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authorBonfaceKilz2021-04-29 21:57:16 +0300
committerGitHub2021-04-29 21:57:16 +0300
commit4c8c5390bdba594c217d7ca0114a80a6b3634e24 (patch)
treeb48693555b97fd21e37b263591685af75a2a4b45 /wqflask/utility/helper_functions.py
parentbab514be0f0d01fc192638b8e7ccd5909b842b23 (diff)
parent881090ff15a5a563bccefcbd08d373c88a64aa31 (diff)
downloadgenenetwork2-4c8c5390bdba594c217d7ca0114a80a6b3634e24.tar.gz
Merge pull request #566 from BonfaceKilz/Feature/Add-upload-data-forms
Chore/Cosmetic-changes
Diffstat (limited to 'wqflask/utility/helper_functions.py')
-rw-r--r--wqflask/utility/helper_functions.py59
1 files changed, 30 insertions, 29 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 46eeb35d..12fd6be5 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -4,20 +4,23 @@ 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 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'])
+ 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'])
+ 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")
@@ -27,9 +30,6 @@ def get_species_dataset_trait(self, start_vars):
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):
@@ -42,28 +42,29 @@ def get_trait_db_obs(self, trait_db_list):
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 = create_trait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
+ 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
+def get_species_groups():
+ """Group each species into a group"""
+ _menu = {}
+ 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 _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())]