Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

6 files changed, 25 insertions, 15 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8652e6b7..1f99df49 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -64,7 +64,7 @@ logger = getLogger(__name__ )
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
 
@@ -77,7 +77,7 @@ def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_sampleli
 
 class Dataset_Types(object):
 
-    def __init__(self, rebuild=False):
+    def __init__(self):
         """Create a dictionary of samples where the value is set to Geno,
 Publish or ProbeSet. E.g.
 
@@ -93,13 +93,9 @@ Publish or ProbeSet. E.g.
 
         """
         self.datasets = {}
-        if rebuild: #ZS: May make this the only option
-            data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content)
-            #data = gen_menu.gen_dropdown_json()
-        else:
-            file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
-            with open(file_name, 'r') as fh:
-                data = json.load(fh)
+        data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown").content)
+        #data = gen_menu.gen_dropdown_json()
+
 
         for species in data['datasets']:
             for group in data['datasets'][species]:
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 7c06356b..15572d97 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -9,6 +9,7 @@
 
 from wqflask import app
 
+
 import logging
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9354ece6..2914d354 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -233,6 +233,7 @@ def show_settings():
 # Cached values
 GN_VERSION         = get_setting('GN_VERSION')
 HOME               = get_setting('HOME')
+SERVER_PORT        = get_setting('SERVER_PORT')
 WEBSERVER_MODE     = get_setting('WEBSERVER_MODE')
 GN2_BASE_URL       = get_setting('GN2_BASE_URL')
 GN2_BRANCH_URL     = get_setting('GN2_BRANCH_URL')
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 64a413c2..adf66fb5 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -36,11 +36,6 @@ def gen_dropdown_json():
                 types=types,
                 datasets=datasets)
 
-    output_file = """./wqflask/static/new/javascript/dataset_menu_structure.json"""
-
-    with open(output_file, 'w') as fh:
-        json.dump(data, fh, indent=3, sort_keys=True)
-
     return data
 
 def get_species():
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index daf818b1..679e38b0 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -5172,6 +5172,23 @@
                   "HSNIH-Rat-PL-RSeq-0818", 
                   "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog"
                ]
+            ],
+            "Prefrontal Cortex mRNA": [
+               [
+                  "864",
+                  "HSNIH-Rat-VoLo-RSeq-0818",
+                  "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "863",
+                  "HSNIH-Rat-PL-RSeq-0818",
+                  "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) rlog"
+               ],
+               [
+                  "861",
+                  "HSNIH-Rat-IL-RSeq-0818",
+                  "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
+               ]
             ]
          }, 
          "HSNIH-RGSMC": {
@@ -7564,4 +7581,4 @@
          ]
       }
    }
-}
\ No newline at end of file
+}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 777d4a2d..777d4a2d 100644..100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html