aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorzsloan2020-04-06 17:41:19 -0500
committerzsloan2020-04-06 17:41:19 -0500
commit9e6b8a2b2adfb4b41867ecd6932ce899872eea9e (patch)
tree3bfbcbd862fa8c935ded7bab0399e4beec795f4e /wqflask
parent984030cbff9c8f49a664df7c693f852f6d09b2e5 (diff)
downloadgenenetwork2-9e6b8a2b2adfb4b41867ecd6932ce899872eea9e.tar.gz
Added Mean column for phenotype traits in search and global search result tables
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py2
-rw-r--r--wqflask/base/trait.py5
-rw-r--r--wqflask/wqflask/do_search.py1
-rw-r--r--wqflask/wqflask/gsearch.py7
-rw-r--r--wqflask/wqflask/search_results.py3
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html6
-rw-r--r--wqflask/wqflask/templates/search_result_page.html7
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%",