def test_csv_export(now, client, answer_type, answer):
im = ImageFactory()
rs = ReaderStudyFactory()
rs.images.add(im)
rs.save()
editor = UserFactory()
rs.add_editor(editor)
reader = UserFactory()
rs.add_reader(reader)
q = QuestionFactory(
question_text="foo", reader_study=rs, answer_type=answer_type
)
a = AnswerFactory(question=q, answer=answer)
a.images.add(im)
a.save()
response = get_view_for_user(
viewname="api:reader-study-export-answers",
reverse_kwargs={"pk": rs.pk},
user=editor,
client=client,
method=client.get,
content_type="application/json",
)
headers = str(response.serialize_headers())
content = str(response.content)
assert response.status_code == 200
assert "Content-Type: text/csv" in headers
assert (
f'filename="{rs.slug}-answers-2020-01-01T00:00:00+00:00.csv"'
in headers
)
assert a.question.question_text in content
assert a.question.get_answer_type_display() in content
assert str(a.question.required) in content
assert a.question.get_image_port_display() in content
if isinstance(answer, dict):
for key in answer:
assert key in content
else:
assert re.sub(r"[\n\r\t]", " ", str(a.answer)) in content
assert im.name in content
assert a.creator.username in content
response = get_view_for_user(
viewname="api:reader-study-export-answers",
reverse_kwargs={"pk": rs.pk},
user=reader,
client=client,
method=client.get,
content_type="application/json",
)
assert response.status_code == 404
def test_assign_score(settings):
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
rs = ReaderStudyFactory(use_display_sets=False)
im = ImageFactory()
q1 = QuestionFactory(reader_study=rs)
q2 = QuestionFactory(reader_study=rs,
answer_type=Question.AnswerType.MULTIPLE_CHOICE)
e, r1, r2 = UserFactory(), UserFactory(), UserFactory()
rs.images.add(im)
rs.add_editor(e)
rs.add_reader(r1)
rs.add_reader(r2)
with capture_on_commit_callbacks(execute=True):
a1 = AnswerFactory(question=q1, creator=r1, answer="foo")
a1.images.add(im)
assert a1.score is None
with capture_on_commit_callbacks(execute=True):
gt = AnswerFactory(question=q1,
creator=e,
answer="foo",
is_ground_truth=True)
gt.images.add(im)
a1.refresh_from_db()
assert a1.score == 1.0
with capture_on_commit_callbacks(execute=True):
a2 = AnswerFactory(question=q1, creator=r2, answer="foo")
a2.images.add(im)
a2.refresh_from_db()
assert a2.score == 1.0
with capture_on_commit_callbacks(execute=True):
a1 = AnswerFactory(question=q2, creator=r1, answer=[])
a1.images.add(im)
a1.refresh_from_db()
assert a1.score is None
with capture_on_commit_callbacks(execute=True):
gt = AnswerFactory(question=q2,
creator=e,
answer=[],
is_ground_truth=True)
gt.images.add(im)
a1.refresh_from_db()
assert a1.score == 1.0
with capture_on_commit_callbacks(execute=True):
a2 = AnswerFactory(question=q2, creator=r2, answer=[])
a2.images.add(im)
a2.refresh_from_db()
assert a2.score == 1.0
def test_mine(client):
im1, im2 = ImageFactory(), ImageFactory()
rs1, rs2 = ReaderStudyFactory(), ReaderStudyFactory()
rs1.images.add(im1)
rs2.images.add(im2)
reader = UserFactory()
rs1.add_reader(reader)
rs2.add_reader(reader)
q1 = QuestionFactory(
reader_study=rs1, answer_type=Question.ANSWER_TYPE_BOOL
)
q2 = QuestionFactory(
reader_study=rs2, answer_type=Question.ANSWER_TYPE_BOOL
)
a1 = AnswerFactory(question=q1, creator=reader, answer=True)
a1.images.add(im1)
a2 = AnswerFactory(question=q2, creator=reader, answer=True)
a2.images.add(im2)
response = get_view_for_user(
viewname="api:reader-studies-answer-mine",
user=reader,
client=client,
method=client.get,
content_type="application/json",
)
response = response.json()
assert response["count"] == 2
response = get_view_for_user(
viewname="api:reader-studies-answer-mine",
user=reader,
client=client,
method=client.get,
data={"question__reader_study": rs1.pk},
content_type="application/json",
)
response = response.json()
assert response["count"] == 1
assert response["results"][0]["pk"] == str(a1.pk)
response = get_view_for_user(
viewname="api:reader-studies-answer-mine",
user=reader,
client=client,
method=client.get,
data={"question__reader_study": rs2.pk},
content_type="application/json",
)
response = response.json()
assert response["count"] == 1
assert response["results"][0]["pk"] == str(a2.pk)
def test_help_markdown_is_scrubbed(client):
rs = ReaderStudyFactory(
help_text_markdown="<b>My Help Text</b><script>naughty</script>")
u = UserFactory()
rs.add_reader(u)
response = get_view_for_user(client=client, url=rs.api_url, user=u)
assert response.status_code == 200
assert response.json()["help_text"] == "<p><b>My Help Text</b>naughty</p>"
def test_question_delete_disabled_for_questions_with_answers(client):
rs = ReaderStudyFactory(use_display_sets=False)
r1, editor = UserFactory(), UserFactory()
rs.add_reader(r1)
rs.add_editor(editor)
q = QuestionFactory(
reader_study=rs,
question_text="q1",
answer_type=Question.AnswerType.BOOL,
)
AnswerFactory(creator=r1, question=q, answer=True)
assert Answer.objects.count() == 1
assert Question.objects.count() == 1
assert not q.is_fully_editable
response = get_view_for_user(
viewname="reader-studies:question-delete",
client=client,
method=client.post,
reverse_kwargs={
"slug": rs.slug,
"pk": q.pk
},
user=editor,
)
assert response.status_code == 403
assert Question.objects.count() == 1
# if answer is deleted, deletion of the question is possible again
get_view_for_user(
viewname="reader-studies:answers-remove",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"user": r1.id},
follow=True,
user=editor,
)
assert Answer.objects.count() == 0
response = get_view_for_user(
viewname="reader-studies:question-delete",
client=client,
method=client.post,
reverse_kwargs={
"slug": rs.slug,
"pk": q.pk
},
user=editor,
)
assert response.status_code == 302
assert Question.objects.count() == 0
def test_assign_answer_image(client, settings):
settings.task_eager_propagates = (True,)
settings.task_always_eager = (True,)
rs = ReaderStudyFactory()
im = ImageFactory()
editor, reader = UserFactory(), UserFactory()
rs.images.add(im)
rs.add_editor(editor)
rs.add_reader(reader)
question = QuestionFactory(
reader_study=rs, answer_type=Question.ANSWER_TYPE_POLYGON_IMAGE
)
us = RawImageUploadSessionFactory(creator=reader)
answer = AnswerFactory(
creator=reader,
question=question,
answer={"upload_session_pk": str(us.pk)},
)
f = StagedFileFactory(
file__from_path=Path(__file__).parent.parent
/ "cases_tests"
/ "resources"
/ "image10x10x10.mha"
)
RawImageFileFactory(upload_session=us, staged_file_id=f.file_id)
response = get_view_for_user(
viewname="api:upload-session-process-images",
reverse_kwargs={"pk": us.pk},
user=reader,
client=client,
method=client.patch,
data={"answer": str(answer.pk)},
content_type="application/json",
)
assert response.status_code == 200
answer.refresh_from_db()
image = us.image_set.first()
assert answer.answer_image == image
assert reader.has_perm("view_image", image)
assert editor.has_perm("view_image", image)
def test_rs_list_permissions(client):
# Users should login
response = get_view_for_user(viewname="reader-studies:list", client=client)
assert response.status_code == 200
assert "Add a new reader study" not in response.rendered_content
creator = get_rs_creator()
# Creators should be able to see the create button
response = get_view_for_user(viewname="reader-studies:list",
client=client,
user=creator)
assert response.status_code == 200
assert "Add a new reader study" in response.rendered_content
rs1, rs2 = ReaderStudyFactory(use_display_sets=False), ReaderStudyFactory(
use_display_sets=False)
reader1 = UserFactory()
# Readers should only be able to see the studies they have access to
response = get_view_for_user(viewname="reader-studies:list",
client=client,
user=reader1)
assert response.status_code == 200
assert "Add a new reader study" not in response.rendered_content
assert rs1.slug not in response.rendered_content
assert rs2.slug not in response.rendered_content
rs1.add_reader(user=reader1)
response = get_view_for_user(viewname="reader-studies:list",
client=client,
user=reader1)
assert response.status_code == 200
assert "Add a new reader study" not in response.rendered_content
assert rs1.slug in response.rendered_content
assert rs2.slug not in response.rendered_content
editor2 = UserFactory()
rs2.add_editor(user=editor2)
# Editors should only be able to see the studies that they have access to
response = get_view_for_user(viewname="reader-studies:list",
client=client,
user=editor2)
assert response.status_code == 200
assert "Add a new reader study" not in response.rendered_content
assert rs1.slug not in response.rendered_content
assert rs2.slug in response.rendered_content
def test_validate_answer():
u = UserFactory()
im1, im2, im3 = ImageFactory(), ImageFactory(), ImageFactory()
rs = ReaderStudyFactory(hanging_list=[
{
"main": im1.name,
"main-overlay": im3.name
},
{
"main": im2.name,
"main-overlay": im3.name
},
])
rs.images.set([im1, im2, im3])
rs.add_reader(u)
q = QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q1",
)
answer = AnswerFactory(
creator=u,
question=q,
answer=True,
)
answer.images.set([im1, im3])
with pytest.raises(ValidationError) as e:
Answer.validate(
creator=u,
question=q,
answer=True,
images=[im1, im3],
)
assert (
e.value.message ==
f"User {u} has already answered this question for this set of images."
)
assert (Answer.validate(
creator=u,
question=q,
answer=True,
images=[im2, im3],
) is None)
def test_reader_study_delete(client):
rs = ReaderStudyFactory(use_display_sets=False)
editor = UserFactory()
reader = UserFactory()
rs.add_editor(editor)
rs.add_reader(reader)
assert ReaderStudy.objects.count() == 1
assert is_following(user=editor, obj=rs)
response = get_view_for_user(
viewname="reader-studies:delete",
client=client,
method=client.get,
reverse_kwargs={"slug": rs.slug},
follow=True,
user=reader,
)
assert response.status_code == 403
assert ReaderStudy.objects.count() == 1
response = get_view_for_user(
viewname="reader-studies:delete",
client=client,
method=client.get,
reverse_kwargs={"slug": rs.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert "Confirm Deletion" in response.rendered_content
response = get_view_for_user(
viewname="reader-studies:delete",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 0
assert not is_following(user=editor, obj=rs)
def test_display_set_description():
rs = ReaderStudyFactory()
reader = UserFactory()
rs.add_reader(reader)
images = [ImageFactory() for _ in range(6)]
ci = ComponentInterface.objects.get(slug="generic-medical-image")
result = {}
for image in images:
ds = DisplaySetFactory(reader_study=rs)
result[ds.pk] = f"<p>{str(image.pk)}</p>"
civ = ComponentInterfaceValueFactory(interface=ci, image=image)
ds.values.add(civ)
rs.case_text = {im.name: str(im.pk) for im in images}
rs.case_text["no_image"] = "not an image"
rs.save()
for ds in rs.display_sets.all():
assert ds.description == result[ds.pk]
def test_case_text_is_scrubbed(client):
u = UserFactory()
im, im1 = ImageFactory(), ImageFactory()
rs = ReaderStudyFactory(
case_text={
im.name: "<b>My Help Text</b><script>naughty</script>",
"not an image name": "Shouldn't appear in result",
im1.name: "Doesn't belong to this study so ignore",
})
rs.images.add(im)
rs.add_reader(u)
response = get_view_for_user(client=client, url=rs.api_url, user=u)
assert response.status_code == 200
# Case should be indexed with the api url
assert response.json()["case_text"] == {
im.api_url: "<p><b>My Help Text</b>naughty</p>"
}
def test_question_delete(client):
rs = ReaderStudyFactory(use_display_sets=False)
r1, editor = UserFactory(), UserFactory()
rs.add_reader(r1)
rs.add_editor(editor)
q = QuestionFactory(
reader_study=rs,
question_text="q1",
answer_type=Question.AnswerType.BOOL,
)
assert Question.objects.count() == 1
response = get_view_for_user(
viewname="reader-studies:question-delete",
client=client,
method=client.post,
reverse_kwargs={
"slug": rs.slug,
"pk": q.pk
},
follow=True,
user=r1,
)
assert response.status_code == 403
response = get_view_for_user(
viewname="reader-studies:question-delete",
client=client,
method=client.post,
reverse_kwargs={
"slug": rs.slug,
"pk": q.pk
},
user=editor,
)
assert response.status_code == 302
assert Question.objects.count() == 0
assert str(rs) in response.url
def test_upload_session_owned_by_answer_creator(client, settings, answer_type):
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
rs = ReaderStudyFactory()
im = ImageFactory()
editor, reader = UserFactory(), UserFactory()
rs.images.add(im)
rs.add_editor(editor)
rs.add_reader(reader)
question = QuestionFactory(reader_study=rs, answer_type=answer_type)
us1 = RawImageUploadSessionFactory(creator=reader)
us2 = RawImageUploadSessionFactory(creator=editor)
answer1 = AnswerFactory(
creator=reader,
question=question,
answer={"upload_session_pk": str(us1.pk)},
)
f = StagedFileFactory(file__from_path=Path(__file__).parent.parent /
"cases_tests" / "resources" / "image10x10x10.mha")
RawImageFileFactory(upload_session=us1, staged_file_id=f.file_id)
response = get_view_for_user(
viewname="api:upload-session-process-images",
reverse_kwargs={"pk": us2.pk},
user=editor,
client=client,
method=client.patch,
data={"answer": str(answer1.pk)},
content_type="application/json",
)
assert response.status_code == 400
assert (b"User does not have permission to add an image to this answer"
in response.rendered_content)
def test_reader_study_copy(client):
rs = ReaderStudyFactory(title="copied")
editor = UserFactory()
editor2 = UserFactory()
reader = UserFactory()
rs.add_reader(reader)
rs.add_editor(editor)
rs.add_editor(editor2)
QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q1",
),
QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q2",
)
im1, im2 = ImageFactory(), ImageFactory()
rs.images.set([im1, im2])
rs.hanging_list = [{"main": im1.name}, {"main": im2.name}]
rs.case_text = {im1.name: "test", im2.name: "test2"}
rs.save()
assert ReaderStudy.objects.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "1"},
user=reader,
follow=True,
)
assert response.status_code == 403
assert ReaderStudy.objects.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "1"},
user=editor,
follow=True,
)
assert response.status_code == 403
assert ReaderStudy.objects.count() == 1
add_perm = Permission.objects.get(
codename=f"add_{ReaderStudy._meta.model_name}"
)
editor.user_permissions.add(add_perm)
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "1"},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 2
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "1"
assert _rs.images.count() == 0
assert _rs.questions.count() == 0
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 1
assert _rs.hanging_list == []
assert _rs.case_text == {}
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "2", "copy_questions": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 3
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "2"
assert _rs.questions.count() == 2
assert _rs.images.count() == 0
assert _rs.hanging_list == []
assert _rs.case_text == {}
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "3", "copy_images": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 4
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "3"
assert _rs.questions.count() == 0
assert _rs.images.count() == 2
assert _rs.hanging_list == []
assert _rs.case_text == {}
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "4", "copy_hanging_list": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert (
"Hanging list and case text can only be copied if the images are copied as well"
in response.rendered_content
)
assert ReaderStudy.objects.count() == 4
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "4", "copy_images": True, "copy_hanging_list": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 5
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "4"
assert _rs.questions.count() == 0
assert _rs.images.count() == 2
assert _rs.hanging_list == rs.hanging_list
assert _rs.case_text == {}
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "5", "copy_images": True, "copy_case_text": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 6
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "5"
assert _rs.questions.count() == 0
assert _rs.images.count() == 2
assert _rs.hanging_list == []
assert _rs.case_text == rs.case_text
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "6", "copy_readers": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 7
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "6"
assert _rs.questions.count() == 0
assert _rs.images.count() == 0
assert _rs.hanging_list == []
assert _rs.case_text == {}
assert _rs.readers_group.user_set.count() == 1
assert _rs.editors_group.user_set.count() == 1
response = get_view_for_user(
viewname="reader-studies:copy",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
data={"title": "7", "copy_editors": True},
user=editor,
follow=True,
)
assert response.status_code == 200
assert ReaderStudy.objects.count() == 8
_rs = ReaderStudy.objects.order_by("created").last()
assert _rs.title == "7"
assert _rs.questions.count() == 0
assert _rs.images.count() == 0
assert _rs.hanging_list == []
assert _rs.case_text == {}
assert _rs.readers_group.user_set.count() == 0
assert _rs.editors_group.user_set.count() == 2
