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 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()
def setUpClass(cls):
cls.project = create_project_with_name(cls.PROJECT_NAME)
return super(TestBamsAPI, cls).setUpClass()
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()