooRealVar*)wSig->var(name);
double mass = vmass->getValV();
double emass = vmass->getError();
datacard<<name<<" param "<<mass<<" "<<emass<<"\n";
sprintf(name,"sigma_m%d_CAT%d",H_MASS[m],i);
RooRealVar *vsigma = (RooRealVar*)wSig->var(name);
double sigma = vsigma->getValV();
double esigma = vsigma->getError();
datacard<<name<<" param "<<sigma<<" "<<esigma<<"\n";
sprintf(name,"Top_mean_CAT%d",i);
RooRealVar *Tvmass = (RooRealVar*)wData->var(name);
double Tmass = Tvmass->getValV();
double Temass = 0.01*Tmass; //Tvmass->getError();
datacard<<name<<" param "<<Tmass<<" "<<Temass<<"\n";
sprintf(name,"Top_sigma_CAT%d",i);
RooRealVar *Tvsigma = (RooRealVar*)wData->var(name);
double Tsigma = Tvsigma->getValV();
double Tesigma = 0.05*Tsigma;//Tvsigma->getError();
datacard<<name<<" param "<<Tsigma<<" "<<Tesigma<<"\n";
sprintf(name,"Z_mean_CAT%d",i);
RooRealVar *Zvmass = (RooRealVar*)wData->var(name);
double Zmass = Zvmass->getValV();
double Zemass = Zvmass->getError();
datacard<<name<<" param "<<Zmass<<" "<<Zemass<<"\n";
sprintf(name,"Z_sigma_CAT%d",i);
RooRealVar *Zvsigma = (RooRealVar*)wData->var(name);
double Zsigma = Zvsigma->getValV();
double Zesigma = Zvsigma->getError();
datacard<<name<<" param "<<Zsigma<<" "<<Zesigma<<"\n";
for(int j=5; j>=0; j--){
if (i>0 && i < 4 && TF && !FreeTF) {
sprintf(name,"trans_%s_p%d_CAT%d",sTRF.Data(),j,i);
if (wData->var(name)) {
cout << name << endl;
datacard<<name<<" param "<<((RooRealVar*)wData->var(name))->getVal()<<" "<<((RooRealVar*)wData->var(name))->getError()<<"\n";
}
}
if (i > 4 && TF && !FreeTF) {
sprintf(name,"trans_%s_p%d_CAT%d",sTRF.Data(),j,i);
if (wData->var(name)) {
cout << name << endl;
datacard<<name<<" param "<<((RooRealVar*)wData->var(name))->getVal()<<" "<<((RooRealVar*)wData->var(name))->getError()<<"\n";
}
}
}
}
datacard.close();
}
fData->Close();
fSig->Close();
}
bool AmeJobMan::updatePath(AmeJob *job, wxString sf1){//only want to use renameTo if same partition
job->m_fn = wxEmptyString;
wxString sf0 = job->getAbsolutePath();
if(sf1==wxEmptyString || sf0==sf1) return true;
//RULES ENABLED?
// if(AmeRules.mImod==AmeRules.M_NOREN) return true;
//POPT("SRC FILE HEALTH");
//SOURCE FILE HEALTHY?
if(!wxFile::Exists(sf0)){
job->setError(wxT("File does not exist."));
//A.gui.println(sf0+" cannot be moved. File not found.");
return false;
}
//POPT("DST FILE HEALTH");
//POPT("updatePath3");
//DESTINATION FILE HEALTHY?
if(wxFile::Exists(sf1)){
wxFile f(sf1);
if(job->m_size==f.Length()){ //could be the same
job->setNewFilePath(sf1);
//A.gui.println(sf0+" will be moved to "+sf1+" later.");
return true;
}
job->setError(wxT("File cannot be moved. Destination file already exists!"));
//A.gui.println(sf0+" cannot be moved to "+sf1+": Destination file already exists!");
return false;
}
//POPT("SRC FOLDER HEALTH");
//DESTINATION FOLDER OK?
wxFileName fn(sf1);
wxFileName parent = fn.GetPath();
if(!parent.DirExists() && !makeDirs(parent)){
job->setError(wxT("Folder")+parent.GetFullPath()+wxT(" cannot be created!"));
//A.gui.println("Folder"+parent+" cannot be created!");
return false;
}
wxGetApp().m_jl->addPath(sf1);
//job.mIdid = -1;
//TRY TO MOVE: WINDOWS
//POPT("TRY MOVE");
wxString p0 = sf0.Lower();
wxString p1 = sf1.Lower();
wxString sok = wxT("Cleanup after successful rename operation.");
if(p0.at(1)==':'||p1.at(1)==':'){ //windows (not network)
if(p0.at(0)==p1.at(0)){
//POPT("NOW MOVE");
if(job->rename(sf1)){
//moveSub(job.m_fc, f);
//A.deleteFile(job.m_fc.getParentFile(), sok);
//AmeJobMan::setJobFile(job, f);
//A.gui.println("Renamed "+sf0+" to "+sf1);
POSTM(MSG_LOG, SP2("Renamed %s to %s", sf0, sf1));
//AmeJobMan::removeFile(sf0);
return true;
}
//A.gui.println(Hyper.error("Renaming failed!")+" ("+sf0+" to "+sf1+")");
return false;
}
job->setNewFilePath(sf1);
//A.gui.println(sf0+" will be moved to "+sf1+" later.");
return true;
}
POPT("NIX");
//TRY TO MOVE: *NIX
if(job->rename(sf1)){ //linux can't rename over partitions
//A.deleteFile(job.m_fc.getParentFile(), sok);
//AmeJobMan.setJobFile(job, f);
//A.gui.println("Renamed"+sf0+" to "+sf1);
return true;
}
job->setNewFilePath(sf0);
//A.gui.println(sf0+" will be moved to "+sf1+" later.");
return true;
//THE END
}
bool PodSync::performSync( const char *pSrc, const char *pDst )
{
DirectoryEnum srcEnumerator;
DirectoryEnum dstEnumerator;
FileInfo srcInfo;
FileInfo dstInfo;
FileInfo *pSrcInfo = &srcInfo;
bool result = false;
// Check that source is valid
if( false == srcInfo.getInfo( pSrc ))
{
rWarning( "Could not get info: %s", pSrc );
return false;
}
// Check that destination is valid
if( false == dstInfo.getInfo( pDst ))
{
rWarning( "Could not get info: %s", pDst );
if( false == makeDirs( pDst ))
{
rError( "Could not create destination: %s", pDst );
return false;
}
else
{
if( false == dstInfo.getInfo( pDst ))
{
rError( "Could not get info: %s", pDst );
return false;
}
}
}
// Check that destination is a directory
if( false == dstInfo.isDir() )
{
rError( "%s is not a directory", pDst );
return false;
}
rInfo( "Source: %s", srcInfo.getName() );
if( true == srcInfo.isDir() )
{
rInfo( "Enumerating %s", srcInfo.getName() );
// Skip . and ..
srcEnumerator.findFirst( pSrc );
srcEnumerator.findNext();
pSrcInfo = srcEnumerator.findNext();
while( 0 != pSrcInfo )
{
result = processOneItem( pSrcInfo, &dstInfo );
if( false == result )
{
rError( "Sync %s failed", pSrcInfo->getName() );
}
pSrcInfo = srcEnumerator.findNext();
}
}
else
{
result = processOneItem( pSrcInfo, &dstInfo );
}
return result;
}
static void generateImgFiles(struct hgdpGeo *geo, char finalEpsFile[PATH_LEN],
char finalPdfFile[PATH_LEN], char finalPngFile[PATH_LEN])
/* Using the frequencies given in geo and the population latitude and longitude
* given above, plot allele frequency pie charts for each population on a world map.
* Work in a temporary trash dir and then move result files to the given paths. */
{
// The Generic Mapping Tools commands must have a writeable ./ and $HOME.
// Use trashDirFile as a directory name, cd to that and work there.
char cwd[PATH_LEN];
if (getcwd(cwd, sizeof(cwd)) == NULL)
errAbort("PATH_LEN (%d) is too short.", PATH_LEN);
struct tempName dirTn;
trashDirFile(&dirTn, "hgc", "hgdpGeo", "");
makeDirs(dirTn.forCgi);
mustChdir(dirTn.forCgi);
char *realHome = getenv("HOME");
setenv("HOME", ".", TRUE);
// Make trash files with coordinate specs for pie charts and full circles:
char rootName[FILENAME_LEN];
splitPath(dirTn.forCgi, NULL, rootName, NULL);
char pieFile[FILENAME_LEN], circleFile[FILENAME_LEN];
safef(pieFile, sizeof(pieFile), "%s_pie.txt", rootName);
safef(circleFile, sizeof(circleFile), "%s_circle.txt", rootName);
FILE *fPie = mustOpen(pieFile, "w");
FILE *fCir = mustOpen(circleFile, "w");
int i;
for (i = 0; i < HGDPGEO_POP_COUNT; i++)
{
FILE *f = (geo->popFreqs[i] == 1.0) ? fCir : fPie;
fprintf(f, "%.4f %.4f 0.65 0 %.4f\n",
pops[i].latitude, pops[i].longitude, geo->popFreqs[i]*360);
}
fclose(fPie);
fclose(fCir);
// Build up an EPS image: copy a baseline EPS (map background), add SNP and allele labels,
// and use ps2xy commands to allele frequency pie charts.
char epsFile[FILENAME_LEN];
safef(epsFile, sizeof(epsFile), "%s.eps", rootName);
char mapBgEps[PATH_LEN];
safef(mapBgEps, sizeof(mapBgEps), "%s/hgcData/hgdpGeoMap.eps", cwd);
copyFile(mapBgEps, epsFile);
FILE *fEps = mustOpen(epsFile, "a");
fprintf(fEps, hgdpGeoLabelFormat, geo->name, geo->name,
geo->ancestralAllele, geo->ancestralAllele, geo->derivedAllele, geo->derivedAllele);
fclose(fEps);
//- run psxy on circle/pie spec trash files for AfrEurAsia and America
char *psxy = cfgOption("hgc.psxyPath");
if (isEmpty(psxy))
errAbort("How did this get called? hg.conf doesn't have hgc.psxyPath.");
runCommandAppend(psxyOrangeAeaCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyPieAeaCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyBlueAeaCmd, psxy, circleFile, epsFile);
runCommandAppend(psxyOrangeAmCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyPieAmCmd, psxy, pieFile, epsFile);
runCommandAppend(psxyBlueAmCmd, psxy, circleFile, epsFile);
// Make PDF and PNG:
struct pipeline *pl;
char pdfFile[FILENAME_LEN], pngFile[FILENAME_LEN];
safef(pdfFile, sizeof(pdfFile), "%s.pdf", rootName);
safef(pngFile, sizeof(pngFile), "%s.png", rootName);
char *ps2pdfCmd[] = {"ps2pdf", epsFile, pdfFile, NULL};
char **cmdsPdf[] = {ps2pdfCmd, NULL};
pl = pipelineOpen(cmdsPdf, pipelineWrite, "/dev/null", NULL);
pipelineClose(&pl);
char *ps2raster = cfgOption("hgc.ps2rasterPath");
char *ghostscript = cfgOption("hgc.ghostscriptPath");
char gsOpt[PATH_LEN];
safef(gsOpt, sizeof(gsOpt), "-G%s", ghostscript);
char *ps2RasterPngCmd[] = {ps2raster, gsOpt, "-P", "-A", "-Tg", "-E150", epsFile, NULL};
char **cmdsPng[] = {ps2RasterPngCmd, NULL};
pl = pipelineOpen(cmdsPng, pipelineRead, "/dev/null", NULL);
pipelineClose(&pl);
// Back to our usual working directory and $HOME:
if (realHome == NULL)
unsetenv("HOME");
else
setenv("HOME", realHome, TRUE);
mustChdir(cwd);
// Move the result files into place:
char tmpPath[PATH_LEN];
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, epsFile);
mustRename(tmpPath, finalEpsFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pdfFile);
mustRename(tmpPath, finalPdfFile);
safef(tmpPath, sizeof(tmpPath), "%s/%s", dirTn.forCgi, pngFile);
mustRename(tmpPath, finalPngFile);
// Clean up the temporary working directory (trash cleaner script doesn't
// remove empty dirs:
removeDir(dirTn.forCgi);
}
