def setup_class_hook(cls):
cls.study = tmtk.Study()
dir_ = os.path.join(cls.studies_dir, 'blueprinted_modifier')
cls.study.Clinical.add_datafile(os.path.join(dir_, 'datafile.tsv'))
cls.modifiers = pd.read_csv(os.path.join(dir_, 'modifiers.txt'),
sep='\t')
cls.modifiers.set_index('modifier_cd', drop=False, inplace=True)
cls.study.Clinical.Modifiers.df = cls.modifiers
cls.study.study_id = 'test'
cls.study.top_node = '\\Public Studies\\Test\\'
cls.study.apply_blueprint(
os.path.join(cls.studies_dir, 'blueprinted_modifier',
'blueprint.json'))
cls.export = tmtk.toolbox.SkinnyExport(cls.study, cls.temp_dir)
cls.export.build_observation_fact()
def setUpClass(cls):
cls.study = tmtk.Study('studies/valid_study/study.params')
def setup_class_hook(cls):
cls.study = tmtk.Study()
dir_ = os.path.join(cls.studies_dir, 'blueprinted')
cls.study.Clinical.add_datafile(os.path.join(dir_, 'datafile.tsv'))
cls.study.apply_blueprint(os.path.join(dir_, 'blueprint.json'))
def setUpClass(cls):
cls.study = tmtk.Study('studies/remap/study.params')
def setUpClass(cls):
cls.study = tmtk.Study('studies/incomplete/study.params')
def setUpClass(cls):
cls.study = tmtk.Study()
cls.study.Clinical.add_datafile('./studies/blueprinted/datafile.tsv')
cls.study.apply_blueprint('./studies/blueprinted/blueprint.json')
def create_study_from_dir(dir_name):
return tmtk.Study(
os.path.join(TestBase.studies_dir, dir_name, 'study.params'))
def setUp(self):
self.study = tmtk.Study('studies/incomplete/study.params')