def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
annotations = Annotations(name='annotations',
exclude='excluded',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={'gender': 'M'})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
experiment = Experiment(data=DataType.betas,
task=Task.table,
method=Method.linreg)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def setUp(self):
data = Data(name='cpg_beta', path=ROOT_DIR, base='fixtures')
experiment = Experiment(type=DataType.cpg,
task='',
method='',
params={})
annotations = Annotations(name='annotations',
exclude=CommonTypes.none.value,
cross_reactive=CrossReactive.exclude.value,
snp=SNP.exclude.value,
chr=Chromosome.non_sex.value,
gene_region=GeneRegion.yes.value,
geo=CommonTypes.any.value,
probe_class=CommonTypes.any.value)
observables = Observables(name='observables', types={'gender': 'vs'})
cells = Cells(name='cells', types=CommonTypes.any.value)
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes)
def setUp(self):
data = Data(name='cpg_beta', path=ROOT_DIR, base='fixtures')
experiment = Experiment(type=None, task=None, method=None, params=None)
annotations = Annotations(name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(
data=None,
task=None,
method=None,
)
annotations = Annotations(name='annotations',
type='450k',
exclude='excluded',
select_dict={
'CROSS_R': ['0'],
'Probe_SNPs': ['empty'],
'Probe_SNPs_10': ['empty'],
'CHR': ['-X', '-Y'],
'UCSC_REFGENE_NAME': ['non-empty'],
'Class': ['ClassA', 'ClassB']
})
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
def check_strategy(self, data_type, task, needed_list):
experiment = Experiment(
data=data_type,
task=task,
method=None,
)
self.config.experiment = experiment
context = Context(self.config)
condition = True
real_list = ['load_strategy', 'get_strategy', 'setup_strategy',
'run_strategy', 'release_strategy', 'save_strategy']
real_list = [getattr(context, x) for x in real_list]
for real, needed in zip(real_list, needed_list):
if type(real) != needed:
condition = False
break
return condition