def test_blastconfig():
"""Test BlastConfig defaults"""
PROGRAM = 'blastn'
DB = 'test-db'
QUERIES = 'test-queries'
cloud_provider = GCPConfig(project='test-project',
region='test-region',
zone='test-zone')
machine_type = 'n1-standard-32'
cfg = BlastConfig(program=PROGRAM,
db=DB,
queries_arg=QUERIES,
cloud_provider=cloud_provider,
machine_type=machine_type)
assert cfg.program == PROGRAM
assert cfg.db == DB
assert cfg.queries_arg == QUERIES
assert cfg.db_source.name == cloud_provider.cloud.name
assert cfg.batch_len == get_query_batch_size(cfg.program)
assert not cfg.queries
assert cfg.options == f'-outfmt {ELB_DFLT_OUTFMT}'
assert cfg.mem_request
assert cfg.mem_limit
assert not cfg.taxidlist
assert cfg.db_mem_margin == ELB_BLASTDB_MEMORY_MARGIN
def test_gcpconfig_from_configparser():
"""Test GCPConfig initialized from a ConfigParser object"""
PROJECT = 'test-project'
REGION = 'test-region'
ZONE = 'test-zone'
NETWORK = 'network'
SUBNET = 'subnet'
confpars = configparser.ConfigParser()
confpars[CFG_CLOUD_PROVIDER] = {
CFG_CP_GCP_PROJECT: PROJECT,
CFG_CP_GCP_REGION: REGION,
CFG_CP_GCP_ZONE: ZONE,
CFG_CP_GCP_NETWORK: NETWORK,
CFG_CP_GCP_SUBNETWORK: SUBNET
}
cfg = GCPConfig.create_from_cfg(confpars)
assert cfg.cloud == CSP.GCP
assert cfg.project == PROJECT
assert cfg.region == REGION
assert cfg.zone == ZONE
assert cfg.network == NETWORK
assert cfg.subnet == SUBNET
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert not errors
def test_gcpconfig():
"""Test GCPConfig defaults"""
PROJECT = 'test-project'
REGION = 'test-region'
ZONE = 'test-zone'
cfg = GCPConfig(project=PROJECT, region=REGION, zone=ZONE)
assert cfg.cloud == CSP.GCP
assert cfg.project == PROJECT
assert cfg.region == REGION
assert cfg.zone == ZONE
assert not cfg.network
assert not cfg.subnet
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert not errors
def test_gcpconfig_from_configparser_missing():
"""Test missing required parameters are reported when initializing
GCPConfig from a ConfigParser object"""
REQUIRED_PARAMS = [CFG_CP_GCP_PROJECT, CFG_CP_GCP_REGION, CFG_CP_GCP_ZONE]
with pytest.raises(ValueError) as err:
cfg = GCPConfig.create_from_cfg(configparser.ConfigParser())
for param in REQUIRED_PARAMS:
assert 'Missing ' + param in str(err.value)
def test_clusterconfig_validation():
"""Test ClusterConfig validation"""
cfg = ClusterConfig(cloud_provider=GCPConfig(project='test-project',
region='test-region',
zone='test-zone'),
results=CloudURI('gs://test-results'),
min_nodes=5)
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert errors
assert [
message for message in errors if 'min-nodes and max-nodes' in message
]
def test_blastconfig_validation():
"""Test BlastConfig validation"""
BAD_URI = 'gs://@BadURI!'
cfg = BlastConfig(program='blastn',
db='test-db',
queries_arg=BAD_URI,
cloud_provider=GCPConfig(project='test-project',
region='test-region',
zone='test-zone'),
machine_type='n1-standard-32')
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert errors
assert [message for message in errors if BAD_URI in message]
def test_gcpconfig_validation():
"""Test GCPConfig validation"""
cfg = GCPConfig(project='test-project',
region='test-region',
zone='test-zone')
cfg.network = 'some-network'
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert errors
assert [
message for message in errors
if 'gcp-network and gcp-subnetwork' in message
]
cfg.network = None
cfg.subnet = 'subnet'
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert errors
assert [
message for message in errors
if 'gcp-network and gcp-subnetwork' in message
]
def test_gcpconfig_from_configparser_errors():
"""Test that incorrect parameter values in ConfigParser are properly
reported"""
confpars = configparser.ConfigParser()
confpars[CFG_CLOUD_PROVIDER] = {
CFG_CP_GCP_PROJECT: 'inval!d-PROJECT',
CFG_CP_GCP_REGION: 'invalie-rEg!on',
CFG_CP_GCP_ZONE: 'inavlid-zone-@#$'
}
with pytest.raises(ValueError) as err:
cfg = GCPConfig.create_from_cfg(confpars)
# test that each invalid parameter value is reported
errors = str(err.value).split('\n')
for key in confpars[CFG_CLOUD_PROVIDER]:
assert [
message for message in errors
if key in message and 'invalid value' in message
and confpars[CFG_CLOUD_PROVIDER][key] in message
]
def test_clusterconfig_gcp():
"""Test ClusterConfig defaults for GCP"""
RESULTS = CloudURI('gs://test-results')
gcp_cfg = GCPConfig(project='test-project',
region='test-region',
zone='test-zone')
cfg = ClusterConfig(cloud_provider=gcp_cfg, results=RESULTS)
assert cfg.name.startswith('elasticblast')
assert cfg.machine_type == ELB_DFLT_GCP_MACHINE_TYPE
assert cfg.pd_size == ELB_DFLT_GCP_PD_SIZE
assert cfg.num_cpus == get_instance_props(gcp_cfg,
cfg.machine_type).ncpus - 1
assert cfg.num_nodes == ELB_DFLT_NUM_NODES
assert cfg.results == RESULTS
assert not cfg.min_nodes
assert not cfg.max_nodes
assert not cfg.use_preemptible
assert not cfg.iops
assert not cfg.labels
assert not cfg.use_local_ssd
assert not cfg.enable_stackdriver
errors = []
cfg.validate(errors, ElbCommand.SUBMIT)
assert not errors