Fixed issue causing anonymous collections to not work on my branch and staging, though still not sure why it's working on production without that change

Added script to convert the dryad format genotype files to BIMBAM

removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable

2 files changed, 43 insertions, 1 deletions

diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index d00b52b8..c605329b 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1966,6 +1966,21 @@
                   "470",
                   "EPFLADEL1013",
                   "EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Exon Level (Oct13) RMA"
+               ],
+               [
+                  "777",
+                  "EL_BXDCDHFDScWAT_0216",
+                  "EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+               ],
+               [
+                  "778",
+                  "EL_BXDHFDScWAT_0216",
+                  "EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+               ],
+               [
+                  "779",
+                  "EL_BXDCDScWAT_0216",
+                  "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA **"
                ]
             ],
             "Adrenal Gland mRNA": [
@@ -3355,6 +3370,15 @@
                ]
             ]
          },
+         "D2GM": {
+            "Retina mRNA": [
+               [
+                  "847",
+                  "JAX_D2GM_RSeq_log2Z_0418",
+                  "JAX Retina (Apr18) RNA-Seq log2-Z"
+               ]
+            ]
+         },
          "EMSR": {},
          "HS": {
             "Hippocampus mRNA": [
@@ -3955,6 +3979,10 @@
             "CXB"
          ],
          [
+            "D2GM",
+            "D2 Glaucoma Model"
+         ],
+         [
             "EMSR",
             "Ethanol-Medicated Stress Reduction"
          ],
@@ -5236,6 +5264,12 @@
                "Spleen mRNA"
             ]
          ],
+         "D2GM": [
+            [
+               "Retina mRNA",
+               "Retina mRNA"
+            ]
+         ],
          "EMSR": [],
          "HS": [
             [
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index d652f2e9..132bae90 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -62,9 +62,17 @@ class AnonUser(object):
             self.anon_id, self.cookie = create_signed_cookie()
         self.key = "anon_collection:v1:{}".format(self.anon_id)
 
-        @after.after_this_request
+        #ZS: This was originally the commented out function below
+        #    For some reason I don't yet understand the commented out code works on production, 
+        #    but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
+        @app.after_request
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
+            return response
+
+        #@after.after_this_request
+        #def set_cookie(response):
+        #    response.set_cookie(self.cookie_name, self.cookie)
 
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,