def test_delete(requireMocking):
# add test sample
tm = TableManager()
table = tm.get_tracking_table()
table.put_item(
Item={
"id": "test-to-delete",
"experiment": "unknown",
"sample": "test-to-delete",
"status": [{
"time": 1524772162698,
"value": "PROCESSING"
}]
})
# check it's there
result = get.get({"pathParameters": {"sample": "test-to-delete"}}, {})
assert json.loads(result['body'])["id"] == "test-to-delete"
# call deletion
result = delete.delete({"pathParameters": {
"sample": "test-to-delete"
}}, {})
# assert test data is gone
assert result['statusCode'] == 204
assert get.get({"pathParameters": {
"sample": "test-to-delete"
}}, {})['statusCode'] == 404
def delete(events, context):
"""deletes the specific element from the storage"""
logger.info("received event: " + json.dumps(events, indent=2))
if 'pathParameters' in events:
if 'sample' in events['pathParameters']:
tm = TableManager()
table = tm.get_tracking_table()
result = table.query(KeyConditionExpression=Key('id').eq(
events['pathParameters']['sample']))
logger.info("found result to delete: %s" % result)
if 'Items' in result and len(result['Items']) > 0:
result = json.dumps(result['Items'][0], use_decimal=True)
result = json.loads(result, use_decimal=True)
# create a response when sample is found
table.delete_item(Key={
'id': result['id'],
'sample': result['id']
})
return {
'statusCode': 204,
'headers': __HTTP_HEADERS__,
'isBase64Encoded': False,
'body': ''
}
else:
# create a response when sample is not found
return {
'statusCode': 404,
'headers': __HTTP_HEADERS__,
'isBase64Encoded': False,
'body': json.dumps({"error": "sample not found"})
}
else:
return {
'statusCode': 422,
'headers': __HTTP_HEADERS__,
'isBase64Encoded': False,
'body': json.dumps({"error": "sample name is not provided!"})
}
else:
return {
'statusCode':
404,
'headers':
__HTTP_HEADERS__,
'isBase64Encoded':
False,
'body':
json.dumps({
"error":
"not supported, need's be called from a http event!"
})
}
def test_get(requireMocking):
# store data
tm = TableManager()
table = tm.get_tracking_table()
table.put_item(Item={
"id": "test",
"experiment": "unknown",
"sample": "test",
"status": [{"time": 1524772162698, "value": "processing"}]
})
# process data
result = get.get({
"pathParameters": {
"sample": "test"
}
}, {})
assert 200 == result['statusCode']
assert 'body' in result
assert "test" == json.loads(result['body'])["id"]
def test_get_with_fileHandle(requireMocking):
# store data
tm = TableManager()
table = tm.get_tracking_table()
table.put_item(Item={
"id": "test",
"experiment": "unknown",
"sample": "test",
"status": [{"time": 1524772162698, "value": "PROCESSING", "fileHandle": "test.mzml"}]
})
# process data
result = get.get({
"pathParameters": {
"sample": "test"
}
}, {})
assert 200 == result['statusCode']
assert 'body' in result
assert 'test' == json.loads(result['body'])['id']
assert 'test.mzml' == json.loads(result['body'])['status'][0]['fileHandle']
def get(events, context):
"""returns the specific sample from the storage"""
if 'pathParameters' in events:
if 'sample' in events['pathParameters']:
tm = TableManager()
table = tm.get_tracking_table()
result = table.query(
KeyConditionExpression=Key('id').eq(events['pathParameters']['sample'])
)
if 'Items' in result and len(result['Items']) > 0:
# create a response when sample is found
return {
"statusCode": 200,
"headers": __HTTP_HEADERS__,
"body": json.dumps(result['Items'][0])
}
else:
# create a response when sample is not found
return {
"statusCode": 404,
"headers": __HTTP_HEADERS__,
"body": json.dumps({"error": "sample not found"})
}
else:
return {
"statusCode": 422,
"headers": __HTTP_HEADERS__,
"body": json.dumps({"error": "sample name is not provided!"})
}
else:
return {
"statusCode": 404,
"headers": __HTTP_HEADERS__,
"body": json.dumps({"error": "not supported, need's be called from a http event!"})
}
def test_sync_currently_processing(requireMocking, mocked_10_sample_job):
tm = TableManager()
for i in range(0, 10):
tracking.create({'body': json.dumps(
{
"job": "12345",
"sample": "abc_{}".format(i),
"state": SCHEDULED
}
)}, {})
assert load_job_samples_with_states("12345")['abc_{}'.format(i)] == "scheduled"
# dummy stasis data which need to be in the system for this test to pass
tm.get_tracking_table().put_item(Item=
{
"experiment": "12345",
"id": "abc_{}".format(i),
"sample": "abc_{}".format(i),
"status": [
{
"fileHandle": "abc_{}.d".format(i),
"priority": 1,
"time": 1563307359163,
"value": "entered"
},
{
"fileHandle": "abc_{}.d".format(i),
"priority": 100,
"time": 1563307360393,
"value": "acquired"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 200,
"time": 1563307361543,
"value": "converted"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 300,
"time": 1563330092360,
"value": "scheduled"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 410,
"time": 1563330183632,
"value": "deconvoluted"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 420,
"time": 1563330184868,
"value": "corrected"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 430,
"time": 1563330189108,
"value": "annotated"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 440,
"time": 1563330190650,
"value": "quantified"
},
{
"fileHandle": "abc_{}.mzml".format(i),
"priority": 450,
"time": 1563330244348,
"value": "replaced"
}
]
}
)
calculate_job_state(job="12345")
assert all(value == str(REPLACED) for value in load_job_samples_with_states("12345").values())