Added Mean column for phenotype traits in search and global search result tables

7 files changed, 28 insertions, 3 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5b32c5ae..ebf3f021 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -710,6 +710,7 @@ class PhenotypeDataSet(DataSet):
                             'Phenotype.Pre_publication_description',
                             'Phenotype.Pre_publication_abbreviation',
                             'Phenotype.Post_publication_abbreviation',
+                            'PublishXRef.mean',
                             'Phenotype.Lab_code',
                             'Publication.PubMed_ID',
                             'Publication.Abstract',
@@ -725,6 +726,7 @@ class PhenotypeDataSet(DataSet):
                                'original_description',
                                'pre_publication_abbreviation',
                                'post_publication_abbreviation',
+                               'mean',
                                'lab_code',
                                'submitter', 'owner',
                                'authorized_users',
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8e779a11..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -354,7 +354,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 SELECT
                         PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
                         Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
-                        Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+                        Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
                         Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
                         Publication.Authors, Publication.Title, Publication.Abstract,
                         Publication.Journal, Publication.Volume, Publication.Pages,
@@ -503,8 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             #LRS and its location
             trait.LRS_score_repr = "N/A"
             trait.LRS_location_repr = "N/A"
-            trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
+            trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
             if dataset.type == 'ProbeSet' and not trait.cellid:
+                trait.mean = ""
                 query = """
                         SELECT
                                 ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b56a858a..05caa100 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -218,6 +218,7 @@ class PhenotypeSearch(DoSearch):
     header_fields = ['Index',
                      'Record',
                      'Description',
+                     'Mean',
                      'Authors',
                      'Year',
                      'Max LRS',
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 12813e9a..3d9b508a 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -139,7 +139,8 @@ class GSearch(object):
                 Publication.`PubMed_ID`,
                 PublishXRef.`LRS`,
                 PublishXRef.`additive`,
-                InbredSet.`InbredSetCode`
+                InbredSet.`InbredSetCode`,
+                PublishXRef.`mean`
                 FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
                 WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
                 AND PublishFreeze.`InbredSetId`=InbredSet.`Id`
@@ -183,6 +184,10 @@ class GSearch(object):
                         this_trait['description'] = line[5].decode('utf-8', 'replace')
                     else:
                         this_trait['description'] = "N/A"
+                    if line[13] != None and line[13] != "":
+                        this_trait['mean'] = line[13]
+                    else:
+                        this_trait['mean'] = "N/A"
                     this_trait['authors'] = line[7]
                     this_trait['year'] = line[8]
                     if this_trait['year'].isdigit():
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 34c647f4..698389ab 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -143,6 +143,9 @@ views.py).
                     trait_dict['pubmed_id'] = this_trait.pubmed_id
                     trait_dict['pubmed_link'] = this_trait.pubmed_link
                 trait_dict['pubmed_text'] = this_trait.pubmed_text
+                trait_dict['mean'] = "N/A"
+                if this_trait.mean != "" and this_trait.mean != None:
+                    trait_dict['mean'] = '%.3f' % this_trait.mean
                 trait_dict['lrs_score'] = this_trait.LRS_score_repr
                 trait_dict['lrs_location'] = this_trait.LRS_location_repr
                 trait_dict['additive'] = "N/A"
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 4d5238ef..f6ffff47 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -190,6 +190,12 @@
                       }
                     },
                     {
+                      'title': "Mean",
+                      'type': "natural",
+                      'width': "10%",
+                      'data': "mean"
+                    },
+                    {
                       'title': "Authors",
                       'type': "natural",
                       'width': "25%",
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 13457030..162bde08 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -350,6 +350,13 @@
                       }
                     },
                     {
+                      'title': "Mean",
+                      'type': "natural",
+                      'width': "110px",
+                      'data': "mean",
+                      'orderSequence': [ "desc", "asc"]
+                    },
+                    {
                       'title': "Authors",
                       'type': "natural",
                       'width': "25%",