Merge git://github.com/zsloan/genenetwork into flask

3 files changed, 8 insertions, 8 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 07fe9cd9..1668940c 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -779,14 +779,14 @@ class MrnaAssayDataSet(DataSet):
 
             #Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
-                self.cursor.execute("""
+                query = """
                     select Geno.Chr, Geno.Mb from Geno, Species
-                    where Species.Name = '%s' and
-                        Geno.Name = '%s' and
+                    where Species.Name = '{}' and
+                        Geno.Name = '{}' and
                         Geno.SpeciesId = Species.Id
-                """ % (species, this_trait.locus))
-                result = self.cursor.fetchone()
-
+                """.format(species, this_trait.locus)
+                result = g.db.execute(query).fetchone()
+                
                 if result:
                     #if result[0] and result[1]:
                     #    lrs_chr = result[0]
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 3429d9c1..401b729c 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -30,7 +30,7 @@ class GeneralTrait(object):
 
     def __init__(self, get_qtl_info=False, **kw):
         # xor assertion
-        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. xor name";
+        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
         if kw.get('dataset_name'):
             self.dataset = create_dataset(kw.get('dataset_name'))
         else:
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 49afb631..a811c3cd 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -52,7 +52,7 @@ ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?sp
 SECUREDIR = GNROOT + 'secure/'
 COMMON_LIB = GNROOT + 'support/admin'
 HTMLPATH = GNROOT + 'web/'
-PYLMM_PATH = HTMLPATH + 'plink/'
+PYLMM_PATH = '/home/zas1024/'
 SNP_PATH = '/mnt/xvdf1/snps/' 
 IMGDIR = HTMLPATH +'image/'
 IMAGESPATH = HTMLPATH + 'images/'