From 0a0d733af4b6c61c381a1c4ec9fa162182a057e9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Jul 2020 14:47:04 -0500
Subject: Fixed some of the logic with how traits are authenticated to avoid
 situation where a trait is authenticated twice

---
 wqflask/base/trait.py | 30 ++++++++----------------------
 1 file changed, 8 insertions(+), 22 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7fc016f3..4c3e790c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -49,7 +49,6 @@ def create_trait(**kw):
     if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
         if the_trait.dataset.type != "Temp":
-
             the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
         return the_trait
     else:
@@ -144,6 +143,7 @@ class GeneralTrait(object):
                 formatted = self.post_publication_description
         else:
             formatted = "Not available"
+
         return formatted
 
     @property
@@ -388,27 +388,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     try:
         response = requests.get(the_url).content
-        if response.strip() == "no-access":
-            trait.view = False
-            return trait
-        else:
-            trait_info = json.loads(response)
-    except:
-        resource_info = get_resource_info(resource_id)
-        if resource_info:
-            default_permissions = resource_info['default_mask']['data']
-        else:
-            default_permissions = webqtlConfig.DEFAULT_PRIVILEGES
-        if 'view' not in default_permissions:
-            trait.view = False
-            return trait
-
+        trait_info = json.loads(response)
+    except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
         if dataset.type == 'Publish':
             query = """
                     SELECT
-                            PublishXRef.Id, Publication.PubMed_ID,
+                            PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
                             Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
-                            Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+                            Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
                             Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
                             Publication.Authors, Publication.Title, Publication.Abstract,
                             Publication.Journal, Publication.Volume, Publication.Pages,
@@ -472,11 +459,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     if trait_info:
         trait.haveinfo = True
-
         for i, field in enumerate(dataset.display_fields):
-            holder = trait_info[i]
-            #if isinstance(trait_info[i], basestring):
-            #    holder = holder.encode('latin1')
+            holder =  trait_info[i]
+            # if isinstance(trait_info[i], basestring):
+            #     holder = unicode(holder.strip(codecs.BOM_UTF8), 'utf-8', "ignore")
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
-- 
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