def test_update_with_one_slot(self):
original_row = ExcelRowInfoGenerator.get_sample_row()
MeasurementImporter(original_row, self.user_id).import_measurement()
self.check_row_is_in_database(original_row)
ch1 = Channel.objects.get_or_create(name="channel1")[0]
ch2 = Channel.objects.get_or_create(name="channel2")[0]
t1 = "t1"
t2 = "t2"
t3 = "t3"
new_row = {
RESEARCHER: str(Researcher.objects.last()),
PROJECT: str(Project.objects.last()),
TECHNOLOGY: str(Technology.objects.last()),
MEASUREMENT_NUMBER: original_row[MEASUREMENT_NUMBER],
DATE: original_row[DATE],
AUTOMATED_PLATEID: original_row.get(AUTOMATED_PLATEID),
AUTOMATED_SLIDEN: original_row[AUTOMATED_SLIDEN],
SLIDE_ID: original_row[SLIDE_ID],
SLIDE_BARCODE: "4",
IMAGE_CYCLE: 4,
TISSUE1: "some",
SAMPLE1: "some",
AGE1: "age1",
TISSUE2: "some2",
SAMPLE2: "some2",
GENOTYPE2: "genotype2",
TISSUE3: "some3",
SAMPLE3: "some3",
AGE3: "some3",
CHANNEL1: str(ch1),
TARGET1: str(t1),
CHANNEL2: str(ch2),
TARGET2: str(t2),
CHANNEL3: str(ch1),
TARGET3: str(t2),
CHANNEL4: str(ch2),
TARGET4: str(t3),
CHANNEL5: str(ch2),
TARGET5: str(t3),
LOW_MAG_REFERENCE: "some",
MAG_BIN_OVERLAP: "some",
SECTION_NUM: "2, 3",
ZPLANES: "some",
NOTES_1: "SMTH2",
NOTES_2: "SMTH2",
POST_STAIN: "smth2",
HARMONY_COPY: "No",
EXPORT_LOCATION: "some",
ARCHIVE_LOCATION: "some",
TEAM_DIR: "some",
}
MeasurementImporter(new_row, self.user_id).import_measurement()
self.check_row_is_in_database(new_row)
self.check_row_is_not_in_database(original_row)
def check_project_cannot_be_created(self, row: RowT, unauthorized_project: Project) -> None:
assert not auth.check_permission(self.user_id, unauthorized_project.id, CREATE_OR_UPDATE_PERMISSION)
row[PROJECT] = unauthorized_project.name
row[MEASUREMENT_NUMBER] = "some"
with self.assertRaises(PermissionError):
MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_not_in_database(row)
def test_append_new_slot_to_existing_manual_measurement(self):
row = ExcelRowInfoGenerator.get_sample_row()
m1 = MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_in_database(row)
new_row_info = {
SLIDE_BARCODE: str(Slide.objects.last().barcode),
AUTOMATED_SLIDEN: 2,
TISSUE1: "slide_2",
SAMPLE1: "slide_2",
TISSUE2: "slide_2_1",
SAMPLE2: "slide_2_1",
}
new_row = row.copy()
new_row.update(new_row_info)
m2 = MeasurementImporter(new_row, self.user_id).import_measurement()
self.check_row_is_in_database(new_row)
self.assertEqual(m1.id, m2.id)
def import_measurements(self) -> None:
for i, row in enumerate(self.get_rows()):
try:
MeasurementImporter(row, self.user_id).import_measurement()
except Exception as e:
logger.error(
f"Failed to import measurement with row number {i + 1}")
logger.error(e)
traceback.print_exc()
def test_authorized_deletion_for_roles(self):
"""
Test that an owner user on a project can delete a measurement.
Test that a viewer or anonymous user on a project cannot delete a measurement.
"""
row = ExcelRowInfoGenerator.get_sample_row()
project_id = get_obj_id_from_name("project", row[PROJECT])
MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_in_database(row)
# check viewer
viewer = User.objects.create(username="******", password="******")
auth.add_role(viewer.id, project_id, Role.VIEWER)
self.try_deleting_row_and_check_it_was_not_deleted(viewer, project_id, row)
# check anonymous
auth.remove_existing_role(viewer.id, project_id)
self.try_deleting_row_and_check_it_was_not_deleted(viewer, project_id, row)
# check owner
MeasurementImporter(row, self.user_id).delete_measurement()
self.check_row_is_not_in_database(row)
def delete_measurements(self):
for i, row in enumerate(self.get_rows()):
try:
if MeasurementImporter(row, self.user_id).delete_measurement():
logger.info(f"Deleted measurement with row number {i + 1}")
else:
logger.info(
f"Measurement with row number {i + 1} does not exist in the database"
)
except Exception as e:
logger.error(
f"Failed to delete measurement with row number {i + 1}")
logger.error(e)
traceback.print_exc()
def test_append_new_slot_to_existing_automated_measurement(self):
"""
Create an automated measurement.
Create a row with the same measurement, different SlideID and samples
Both rows must belong to the same measurement.
"""
row = ExcelRowInfoGenerator.get_sample_row()
m1 = MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_in_database(row)
new_row_info = {
SLIDE_BARCODE: str(Slide.objects.first().barcode),
AUTOMATED_SLIDEN: 2,
SLIDE_ID: "slide_2",
TISSUE1: "slide_2",
SAMPLE1: "slide_2",
TISSUE2: "slide_2_1",
SAMPLE2: "slide_2_1",
}
new_row = row.copy()
new_row.update(new_row_info)
m2 = MeasurementImporter(new_row, self.user_id).import_measurement()
self.check_row_is_in_database(new_row)
self.assertEqual(m1.id, m2.id)
def test_authorized_creation_for_roles(self):
"""
Test that a user with owner role on a project can create a measurement.
Test that a user with viewer role on a project cannot create a measurement.
Test a user without any role on a project cannot create a measurement.
"""
row = ExcelRowInfoGenerator.get_sample_row()
user = User.objects.create(username="******", password="******")
authorized_project_name = row[PROJECT]
auth.add_role(user.id, get_obj_id_from_name("project", authorized_project_name), Role.OWNER)
MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_in_database(row)
project_without_role = Project.objects.create(name="project_without_role")
self.check_project_cannot_be_created(row.copy(), project_without_role)
auth.add_role(self.user_id, project_without_role.id, Role.VIEWER)
self.check_project_cannot_be_created(row.copy(), project_without_role)
def try_deleting_row_and_check_it_was_not_deleted(self, user: User, project_id: int, row: RowT):
assert not auth.check_permission(user.id, project_id, DELETE_PERMISSION)
with self.assertRaises(PermissionError):
MeasurementImporter(row, user.id).delete_measurement()
self.check_row_is_in_database(row)
def test_create_with_one_slot(self):
row = ExcelRowInfoGenerator.get_sample_row()
MeasurementImporter(row, self.user_id).import_measurement()
self.check_row_is_in_database(row)