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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(":")
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
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