def import_data_stage02_isotopomer_fittedNetFluxDifferences_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_data_stage02_isotopomer_fittedNetFluxDifferences(data.data);
data.clear_data();
def import_standards_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_standards(data.data);
data.clear_data();
def import_dataStage01IsotopomerAveragesNormSum_updateUsedAndComment(self,filename):
'''table updates'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01IsotopomerAveragesNormSum_usedAndComment(data.data);
data.clear_data();
def import_MSComponents_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_MSComponents(data.data);
data.clear_data();
def import_dataStage03QuantificationMetabolomicsData_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage03MetabolomicsData(data.data);
data.clear_data();
def import_biologicalMaterialGeneReferences_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_biologicalMaterialGeneReferences(data.data);
data.clear_data();
def import_biologicalMaterialDescription_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_biologicalMaterialDescription(data.data);
data.clear_data();
def import_dataStage01ResequencingLineage_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_dataStage01ResequencingLineage(data.data);
data.clear_data();
def import_dataStage01Normalized_update_unique(self,filename):
'''table updates'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01Normalized_unique(data.data);
data.clear_data();
def import_data_stage02_physiology_pairWiseTest_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_data_stage02_physiology_pairWiseTest(data.data);
data.clear_data();
def import_quantitationMethod_add(self,QMethod_id_I, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_quantitationMethod(QMethod_id_I, data.data);
data.clear_data();
def import_dataStage01RNASequencingGenesFpkmTracking_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01RNASequencingGenesFpkmTracking(data.data);
data.clear_data();
def import_mutations(self,filenames_I=[]):
"""import mutations for multiple experiments/samples"""
io = base_importData();
for filename in filenames_I:
io.read_csv(filename);
self.mutations.extend(self.format_mutationData(io.data));
io.clear_data();
def import_dataStage02PhysiologySamplingParameters_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_dataStage02PhysiologySamplingParameters(data.data);
data.clear_data();
def import_data_stage03_quantification_analysis_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_data_stage03_quantification_analysis(data.data);
data.clear_data();
def import_dataStage01Normalized_update_id(self,filename):
'''table updates'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01Normalized_id(data.data,used_comment_only_I=True);
data.clear_data();
def import_dataStage03QuantificationSimulatedData_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_dataStage03QuantificationSimulatedData(data.data);
data.clear_data();
def import_geneExpDiff(
self,
filename_I,
experiment_id_1_I=None,
experiment_id_2_I=None,
sample_name_abbreviation_1_I=None,
sample_name_abbreviation_2_I=None,
):
"""import geneExpDiff
INPUT:
filename_I = input filename
OPTIONAL INPUT:
the following are optional for analyzing a single sample,
but required when analyzing multiple samples
experiment_id_1_I = string, name of the experiment that generated the samples
experiment_id_I = string, name of the experiment that generated the samples
sample_name_abbreviation_1_I = string, name of the sample
sample_name_abbreviation_2_I = string, name of the sample
"""
io = base_importData()
io.read_tab(filename_I)
geneExpDiff = self.format_geneExpDiff(io.data)
for d in geneExpDiff:
d["experiment_id_1"] = experiment_id_1_I
d["experiment_id_2"] = experiment_id_2_I
d["sample_name_abbreviation_1"] = sample_name_abbreviation_1_I
d["sample_name_abbreviation_2"] = sample_name_abbreviation_2_I
self.geneExpDiff = geneExpDiff
def import_biologicalMaterialMassVolumeConversion_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_biologicalMaterialMassVolumeConversion(data.data);
data.clear_data();
def import_sampleDescription_update(self, filename):
'''table updates'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_sampleDescription(data.data);
data.clear_data();
def import_MSSourceParameters_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_MSSourceParameters(data.data);
data.clear_data();
def import_dataStage01PhysiologyData_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01PhysiologyData(data.data);
data.clear_data();
def import_data_stage02_isotopomer_tracers_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_data_stage02_isotopomer_tracers(data.data);
data.clear_data();
def import_dataStage01ResequencingHistogram_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01ResequencingHistogram(data.data);
data.clear_data();
def import_standardsOrdering_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_standardsOrdering(data.data);
data.clear_data();
def import_dataStage01MQResultsTable_update(self,filename):
'''table updates'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_dataStage01MQResultsTable(data.data);
data.clear_data();
def import_calibrationFile_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
# split into seperate data structures based on the destined table add
sample_data = [];
experiment_data = [];
for d in data.data:
sample_data.append({'sample_name':d['sample_name'],
'sample_type':d['sample_type'],
'calibrator_id':d['calibrator_id'],
'calibrator_level':d['calibrator_level'],
'sample_id':d['sample_id'],
'sample_dilution':d['sample_dilution']});
experiment_data.append({'exp_type_id':d['exp_type_id'],
'id':d['experiment_id'],
'sample_name':d['sample_name'],
'experimentor_id':d['experimentor_id'],
'extraction_method_id':d['extraction_method_id'],
'acquisition_method_id':d['acquisition_method_id'],
'quantitation_method_id':d['quantitation_method_id'],
'internal_standard_id':d['is_id']});
# add data to the database:
self.add_sample(sample_data);
self.add_experiment(experiment_data);
# deallocate memory
data.clear_data();
def import_visualizationUser_update(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.update_visualizationUser(data.data);
data.clear_data();
def import_dataStage02PhysiologySimulation_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_dataStage02PhysiologySimulation(data.data);
data.clear_data();
def import_visualizationProject_add(self, filename):
'''table adds'''
data = base_importData();
data.read_csv(filename);
data.format_data();
self.add_visualizationProject(data.data);
data.clear_data();
