def setUpClass(cls): cls.user = helpers.create_user(db, 'name', 'password', 'email') cls.project = create_project_with_name(PROJECT_NAME) cls.project1 = create_project_with_name(PROJECT_NAME + '2') cls.normal_bam = create_bam_with_name(cls.project['id'], 'normal', uri='/bam/path/normal.bam') cls.tumor_bam = create_bam_with_name(cls.project['id'], 'tumor', uri='/bam/path/tumor.bam') with tables(db.engine, 'vcfs') as (con, runs): res = runs.insert( {'uri': 'file://path/to/something.vcf', 'project_id': cls.project['id'], 'normal_bam_id': cls.normal_bam['id'], 'tumor_bam_id': cls.tumor_bam['id'], 'vcf_header': ''} ).returning(*runs.c).execute() cls.run = dict(res.fetchone()) cls.run2 = create_run_with_uri(cls.project['id'], 'http://someuri.vcf') cls.comment1 = create_comment_with_text(cls.run['id'], 'this is some text') cls.comment2 = create_comment_with_text(cls.run['id'], 'more text')
def setUpClass(cls): cls.project = create_project_with_name(cls.PROJECT_NAME) cls.bam = create_bam_with_name( cls.project['id'], cls.PROJECT_NAME, uri=cls.BAM_PATH) return super(TestRunsAPI, cls).setUpClass()