from base import data_set from base.trait import create_trait from base.species import TheSpecies from utility import hmac from flask import Flask, g import logging logger = logging.getLogger(__name__ ) def get_species_dataset_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" if "temp_trait" in list(start_vars.keys()): if start_vars['temp_trait'] == "True": self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group']) else: self.dataset = data_set.create_dataset(start_vars['dataset']) else: self.dataset = data_set.create_dataset(start_vars['dataset']) logger.debug("After creating dataset") self.species = TheSpecies(dataset=self.dataset) logger.debug("After creating species") self.this_trait = create_trait(dataset=self.dataset, name=start_vars['trait_id'], cellid=None, get_qtl_info=True) logger.debug("After creating trait") #if read_genotype: #self.dataset.group.read_genotype_file() #self.genotype = self.dataset.group.genotype def get_trait_db_obs(self, trait_db_list): if isinstance(trait_db_list, str): trait_db_list = trait_db_list.split(",") self.trait_list = [] for trait in trait_db_list: data, _separator, hmac_string = trait.rpartition(':') data = data.strip() assert hmac_string==hmac.hmac_creation(data), "Data tampering?" trait_name, dataset_name = data.split(":")[:2] if dataset_name == "Temp": dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2]) else: dataset_ob = data_set.create_dataset(dataset_name) trait_ob = create_trait(dataset=dataset_ob, name=trait_name, cellid=None) if trait_ob: self.trait_list.append((trait_ob, dataset_ob)) def get_species_groups(): species_query = "SELECT SpeciesId, MenuName FROM Species" species_ids_and_names = g.db.execute(species_query).fetchall() species_and_groups = [] for species_id, species_name in species_ids_and_names: this_species_groups = {} this_species_groups['species'] = species_name groups_query = "SELECT InbredSetName FROM InbredSet WHERE SpeciesId = %s" % (species_id) groups = [group[0] for group in g.db.execute(groups_query).fetchall()] this_species_groups['groups'] = groups species_and_groups.append(this_species_groups) return species_and_groups