def test_get_runs(self):
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
run_date = datetime.date(2019, 2, 15)
run = SequencingRun(id=2, run_date=run_date, machine_id='M00123',
run_number='2', flowcell_id='A',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
# Get all runs
response = self.client.get('/api/v0/runs')
assert len(response.json['runs']) == 2
# Get a specific run
response = self.client.get('/api/v0/runs?run_barcode=190110_M00123_0001_000000001')
assert len(response.json['runs']) == 1
# Assert invalid barcode is caught
response = self.client.get('/api/v0/runs?run_barcode=1')
assert response.status_code == 400
# Fetch an unknown run
response = self.client.get('/api/v0/runs?run_barcode=190110_M00124_0001_000000001')
assert response.status_code == 404
def test_download_file(self):
''' Test GET /<sequencing_run_id>/file works '''
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
boto3.clients['s3'].upload_file(Filename="test_data/SampleSheet.csv",
Bucket='somebucket',
Key="/PHIX3_test/SampleSheet.csv")
# Test if we don't provide a file, the response is http 400
response = self.client.get('/api/v0/runs/1/file')
assert response.status_code == 400
# Test if we don't provide a valid run, the response is http 404
response = self.client.get('/api/v0/runs/2/file?file=SampleSheet.csv')
assert response.status_code == 404
# Test we can download a file
response = self.client.get('/api/v0/runs/1/file?file=SampleSheet.csv')
# Check
assert response.status_code == 200
# Test if we don't provide a valid file, the response is http 404
response = self.client.get('/api/v0/runs/1/file?file=nofile')
assert response.status_code == 404
def test_post_demultiplex_scrnaseq(self):
# Set up test case
data = {'ASSAY': 'scRNASeq'}
# Set up supporting mocks
resp = boto3.clients["iam"].create_role(
RoleName="TestRole", AssumeRolePolicyDocument="some_policy")
iam_arn = resp["Role"]["Arn"]
boto3.clients['lambda'].create_function(
FunctionName="somelambdafn",
Runtime="python3.6",
Role=iam_arn,
Handler="lambda_function.lambda_handler",
Code={"ZipFile": get_test_zip_file1()},
Description="test lambda function",
Timeout=3,
MemorySize=128,
Publish=True)
self.app.config['SCRNASEQ_LAMBDA_FN'] = "somelambdafn"
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
# Test
response = self.client.post('/api/v0/runs/1/demultiplex?user=testuser', json=data)
# Check results
self.assertEqual(response.status_code, 200)
def test_get_samplesheet_runexists_nosamplesheet(self):
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
response = self.client.get('/api/v0/runs/1/sample_sheet')
assert response.status_code == 404
def post(self):
# TODO: Secure with auth_tokens
if not request.json:
abort(400)
if not SequencingRun.is_data_valid(request.json):
abort(403)
# 1. Make sure the run doesn't exist in ngs360
s3_run_folder_path = request.json['s3_run_folder_path']
run = SequencingRun.query.filter_by(
s3_run_folder_path=s3_run_folder_path).first()
if run is None:
if len(request.json['run_date']) == 6:
# assume format is YYMMDD
run_date = datetime.datetime.strptime(request.json['run_date'],
'%y%m%d')
else:
# assume format is m/d/y h:m:s eg 2/2/2018 2:06:49 PM
run_date = datetime.datetime.strptime(request.json['run_date'],
'%m/%d/%Y %I:%M:%S %p')
machine_id = request.json['machine_id']
run_number = request.json['run_number']
flowcell_id = request.json['flowcell_id']
experiment_name = request.json['experiment_name']
run = SequencingRun(run_date=run_date,
machine_id=machine_id,
run_number=run_number,
flowcell_id=flowcell_id,
experiment_name=experiment_name,
s3_run_folder_path=s3_run_folder_path)
db.session.add(run)
db.session.commit()
else:
abort(409)
run = SequencingRun.query.filter_by(
s3_run_folder_path=s3_run_folder_path).first()
return {'run': run.to_dict()}, 201
def test_get_samplesheet(self):
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
boto3.clients['s3'].upload_file(Filename="test_data/SampleSheet.csv",
Bucket='somebucket',
Key="/PHIX3_test/SampleSheet.csv")
# Test
response = self.client.get('/api/v0/runs/1/sample_sheet')
# Check
assert response.status_code == 200
assert response.json == {'Summary': {'experiment_name': 'PHIX3 test',
'flowcell_id': '000000001',
'id': 1,
'machine_id': 'M00123',
'run_date': '2019-01-10',
'run_number': '1',
's3_run_folder_path': 's3://somebucket/PHIX3_test'},
'Header': {'Application': 'FASTQ Only',
'Assay': 'someassay',
'Chemistry': 'Amplicon',
'Date': '1/8/2018',
'Description': 'PHIX3 test',
'Experiment Name': 'PHIX3 test',
'IEMFileVersion': '4',
'Investigator Name': 'John',
'Workflow': 'GenerateFASTQ'},
'Reads': [151, 151],
'Settings': {'Adapter': 'CTGTCTCTTATACACATCT',
'ReverseComplement': '0'},
'DataCols': ['Sample_ID', 'Sample_Name', 'Sample_Plate',
'Sample_Well', 'I7_Index_ID', 'index', 'I5_Index_ID',
'index2', 'Sample_Project', 'Description'],
'Data': [{'Description': '',
'I5_Index_ID': 'S502-A',
'I7_Index_ID': 'N701-A',
'Sample_ID': 'sample1',
'Sample_Name': 'sample1',
'Sample_Plate': '',
'Sample_Project': 'P-00000000-0001',
'Sample_Well': '',
'index': 'TAAGGCGA',
'index2': 'CTCTCTAT'}]
}
def test_put_samples(self):
# Set up test parameters
data = [{'sampleid': 'samplea', 'projectid': 'P-00000000-0001'}]
# Set up supporting mocks
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
# Test
response = self.client.put('/api/v0/runs/1/samples', json=data)
# Check Results
self.assertEqual(response.json['Status'], "OK")
def test_get_run_metrics_notdemuxed(self):
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
response = self.client.get('/api/v0/runs/1/metrics')
assert response.status_code == 404
assert response.json == {"Status": "error",
"Message": "s3://somebucket/PHIX3_test/Stats/Stats.json not found"}
def test_upload_file(self):
''' Test POST /<sequencing_run_id>/file works '''
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
files = {"file": (open("test_data/SampleSheet.csv", 'rb'), 'SampleSheet.csv'),
"filename": "SampleSheet.csv"
}
response = self.client.post('/api/v0/runs/1/file', data=files, content_type='multipart/form-data')
assert response.json['status'] == 'File, SampleSheet.csv, uploaded'
def test_get_run_metrics(self):
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
boto3.resources['s3'].create_bucket(Bucket='somebucket')
boto3.clients['s3'].put_object(Bucket='somebucket',
Key="/PHIX3_test/Stats/Stats.json",
Body='{"metrics": "test"}')
response = self.client.get('/api/v0/runs/1/metrics')
assert response.status_code == 200
assert response.json == {"metrics": "test"}
def test_get_project(self):
# Set up test case
# Set up supporting mocks
project = Project(id='P-00000000-0001', xpress_project_id=12345)
db.session.add(project)
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1,
run_date=run_date,
machine_id='M00123',
run_number='1',
flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
run_to_samples = RunToSamples(id=1,
sequencing_run_id=1,
sample_id='sample_a',
project_id='P-00000000-0001')
db.session.add(run_to_samples)
db.session.commit()
# Test
response = self.client.get('/api/v0/projects/P-00000000-0001')
# Check
assert response.status_code == 200
assert response.json['id'] == 'P-00000000-0001'
assert response.json['sequencing_runs'] == [{
'experiment_name':
'PHIX3 test',
'flowcell_id':
'000000001',
'id':
1,
'machine_id':
'M00123',
'run_date':
'2019-01-10',
'run_number':
'1',
's3_run_folder_path':
's3://somebucket/PHIX3_test'
}]
assert response.json['xpress_project_id'] == 12345
assert 'project_details' in response.json
def test_post_demultiplex_edgeseq(self):
# Set up test case
data = {'ASSAY': 'EdgeSeq'}
# Set up supporting mocks
boto3.clients['batch'].register_job_definition(
jobDefinitionName="job",
type="container",
containerProperties={
"image": "busybox",
"vcpus": 1,
"memory": 128,
"command": ["sleep", "10"],
})
resp = boto3.clients["iam"].create_role(
RoleName="TestRole", AssumeRolePolicyDocument="some_policy")
iam_arn = resp["Role"]["Arn"]
env = boto3.clients['batch'].create_compute_environment(
computeEnvironmentName='compute_name',
type="UNMANAGED",
state="ENABLED",
serviceRole=iam_arn)
boto3.clients['batch'].create_job_queue(
jobQueueName="queue",
state="ENABLED",
priority=123,
computeEnvironmentOrder=[{"order": 123, "computeEnvironment": env['computeEnvironmentArn']}])
self.app.config['BCL2FASTQ_JOB'] = "job"
self.app.config['BCL2FASTQ_QUEUE'] = "queue"
run_date = datetime.date(2019, 1, 10)
run = SequencingRun(id=1, run_date=run_date, machine_id='M00123',
run_number='1', flowcell_id='000000001',
experiment_name='PHIX3 test',
s3_run_folder_path='s3://somebucket/PHIX3_test')
db.session.add(run)
db.session.commit()
# Test
response = self.client.post('/api/v0/runs/1/demultiplex?user=testuser', json=data)
# Check results
self.assertEqual(response.status_code, 200)
self.assertTrue('jobName' in response.json)
self.assertTrue('jobId' in response.json)