From f9bb77224092c38b8a14c9bca1044dcb843bcbae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Mar 2021 21:03:17 +0000
Subject: Added URL as second value for RRID case attributes, so it can be
 displayed in the trait page sample table

---
 wqflask/wqflask/show_trait/SampleList.py | 13 +++++++++++--
 wqflask/wqflask/show_trait/show_trait.py |  1 +
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ece485ae..6017f895 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -2,13 +2,12 @@ import re
 import itertools
 
 from flask import g
-from base import webqtlCaseData
+from base import webqtlCaseData, webqtlConfig
 from pprint import pformat as pf
 
 from utility import Plot
 from utility import Bunch
 
-
 class SampleList(object):
     def __init__(self,
                  dataset,
@@ -70,6 +69,16 @@ class SampleList(object):
                 sample.extra_attributes = self.sample_attribute_values.get(
                     sample_name, {})
 
+                #ZS: Add a url so RRID case attributes can be displayed as links
+                if 'rrid' in sample.extra_attributes:
+                    if len(sample.extra_attributes['rrid'].split(":")) > 1:
+                        the_rrid = sample.extra_attributes['rrid'].split(":")[1]
+                        sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']]
+                        if self.dataset.group.species == "mouse":
+                            sample.extra_attributes['rrid'].append(webqtlConfig.RRID_MOUSE_URL % the_rrid)
+                        elif self.dataset.group.species == "rat":
+                            sample.extra_attributes['rrid'].append(webqtlConfig.RRID_RAT_URL % the_rrid)
+
             self.sample_list.append(sample)
 
         self.se_exists = any(sample.variance for sample in self.sample_list)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index cf3accaa..878c41c0 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -269,6 +269,7 @@ class ShowTrait(object):
                        short_description = short_description,
                        unit_type = trait_units,
                        dataset_type = self.dataset.type,
+                       species = self.dataset.group.species,
                        scales_in_geno = self.scales_in_geno,
                        data_scale = self.dataset.data_scale,
                        sample_group_types = self.sample_group_types,
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