def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
if name == None:
self.name, self.id, self.genetic_type = fetchone(
dataset.query_for_group)
else:
self.name, self.id, self.genetic_type = fetchone(
"SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'"
% name)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
self.accession_id = self.get_accession_id()
self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
self.genofile = None
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
If the data set name parameter is not found in the 'Name' field of
the data set table, check if it is actually the FullName or
ShortName instead.
This is not meant to retrieve the data set info if no name at
all is passed.
"""
try:
if self.type == "ProbeSet":
query_args = tuple(escape(x) for x in (
str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
FROM ProbeSetFreeze, ProbeFreeze, Tissue
WHERE ProbeSetFreeze.public > %s
AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
AND ProbeFreeze.TissueId = Tissue.Id
AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
""" % (query_args),"/dataset/"+self.name+".json",
lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
)
else:
query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
self.tissue = "N/A"
self.id, self.name, self.fullname, self.shortname = fetchone("""
SELECT Id, Name, FullName, ShortName
FROM %s
WHERE public > %s AND
(Name = '%s' OR FullName = '%s' OR ShortName = '%s')
""" % (query_args))
except TypeError:
logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
if name == None:
self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
else:
self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
self.accession_id = self.get_accession_id()
self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
self.genofile = None
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
If the data set name parameter is not found in the 'Name' field of
the data set table, check if it is actually the FullName or
ShortName instead.
This is not meant to retrieve the data set info if no name at
all is passed.
"""
try:
if self.type == "ProbeSet":
query_args = tuple(escape(x) for x in (
str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
FROM ProbeSetFreeze, ProbeFreeze, Tissue
WHERE ProbeSetFreeze.public > %s
AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
AND ProbeFreeze.TissueId = Tissue.Id
AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
""" % (query_args),"/dataset/"+self.name+".json",
lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
)
else:
query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
self.tissue = "N/A"
self.id, self.name, self.fullname, self.shortname = fetchone("""
SELECT Id, Name, FullName, ShortName
FROM %s
WHERE public > %s AND
(Name = '%s' OR FullName = '%s' OR ShortName = '%s')
""" % (query_args))
except TypeError:
logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
def __init__(self, dataset):
"""This sets self.group and self.group_id"""
#logger.debug("DATASET NAME2:", dataset.name)
self.name, self.id = fetchone(dataset.query_for_group)
if self.name == 'BXD300':
self.name = "BXD"
self.f1list = None
self.parlist = None
self.get_f1_parent_strains()
#logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list))
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
self.allsamples = None
self._datasets = None
