From ecb0a828de3ba744da82a45e1dc7a55906fd5fb1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 May 2020 19:38:27 -0500
Subject: Fixed blatseq issue and geno correlation issue

---
 wqflask/base/data_set.py                           |  3 +--
 wqflask/wqflask/show_trait/show_trait.py           | 26 +++++++++++-----------
 .../wqflask/static/new/javascript/show_trait.js    |  2 +-
 wqflask/wqflask/templates/show_trait_details.html  |  2 +-
 4 files changed, 16 insertions(+), 17 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5f08c34c..1457ba8d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -165,12 +165,11 @@ Publish or ProbeSet. E.g.
 
             geno_query =    """
                                 SELECT
-                                    GenoFreezeId
+                                    GenoFreeze.Id
                                 FROM
                                     GenoFreeze
                                 WHERE
                                     GenoFreeze.Name = "{0}"
-                                {1}
                             """.format(name)
 
             results = g.db.execute(geno_query).fetchall()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f73079f8..072d7f8c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -73,16 +73,16 @@ class ShowTrait(object):
 
         #ZS: Get verify/rna-seq link URLs
         try:
-            blatsequence = self.this_trait.blatseq
+            blatsequence = self.this_trait.sequence
             if not blatsequence:
                 #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
                 query1 = """SELECT Probe.Sequence, Probe.Name
-                           FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
-                           WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                                 ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                 ProbeSetFreeze.Name = '%s' AND
-                                 ProbeSet.Name = '%s' AND
-                                 Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+                            FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
+                            WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                                    ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+                                    ProbeSetFreeze.Name = '%s' AND
+                                    ProbeSet.Name = '%s' AND
+                                    Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
                 seqs = g.db.execute(query1).fetchall()
                 if not seqs:
                     raise ValueError
@@ -98,10 +98,10 @@ class ShowTrait(object):
             query2 = """SELECT Probe.Sequence, Probe.Name
                         FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
                         WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                              ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                              ProbeSetFreeze.Name = '%s' AND
-                              ProbeSet.Name = '%s' AND
-                              Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+                                ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+                                ProbeSetFreeze.Name = '%s' AND
+                                ProbeSet.Name = '%s' AND
+                                Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
 
             seqs = g.db.execute(query2).fetchall()
             for seqt in seqs:
@@ -121,8 +121,8 @@ class ShowTrait(object):
                 self.UCSC_BLAT_URL = ""
                 self.UTHSC_BLAT_URL = ""
         except:
-            self.UCSC_BLAT_URL = ""
-            self.UTHSC_BLAT_URL = ""
+           self.UCSC_BLAT_URL = ""
+           self.UTHSC_BLAT_URL = ""
 
         if self.dataset.type == "ProbeSet":
             self.show_probes = "True"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index d94a2347..785e5332 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -518,7 +518,7 @@ submit_special = function(url) {
   return $("#trait_data_form").submit();
 };
 
-var corr_input_list = ['corr_type', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
                         'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
 $(".corr_compute").on("click", (function(_this) {
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 20dee54e..62268a54 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -212,7 +212,7 @@
         <a href="#redirect">
         <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
         </a>
-        {% if this_trait.dataset.type == 'ProbeSet' %}
+        {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
         <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
         <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
-- 
cgit v1.2.3