From 6c03a5aeb95f37c477bed3f432790329a0bd5038 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 11 Apr 2016 21:46:04 +0000
Subject: Figured out how to load results into dataTable using AJAX, but still
 need to get it working with Scroller correctly

Added code getting the description, etc to trait.py since it was missed from last commit
---
 wqflask/base/trait.py | 55 +++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 51 insertions(+), 4 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ce3a7608..0bc10b97 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -2,7 +2,7 @@ from __future__ import absolute_import, division, print_function
 
 import string
 import resource
-
+import codecs
 
 from htmlgen import HTMLgen2 as HT
 
@@ -309,13 +309,50 @@ class GeneralTrait(object):
                     holder = unicode(trait_info[i], "utf8", "ignore")
                 setattr(self, field, holder)
 
+            description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
+            target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+
+            if len(description_string) > 1 and description_string != 'None':
+                description_display = description_string
+            else:
+                description_display = self.symbol
+
+            if (len(description_display) > 1 and description_display != 'N/A' and
+                    len(target_string) > 1 and target_string != 'None'):
+                description_display = description_display + '; ' + target_string.strip()
+
+            # Save it for the jinja2 template
+            self.description_display = description_display
+
+            #XZ: trait_location_value is used for sorting
+            trait_location_repr = 'N/A'
+            trait_location_value = 1000000
+
+            if self.chr and self.mb:
+                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+                #This is so we can convert the location to a number used for sorting
+                trait_location_value = convert_location_to_value(self.chr, self.mb)
+                #try:
+                #    trait_location_value = int(self.chr)*1000 + self.mb
+                #except ValueError:
+                #    if self.chr.upper() == 'X':
+                #        trait_location_value = 20*1000 + self.mb
+                #    else:
+                #        trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
+                #                               self.mb)
+
+                #ZS: Put this in function currently called "convert_location_to_value"
+                self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
+                self.location_value = trait_location_value
+                
+                
             if self.dataset.type == 'Publish':
                 self.confidential = 0
                 if self.pre_publication_description and not self.pubmed_id:
                     self.confidential = 1
-                    
-                description = self.post_publication_description
                 
+                description = self.post_publication_description
+            
                 #If the dataset is confidential and the user has access to confidential
                 #phenotype traits, then display the pre-publication description instead
                 #of the post-publication description
@@ -662,7 +699,17 @@ class GeneralTrait(object):
                 ZValue = ZValue*sqrt(self.overlap-3)
                 self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
 
-
+def convert_location_to_value(chromosome, mb):
+    try:
+        location_value = int(chromosome)*1000 + float(mb)
+    except ValueError:
+        if chromosome.upper() == 'X':
+            location_value = 20*1000 + float(mb)
+        else:
+            location_value = (ord(str(chromosome).upper()[0])*1000 +
+                              float(mb))
+    
+    return location_value
 
 @app.route("/trait/get_sample_data")
 def get_sample_data():
-- 
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