def test_update_config2(run_task_awsem_event_data2):
data = run_task_awsem_event_data2
config = data['config']
update_config(config, data['args']['app_name'], data['args']['input_files'], data['args']['input_parameters'])
assert config['instance_type'] == 't2.xlarge'
assert config['EBS_optimized'] is False
assert config['ebs_size'] >= 10
assert config['copy_to_s3'] is True # check the other fields are preserved in the returned config
def test_update_config5(run_task_awsem_event_omit_fields2):
data = run_task_awsem_event_omit_fields2
config = data['config']
update_config(config, data['args'].get('app_name', ''),
data['args']['input_files'], {})
assert config['instance_type'] == 't3.micro'
assert config['EBS_optimized'] is True
assert config['ebs_size'] >= 10
assert config['shutdown_min'] == "now"
def test_update_config3(run_task_awsem_event_data_chipseq):
data = run_task_awsem_event_data_chipseq
config = data['config']
update_config(config, data['args']['app_name'],
data['args']['input_files'],
data['args']['input_parameters'])
assert config['instance_type'] == 'c5.4xlarge'
assert config['EBS_optimized'] is True
assert config['ebs_size'] == 87
def test_update_config(run_task_awsem_event_data):
data = run_task_awsem_event_data
config = data['config']
update_config(config, data['args']['app_name'],
data['args']['input_files'],
data['args']['input_parameters'])
assert config['instance_type'] == 't3.micro'
assert config['EBS_optimized'] is True
assert config['ebs_size'] >= 10
assert config[
'shutdown_min'] == 30 # check the other fields are preserved in the returned config
def handler(event, context):
'''
config:
instance_type: EC2 instance type
ebs_size: EBS storage size in GB
ebs_type: EBS storage type (available values: gp2, io1, st1, sc1, standard (default: io1)
ebs_iops: EBS storage IOPS
password: password for ssh connection for user ec2-user
EBS_optimized: Use this flag if the instance type is EBS-optimized (default: EBS-optimized)
shutdown_min: Number of minutes before shutdown after the jobs are finished. (default now)
copy_to_s3: Upload or copy the json file to S3 bucket json_bucket
launch_instance: Launch instance based on the json file
log_bucket: bucket for collecting logs (started, postrun, success, error, log)
args:
cwl_main_filename: main cwl file name
cwl_child_filenames: names of the other cwl files used by main cwl file, delimiated by comma
app_name: name of the app
app_version: version of the app
cwl_directory_url: the url and subdirectories for the main cwl file
cwl_version: the version of cwl (either 'draft3' or 'v1')
input_reference_files_directory: bucket name and subdirectory for input reference files
output_S3_bucket: bucket name and subdirectory for output files and logs
input_files: input files in json format (parametername: {'bucket_name':bucketname, 'object_key':filename})
secondary_files: secondary files in json format (parametername: {'bucket_name':bucketnname, 'object_ke':filename})
input_parameters: input parameters in json format (parametername:value)
'''
# read default variables in config
CONFIG_FIELD = "config"
CONFIG_KEYS = [
"EBS_optimized", "shutdown_min", "copy_to_s3", "instance_type",
"ebs_size", "launch_instance", "key_name", "ebs_type", "ebs_iops",
"json_bucket", "password", "log_bucket"
]
ARGS_FIELD = "args"
ARGS_KEYS = [
"cwl_main_filename", "cwl_child_filenames", "app_name", "app_version",
"input_files", "output_S3_bucket", "cwl_directory_url",
"input_parameters", "secondary_files", "output_target",
"secondary_output_target"
]
cfg = event.get(CONFIG_FIELD)
for k in CONFIG_KEYS:
assert k in cfg, "%s not in config_field" % k
args = event.get(ARGS_FIELD)
for k in ARGS_KEYS:
assert k in args, "%s not in args field" % k
# args: parameters needed by the instance to run a workflow
# cfg: parameters needed to launch an instance
cfg['job_tag'] = args.get('app_name')
cfg['userdata_dir'] = '/tmp/userdata'
# local directory in which the json file will be first created.
cfg['json_dir'] = '/tmp/json'
# AMI and script directory according to cwl version
if args['cwl_version'] == 'v1':
cfg['ami_id'] = os.environ.get('AMI_ID_CWL_V1')
cfg['script_url'] = 'https://raw.githubusercontent.com/' + \
os.environ.get('TIBANNA_REPO_NAME') + '/' + \
os.environ.get('TIBANNA_REPO_BRANCH') + '/awsf_cwl_v1/'
else:
cfg['ami_id'] = os.environ.get('AMI_ID_CWL_DRAFT3')
cfg['script_url'] = 'https://raw.githubusercontent.com/' + \
os.environ.get('TIBANNA_REPO_NAME') + '/' + \
os.environ.get('TIBANNA_REPO_BRANCH') + '/awsf_cwl_draft3/'
utils.update_config(cfg, args['app_name'], args['input_files'],
args['input_parameters'])
# create json and copy to s3
jobid = utils.create_json(event, '')
# launch instance and execute workflow
if cfg.get('launch_instance'):
launch_instance_log = utils.launch_instance(cfg, jobid)
event.update({'jobid': jobid})
event.update(launch_instance_log)
return (event)
