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-rw-r--r--wqflask/base/trait.py44
1 files changed, 22 insertions, 22 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index a71d8157..b51b8c72 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -69,11 +69,11 @@ class GeneralTrait(object):
self.retrieve_info(get_qtl_info=get_qtl_info)
if get_sample_info != False:
self.retrieve_sample_data()
-
-
+
+
def jsonable(self):
"""Return a dict suitable for using as json
-
+
Actual turning into json doesn't happen here though"""
return dict(name=self.name,
dataset=self.dataset.name,
@@ -258,10 +258,10 @@ class GeneralTrait(object):
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id = %s
""" % (self.name, self.dataset.id)
-
+
trait_info = g.db.execute(query).fetchone()
-
-
+
+
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif self.dataset.type == 'ProbeSet':
@@ -310,27 +310,27 @@ class GeneralTrait(object):
if isinstance(trait_info[i], basestring):
holder = unicode(trait_info[i], "utf8", "ignore")
setattr(self, field, holder)
-
+
if self.dataset.type == 'Publish':
self.confidential = 0
if self.pre_publication_description and not self.pubmed_id:
self.confidential = 1
-
+
description = self.post_publication_description
-
+
#If the dataset is confidential and the user has access to confidential
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if self.confidential:
self.description_display = ""
-
+
#if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
# privilege=self.dataset.privilege,
# userName=self.dataset.userName,
# authorized_users=self.authorized_users):
- #
+ #
# description = self.pre_publication_description
-
+
if description:
self.description_display = description.strip()
else:
@@ -343,8 +343,8 @@ class GeneralTrait(object):
if self.pubmed_id:
self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
-
-
+
+
self.homologeneid = None
if self.dataset.type == 'ProbeSet' and self.dataset.group:
if self.geneid:
@@ -374,7 +374,7 @@ class GeneralTrait(object):
if result:
self.homologeneid = result[0]
-
+
description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
@@ -410,7 +410,7 @@ class GeneralTrait(object):
#ZS: Put this in function currently called "convert_location_to_value"
self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
self.location_value = trait_location_value
-
+
if get_qtl_info:
#LRS and its location
@@ -481,7 +481,7 @@ class GeneralTrait(object):
self.locus = self.locus_chr = self.locus_mb = self.additive = ""
else:
self.locus = self.lrs = self.additive = ""
-
+
if (self.dataset.type == 'Publish' or self.dataset.type == "ProbeSet") and self.locus_chr != "" and self.locus_mb != "":
#XZ: LRS_location_value is used for sorting
try:
@@ -493,7 +493,7 @@ class GeneralTrait(object):
LRS_location_value = ord(str(self.locus_chr).upper()[0])*1000 + float(self.locus_mb)
self.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (self.locus_chr, float(self.locus_mb))
- if self.lrs != "":
+ if self.lrs != "":
self.LRS_score_repr = LRS_score_repr = '%3.1f' % self.lrs
self.LRS_score_value = LRS_score_value = self.lrs
else:
@@ -712,7 +712,7 @@ def convert_location_to_value(chromosome, mb):
else:
location_value = (ord(str(chromosome).upper()[0])*1000 +
float(mb))
-
+
return location_value
@app.route("/trait/get_sample_data")
@@ -720,11 +720,11 @@ def get_sample_data():
params = request.args
trait = params['trait']
dataset = params['dataset']
-
+
trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
-
+
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():
# jsonable_sample_data[sample] = trait_ob.data[sample].value