From 8aa6cc5c1cf85ae9f3ac6c87ff0c354af5c947c7 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 7 Dec 2012 14:12:14 -0600
Subject: Got show_trait page to appear again for phenotype traits

Need to see why other samples list doesn't appear for traits in BXDPublishedPhenotypes
---
 wqflask/wqflask/do_search.py                      | 26 ++++-------------------
 wqflask/wqflask/show_trait/SampleList.py          |  3 ++-
 wqflask/wqflask/show_trait/show_trait.py          |  3 ++-
 wqflask/wqflask/templates/show_trait_details.html |  5 ++++-
 4 files changed, 12 insertions(+), 25 deletions(-)

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 403f1b5e..3ce613e9 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -198,26 +198,6 @@ class PhenotypeSearch(DoSearch):
 
         query = self.compile_final_query(where_clause = self.get_fields_clause())
 
-#        self.query = """SELECT PublishXRef.Id,
-#PublishFreeze.createtime as thistable,
-#Publication.PubMed_ID as Publication_PubMed_ID,
-#Phenotype.Post_publication_description as Phenotype_Name FROM Phenotype,
-#PublishFreeze, Publication, PublishXRef WHERE (Phenotype.Post_publication_description
-#REGEXP "[[:<:]]brain[[:>:]]" OR Phenotype.Pre_publication_description REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Pre_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Post_publication_abbreviation REGEXP "[[:<:]]brain[[:>:]]"
-#OR Phenotype.Lab_code REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.PubMed_ID REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Abstract REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Title REGEXP "[[:<:]]brain[[:>:]]"
-#OR Publication.Authors REGEXP "[[:<:]]brain[[:>:]]"
-#OR PublishXRef.Id REGEXP "[[:<:]]brain[[:>:]]")
-#and PublishXRef.InbredSetId = 1
-#and PublishXRef.PhenotypeId = Phenotype.Id
-#and PublishXRef.PublicationId = Publication.Id
-#and PublishFreeze.Id = 1;"""
-
-
         results = self.execute(query)
         print("in [df] run results are:", results)
         return results
@@ -461,7 +441,8 @@ class CisTransLrsSearch(LrsSearch):
 
 
 class CisLrsSearch(CisTransLrsSearch):
-    """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
+    """
+    Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
 
     A cisLRS search can take 3 forms:
     - cisLRS=(min_LRS max_LRS)
@@ -484,9 +465,10 @@ class CisLrsSearch(CisTransLrsSearch):
 class TransLrsSearch(CisTransLrsSearch):
     """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
 
-    A transLRS search can take 2 forms:
+    A transLRS search can take 3 forms:
     - transLRS=(min_LRS max_LRS)
     - transLRS=(min_LRS max_LRS mb_buffer)
+    - transLRS>min_LRS
     where min/max_LRS represent the range of LRS scores and the mb_buffer is the range around
     a particular QTL where its eQTL would be considered "cis". If there is no third parameter,
     mb_buffer will default to 5 megabases.
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 0c752617..d98a810a 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -56,7 +56,8 @@ class SampleList(object):
             if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
                 sample.extra_attributes = self.get_extra_attribute_values(sample_name)
                 print("sample.extra_attributes is", pf(sample.extra_attributes))
-                self.sample_list.append(sample)
+            
+            self.sample_list.append(sample)
 
         print("self.attributes is", pf(self.attributes))
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d1c60877..0f593216 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1627,10 +1627,11 @@ class ShowTrait(object):
                                         this_trait=this_trait,
                                         sample_group_type='primary',
                                         header="%s Only" % (self.dataset.group.name))
+        print("primary_samples is: ", pf(primary_samples))
+
 
         other_sample_names = []
         for sample in this_trait.data.keys():
-            print("hjk - sample is:", sample)
             if sample not in all_samples_ordered:
                 all_samples_ordered.append(sample)
                 other_sample_names.append(sample)
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 4b3862c7..c3abfc9f 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -12,6 +12,7 @@
         </a>
     </dd>
 
+    {% if this_trait.probe_set_specificity %}
     <dt>
         <a href="/blatInfo.html" target="_blank"
            title="Values higher than 2 for the specificity are good">
@@ -19,9 +20,11 @@
         </a>
     </dt>
     <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
-
+    {% endif %}
+    {% if this_trait.probe_set_blat_score %}
     <dt>BLAT Score</dt>
     <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
+    {% endif %}
 </dl>
 
 
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