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