def test_load_case_BadPath(mock_app, institute_obj, case_obj):
# GIVEN a config setup with an incorrect path configured
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
res = store.institute_collection.find({"_id": "cust000"})
assert sum(1 for i in res) == 1
# Make sure the scout config file is available
assert os.path.exists(load_path)
temp_conf = os.path.join(tempfile.gettempdir(), "temp.conf")
content = []
with open(load_path) as f:
content = f.readlines()
# Remove a mandatory key value from config value content
content.remove("vcf_snv: scout/demo/643594.clinical.vcf.gz\n")
content.append(
"vcf_snv: scout/demo/incorrect_path/643594.clinical.vcf.gz\n")
with open(temp_conf, mode="wt") as f:
f.write("".join(content))
# WHEN: config is loaded
result = runner.invoke(cli, ["load", "case", temp_conf])
# THEN KeyError is caught and exit value is non-zero
assert result.exit_code == 1
assert "Error opening" in result.output
def test_load_case_KeyMissing(mock_app, institute_obj, case_obj):
# GIVEN a config setup with 'sample_id' missing
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
res = store.institute_collection.find({"_id": "cust000"})
assert sum(1 for i in res) == 1
# Make sure the scout config file is available
assert os.path.exists(load_path)
temp_conf = os.path.join(tempfile.gettempdir(), "temp.conf")
content = []
with open(load_path) as f:
content = f.readlines()
# Remove a mandatory key value from config value content
content.remove("family: 'internal_id'\n")
with open(temp_conf, mode="wt") as f:
f.write("".join(content))
# WHEN: config is loaded
result = runner.invoke(cli, ["load", "case", temp_conf])
# THEN KeyError is caught and exit value is non-zero
assert result.exit_code != 0
def test_load_case_NoConf(mock_app, institute_obj, case_obj):
# GIVEN a load command missing path to config
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
res = store.institute_collection.find({"_id": "cust000"})
assert sum(1 for i in res) == 1
no_load_path = ""
# WHEN load command is run
result = runner.invoke(cli, ["load", "case", no_load_path])
# THEN error in exit status
assert result.exit_code != 0
def test_load_case(mock_app, institute_obj, case_obj):
"""Testing the scout load case command"""
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj['_id'])
assert store.case_collection.find().count() == 0
assert store.institute_collection.find({'_id': 'cust000'}).count() == 1
# Make sure the scout config file is available
assert os.path.exists(load_path)
# Test command to upload case using demo resources:
result = runner.invoke(cli, ['load', 'case', load_path])
assert result.exit_code == 0
assert store.case_collection.find().count() == 1
def test_load_case_from_yaml(mock_app, institute_obj, case_obj):
"""Testing the scout load case command"""
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
res = store.institute_collection.find({"_id": "cust000"})
assert sum(1 for i in res) == 1
# Make sure the scout config file is available
assert os.path.exists(load_path)
# Test command to upload case using demo resources:
result = runner.invoke(cli, ["load", "case", load_path])
assert result.exit_code == 0
assert sum(1 for i in store.case_collection.find()) == 1
def test_load_case_from_ped(mock_app, institute_obj, case_obj):
"""Test loading a case into scout from a ped file. It requires providing case genome build in the prompt."""
# GIVEN a database with no cases
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
case_owner = institute_obj["_id"]
# WHEN case is loaded using a ped file it will also require a genome build
runner = mock_app.test_cli_runner()
result = runner.invoke(
cli, ["load", "case", "--owner", case_owner, "--ped", ped_path],
input="37")
# THEN case should be saved correctly
assert result.exit_code == 0
case_obj = store.case_collection.find_one()
# WITH the expected genome build
assert case_obj["genome_build"] == 37
def test_load_case_SyntaxError(mock_app, institute_obj, case_obj, monkeypatch):
"""Test loading a case with a config file that will trigger KeyError"""
runner = mock_app.test_cli_runner()
# GIVEN a patched `parse_case` function that will raise KeyError
def mock_parse_case(*args): # noqa
raise SyntaxError
monkeypatch.setattr(case, "add_smn_info", mock_parse_case)
# GIVEN a database with no cases
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
# WHEN case is loaded using a a yaml file
runner = mock_app.test_cli_runner()
result = runner.invoke(cli, ["load", "case", load_path])
# THEN call will fail with KeyError
assert result.exit_code == 1
assert "SyntaxError" in result.output
def test_load_case_KeyError(mock_app, institute_obj, case_obj):
# GIVEN a config setup with 'sample_id' missing
runner = mock_app.test_cli_runner()
assert runner
# remove case from real populated database using adapter
store.delete_case(case_id=case_obj["_id"])
assert store.case_collection.find_one() is None
res = store.institute_collection.find({"_id": "cust000"})
assert sum(1 for i in res) == 1
# Make sure the scout config file is available
assert os.path.exists(load_path)
temp_conf = os.path.join(tempfile.gettempdir(), "temp.conf")
shutil.copy2(load_path, temp_conf)
sed_change = "sed -i -e 's/sample_id/SAMPLE_ID/g' "
os.system(sed_change + temp_conf)
# WHEN: config is loaded
result = runner.invoke(cli, ["load", "case", temp_conf])
# THEN KeyError is caught and exit value is non-zero
assert result.exit_code != 0
os.remove(temp_conf) # clean up