def export_dataStage02IsotopomerFluxMap_js(self,analysis_id_I,simulation_id_I = None,data_dir_I="tmp"):
'''Export flux map for viewing'''
MFAmethods = MFA_methods();
# Get the simulation information
if simulation_id_I:
simulation_id = simulation_id_I;
else:
simulation_ids = [];
simulation_ids = self.get_simulationID_analysisID_dataStage02IsotopomerAnalysis(analysis_id_I);
if not simulation_ids:
print('No simulation found for the analysis_id ' + analysis_id_I);
elif len(simulation_ids)>1:
print('More than 1 simulation found for the analysis_id ' + analysis_id_I);
simulation_id_I = simulation_ids[0];
else:
simulation_id_I = simulation_ids[0];
# Get the flux information
flux = [];
flux_tmp = [];
#flux = self.get_rowsEscherFluxList_simulationID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id_I);
flux_tmp = self.get_rows_simulationID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id_I);
for i,row in enumerate(flux_tmp):
observable = MFAmethods.check_observableExchangeFlux(row['flux'],row['flux_lb'],row['flux_ub']);
if not row['flux'] is None and row['flux']!=0.0 and numpy.abs(row['flux']) < 10.0:
flux_tmp[i]['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
flux_tmp[i]['flux_units'] = self.remove_jsRegularExpressions(row['flux_units']);
if observable: flux_tmp[i]['observable'] = 'Yes';
else: flux_tmp[i]['observable'] = 'No';
flux.append(flux_tmp[i]);
elif row['flux']==0.0 and numpy.abs(numpy.mean([row['flux_lb'],row['flux_ub']]))<10.0:
flux_tmp[i]['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
flux_tmp[i]['flux_units'] = self.remove_jsRegularExpressions(row['flux_units']);
#flux_tmp[i]['flux'] = numpy.mean([row['flux_lb'],row['flux_ub']]);
if observable: flux_tmp[i]['observable'] = 'Yes';
else: flux_tmp[i]['observable'] = 'No';
flux.append(flux_tmp[i]);
# Get the map information
map = [];
map = self.get_rows_modelID_modelsEschermaps('iJO1366');
# dump chart parameters to a js files
data1_keys = ['simulation_id','rxn_id','simulation_dateAndTime','flux_units','observable'
];
data1_nestkeys = ['simulation_id'];
data1_keymap = {'values':'flux','key':'rxn_id'};
data2_keys = ['model_id','eschermap_id'
];
data2_nestkeys = ['model_id'];
data2_keymap = {'data':'eschermap_json'};
# make the data object
dataobject_O = [{"data":flux,"datakeys":data1_keys,"datanestkeys":data1_nestkeys},
{"data":map,"datakeys":data2_keys,"datanestkeys":data2_nestkeys}];
# make the tile parameter objects
formtileparameters1_O = {'tileheader':'Filter menu','tiletype':'html','tileid':"filtermenu1",'rowid':"row1",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-6"};
formparameters1_O = {'htmlid':'filtermenuform1',"htmltype":'form_01',"formsubmitbuttonidtext":{'id':'submit1','text':'submit'},"formresetbuttonidtext":{'id':'reset1','text':'reset'},"formupdatebuttonidtext":{'id':'update1','text':'update'}};
formtileparameters1_O.update(formparameters1_O);
formtileparameters2_O = {'tileheader':'Filter menu','tiletype':'html','tileid':"filtermenu2",'rowid':"row1",'colid':"col2",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-6"};
formparameters2_O = {'htmlid':'filtermenuform2',"htmltype":'form_01',"formsubmitbuttonidtext":{'id':'submit2','text':'submit'},"formresetbuttonidtext":{'id':'reset2','text':'reset'},"formupdatebuttonidtext":{'id':'update2','text':'update'}};
formtileparameters2_O.update(formparameters2_O);
htmlparameters_O = {"htmlkeymap":[data1_keymap,data2_keymap],
'htmltype':'escher_01','htmlid':'html1',
'escherdataindex':{"reactiondata":0,"mapdata":1},
'escherembeddedcss':None,
'escheroptions':None};
htmltileparameters_O = {'tileheader':'Escher map','tiletype':'html','tileid':"tile1",'rowid':"row2",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-12"};
htmltileparameters_O.update(htmlparameters_O);
tableparameters_O = {"tabletype":'responsivetable_01',
'tableid':'table1',
"tablefilters":None,
"tableclass":"table table-condensed table-hover",
'tableformtileid':'filtermenu1','tableresetbuttonid':'reset1','tablesubmitbuttonid':'submit1'};
tabletileparameters_O = {'tileheader':'Flux precision','tiletype':'table','tileid':"tile2",'rowid':"row3",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-12"};
tabletileparameters_O.update(tableparameters_O);
parametersobject_O = [formtileparameters1_O,formtileparameters2_O,htmltileparameters_O,tabletileparameters_O];
tile2datamap_O = {"filtermenu1":[0],"filtermenu2":[1],"tile1":[0,1],"tile2":[0]};
filtermenuobject_O = [{"filtermenuid":"filtermenu1","filtermenuhtmlid":"filtermenuform1",
"filtermenusubmitbuttonid":"submit1","filtermenuresetbuttonid":"reset1",
"filtermenuupdatebuttonid":"update1"},{"filtermenuid":"filtermenu2","filtermenuhtmlid":"filtermenuform2",
"filtermenusubmitbuttonid":"submit2","filtermenuresetbuttonid":"reset2",
"filtermenuupdatebuttonid":"update2"}];
# dump the data to a json file
ddtutilities = ddt_container(parameters_I = parametersobject_O,data_I = dataobject_O,tile2datamap_I = tile2datamap_O,filtermenu_I = filtermenuobject_O);
if data_dir_I=='tmp':
filename_str = self.settings['visualization_data'] + '/tmp/ddt_data.js'
elif data_dir_I=='data_json':
data_json_O = ddtutilities.get_allObjects_js();
return data_json_O;
with open(filename_str,'w') as file:
file.write(ddtutilities.get_allObjects());
def export_dataStage02IsotopomerFittedExchangeFluxes_js(self,analysis_id_I = None,
simulation_ids_I = [],
bullet_chart_I = True,
data_dir_I="tmp"):
'''Plot the flux precision for a given set of simulations and a given set of reactions
Input:
analysis_id_I = string, analysis id
Optional Input:
simulation_ids_I = [] of strings, simulation_ids in a specific order
bullet_chart_I = True: show the flux estimation +/- StDev
False: show the 95% confidence invervals and flux estimation +/- StDev
'''
MFAmethods = MFA_methods();
#Input:
# analysis_id_I or
# simulation_ids_I
if simulation_ids_I:
simulation_ids = simulation_ids_I;
else:
simulation_ids = [];
simulation_ids = self.get_simulationID_analysisID_dataStage02IsotopomerAnalysis(analysis_id_I);
data_O =[];
for simulation_id in simulation_ids:
# get the flux information for each simulation
flux_data = [];
flux_data = self.get_rows_simulationID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id);
#min_flux,max_flux = None,None;
#min_flux,max_flux = self.get_fluxMinAndMax_simulationID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id)
for i,row in enumerate(flux_data):
observable = MFAmethods.check_observableExchangeFlux(row['flux'],row['flux_lb'],row['flux_ub']);
if not row['flux'] is None:
row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
#row['flux_units'] = row['flux_units'].replace('*','x');
row['flux_lb_stdev'] = row['flux'] - row['flux_stdev'];
row['flux_ub_stdev'] = row['flux'] + row['flux_stdev'];
row['flux_mean'] = numpy.mean([row['flux_lb'],row['flux_ub']]);
if observable: row['observable'] = 'Yes';
else: row['observable'] = 'No';
data_O.append(row);
#if not row['flux'] is None and observable:
# row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
# row['flux_units'] = row['flux_units'].replace('*','x');
# row['flux_lb_stdev'] = row['flux'] - row['flux_stdev'];
# row['flux_ub_stdev'] = row['flux'] + row['flux_stdev'];
# row['flux_mean'] = numpy.mean([row['flux_lb'],row['flux_ub']]);
# data_O.append(row);
#elif not row['flux'] is None and not observable:
# row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
# row['flux_units'] = row['flux_units'].replace('*','x');
# row['flux_lb'] = None;
# row['flux_ub'] = None;
# row['flux_mean'] = None;
# data_O.append(row);
#elif row['flux']==0.0 and observable:
# row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
# row['flux_units'] = row['flux_units'].replace('*','x');
# row['flux_lb_stdev'] = 0.0;
# row['flux_ub_stdev'] = 0.0;
# row['flux_mean'] = numpy.mean([row['flux_lb'],row['flux_ub']]);
# data_O.append(row);
#elif row['flux']==0.0 and not observable:
# row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
# row['flux_units'] = row['flux_units'].replace('*','x');
# row['flux_lb'] = None;
# row['flux_ub'] = None;
# #row['flux_mean'] = None;
# row['flux_lb_stdev'] = None;
# row['flux_ub_stdev'] = None;
# row['flux']=None;
# data_O.append(row);
elif row['flux']==0.0:
row['simulation_dateAndTime'] = self.convert_datetime2string(row['simulation_dateAndTime']);
row['flux_units'] = row['flux_units'].replace('*','x');
row['flux_lb_stdev'] = 0.0;
row['flux_ub_stdev'] = 0.0;
row['flux_mean'] = numpy.mean([row['flux_lb'],row['flux_ub']]);
if observable: row['observable'] = 'Yes';
else: row['observable'] = 'No';
data_O.append(row);
# dump chart parameters to a js files
data1_keys = ['simulation_id','rxn_id','simulation_dateAndTime','flux_units','observable'
];
data1_nestkeys = ['rxn_id'];
if bullet_chart_I:
data1_keymap = {'xdata':'rxn_id',
'ydatamean':'flux',
'ydatalb':'flux_lb_stdev',
'ydataub':'flux_ub_stdev',
'serieslabel':'simulation_id',
'featureslabel':'rxn_id'};
else:
data1_keymap = {'xdata':'rxn_id',
#'ydata':'flux',
'ydatamean':'flux_mean',
'ydatalb':'flux_lb',
'ydataub':'flux_ub',
#'ydatamin':'min',
#'ydatamax':'max',
'ydataiq1':'flux_lb_stdev',
'ydataiq3':'flux_ub_stdev',
'ydatamedian':'flux',
'serieslabel':'simulation_id',
'featureslabel':'rxn_id'};
# make the data object
dataobject_O = [{"data":data_O,"datakeys":data1_keys,"datanestkeys":data1_nestkeys}];
# make the tile parameter objects
formtileparameters_O = {'tileheader':'Filter menu','tiletype':'html','tileid':"filtermenu1",'rowid':"row1",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-12"};
formparameters_O = {'htmlid':'filtermenuform1',"htmltype":'form_01',"formsubmitbuttonidtext":{'id':'submit1','text':'submit'},"formresetbuttonidtext":{'id':'reset1','text':'reset'},"formupdatebuttonidtext":{'id':'update1','text':'update'}};
formtileparameters_O.update(formparameters_O);
svgparameters_O = {"svgtype":'boxandwhiskersplot2d_02',"svgkeymap":[data1_keymap,data1_keymap],
'svgid':'svg1',
"svgmargin":{ 'top': 50, 'right': 350, 'bottom': 50, 'left': 50 },
"svgwidth":750,"svgheight":350,
"svgx1axislabel":"rxn_id","svgy1axislabel":"flux",
'svgformtileid':'filtermenu1','svgresetbuttonid':'reset1','svgsubmitbuttonid':'submit1'};
svgtileparameters_O = {'tileheader':'Flux precision','tiletype':'svg','tileid':"tile2",'rowid':"row1",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-12"};
svgtileparameters_O.update(svgparameters_O);
tableparameters_O = {"tabletype":'responsivetable_01',
'tableid':'table1',
"tablefilters":None,
"tableclass":"table table-condensed table-hover",
'tableformtileid':'filtermenu1','tableresetbuttonid':'reset1','tablesubmitbuttonid':'submit1'};
tabletileparameters_O = {'tileheader':'Flux precision','tiletype':'table','tileid':"tile3",'rowid':"row1",'colid':"col1",
'tileclass':"panel panel-default",'rowclass':"row",'colclass':"col-sm-12"};
tabletileparameters_O.update(tableparameters_O);
parametersobject_O = [formtileparameters_O,svgtileparameters_O,tabletileparameters_O];
tile2datamap_O = {"filtermenu1":[0],"tile2":[0],"tile3":[0]};
# dump the data to a json file
ddtutilities = ddt_container(parameters_I = parametersobject_O,data_I = dataobject_O,tile2datamap_I = tile2datamap_O,filtermenu_I = None);
if data_dir_I=='tmp':
filename_str = self.settings['visualization_data'] + '/tmp/ddt_data.js'
elif data_dir_I=='data_json':
data_json_O = ddtutilities.get_allObjects_js();
return data_json_O;
with open(filename_str,'w') as file:
file.write(ddtutilities.get_allObjects());
