From 2eeaf2f6df9deb3f89db0b5821d784b93eb4bc36 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Tue, 12 May 2015 14:10:04 +0300
Subject: Fix #35

* 'aliases' and 'location' are shown only where relevant
* descriptions for phenotype datasets are provided at the top
---
 wqflask/base/trait.py                             | 28 ++++++++++++++++++-----
 wqflask/wqflask/templates/show_trait.html         | 10 +++++---
 wqflask/wqflask/templates/show_trait_details.html |  6 ++++-
 3 files changed, 34 insertions(+), 10 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index f3648b80..8930c917 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -53,7 +53,8 @@ class GeneralTrait(object):
         self.pvalue = None
         self.mean = None
         self.num_overlap = None
-
+        self.strand_probe = None
+        self.symbol = None
 
         if kw.get('fullname'):
             name2 = value.split("::")
@@ -532,13 +533,28 @@ class GeneralTrait(object):
             setDescription.append(self.dataset.genHTML(Class='cori'))
         return setDescription
 
+    @property
+    def name_header_fmt(self):
+        '''Return a human-readable name for use in page header'''
+        if self.dataset.type == 'ProbeSet':
+            return self.symbol
+        elif self.dataset.type == 'Geno':
+            return self.name
+        elif self.dataset.type == 'Publish':
+            return self.post_publication_abbreviation
+        else:
+            return "unnamed"
+
     @property
     def description_fmt(self):
         '''Return a text formated description'''
-        if self.description:
-            formatted = self.description
-            if self.probe_target_description:
-                formatted += "; " + self.probe_target_description
+        if self.dataset.type == 'ProbeSet':
+            if self.description:
+                formatted = self.description
+                if self.probe_target_description:
+                    formatted += "; " + self.probe_target_description
+        elif self.dataset.type == 'Publish':
+            formatted = self.post_publication_description
         else:
             formatted = "Not available"
         return formatted.capitalize()
@@ -652,4 +668,4 @@ def get_sample_data():
     #    jsonable_sample_data[sample] = trait_ob.data[sample].value
     #
     #return jsonable_sample_data
-    
\ No newline at end of file
+
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a1723ef8..d6f22f41 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -13,8 +13,12 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-    {{ header("{}".format(this_trait.symbol),
-        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+    {% if this_trait.dataset.type != 'Geno' %}
+	{{ header("{}".format(this_trait.name_header_fmt),
+	    '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+    {% else %}
+	{{ header("{}".format(this_trait.name_header_fmt)) }}
+    {% endif %}
 
 
     <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
@@ -31,7 +35,7 @@
             <div class="page-header">
                 <h1>{{ dataset.group.species.capitalize() }} -
                     {{ dataset.group.name }} -
-                    {{ this_trait.symbol }}
+                    {{ this_trait.name_header_fmt }}
                 </h1>
             </div>
             
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 0afac1f7..e1780e42 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,9 +1,13 @@
 <dl class="dl-horizontal">
+    {% if this_trait.dataset.type == 'ProbeSet' %}
     <dt>Aliases</dt>
     <dd>{{ this_trait.alias_fmt }}</dd>
+    {% endif %}
 
+    {% if this_trait.dataset.type != 'Publish' %}
     <dt>Location</dt>
     <dd>{{ this_trait.location_fmt }}</dd>
+    {% endif %}
 
     <dt>Database</dt>
     <dd>
@@ -16,7 +20,7 @@
     <dt>
         <a href="/blatInfo.html" target="_blank"
            title="Values higher than 2 for the specificity are good">
-            BLAT Specifity
+            BLAT Specificity
         </a>
     </dt>
     <dd>{{ "%0.3f" | format(this_trait.probe_set_specificity|float) }}</dd>
-- 
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