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):
"""
2008-02-28
"""
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):
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):
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):
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)
