Replaced Histogram and Bar Chart with Plotly version and added new Box Plot with Plotly

GEMMA now has option to select genotypes

Updated dataset select dropdowns to be ordered correctly

Fixed dataset select dropdowns for correlations to not show confidential datasets

Added Skewness and Kurtosis to Basic Statistics table

Fixed Verify and RNA-seq buttons on trait page

Temporarily hardcoded Reference page until we get it to link with database

2 files changed, 7 insertions, 3 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index dbdbb51c..6649f8af 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -111,7 +111,7 @@ Publish or ProbeSet. E.g.
                             new_type = "ProbeSet"
                         self.datasets[short_dataset_name] = new_type
         # Set LOG_LEVEL_DEBUG=5 to see the following:
-        logger.debugf(5,"datasets",self.datasets)
+        logger.debugf(5, "datasets",self.datasets)
 
     def __call__(self, name):
         return self.datasets[name]
@@ -426,13 +426,15 @@ def datasets(group_name, this_group = None):
           FROM PublishFreeze,InbredSet
           WHERE PublishFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name = '%s'
-            and PublishFreeze.public > %s)
+            and PublishFreeze.public > %s
+            and PublishFreeze.confidentiality < 1)
          UNION
          (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
           FROM GenoFreeze, InbredSet
           WHERE GenoFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name = '%s'
-            and GenoFreeze.public > %s)
+            and GenoFreeze.public > %s
+            and GenoFreeze.confidentiality < 1)
          UNION
          (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
           FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -441,6 +443,7 @@ def datasets(group_name, this_group = None):
             and ProbeFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name like %s
             and ProbeSetFreeze.public > %s
+            and ProbeSetFreeze.confidentiality < 1
           ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
         ''' % (group_name, webqtlConfig.PUBLICTHRESH,
               group_name, webqtlConfig.PUBLICTHRESH,
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index c3f1e76a..1ef2bc26 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -49,6 +49,7 @@ PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=
 UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
 UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
 ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
 DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'