From e4621a2a759f55659b5c631baec5e5f497e0cff1 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Thu, 18 Jun 2015 19:55:41 +0300
Subject: add missing line to webqtlUtil

---
 wqflask/utility/webqtlUtil.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'wqflask')

diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4d7981d9..ab746228 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -43,6 +43,7 @@ ParInfo ={
 'BXH':['BHF1', 'HBF1',  'C57BL/6J', 'C3H/HeJ'],
 'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
 'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
 'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-- 
cgit v1.2.3


From 45ebe51fbee7da1617b01cff7b9ab404d6ad1aa7 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Thu, 18 Jun 2015 20:05:49 +0300
Subject: fix all_samples_ordered

move duplicated code into a method,
handle the case of missing f1/f12 correctly
---
 wqflask/base/data_set.py                 | 6 ++++++
 wqflask/base/trait.py                    | 9 +--------
 wqflask/wqflask/show_trait/show_trait.py | 9 +--------
 3 files changed, 8 insertions(+), 16 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index acfee3d4..b17396e5 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -392,6 +392,12 @@ class DatasetGroup(object):
             Redis.set(key, json.dumps(self.samplelist))
             Redis.expire(key, 60*5)
 
+    def all_samples_ordered(self):
+        result = []
+        lists = (self.parlist, self.f1list, self.samplelist)
+        [result.extend(l) for l in lists if l]
+        return result
+
     def read_genotype_file(self):
         '''Read genotype from .geno file instead of database'''
         #if self.group == 'BXD300':
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7f1170a9..2e0e86fb 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -251,14 +251,7 @@ class GeneralTrait(object):
         # Todo: is this necessary? If not remove
         self.data.clear()
 
-        if self.dataset.group.parlist:
-            all_samples_ordered = (self.dataset.group.parlist +
-                                   self.dataset.group.f1list +
-                                   self.dataset.group.samplelist)
-        elif self.dataset.group.f1list:
-            all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
-        else:
-            all_samples_ordered = self.dataset.group.samplelist
+        all_samples_ordered = self.dataset.group.all_samples_ordered()
 
         if results:
             for item in results:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index bd827086..61305e9b 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1148,14 +1148,7 @@ class ShowTrait(object):
 
 
     def make_sample_lists(self, this_trait):
-        if self.dataset.group.parlist:
-            all_samples_ordered = (self.dataset.group.parlist +
-                                   self.dataset.group.f1list +
-                                   self.dataset.group.samplelist)
-        elif self.dataset.group.f1list:
-            all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
-        else:
-            all_samples_ordered = list(self.dataset.group.samplelist)
+        all_samples_ordered = self.dataset.group.all_samples_ordered()
 
         primary_sample_names = list(all_samples_ordered)
 
-- 
cgit v1.2.3