1 files changed, 69 insertions, 0 deletions
diff --git a/gn2/utility/helper_functions.py b/gn2/utility/helper_functions.py
new file mode 100644
index 00000000..fc101959
--- /dev/null
+++ b/gn2/utility/helper_functions.py
@@ -0,0 +1,69 @@
+from gn2.base import data_set
+from gn2.base.trait import create_trait
+from gn2.base.species import TheSpecies
+
+from gn2.utility import hmac
+from gn2.utility.tools import get_setting
+
+from gn2.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())]