diff options
Diffstat (limited to 'wqflask/utility/helper_functions.py')
| -rw-r--r-- | wqflask/utility/helper_functions.py | 82 |
1 files changed, 39 insertions, 43 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index e7c04fef..27dd0729 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -1,72 +1,68 @@ -from __future__ import absolute_import, print_function, division - -from base.trait import GeneralTrait 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 +from flask import g import logging -logger = logging.getLogger(__name__ ) +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 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']) + 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.dataset = data_set.create_dataset(start_vars['dataset']) self.species = TheSpecies(dataset=self.dataset) - logger.debug("After creating species") - self.this_trait = GeneralTrait(dataset=self.dataset, + 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, basestring): + 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(":") + 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]) + 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 = GeneralTrait(dataset=dataset_ob, - name=trait_name, - cellid=None) - self.trait_list.append((trait_ob, dataset_ob)) - -def get_species_groups(): + trait_ob = create_trait(dataset=dataset_ob, + name=trait_name, + cellid=None) + if trait_ob: + self.trait_list.append((trait_ob, dataset_ob)) - 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) +def get_species_groups(): + """Group each species into a group""" + _menu = {} - return species_and_groups + for species, group_name in g.db.execute( + "SELECT s.MenuName, i.InbredSetName FROM InbredSet i " + "INNER JOIN Species s ON s.SpeciesId = i.SpeciesId " + "ORDER BY i.SpeciesId ASC, i.Name ASC").fetchall(): + if species in _menu: + if _menu.get(species): + _menu = _menu[species].append(group_name) + else: + _menu[species] = [group_name] + return [{"species": key, + "groups": value} for key, value in + list(_menu.items())] |