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authorZachary Sloan2014-06-25 20:19:02 +0000
committerZachary Sloan2014-06-25 20:19:02 +0000
commitdf6a70c9a06bc30856a1bc46023bd67e5325f5c9 (patch)
treec7ed438dbc627043785337c0a81ce7988e16d50c /wqflask/base
parent33cf7a7dafc0bf338f98eb793ffd87d4442a58fd (diff)
downloadgenenetwork2-df6a70c9a06bc30856a1bc46023bd67e5325f5c9.tar.gz
Added Karl's correlation matrix code
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
Diffstat (limited to 'wqflask/base')
-rwxr-xr-xwqflask/base/data_set.py10
-rwxr-xr-xwqflask/base/species.py6
-rwxr-xr-xwqflask/base/trait.py2
3 files changed, 13 insertions, 5 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a2b13748..843862aa 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -164,6 +164,7 @@ class Markers(object):
marker['chr'] = int(marker['chr'])
else:
marker['chr'] = 19
+ print("Mb:", marker['Mb'])
marker['Mb'] = float(marker['Mb'])
self.markers = markers
@@ -670,6 +671,7 @@ class PhenotypeDataSet(DataSet):
def get_trait_info(self, trait_list, species = ''):
for this_trait in trait_list:
+
if not this_trait.haveinfo:
this_trait.retrieve_info(get_qtl_info=True)
@@ -679,6 +681,7 @@ class PhenotypeDataSet(DataSet):
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if this_trait.confidential:
+ this_trait.description_display = ""
continue # for now
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -688,7 +691,12 @@ class PhenotypeDataSet(DataSet):
description = this_trait.pre_publication_description
- this_trait.description_display = description.strip()
+ if len(description) > 0:
+ this_trait.description_display = description.strip()
+ else:
+ this_trait.description_display = ""
+
+ print("this_trait.description_display is:", this_trait.description_display)
if not this_trait.year.isdigit():
this_trait.pubmed_text = "N/A"
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index ebc2bfed..52bd8297 100755
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -13,7 +13,7 @@ from pprint import pformat as pf
class TheSpecies(object):
def __init__(self, dataset):
self.dataset = dataset
- print("self.dataset is:", pf(self.dataset.__dict__))
+ #print("self.dataset is:", pf(self.dataset.__dict__))
self.chromosomes = Chromosomes(self.dataset)
self.genome_mb_length = self.chromosomes.get_genome_mb_length()
@@ -56,8 +56,8 @@ class Chromosomes(object):
InbredSet.Name = %s
Order by OrderId
""", self.dataset.group.name).fetchall()
- print("group: ", self.dataset.group.name)
- print("bike:", results)
+ #print("group: ", self.dataset.group.name)
+ #print("bike:", results)
for item in results:
self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 3f80d4a4..2bbd1f2a 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -645,7 +645,7 @@ def get_sample_data():
trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
- return json.dumps({key: value.value for key, value in trait_ob.data.iteritems() })
+ return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
#jsonable_sample_data = {}
#for sample in trait_ob.data.iteritems():