Merge branch 'master' of github.com:genenetwork/genenetwork2 into gn-master

3 files changed, 13 insertions, 4 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d6a46c2e..5603fe2e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -158,7 +158,10 @@ class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
         json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json'))
-        markers = json.load(json_data_fh)
+        try:
+            markers = json.load(json_data_fh)
+        except:
+            markers = []
     
         for marker in markers:
             if (marker['chr'] != "X") and (marker['chr'] != "Y"):
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 54a7ce8e..ba82057a 100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -19,7 +19,7 @@ class MrnaAssayTissueData(object):
         if self.gene_symbols == None:
             self.gene_symbols = []
         
-        print("self.gene_symbols:", self.gene_symbols)
+        #print("self.gene_symbols:", self.gene_symbols)
         
         self.data = collections.defaultdict(Bunch)
             
@@ -57,9 +57,15 @@ class MrnaAssayTissueData(object):
 
         results = g.db.execute(query).fetchall()
         
+        lower_symbols = []
+        for gene_symbol in gene_symbols:
+            if gene_symbol != None:
+                lower_symbols.append(gene_symbol.lower())
+
         for result in results:
             symbol = result[0]
-            if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]:
+            #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]:
+            if symbol.lower() in lower_symbols:
                 #gene_symbols.append(symbol)
                 symbol = symbol.lower()
                 
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 330fec56..4f9b3af3 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -55,7 +55,7 @@ COMMON_LIB = GNROOT + 'support/admin'
 HTMLPATH = GNROOT + 'genotype_files/'
 PYLMM_PATH = '/home/zas1024/plink_gemma/'
 SNP_PATH = '/home/zas1024/snps/' 
-IMGDIR = GNROOT + '/wqflask/wqflask/images/'
+IMGDIR = GNROOT + '/wqflask/output/'
 IMAGESPATH = HTMLPATH + 'images/'
 UPLOADPATH = IMAGESPATH + 'upload/'
 TMPDIR = '/home/zas1024/tmp/' # Will remove this and dependent items later