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authorPjotr Prins2016-09-09 08:35:18 +0200
committerPjotr Prins2016-09-09 08:35:18 +0200
commit8744bf9c11481c910d029c3e6b1ae1adde27c271 (patch)
treeedfab9ad67d190ef22fe2c876583a9f2380d5f86 /wqflask/base
parent7cc37bf2efba6873fccd0f1756c89d25400afd47 (diff)
parentccf8474f5f94891782891bd3677e6ddf5d08d24a (diff)
downloadgenenetwork2-8744bf9c11481c910d029c3e6b1ae1adde27c271.tar.gz
Merge branch 'master' of github.com:genenetwork/genenetwork2
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py2
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py6
-rw-r--r--wqflask/base/trait.py16
-rw-r--r--wqflask/base/webqtlCaseData.py4
4 files changed, 16 insertions, 12 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d0ec3f3c..1b4e1195 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -106,7 +106,7 @@ Publish or ProbeSet. E.g.
new_type = "Geno"
else:
new_type = "ProbeSet"
- self.datasets[short_dataset_name] = new_type
+ self.datasets[short_dataset_name] = new_type
logger.info("datasets",self.datasets)
def __call__(self, name):
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index e99ef7b5..eb836e6c 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -57,7 +57,7 @@ class MrnaAssayTissueData(object):
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''.format(in_clause)
- logger.sql(query)
+
results = g.db.execute(query).fetchall()
lower_symbols = []
@@ -91,7 +91,7 @@ class MrnaAssayTissueData(object):
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
-
+
symbol_values_dict = {}
if len(id_list) > 0:
@@ -100,8 +100,6 @@ class MrnaAssayTissueData(object):
WHERE TissueProbeSetData.Id IN {} and
TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
- logger.sql('tissue query',query)
-
results = g.db.execute(query).fetchall()
for result in results:
if result.Symbol.lower() not in symbol_values_dict:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 9566c192..900e050c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -116,7 +116,6 @@ class GeneralTrait(object):
return stringy
-
def display_name(self):
stringy = ""
if self.dataset and self.name:
@@ -323,7 +322,7 @@ class GeneralTrait(object):
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if self.confidential:
- self.description_display = ""
+ self.description_display = self.pre_publication_description
#if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
# privilege=self.dataset.privilege,
@@ -331,11 +330,11 @@ class GeneralTrait(object):
# authorized_users=self.authorized_users):
#
# description = self.pre_publication_description
-
- if description:
- self.description_display = description.strip()
else:
- self.description_display = ""
+ if description:
+ self.description_display = description.strip()
+ else:
+ self.description_display = ""
if not self.year.isdigit():
self.pubmed_text = "N/A"
@@ -613,7 +612,10 @@ class GeneralTrait(object):
if self.probe_target_description:
formatted += "; " + self.probe_target_description
elif self.dataset.type == 'Publish':
- formatted = self.post_publication_description
+ if self.confidential:
+ formatted = self.pre_publication_description
+ else:
+ formatted = self.post_publication_description
else:
formatted = "Not available"
return formatted.capitalize()
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index c80fcb65..8df9939e 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -52,6 +52,10 @@ class webqtlCaseData(object):
str += " variance=%2.3f" % self.variance
if self.num_cases != None:
str += " ndata=%d" % self.num_cases
+ if self.name != None:
+ str += " name=%s" % self.name
+ if self.name2 != None:
+ str += " name2=%s" % self.name2
return str
@property