about summary refs log tree commit diff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/webqtlConfig.py8
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py8
2 files changed, 10 insertions, 6 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index d0016b33..f6140ac3 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -8,7 +8,7 @@
 # 
 #########################################
 
-from utility.tools import mk_dir, assert_dir, flat_files, TEMPDIR
+from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR
 
 #Debug Level
 #1 for debug, mod python will reload import each time
@@ -69,7 +69,11 @@ GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'/generated_text/')
 
 # Flat file directories
 GENODIR              = flat_files('genotype')+'/'
-JSON_GENODIR         = flat_files('json')+'/'
+JSON_GENODIR         = flat_files('genotype/json')+'/'
+if not valid_path(JSON_GENODIR):
+    # fall back on old location (move the dir, FIXME)
+    JSON_GENODIR = flat_files('json')
+assert_dir(GENODIR)
 
 PORTADDR = "http://50.16.251.170"
 
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6d8dd76a..c1ad1c84 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -161,7 +161,7 @@ class CorrelationResults(object):
             self.correlation_data = {}
 
             db_filename = self.getFileName(target_db_name = self.target_dataset.name)
-            cache_available = db_filename in os.listdir(webqtlConfig.TEXTDIR)
+            cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR)
             
             if self.corr_type == "tissue":
                 self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol")
@@ -179,7 +179,7 @@ class CorrelationResults(object):
                     
             elif self.corr_type == "sample":
                 if self.dataset.type == "ProbeSet" and cache_available:
-                    dataset_file = open(webqtlConfig.TEXTDIR+db_filename,'r')
+                    dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
 
                     #XZ, 01/08/2009: read the first line
                     line = dataset_file.readline()
@@ -571,7 +571,7 @@ class CorrelationResults(object):
 
         #db_filename = self.getFileName(target_db_name=self.target_db_name)
         #
-        #cache_available = db_filename in os.listdir(webqtlConfig.TEXTDIR)
+        #cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR)
 
          # If the cache file exists, do a cached correlation for probeset data
         if self.dataset.type == "ProbeSet":
@@ -1308,7 +1308,7 @@ class CorrelationResults(object):
             # return allcorrelations
             
 	
-        datasetFile = open(webqtlConfig.TEXTDIR+db_filename,'r')
+        datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
     
         print("Invoking parallel computing")
         input_line_list = datasetFile.readlines()