Merge branch 'testing' into Feature/Add-upload-data-forms

7 files changed, 25 insertions, 18 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 968b6d4b..5574128d 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -337,6 +337,10 @@ def jsonable(trait):
                     dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
+    elif dataset.name == "Temp":
+        return dict(name=trait.name,
+                    dataset="Temp",
+                    dataset_name="Temp")
     else:
         return dict()
 
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index e0ae3414..12fd6be5 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -39,8 +39,8 @@ def get_trait_db_obs(self, trait_db_list):
     for trait in trait_db_list:
         data, _separator, hmac_string = trait.rpartition(':')
         data = data.strip()
-        assert hmac_string == hmac.hmac_creation(data), "Data tampering?"
-        trait_name, dataset_name = data.split(":")
+        assert hmac_string==hmac.hmac_creation(data), "Data tampering?"
+        trait_name, dataset_name = data.split(":")[:2]
         if dataset_name == "Temp":
             dataset_ob = data_set.create_dataset(
                 dataset_name=dataset_name, dataset_type="Temp",
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 83ebcdf9..06c9300a 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -146,7 +146,12 @@ def gen_covariates_file(this_dataset, covariates, samples):
     for covariate in covariate_list:
         this_covariate_data = []
         trait_name = covariate.split(":")[0]
-        dataset_ob = create_dataset(covariate.split(":")[1])
+        dataset_name = covariate.split(":")[1]
+        if dataset_name == "Temp":
+            temp_group = trait_name.split("_")[2]
+            dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+        else:
+            dataset_ob = create_dataset(covariate.split(":")[1])
         trait_ob = create_trait(dataset=dataset_ob,
                                 name=trait_name,
                                 cellid=None)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index f5ee5303..c99fce01 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -182,15 +182,3 @@ class NetworkGraph:
                             samples=self.all_sample_list,
                             sample_data=self.sample_data,
                             elements=self.elements,)
-
-    def get_trait_db_obs(self, trait_db_list):
-        self.trait_list = []
-        for i, trait_db in enumerate(trait_db_list):
-            if i == (len(trait_db_list) - 1):
-                break
-            trait_name, dataset_name = trait_db.split(":")
-            dataset_ob = data_set.create_dataset(dataset_name)
-            trait_ob = create_trait(dataset=dataset_ob,
-                                    name=trait_name,
-                                    cellid=None)
-            self.trait_list.append((trait_ob, dataset_ob))
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 36500a8d..fd7c132b 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -119,7 +119,7 @@ class SearchResultPage:
                 trait_dict['dataset'] = this_trait.dataset.name
                 trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
                 if this_trait.dataset.type == "ProbeSet":
-                    trait_dict['symbol'] = this_trait.symbol
+                    trait_dict['symbol'] = this_trait.symbol if this_trait.symbol else "N/A"
                     trait_dict['description'] = "N/A"
                     if this_trait.description_display:
                         trait_dict['description'] = this_trait.description_display
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index ecb1220d..48b9b7be 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -326,4 +326,15 @@ $(function() {
       } );
   }
 
+  apply_default = function() {
+    let default_collection_id = $.cookie('default_collection');
+    if (default_collection_id) {
+      let the_option = $('[name=existing_collection] option').filter(function() {
+        return ($(this).text().split(":")[0] == default_collection_id);
+      })
+      the_option.prop('selected', true);
+    }
+  }
+  apply_default();
+
 });
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ccb2ac5a..e6f22deb 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -191,7 +191,7 @@
                     Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
                 </li>
                 <li>
-                    <a href="http://www.iniastress.org/">NIAAA</a>
+                    <a href="https://www.ohsu.edu/iniastress-consortium">NIAAA</a>
                     Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
                 </li>
                 <li>
@@ -257,7 +257,6 @@
     <script src="{{ url_for('js', filename='jquery-ui/jquery-ui.min.js') }}" type="text/javascript"></script>
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
-    <!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
 
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>