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

5 files changed, 116 insertions, 4 deletions

diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
new file mode 100644
index 00000000..e833b395
--- /dev/null
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+"""
+Convert data dryad files to a BIMBAM _geno and _snps file
+
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+
+
+def read_dryad_file(filename):
+    exclude_count = 0
+    marker_list = []
+    sample_dict = {}
+    sample_list = []
+    geno_rows = []
+    with open(filename, 'r') as the_file:
+        for i, line in enumerate(the_file):
+            if i > 0:
+                if line.split(" ")[1] == "no":
+                    sample_name = line.split(" ")[0]
+                    sample_list.append(sample_name)
+                    sample_dict[sample_name] = line.split(" ")[2:]
+                else:
+                    exclude_count += 1
+            else:
+                marker_list = line.split(" ")[2:]
+
+    for i, marker in enumerate(marker_list):
+        this_row = []
+        this_row.append(marker)
+        this_row.append("X")
+        this_row.append("Y")
+        for sample in sample_list:
+            this_row.append(sample_dict[sample][i])
+        geno_rows.append(this_row)
+
+    print(exclude_count)
+
+    return geno_rows
+
+    #for i, marker in enumerate(marker_list):
+    #    this_row = []
+    #    this_row.append(marker)
+    #    this_row.append("X")
+    #    this_row.append("Y")
+    #    with open(filename, 'r') as the_file:
+    #        for j, line in enumerate(the_file):
+    #            if j > 0:
+    #                this_row.append(line.split(" ")[i+2])
+    #        print("row: " + str(i))
+    #        geno_rows.append(this_row)
+    #            
+    #return geno_rows
+
+def write_bimbam_files(geno_rows):
+    with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
+        for row in geno_rows:
+            geno_fh.write(", ".join(row) + "\n")
+
+def convert_dryad_to_bimbam(filename):
+    geno_file_rows = read_dryad_file(filename)
+    write_bimbam_files(geno_file_rows)
+
+if __name__=="__main__":
+    input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
+    convert_dryad_to_bimbam(input_filename)
\ No newline at end of file
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 2825c6ea..18b2dac9 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -63,7 +63,7 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
-def parse_db_uri(db_uri):
+def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
     parsed_uri = urlparse.urlparse(SQL_URI)
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index c11073fb..41a3aad8 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -59,7 +59,7 @@ def set_data(dataset_name):
     orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
 
     sample_list = []
-    with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh:
+    with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh:
         for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)):
             trait_dict = {}
             sample_list = []
@@ -118,7 +118,7 @@ if __name__ == '__main__':
 
     #out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
 
-    #success, _ = bulk(es, set_data(sys.argv[1]))
+    success, _ = bulk(es, set_data(sys.argv[1]))
 
     response = es.search(
         index = "traits", doc_type = "trait", body = {
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,