From 204a308be0f741726b9a620d88fbc22b22124c81 Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Fri, 29 Dec 2023 18:55:37 +0000
Subject: Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.
---
 wqflask/utility/helper_functions.py | 69 -------------------------------------
 1 file changed, 69 deletions(-)
 delete mode 100644 wqflask/utility/helper_functions.py

(limited to 'wqflask/utility/helper_functions.py')

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
deleted file mode 100644
index 8b20bd74..00000000
--- a/wqflask/utility/helper_functions.py
+++ /dev/null
@@ -1,69 +0,0 @@
-from base import data_set
-from base.trait import create_trait
-from base.species import TheSpecies
-
-from utility import hmac
-from utility.tools import get_setting
-
-from wqflask.database import database_connection
-
-
-def get_species_dataset_trait(self, start_vars):
-    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'])
-    self.species = TheSpecies(dataset=self.dataset)
-    self.this_trait = create_trait(dataset=self.dataset,
-                                   name=start_vars['trait_id'],
-                                   cellid=None,
-                                   get_qtl_info=True)
-
-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():
-    """Group each species into a group"""
-    _menu = {}
-    species, group_name = None, None
-    with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor:
-        cursor.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"
-        )
-        for species, group_name in cursor.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())]
-- 
cgit v1.2.3