def __init__(self, **keywords): """ 2008-02-28 """ argument_default_dict = {('hostname',1, ):'papaya.usc.edu',\ ('dbname',1, ):'stock_250k',\ ('schema',0, ):'',\ ('user',1, ):None,\ ('passwd',1, ):None,\ ('output_fname',0, ):None,\ ('raw_phenotype_table',1, ):'at.phenotype',\ ('experiment_table',1, ):'at.experiment',\ ('phenotype_table',1, ):'stock_250k.phenotype',\ ('phenotype_avg_table',1, ):'stock_250k.phenotype_avg',\ ('method_table',1, ):'stock_250k.phenotype_method',\ ('commit',0, int):0,\ ('debug',0, int):0,\ ('report',0, int):0} """ 2008-02-28 argument_default_dict is a dictionary of default arguments, the key is a tuple, ('argument_name', is_argument_required, argument_type) argument_type is optional """ #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self) self.debug = self.ad['debug'] self.report = self.ad['report']
def __init__(self, **keywords): """ 2008-04-12 add experimenter, mapping_file """ from pymodule import process_function_arguments argument_default_dict = {('curs',1, ): None,\ ('array_info_table',1, ):None,\ ('user',1, ):None,\ ('experimenter',0,):None,\ ('mapping_file',0,):None,\ ('debug',0, int):0,\ ('report',0, int):0} """ 2008-02-28 argument_default_dict is a dictionary of default arguments, the key is a tuple, ('argument_name', is_argument_required, argument_type) argument_type is optional """ #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self, howto_deal_with_required_none=2) if not self.experimenter: self.experimenter = self.user self.md5sum2array_id, self.max_array_id = self.get_md5sum2array_id(self.curs, self.array_info_table) if self.mapping_file: #2008-04-23 check if mapping is there or not (empty dictionary). self.array_file_basename2ecotypeid_tuple = self.readMappingFile(self.mapping_file) else: self.array_file_basename2ecotypeid_tuple = {}
def __init__(self, **keywords): """ 2008-04-12 add experimenter, mapping_file """ from pymodule import process_function_arguments argument_default_dict = {('curs',1, ): None,\ ('array_info_table',1, ):None,\ ('user',1, ):None,\ ('experimenter',0,):None,\ ('mapping_file',0,):None,\ ('debug',0, int):0,\ ('report',0, int):0} """ 2008-02-28 argument_default_dict is a dictionary of default arguments, the key is a tuple, ('argument_name', is_argument_required, argument_type) argument_type is optional """ #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self, howto_deal_with_required_none=2) if not self.experimenter: self.experimenter = self.user self.md5sum2array_id, self.max_array_id = self.get_md5sum2array_id( self.curs, self.array_info_table) if self.mapping_file: #2008-04-23 check if mapping is there or not (empty dictionary). self.array_file_basename2ecotypeid_tuple = self.readMappingFile( self.mapping_file) else: self.array_file_basename2ecotypeid_tuple = {}
def __init__(self, **keywords): """ 2008-03-11 """ from pymodule import process_function_arguments, turn_option_default_dict2argument_default_dict argument_default_dict = turn_option_default_dict2argument_default_dict(self.option_default_dict) #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
def __init__(self, **keywords): from pymodule import process_function_arguments, turn_option_default_dict2argument_default_dict argument_default_dict = turn_option_default_dict2argument_default_dict(self.option_default_dict) self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self) self._threadlocal = threading.local() self.tables = {} self.mappers = {} self._engine = None
def __init__(self, **keywords): """ 2008-04-08 """ from pymodule import process_function_arguments, turn_option_default_dict2argument_default_dict argument_default_dict = turn_option_default_dict2argument_default_dict(self.option_default_dict) #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
def __init__(self, **keywords): argument_default_dict = {('SNPData1', 1, ): None,\ ('SNPData2', 1, ): None,\ ('curs', 0, ): None,\ ('QC_method_id', 1, int):3,\ ('user', 0,): '',\ ('columns_to_be_selected', 0, ):'s1.name, s2.name'} self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self, howto_deal_with_required_none=2) self.columns_to_be_selected = 's1.name, s2.name' self.QC_method_id = 3 #2008-05-06 set to 3 to use the Cmp250kVs149SNP.py's col matching function self.update_row_col_matching()
def __init__(self, **keywords): """ 2008-04-12 add experimenter, mapping_file 2008-04-09 array_data_table, probes_table, strain_info_table are no longer required. but leave them in the argument_default_dict. 2008-02-28 """ from pymodule import process_function_arguments, turn_option_default_dict2argument_default_dict """ #2008-04-23 old dictionary argument_default_dict = {('hostname',1, ):'papaya.usc.edu',\ ('dbname',1, ):'stock_250k',\ ('user',1, ):None,\ ('passwd',1, ):None,\ ('experimenter',0,):None,\ ('mapping_file',1,):None,\ ('input_dir',1, ):None,\ ('output_dir',1, ):'/Network/Data/250k/db/raw_data/',\ ('array_data_table',0, ):'array_data',\ ('probes_table',0, ):'probes',\ ('strain_info_table',0, ):'strain_info',\ ('array_info_table',1, ):'array_info',\ ('commit',0, int):0,\ ('debug',0, int):0,\ ('report',0, int):0} """ argument_default_dict = turn_option_default_dict2argument_default_dict( self.option_default_dict) """ 2008-02-28 argument_default_dict is a dictionary of default arguments the key is a tuple, ('argument_name', is_argument_required, argument_type) argument_type is optional """ #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self)
def __init__(self, **keywords): """ 2008-04-12 add experimenter, mapping_file 2008-04-09 array_data_table, probes_table, strain_info_table are no longer required. but leave them in the argument_default_dict. 2008-02-28 """ from pymodule import process_function_arguments, turn_option_default_dict2argument_default_dict """ #2008-04-23 old dictionary argument_default_dict = {('hostname',1, ):'papaya.usc.edu',\ ('dbname',1, ):'stock_250k',\ ('user',1, ):None,\ ('passwd',1, ):None,\ ('experimenter',0,):None,\ ('mapping_file',1,):None,\ ('input_dir',1, ):None,\ ('output_dir',1, ):'/Network/Data/250k/db/raw_data/',\ ('array_data_table',0, ):'array_data',\ ('probes_table',0, ):'probes',\ ('strain_info_table',0, ):'strain_info',\ ('array_info_table',1, ):'array_info',\ ('commit',0, int):0,\ ('debug',0, int):0,\ ('report',0, int):0} """ argument_default_dict = turn_option_default_dict2argument_default_dict(self.option_default_dict) """ 2008-02-28 argument_default_dict is a dictionary of default arguments the key is a tuple, ('argument_name', is_argument_required, argument_type) argument_type is optional """ #argument dictionary self.ad = process_function_arguments(keywords, argument_default_dict, error_doc=self.__doc__, class_to_have_attr=self)