def __init__(self, search_term, search_operator=None, dataset=None): self.search_term = search_term # Make sure search_operator is something we expect assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset if self.dataset: logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) logger.debug("self.dataset.group is: ", pf(self.dataset.group)) # Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def __init__(self, search_term, search_operator=None, dataset=None): self.search_term = search_term # Make sure search_operator is something we expect assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator" self.search_operator = search_operator self.dataset = dataset if self.dataset: logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset)) logger.debug("self.dataset.group is: ", pf(self.dataset.group)) #Get group information for dataset and the species id self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def retrieve_sample_data(self, trait): query = """ SELECT Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) WHERE Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoFreeze.Name = %s AND GenoXRef.DataId = GenoData.Id AND GenoData.StrainId = Strain.Id Order BY Strain.Name """ logger.sql(query) results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() return results