Merge branch 'testing' into bug/network_graph_fixes

6 files changed, 39 insertions, 38 deletions

diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 204ff59a..df926884 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,7 +2,7 @@ from pprint import pformat as pf
 
 # Todo: Move these out of __init__
 
-class Bunch(object):
+class Bunch:
     """Like a dictionary but using object notation"""
     def __init__(self,  **kw):
             self.__dict__ = kw
@@ -11,7 +11,7 @@ class Bunch(object):
         return pf(self.__dict__)
 
 
-class Struct(object):
+class Struct:
     '''The recursive class for building and representing objects with.
 
     From http://stackoverflow.com/a/6573827/1175849
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index ea5a0ab6..91ea91e8 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,7 +6,7 @@ from utility.tools import LOG_BENCH
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
-class Bench(object):
+class Bench:
     entries = collections.OrderedDict()
 
     def __init__(self, name=None, write_output=LOG_BENCH):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 81085ffe..0a381c9b 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,7 @@
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-class genotype(object):
+class genotype:
     """
     Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
     """
@@ -119,7 +119,7 @@ class genotype(object):
 
             self.chromosomes.append(chr_ob)
 
-class Chr(object):
+class Chr:
     def __init__(self, name, geno_ob):
         self.name = name
         self.loci = []
@@ -140,7 +140,7 @@ class Chr(object):
     def add_marker(self, marker_row):
         self.loci.append(Locus(self.geno_ob, marker_row))
 
-class Locus(object):
+class Locus:
     def __init__(self, geno_ob, marker_row = None):
         self.chr = None
         self.name = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 0b736176..f8e96d19 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,7 +12,7 @@ import simplejson as json
 
 from pprint import pformat as pf
 
-class Marker(object):
+class Marker:
   def __init__(self):
     self.name = None
     self.chr = None
@@ -21,7 +21,7 @@ class Marker(object):
     self.genotypes = []
 
 
-class ConvertGenoFile(object):
+class ConvertGenoFile:
 
   def __init__(self, input_file):
     self.mb_exists = False
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())]
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 4144ae00..b2cbd458 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,7 +2,7 @@ from redis import Redis
 
 import simplejson as json
 
-class TempData(object):
+class TempData:
 
     def __init__(self, temp_uuid):
         self.temp_uuid = temp_uuid