def execute_findShortestPaths(self,
analysis_id_I,
algorithms_params_I,
nodes_startAndStop_I,
exclusion_list_I=[],
weights_I=[],
):
'''
compute the shortest paths
INPUT:
model_id_I
algorithms_params_I
nodes_startAndStop_I
simulation_id_I
exclusion_list_I
OUTPUT:
'''
exCOBRA01 = models_COBRA_execute(self.session,self.engine,self.settings);
exCOBRA01.initialize_supportedTables();
physiology_analysis_query = stage02_physiology_analysis_query(self.session,self.engine,self.settings);
physiology_analysis_query.initialize_supportedTables();
data_O=[];
data_graphs_O=[];
rows = physiology_analysis_query.getJoin_analysisID_dataStage02PhysiologyAnalysisAndSimulation(analysis_id_I);
for row in rows:
weights = [];
if type(weights_I)==type([]):
weights = weights_I;
weights_str = '[]';
elif type(weights_I)==type(''):
if weights_I == 'stage02_physiology_sampledData_query':
weights = self.import_graphWeights_sampledData(row['simulation_id']);
weights_str = 'stage02_physiology_sampledData_query';
elif weights_I == 'stage02_physiology_simulatedData_query':
weights = self.import_graphWeights_simulatedData(row['simulation_id']);
weights_str = 'stage02_physiology_simulatedData_query';
else:
print('weights source not recognized');
# run the analysis for different algorithms/params
for ap in algorithms_params_I:
shortestPaths = exCOBRA01.execute_findShortestPath_nodes(
row['model_id'],
nodes_startAndStop_I = nodes_startAndStop_I,
algorithm_I=ap['algorithm'],
exclusion_list_I=exclusion_list_I,
params_I=ap['params'],
weights_I=weights
)
for sp in shortestPaths:
tmp = {};
tmp['analysis_id']=analysis_id_I
tmp['simulation_id']=row['simulation_id']
tmp['weights']=weights_str;
tmp['used_']=True;
tmp['comment_']=None;
tmp['params']=sp['params']
tmp['path_start']=sp['start']
tmp['algorithm']=sp['algorithm']
tmp['path_stop']=sp['stop']
tmp1 = copy.copy(tmp);
tmp1['path_n']=sp['path_n']
tmp1['path_iq_1']=sp['path_iq_1']
tmp1['path_var']=sp['path_var']
tmp1['path_ci_lb']=sp['path_ci_lb']
tmp1['path_cv']=sp['path_cv']
tmp1['path_iq_3']=sp['path_iq_3']
tmp1['path_ci_ub']=sp['path_ci_ub']
tmp1['path_average']=sp['path_average']
tmp1['path_max']=sp['path_max']
tmp1['path_median']=sp['path_median']
tmp1['path_ci_level']=sp['path_ci_level']
tmp1['path_min']=sp['path_min']
data_O.append(tmp1);
for path in sp['all_paths']:
tmp2 = copy.copy(tmp);
tmp2['paths']=path;
data_graphs_O.append(tmp2);
#for sp in shortestPaths:
#dict_keys(['stop', 'params', 'path_n', 'all_paths', 'path_iq_1', 'path_var', 'path_ci_lb', 'path_cv', 'path_iq_3', 'path_ci_ub', 'path_average', 'path_max', 'path_median', 'start', 'algorithm', 'path_ci_level', 'path_min'])
# str = "start: %s, stop: %s, min: %s, max: %s, average: %s, " \
# %(sp['start'],sp['stop'],sp['path_min'],
# sp['path_max'],sp['path_average'])
# print(str)
self.add_rows_table('data_stage02_physiology_graphData_shortestPathStats',data_O);
self.add_rows_table('data_stage02_physiology_graphData_shortestPaths',data_graphs_O);
sys.path.append(pg_settings.datadir_settings['github']+'/SBaaS_models') sys.path.append(pg_settings.datadir_settings['github']+'/SBaaS_LIMS') sys.path.append(pg_settings.datadir_settings['github']+'/SBaaS_COBRA') # SBaaS dependencies paths: sys.path.append(pg_settings.datadir_settings['github']+'/io_utilities') sys.path.append(pg_settings.datadir_settings['github']+'/python_statistics') sys.path.append(pg_settings.datadir_settings['github']+'/r_statistics') sys.path.append(pg_settings.datadir_settings['github']+'/listDict') sys.path.append(pg_settings.datadir_settings['github']+'/ddt_python') sys.path.append(pg_settings.datadir_settings['github']+'/molmass') sys.path.append(pg_settings.datadir_settings['github']+'/genomeScale_MFA') sys.path.append(pg_settings.datadir_settings['github']+'/genomeScale_MFA_INCA') #make the COBRA table from SBaaS_models.models_COBRA_execute import models_COBRA_execute cobra01 = models_COBRA_execute(session,engine,pg_settings.datadir_settings); cobra01.initialize_supportedTables() cobra01.initialize_tables() #make the BioCyc table from SBaaS_models.models_BioCyc_execute import models_BioCyc_execute biocyc01 = models_BioCyc_execute(session,engine,pg_settings.datadir_settings); biocyc01.initialize_supportedTables() biocyc01.initialize_tables() #BioCyc dependencies from SBaaS_models.models_BioCyc_dependencies import models_BioCyc_dependencies biocyc01_dep = models_BioCyc_dependencies(); #BioCyc dependencies from SBaaS_models.models_COBRA_dependencies import models_COBRA_dependencies
