Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloan

2 files changed, 22 insertions, 0 deletions

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 377f6b26..cf16879f 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -5,6 +5,9 @@ from base import data_set
 from base.species import TheSpecies
 
 from wqflask import user_manager
+
+from flask import Flask, g
+
 import logging
 logger = logging.getLogger(__name__ )
 
@@ -41,3 +44,20 @@ def get_trait_db_obs(self, trait_db_list):
                                name=trait_name,
                                cellid=None)
         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
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9860f63e..82ef136f 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -217,9 +217,11 @@ USE_REDIS          = get_setting_bool('USE_REDIS')
 USE_GN_SERVER      = get_setting_bool('USE_GN_SERVER')
 
 GENENETWORK_FILES  = get_setting('GENENETWORK_FILES')
+TEMP_TRAITS        = get_setting('TEMP_TRAITS')
 
 PYLMM_COMMAND      = pylmm_command()
 GEMMA_COMMAND      = gemma_command()
+GEMMA_RESULTS_PATH = get_setting('GEMMA_RESULTS_PATH')
 PLINK_COMMAND      = plink_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR