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authorPjotr Prins2016-05-29 17:20:20 +0000
committerPjotr Prins2016-05-29 17:20:20 +0000
commit4b083f2cdfa493f7b2ccc3c30cc5bb6cad694d3a (patch)
treec2c2503d88868f13b06dd66328720486e72f647a /wqflask/base
parent33d817c81b4b22bc051dbde2b26c5d4de028369e (diff)
parent0d22d3bc72cfc35cb23efce3d1687477880a5b3e (diff)
downloadgenenetwork2-4b083f2cdfa493f7b2ccc3c30cc5bb6cad694d3a.tar.gz
Merge branch 'master' of github.com:genenetwork/genenetwork2
Diffstat (limited to 'wqflask/base')
-rw-r--r--wqflask/base/data_set.py6
-rw-r--r--wqflask/base/trait.py14
-rwxr-xr-xwqflask/base/webqtlCaseData.py3
-rw-r--r--[-rwxr-xr-x]wqflask/base/webqtlConfig.py2
4 files changed, 14 insertions, 11 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 053b45fc..4953e728 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -711,7 +711,7 @@ class PhenotypeDataSet(DataSet):
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, PublishData.value, PublishSE.error, NStrain.count
+ Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
FROM
(PublishData, Strain, PublishXRef, PublishFreeze)
left join PublishSE on
@@ -803,7 +803,7 @@ class GenotypeDataSet(DataSet):
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
+ Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
@@ -1031,7 +1031,7 @@ class MrnaAssayDataSet(DataSet):
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
+ Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2
FROM
(ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6c5ca8b2..d1c0be83 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -180,13 +180,15 @@ class GeneralTrait(object):
samples = []
vals = []
the_vars = []
+ sample_aliases = []
for sample_name, sample_data in self.data.items():
if sample_data.value != None:
if not include_variance or sample_data.variance != None:
samples.append(sample_name)
vals.append(sample_data.value)
the_vars.append(sample_data.variance)
- return samples, vals, the_vars
+ sample_aliases.append(sample_data.name2)
+ return samples, vals, the_vars, sample_aliases
#
@@ -230,7 +232,7 @@ class GeneralTrait(object):
if results:
for item in results:
- name, value, variance, num_cases = item
+ name, value, variance, num_cases, name2 = item
if not samplelist or (samplelist and name in samplelist):
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
@@ -313,9 +315,9 @@ class GeneralTrait(object):
self.confidential = 0
if self.pre_publication_description and not self.pubmed_id:
self.confidential = 1
-
- description = self.post_publication_description
+ 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
@@ -329,7 +331,7 @@ class GeneralTrait(object):
#
# description = self.pre_publication_description
- if len(description) > 0:
+ if description:
self.description_display = description.strip()
else:
self.description_display = ""
@@ -479,7 +481,7 @@ class GeneralTrait(object):
else:
self.locus = self.lrs = self.additive = ""
- if self.locus_chr != "" and self.locus_mb != "":
+ 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:
LRS_location_value = int(self.locus_chr)*1000 + float(self.locus_mb)
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 42763aed..99a34866 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -29,8 +29,9 @@ print("Mr. Mojo Risin 2")
class webqtlCaseData(object):
"""one case data in one trait"""
- def __init__(self, name, value=None, variance=None, num_cases=None):
+ def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
self.name = name
+ self.name2 = name2 # Other name (for traits like BXD65a)
self.value = value # Trait Value
self.variance = variance # Trait Variance
self.num_cases = num_cases # Number of individuals/cases
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 0358bcbf..d0016b33 100755..100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -69,7 +69,7 @@ GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/')
# Flat file directories
GENODIR = flat_files('genotype')+'/'
-JSON_GENODIR = assert_dir(GENODIR+'json/')
+JSON_GENODIR = flat_files('json')+'/'
PORTADDR = "http://50.16.251.170"