def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist == None:
samplelist = []
if dataset.type == "Temp":
results = Redis.get(trait.name).split()
else:
results = dataset.retrieve_sample_data(trait.name)
# Todo: is this necessary? If not remove
trait.data.clear()
if results:
if dataset.type == "Temp":
all_samples_ordered = dataset.group.all_samples_ordered()
for i, item in enumerate(results):
try:
trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
except:
pass
else:
for item in results:
name, value, variance, num_cases, name2 = item
if not samplelist or (samplelist and name in samplelist):
trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
return trait
def __init__(self, dataset, sample_names, this_trait, sample_group_type,
header):
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
self.sample_attribute_values = {}
self.get_attributes()
print("camera: attributes are:", pf(self.attributes))
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
#ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
print("No sample %s, let's create it now" % sample_name)
sample = webqtlCaseData.webqtlCaseData(sample_name)
#sampleNameAdd = ''
#if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
# sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
sample.extra_info = {}
if self.dataset.group.name == 'AXBXA' and sample_name in (
'AXB18/19/20', 'AXB13/14', 'BXA8/17'):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
print(" type of sample:", type(sample))
if sample_group_type == 'primary':
sample.this_id = "Primary_" + str(counter)
else:
sample.this_id = "Other_" + str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
print("sample.extra_attributes is",
pf(sample.extra_attributes))
self.sample_list.append(sample)
print("self.attributes is", pf(self.attributes))
self.do_outliers()
#do_outliers(the_samples)
print("*the_samples are [%i]: %s" %
(len(self.sample_list), pf(self.sample_list)))
for sample in self.sample_list:
print("apple:", type(sample), sample)
def __init__(self,
dataset,
sample_names,
this_trait,
sample_group_type,
header):
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
self.sample_attribute_values = {}
self.get_attributes()
print("camera: attributes are:", pf(self.attributes))
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
#ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
print("No sample %s, let's create it now" % sample_name)
sample = webqtlCaseData.webqtlCaseData(sample_name)
#sampleNameAdd = ''
#if fd.RISet == 'AXBXA' and sampleName in ('AXB18/19/20','AXB13/14','BXA8/17'):
# sampleNameAdd = HT.Href(url='/mouseCross.html#AXB/BXA', text=HT.Sup('#'), Class='fs12', target="_blank")
sample.extra_info = {}
if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
print(" type of sample:", type(sample))
if sample_group_type == 'primary':
sample.this_id = "Primary_" + str(counter)
else:
sample.this_id = "Other_" + str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
print("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
print("self.attributes is", pf(self.attributes))
self.do_outliers()
#do_outliers(the_samples)
print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list)))
for sample in self.sample_list:
print("apple:", type(sample), sample)
def retrieve_sample_data(self, samplelist=None):
if samplelist == None:
samplelist = []
#assert self.dataset
#if self.cellid:
# #Probe Data
# query = '''
# SELECT
# Strain.Name, ProbeData.value, ProbeSE.error, ProbeData.Id
# FROM
# (ProbeData, ProbeFreeze, ProbeSetFreeze, ProbeXRef,
# Strain, Probe, ProbeSet)
# left join ProbeSE on
# (ProbeSE.DataId = ProbeData.Id AND ProbeSE.StrainId = ProbeData.StrainId)
# WHERE
# Probe.Name = '%s' AND ProbeSet.Name = '%s' AND
# Probe.ProbeSetId = ProbeSet.Id AND
# ProbeXRef.ProbeId = Probe.Id AND
# ProbeXRef.ProbeFreezeId = ProbeFreeze.Id AND
# ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
# ProbeSetFreeze.Name = '%s' AND
# ProbeXRef.DataId = ProbeData.Id AND
# ProbeData.StrainId = Strain.Id
# Order BY
# Strain.Name
# ''' % (self.cellid, self.name, self.dataset.name)
#
#else:
results = self.dataset.retrieve_sample_data(self.name)
# Todo: is this necessary? If not remove
self.data.clear()
if self.dataset.group.parlist:
all_samples_ordered = (self.dataset.group.parlist +
self.dataset.group.f1list +
self.dataset.group.samplelist)
elif self.dataset.group.f1list:
all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
else:
all_samples_ordered = self.dataset.group.samplelist
if results:
for item in results:
name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
def retrieve_sample_data(self, samplelist=None):
if samplelist == None:
samplelist = []
results = self.dataset.retrieve_sample_data(self.name)
# Todo: is this necessary? If not remove
self.data.clear()
all_samples_ordered = self.dataset.group.all_samples_ordered()
if results:
for item in results:
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)
def retrieve_sample_data(self, samplelist=None):
if samplelist == None:
samplelist = []
results = self.dataset.retrieve_sample_data(self.name)
# Todo: is this necessary? If not remove
self.data.clear()
all_samples_ordered = self.dataset.group.all_samples_ordered()
if results:
for item in results:
name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
def __init__(self,
dataset,
sample_names,
this_trait,
sample_group_type="primary",
header="Samples"):
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
self.sample_attribute_values = {}
self.get_attributes()
if self.this_trait and self.dataset:
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
# ZS: self.this_trait will be a list if it is a Temp trait
if isinstance(self.this_trait, list):
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
if counter <= len(self.this_trait):
if isinstance(self.this_trait[counter - 1],
(bytes, bytearray)):
if (self.this_trait[counter -
1].decode("utf-8").lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
value=float(self.this_trait[counter - 1]))
else:
if (self.this_trait[counter - 1].lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
value=float(self.this_trait[counter - 1]))
else:
# ZS - If there's no value for the sample/strain,
# create the sample object (so samples with no value
# are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
if (self.dataset.group.name == 'AXBXA'
and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
sample.this_id = str(counter)
# ZS: For extra attribute columns; currently only used by
# several datasets
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
self.sample_list.append(sample)
self.se_exists = any(sample.variance for sample in self.sample_list)
self.num_cases_exists = any(sample.num_cases
for sample in self.sample_list)
first_attr_col = self.get_first_attr_col()
for sample in self.sample_list:
sample.first_attr_col = first_attr_col
self.do_outliers()
def __init__(self,
dataset,
sample_names,
this_trait,
sample_group_type="primary",
header="Samples"):
self.dataset = dataset
self.this_trait = this_trait
self.sample_group_type = sample_group_type # primary or other
self.header = header
self.sample_list = [] # The actual list
self.sample_attribute_values = {}
self.get_attributes()
#self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
if self.this_trait and self.dataset:
self.get_extra_attribute_values()
for counter, sample_name in enumerate(sample_names, 1):
sample_name = sample_name.replace("_2nd_", "")
if type(
self.this_trait
) is list: #ZS: self.this_trait will be a list if it is a Temp trait
if counter <= len(self.this_trait) and str(
self.this_trait[counter - 1]).upper() != 'X':
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
value=float(self.this_trait[counter - 1]))
else:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
else:
#ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
try:
sample = self.this_trait.data[sample_name]
except KeyError:
#logger.debug("No sample %s, let's create it now" % sample_name)
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
if self.dataset.group.name == 'AXBXA' and sample_name in (
'AXB18/19/20', 'AXB13/14', 'BXA8/17'):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
sample.this_id = str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
#logger.debug("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
#logger.debug("attribute vals are", pf(self.sample_attribute_values))
self.do_outliers()
def setUp(self):
self.w = webqtlCaseData(name="Test",
value=0,
variance=0.0,
num_cases=10,
name2="Test2")
