def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def mark_validation(institute_id, case_name, variant_id):
"""Mark a variant as sanger validated."""
institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
variant_obj = store.variant(variant_id)
user_obj = store.user(current_user.email)
validate_type = request.form['type'] or None
link = url_for('variants.variant', institute_id=institute_id, case_name=case_name,
variant_id=variant_id)
store.validate(institute_obj, case_obj, user_obj, link, variant_obj, validate_type)
return redirect(request.referrer or link)
def test_export_verified(mock_app, case_obj, user_obj, institute_obj):
"""Test the CLI command that exports verified variants into excel files"""
runner = mock_app.test_cli_runner()
assert runner
# Load snv variants using the cli
result = runner.invoke(cli, [
'load',
'variants',
case_obj['_id'],
'--snv',
])
assert store.variant_collection.find_one() is not None
# Test the cli without verified variants available
result = runner.invoke(cli, ['export', 'verified'])
assert result.exit_code == 0
assert 'There are no verified variants for institute cust000 in database!' in result.output
# Set a variant as verified
variant_obj = store.variant_collection.find_one()
# Validate the above variant:
store.validate(institute=institute_obj,
case=case_obj,
user=user_obj,
link='link_to_var',
variant=variant_obj,
validate_type='True positive')
var_res = store.variant_collection.find({'validation': 'True positive'})
assert sum(1 for i in var_res) == 1
event_res = store.event_collection.find({'verb': 'validate'})
assert sum(1 for i in event_res) == 1
# Test the cli without parameters
result = runner.invoke(cli, ['export', 'verified', '--test'])
assert result.exit_code == 0
# Variant should be found now
assert 'Success. Verified variants file contains' in result.output
# Test the cli with with a wrong collaborator param
result = runner.invoke(cli,
['export', 'verified', '--test', '-c', 'cust666'])
assert result.exit_code == 0
# Variant should not be found now
assert 'There are no verified variants for institute cust666 in database!' in result.output
# Test the cli with the right collaborator param
result = runner.invoke(
cli, ['export', 'verified', '--test', '-c', case_obj['owner']])
assert result.exit_code == 0
# Variant should be found again
assert 'Success. Verified variants file contains' in result.output
def test_export_verified(mock_app, case_obj, user_obj, institute_obj):
"""Test the CLI command that exports verified variants into excel files"""
runner = mock_app.test_cli_runner()
assert runner
# Load snv variants using the cli
result = runner.invoke(cli, ["load", "variants", case_obj["_id"], "--snv"])
assert store.variant_collection.find_one() is not None
# Test the cli without verified variants available
result = runner.invoke(cli, ["export", "verified"])
assert result.exit_code == 0
assert ("There are no verified variants for institute cust000 in database!"
in result.output)
# Set a variant as verified
variant_obj = store.variant_collection.find_one()
# Validate the above variant:
store.validate(
institute=institute_obj,
case=case_obj,
user=user_obj,
link="link_to_var",
variant=variant_obj,
validate_type="True positive",
)
var_res = store.variant_collection.find({"validation": "True positive"})
assert sum(1 for i in var_res) == 1
event_res = store.event_collection.find({"verb": "validate"})
assert sum(1 for i in event_res) == 1
# Test the cli without parameters
result = runner.invoke(cli, ["export", "verified", "--test"])
assert result.exit_code == 0
# Variant should be found now
assert "Success. Verified variants file contains" in result.output
# Test the cli with with a wrong collaborator param
result = runner.invoke(cli,
["export", "verified", "--test", "-c", "cust666"])
assert result.exit_code == 0
# Variant should not be found now
assert ("There are no verified variants for institute cust666 in database!"
in result.output)
# Test the cli with the right collaborator param
result = runner.invoke(
cli, ["export", "verified", "--test", "-c", case_obj["owner"]])
assert result.exit_code == 0
# Variant should be found again
assert "Success. Verified variants file contains" in result.output
def test_reload_variants(mock_app, case_obj, user_obj, institute_obj):
"""Testing loading again variants after rerun"""
runner = mock_app.test_cli_runner()
assert runner
# Given an empty variant database
assert sum(1 for i in store.variant_collection.find()) == 0
# After using the CLI uploading SNV variants for a case
result = runner.invoke(
cli,
["load", "variants", case_obj["_id"], "--snv", "--rank-treshold", 10])
assert result.exit_code == 0
# Variants collection should be populated
assert sum(1 for i in store.variant_collection.find()) > 0
## Order Sanger for one variant and set it to validated
one_variant = store.variant_collection.find_one()
store.order_verification(
institute=institute_obj,
case=case_obj,
user=user_obj,
link="sanger_link",
variant=one_variant,
)
# then one variant should have an associated Sanger event
assert (sum(1 for i in store.event_collection.find({
"verb": "sanger",
"category": "variant"
})) == 1)
store.validate(
institute=institute_obj,
case=case_obj,
user=user_obj,
link="validated_link",
variant=one_variant,
validate_type="True positive",
)
# then one variant should have an associated Sanger event
assert (sum(1 for i in store.event_collection.find({
"verb": "validate",
"category": "variant"
})) == 1)
# Check that the variant is validated
new_variant = store.variant_collection.find_one(
{"display_name": one_variant["display_name"]})
assert new_variant["validation"] == "True positive"
# force re-upload the same variants using the command line:
result = runner.invoke(
cli,
[
"load",
"variants",
case_obj["_id"],
"--snv",
"--rank-treshold",
10,
"--force",
],
)
assert result.exit_code == 0
# Then the variant from before should be already validated:
new_variant = store.variant_collection.find_one(
{"display_name": one_variant["display_name"]})
assert new_variant["validation"] == "True positive"
# And 2 Sanger events shouls be found associated with the variants
assert (sum(1 for i in store.event_collection.find({
"verb": "sanger",
"category": "variant"
})) == 2)