class TestBifrostEnterobase:
component_name = "enterobase__v1_1_5__"
current_dir = os.getcwd()
test_dir = "/bifrost/test_data/output/test__enterobase/"
json_entries = [{
"_id": {
"$oid": "000000000000000000000001"
},
"name": "SRR2094561",
"components": [],
"categories": {
"paired_reads": {
"summary": {
"data": [
"/bifrost/test_data/samples/SRR2094561_1.fastq.gz",
"/bifrost/test_data/samples/SRR2094561_2.fastq.gz"
]
}
},
"mlst": {
"summary": {
"sequence_type": {
"senterica": "34"
}
}
},
"species_detection": {
"summary": {
"species": "Salmonella enterica"
}
}
}
}]
bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
@classmethod
def setup_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
col = db["samples"]
col.insert_many(cls.bson_entries)
launcher.initialize()
os.chdir(cls.current_dir)
@classmethod
def teardown_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
@staticmethod
def clear_all_collections(db):
db.drop_collection("components")
db.drop_collection("hosts")
db.drop_collection("run_components")
db.drop_collection("runs")
db.drop_collection("sample_components")
db.drop_collection("samples")
def test_info(self):
launcher.run_pipeline(["--info"])
def test_help(self):
launcher.run_pipeline(["--help"])
def test_pipeline(self):
if os.path.isdir(self.test_dir):
shutil.rmtree(self.test_dir)
os.mkdir(self.test_dir)
test_args = ["--sample_name", "SRR2094561", "--outdir", self.test_dir]
launcher.main(args=test_args)
assert os.path.isfile(
f"{self.test_dir}/{self.component_name}/datadump_complete")
shutil.rmtree(self.test_dir)
assert not os.path.isdir(f"{self.test_dir}/{self.component_name}")
class TestRunComponents:
json_entries_runs = [{
"_id": {
"$oid": "000000000000000000000001"
},
"name": "test_run1",
"samples": [],
"components": [],
"hosts": []
}]
bson_entries_runs = [
database_interface.json_to_bson(i) for i in json_entries_runs
]
json_entries_components = [{
"_id": {
"$oid": "0000000000000000000000b1"
},
"name": "test_component1"
}]
bson_entries_components = [
database_interface.json_to_bson(i) for i in json_entries_components
]
json_entries = [{
"_id": {
"$oid": "000000000000000000000001"
},
"name": "test_sample_component1",
"sample": {
"_id": {
"$oid": "0000000000000000000000a1"
},
"name": "test_sample1"
},
"component": {
"_id": {
"$oid": "0000000000000000000000b1"
},
"name": "test_component1"
}
}]
bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
@classmethod
def setup_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
col = db["runs"]
col.insert_many(cls.bson_entries_runs)
col = db["components"]
col.insert_many(cls.bson_entries_components)
col = db["run_components"]
col.insert_many(cls.bson_entries)
@classmethod
def teardown_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
@staticmethod
def clear_all_collections(db):
db.drop_collection("components")
db.drop_collection("hosts")
db.drop_collection("run_components")
db.drop_collection("runs")
db.drop_collection("sample_components")
db.drop_collection("samples")
def test_run_component_create(self):
run = Run(value=self.json_entries_runs[0])
component = Component(value=self.json_entries_components[0])
test_run_component = RunComponent(
run_reference=run.to_reference(),
component_reference=component.to_reference())
test_run_component.save()
assert "_id" in test_run_component.json
def test_run_component_load(self):
_id = "000000000000000000000001"
name = "test_run_component1"
# Test load on just _id
reference = RunComponentReference(_id=_id)
run_component = RunComponent.load(reference)
json = run_component.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del run_component
# Test load on just name
refrence = RunComponentReference(name=name)
run_component = RunComponent.load(reference)
json = run_component.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del run_component
# Test load on both _id and name
reference = RunComponentReference(_id=_id, name=name)
run_component = RunComponent.load(reference)
json = run_component.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del run_component
# Test load on both _id and name
reference = RunComponentReference(value=self.json_entries[0])
run_component = RunComponent.load(reference)
json = run_component.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del run_component
def test_run_component_delete(self):
_id = "000000000000000000000001"
name = "test_run_component"
run_component = RunComponent.load(
RunComponentReference(_id=_id, name=name))
assert run_component.delete() == True
class TestBifrostRunLauncher:
component_name = "run_launcher__v2_2_7"
test_dir = "/bifrost/test_data/output/test__run_launcher/"
current_dir = os.getcwd()
json_entries = [{
"_id": {
"$oid": "000000000000000000000001"
},
"name": "test_component1"
}]
bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
@classmethod
def setup_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
launcher.initialize()
@classmethod
def teardown_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
@staticmethod
def clear_all_collections(db):
db.drop_collection("components")
db.drop_collection("hosts")
db.drop_collection("run_components")
db.drop_collection("runs")
db.drop_collection("sample_components")
db.drop_collection("samples")
def test_info(self):
launcher.run_pipeline(["--info"])
def test_help(self):
launcher.run_pipeline(["--help"])
def test_pipeline(self):
bifrost_config_and_data_path = "/bifrost/test_data"
if os.path.isdir(self.test_dir):
shutil.rmtree(self.test_dir)
os.mkdir(self.test_dir)
test_args = [
"--outdir", f"{self.test_dir}/{self.component_name}",
"--pre_script", f"{bifrost_config_and_data_path}/pre.sh",
"--per_sample_script",
f"{bifrost_config_and_data_path}/per_sample.sh", "--post_script",
f"{bifrost_config_and_data_path}/post.sh", "--run_metadata",
f"{bifrost_config_and_data_path}/run_metadata.tsv",
"--reads_folder", f"{bifrost_config_and_data_path}/samples",
"--run_name", "bifrost_test", "--run_type", "test",
"--component_subset",
"bifrost_min_read_check_v2_2_8,bifrost_whats_my_species_v2_2_11__171019,bifrost_cge_mlst_v2_2_6__210314",
"--sample_subset", "S1"
]
launcher.main(args=test_args)
#clear collection
assert os.path.isfile(
f"{self.test_dir}/{self.component_name}/run_script.sh")
assert os.path.isfile(
f"{self.test_dir}/{self.component_name}/run.yaml")
assert os.path.isfile(
f"{self.test_dir}/{self.component_name}/samples.yaml")
class TestHosts:
json_entries = [{
"_id": {
"$oid": "000000000000000000000001"
},
"name": "test_host1",
"samples": []
}]
bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
@classmethod
def setup_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
col = db["hosts"]
col.insert_many(cls.bson_entries)
@classmethod
def teardown_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
@staticmethod
def clear_all_collections(db):
db.drop_collection("components")
db.drop_collection("hosts")
db.drop_collection("run_components")
db.drop_collection("runs")
db.drop_collection("sample_components")
db.drop_collection("samples")
def test_host_create(self):
test_host = Host(name="test_host")
test_host.save()
assert "_id" in test_host.json
def test_host_create_from_ref(self):
_id = "000000000000000000000001"
name = "test_host"
host = Host.load(HostReference(_id=_id, name=name))
assert host.delete() == True
test_host = Host(value=self.json_entries[0])
test_host.save()
json = host.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
def test_host_load(self):
_id = "000000000000000000000001"
name = "test_host1"
# Test load on just _id
reference = HostReference(_id=_id)
host = Host.load(reference)
json = host.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del host
# Test load on just name
refrence = HostReference(name=name)
host = Host.load(reference)
json = host.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del host
# Test load on both _id and name
reference = HostReference(_id=_id, name=name)
host = Host.load(reference)
json = host.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del host
# Test load on both _id and name
reference = HostReference(value=self.json_entries[0])
host = Host.load(reference)
json = host.json
json.pop("version", None)
json.pop("metadata", None)
assert json == self.json_entries[0]
del host
def test_host_delete(self):
_id = "000000000000000000000001"
name = "test_host"
host = Host.load(HostReference(_id=_id, name=name))
assert host.delete() == True
class TestCGEVirulencefinder:
component_name = "cge_virulencefinder__v2_0_1"
component_name = component_name + "__0479a98"
current_dir = os.getcwd()
test_dir = "/bifrost/test_data/output/test__cge_virulencefinder/"
json_entries = [
{
"_id": {"$oid": "000000000000000000000001"},
"name": "S1",
"components": [],
"categories": {
"paired_reads": {
"summary": {
"data": ["/bifrost/test_data/samples/S1_R1.fastq.gz",
"/bifrost/test_data/samples/S1_R2.fastq.gz"]
}
},
"species_detection": {
"summary": {
"species": "Staphylococcus aureus"
}
}
}
}
]
bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
@classmethod
def setup_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
col = db["samples"]
col.insert_many(cls.bson_entries)
launcher.initialize()
os.chdir(cls.current_dir)
@classmethod
def teardown_class(cls):
client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
db = client.get_database()
cls.clear_all_collections(db)
@staticmethod
def clear_all_collections(db):
db.drop_collection("components")
db.drop_collection("hosts")
db.drop_collection("run_components")
db.drop_collection("runs")
db.drop_collection("sample_components")
db.drop_collection("samples")
def test_info(self):
launcher.run_pipeline(["--info"])
def test_help(self):
launcher.run_pipeline(["--help"])
def test_pipeline(self):
if os.path.isdir(self.test_dir):
shutil.rmtree(self.test_dir)
os.mkdir(self.test_dir)
test_args = [
"--sample_name", "S1",
"--outdir", self.test_dir
]
launcher.main(args=test_args)
assert os.path.isfile(f"{self.test_dir}/{self.component_name}/datadump_complete")
shutil.rmtree(self.test_dir)
assert not os.path.isdir(f"{self.test_dir}/{self.component_name}")