def setUpClass(cls): cls.project = create_project_with_name('my project') cls.chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.vcf') _extract(cls.chr_run['id']) cls.no_chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.nochr.vcf') _extract(cls.no_chr_run['id']) return super(TestGenotypesAPI, cls).setUpClass()
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('Downloadable project') cls.run = create_run_with_uri(cls.project['id'], '/tests/data/somatic_hg19_14muts.vcf') _extract(cls.run['id']) return super(TestDownload, cls).setUpClass()
def setUpClass(cls): cls.project = create_project_with_name('my project') cls.chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.vcf') _extract(cls.chr_run['id']) cls.no_chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.nochr.vcf') _extract(cls.no_chr_run['id'])
def setUp(self): self.project = create_project_with_name('my project') self.run = create_run_with_uri(self.project['id'], '/tests/data/snv.vcf')
def setUpClass(cls): cls.project = create_project_with_name("project") cls.run = create_run_with_uri(cls.project["id"], "hdfs://somevcf.vcf") return super(TestCommentsAPI, cls).setUpClass()
def setUpClass(cls): cls.project = create_project_with_name('project') cls.run = create_run_with_uri(cls.project['id'], 'http://somevcf.vcf') return super(TestCommentsAPI, cls).setUpClass()