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_ground_truth_is_excluded(client):
im = ImageFactory()
rs = ReaderStudyFactory()
rs.images.add(im)
editor = UserFactory()
rs.add_editor(editor)
rs.add_reader(editor)
q = QuestionFactory(reader_study=rs, answer_type=Question.AnswerType.BOOL)
a1 = AnswerFactory(question=q,
creator=editor,
answer=True,
is_ground_truth=True)
a1.images.add(im)
a2 = AnswerFactory(question=q,
creator=editor,
answer=True,
is_ground_truth=False)
a2.images.add(im)
response = get_view_for_user(
viewname="api:reader-studies-answer-mine",
user=editor,
client=client,
method=client.get,
content_type="application/json",
)
results = response.json()["results"]
assert len(results) == 1
assert results[0]["pk"] == str(a2.pk)
def test_user_upload_to_display_set_without_interface(client, settings):
# Override the celery settings
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
user = UserFactory()
rs = ReaderStudyFactory(use_display_sets=False)
rs.add_editor(user=user)
ci = ComponentInterface.objects.filter(slug="generic-overlay").get()
civ = ComponentInterfaceValueFactory(interface=ci)
ds = DisplaySetFactory(reader_study=rs)
ds.values.add(civ)
assert ds.values.count() == 1
upload = create_upload_from_file(
file_path=Path(__file__).parent / "resources" / "image10x10x10.mha",
creator=user,
)
with capture_on_commit_callbacks(execute=True):
response = get_view_for_user(
viewname="api:upload-session-list",
user=user,
client=client,
method=client.post,
content_type="application/json",
data={
"uploads": [upload.api_url],
"display_set": ds.pk
},
HTTP_X_FORWARDED_PROTO="https",
)
assert response.status_code == 400
assert ("An interface needs to be defined to upload to a display set."
in response.json()["non_field_errors"])
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_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_remove_image_api_view(client):
rs = ReaderStudyFactory()
reader, editor = UserFactory(), UserFactory()
rs.add_reader(reader)
rs.add_editor(editor)
response = get_view_for_user(
viewname="api:reader-study-remove-image",
reverse_kwargs={"pk": rs.pk},
user=reader,
client=client,
method=client.patch,
data={"image": 1},
content_type="application/json",
follow=True,
)
assert response.status_code == 403
response = get_view_for_user(
viewname="api:reader-study-remove-image",
reverse_kwargs={"pk": rs.pk},
user=editor,
client=client,
method=client.patch,
data={"image": 1},
content_type="application/json",
follow=True,
)
assert response.status_code == 200
assert "Image could not be removed from reader study." in str(
response.content
)
im = ImageFactory()
rs.images.add(im)
assert im in rs.images.all()
response = get_view_for_user(
viewname="api:reader-study-remove-image",
reverse_kwargs={"pk": rs.pk},
user=editor,
client=client,
method=client.patch,
data={"image": im.pk},
content_type="application/json",
follow=True,
)
assert response.status_code == 200
assert "Image removed from reader study." in str(response.content)
assert im not in rs.images.all()
def test_session_with_user_upload_to_readerstudy(client, settings):
# Override the celery settings
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
user = UserFactory()
rs = ReaderStudyFactory(use_display_sets=False)
rs.add_editor(user=user)
upload = create_upload_from_file(
file_path=Path(__file__).parent / "resources" / "image10x10x10.mha",
creator=user,
)
# try upload with interface
with capture_on_commit_callbacks(execute=True):
response = get_view_for_user(
viewname="api:upload-session-list",
user=user,
client=client,
method=client.post,
content_type="application/json",
data={
"uploads": [upload.api_url],
"reader_study": rs.slug,
"interface": "generic-overlay",
},
HTTP_X_FORWARDED_PROTO="https",
)
assert response.status_code == 400
assert (
"An interface can only be defined for archive, archive item or display set uploads."
in response.json()["non_field_errors"])
# try without interface
with capture_on_commit_callbacks(execute=True):
response = get_view_for_user(
viewname="api:upload-session-list",
user=user,
client=client,
method=client.post,
content_type="application/json",
data={
"uploads": [upload.api_url],
"reader_study": rs.slug
},
HTTP_X_FORWARDED_PROTO="https",
)
assert response.status_code == 201
upload_session = response.json()
assert upload_session["uploads"] == [upload.api_url]
def test_upload_some_images(client: Client, challenge_set, settings):
# Override the celery settings
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
user = UserFactory()
# Use reader studies as this uses UploadRawImagesForm
rs = ReaderStudyFactory(use_display_sets=False)
rs.add_editor(user)
response = get_view_for_user(
client=client,
viewname="reader-studies:add-images",
user=user,
reverse_kwargs={"slug": rs.slug},
)
assert response.status_code == 200
assert rs.images.count() == 0
assert RawImageUploadSession.objects.count() == 0
user_upload = create_upload_from_file(file_path=RESOURCE_PATH /
"image10x10x10.mha",
creator=user)
with capture_on_commit_callbacks(execute=True):
response = get_view_for_user(
data={"user_uploads": [user_upload.pk]},
client=client,
viewname="reader-studies:add-images",
user=user,
reverse_kwargs={"slug": rs.slug},
method=client.post,
)
assert response.status_code == 302
assert rs.images.count() == 1
sessions = RawImageUploadSession.objects.all()
assert len(sessions) == 1
response = get_view_for_user(url=sessions[0].get_absolute_url(),
client=client,
user=user)
assert response.status_code == 200
response = get_view_for_user(
url=sessions[0].get_absolute_url(),
client=client,
user=UserFactory(is_staff=True),
)
assert response.status_code == 403
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)
class TwoReaderStudies:
def __init__(self):
self.creator = get_rs_creator()
self.rs1, self.rs2 = ReaderStudyFactory(
use_display_sets=False), ReaderStudyFactory(use_display_sets=False)
self.editor1, self.reader1, self.editor2, self.reader2 = (
UserFactory(),
UserFactory(),
UserFactory(),
UserFactory(),
)
self.rs1.add_editor(user=self.editor1)
self.rs2.add_editor(user=self.editor2)
self.rs1.add_reader(user=self.reader1)
self.rs2.add_reader(user=self.reader2)
self.u = UserFactory()
def test_upload_some_images(client: Client, challenge_set, settings):
# Override the celery settings
settings.task_eager_propagates = (True,)
settings.task_always_eager = (True,)
user = UserFactory()
# Use reader studies as this uses UploadRawImagesForm
rs = ReaderStudyFactory()
rs.add_editor(user)
response = get_view_for_user(
client=client,
viewname="reader-studies:add-images",
user=user,
reverse_kwargs={"slug": rs.slug},
)
assert response.status_code == 200
assert rs.images.count() == 0
assert RawImageUploadSession.objects.count() == 0
file1 = create_file_from_filepath(RESOURCE_PATH / "image10x10x10.mha")
response = get_view_for_user(
data={"files": f"{file1.uuid}"},
client=client,
viewname="reader-studies:add-images",
user=user,
reverse_kwargs={"slug": rs.slug},
method=client.post,
)
assert response.status_code == 302
assert rs.images.count() == 1
sessions = RawImageUploadSession.objects.all()
assert len(sessions) == 1
response = get_view_for_user(
url=sessions[0].get_absolute_url(), client=client, user=user
)
assert response.status_code == 200
response = get_view_for_user(
url=sessions[0].get_absolute_url(),
client=client,
user=UserFactory(is_staff=True),
)
assert response.status_code == 403
def test_assign_score(settings):
settings.task_eager_propagates = (True,)
settings.task_always_eager = (True,)
rs = ReaderStudyFactory()
im = ImageFactory()
q1 = QuestionFactory(reader_study=rs)
q2 = QuestionFactory(
reader_study=rs, answer_type=Question.ANSWER_TYPE_MULTIPLE_CHOICE
)
e, r1, r2 = UserFactory(), UserFactory(), UserFactory()
rs.images.add(im)
rs.add_editor(e)
rs.add_reader(r1)
rs.add_reader(r2)
a1 = AnswerFactory(question=q1, creator=r1, answer="foo")
a1.images.add(im)
assert a1.score is None
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
a2 = AnswerFactory(question=q1, creator=r2, answer="foo")
a2.images.add(im)
a2.refresh_from_db()
assert a2.score == 1.0
a1 = AnswerFactory(question=q2, creator=r1, answer=[])
a1.images.add(im)
assert a1.score is None
gt = AnswerFactory(question=q2, creator=e, answer=[], is_ground_truth=True)
gt.images.add(im)
a1.refresh_from_db()
assert a1.score == 1.0
a2 = AnswerFactory(question=q2, creator=r2, answer=[])
a2.images.add(im)
a2.refresh_from_db()
assert a2.score == 1.0
def test_generate_hanging_list_api_view(generate_hanging_list, client):
rs = ReaderStudyFactory()
editor = UserFactory()
rs.add_editor(editor)
response = get_view_for_user(
viewname="api:reader-study-generate-hanging-list",
reverse_kwargs={"pk": rs.pk},
user=editor,
client=client,
method=client.patch,
follow=True,
)
assert response.status_code == 200
assert "Hanging list generated." in str(response.content)
generate_hanging_list.assert_called_once()
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_api_list_is_filtered(client):
rs1, rs2 = ReaderStudyFactory(), ReaderStudyFactory()
rs1_editor = UserFactory()
rs1.add_editor(rs1_editor)
q1, q2 = (
QuestionFactory(reader_study=rs1),
QuestionFactory(reader_study=rs2),
)
a1, _ = (
AnswerFactory(question=q1, answer=True),
AnswerFactory(question=q2, answer=False),
)
response = get_view_for_user(viewname="api:reader-study-list",
user=rs1_editor,
client=client)
assert response.status_code == 200
assert response.json()["count"] == 1
response = get_view_for_user(
viewname="api:reader-study-detail",
reverse_kwargs={"pk": rs1.pk},
user=rs1_editor,
client=client,
)
assert response.status_code == 200
assert len(response.json()["questions"]) == 1
response = get_view_for_user(
viewname="api:reader-studies-question-list",
user=rs1_editor,
client=client,
)
assert response.status_code == 200
assert response.json()["count"] == 1
assert response.json()["results"][0]["pk"] == str(q1.pk)
response = get_view_for_user(
viewname="api:reader-studies-answer-list",
user=rs1_editor,
client=client,
)
assert response.status_code == 200
assert response.json()["count"] == 1
assert response.json()["results"][0]["pk"] == str(a1.pk)
def test_answer_remove(client):
rs = ReaderStudyFactory()
r1, r2, editor = UserFactory(), UserFactory(), UserFactory()
rs.add_reader(r1)
rs.add_reader(r2)
rs.add_editor(editor)
q = QuestionFactory(
reader_study=rs,
question_text="q1",
answer_type=Question.ANSWER_TYPE_BOOL,
)
im = ImageFactory()
a1 = AnswerFactory(creator=r1, question=q, answer=True)
a1.images.set([im])
a2 = AnswerFactory(creator=r2, question=q, answer=True)
a2.images.set([im])
assert Answer.objects.count() == 2
response = 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=r1,
)
assert response.status_code == 403
response = 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 response.status_code == 200
assert Answer.objects.count() == 1
assert Answer.objects.filter(creator=r1).count() == 0
assert Answer.objects.filter(creator=r2).count() == 1
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_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 reader_study_with_gt():
rs = ReaderStudyFactory()
im1, im2 = ImageFactory(name="im1"), ImageFactory(name="im2")
q1, q2, q3 = [
QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q1",
),
QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q2",
),
QuestionFactory(
reader_study=rs,
answer_type=Question.AnswerType.BOOL,
question_text="q3",
),
]
r1, r2, editor = UserFactory(), UserFactory(), UserFactory()
rs.add_reader(r1)
rs.add_reader(r2)
rs.add_editor(editor)
rs.images.set([im1, im2])
rs.hanging_list = [{"main": im1.name}, {"main": im2.name}]
rs.save()
for question in [q1, q2, q3]:
for im in [im1, im2]:
ans = AnswerFactory(
question=question,
creator=editor,
answer=True,
is_ground_truth=True,
)
ans.images.add(im)
return rs
def test_reader_study_display_set_list(client):
user = UserFactory()
rs = ReaderStudyFactory(use_display_sets=True)
rs.add_editor(user)
civ = ComponentInterfaceValueFactory(image=ImageFactory())
ds = DisplaySetFactory(reader_study=rs)
ds.values.add(civ)
response = get_view_for_user(
viewname="reader-studies:display_sets",
reverse_kwargs={"slug": rs.slug},
client=client,
user=user,
)
assert response.status_code == 200
response = get_view_for_user(
viewname="reader-studies:display_sets",
reverse_kwargs={"slug": rs.slug},
client=client,
user=user,
method=client.get,
follow=True,
data={
"length": 10,
"draw": 1,
"order[0][dir]": "desc",
"order[0][column]": 0,
},
**{"HTTP_X_REQUESTED_WITH": "XMLHttpRequest"},
)
resp = response.json()
assert str(ds.pk) in resp["data"][0][0]
def test_csv_export(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-studies-answer-list",
params={"question__reader_study": str(rs.pk)},
user=editor,
client=client,
method=client.get,
HTTP_ACCEPT="text/csv",
)
headers = str(response.serialize_headers())
content = str(response.content)
assert response.status_code == 200
assert "Content-Type: text/csv" in headers
if isinstance(answer, dict):
for key in answer:
assert key in content
else:
assert re.sub(r"\n", r"\\n", str(a.answer)) in content
assert a.creator.username in content
response = get_view_for_user(
viewname="api:reader-studies-question-list",
params={"reader_study": str(rs.pk)},
user=editor,
client=client,
method=client.get,
HTTP_ACCEPT="text/csv",
)
headers = str(response.serialize_headers())
content = str(response.content)
assert response.status_code == 200
assert "Content-Type: text/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
response = get_view_for_user(
viewname="api:image-list",
params={"readerstudies": str(rs.pk)},
user=editor,
client=client,
method=client.get,
HTTP_ACCEPT="text/csv",
)
headers = str(response.serialize_headers())
content = str(response.content)
assert response.status_code == 200
assert "Content-Type: text/csv" in headers
assert im.name in content
def test_progress_for_user(settings):
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
rs = ReaderStudyFactory()
im1, im2 = ImageFactory(name="im1"), ImageFactory(name="im2")
q1, q2, q3 = [
QuestionFactory(reader_study=rs),
QuestionFactory(reader_study=rs),
QuestionFactory(reader_study=rs),
]
reader = UserFactory()
rs.add_reader(reader)
question_perc = 100 / 6
assert rs.get_progress_for_user(reader) == {
"diff": 0.0,
"hangings": 0.0,
"questions": 0.0,
}
rs.images.set([im1, im2])
rs.hanging_list = [{"main": im1.name}, {"main": im2.name}]
rs.save()
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == 0
a11 = AnswerFactory(question=q1, answer="foo", creator=reader)
a11.images.add(im1)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == pytest.approx(question_perc)
a21 = AnswerFactory(question=q1, answer="foo", creator=reader)
a21.images.add(im2)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == pytest.approx(question_perc * 2)
a12 = AnswerFactory(question=q2, answer="foo", creator=reader)
a12.images.add(im1)
a13 = AnswerFactory(question=q3, answer="foo", creator=reader)
a13.images.add(im1)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 50
assert progress["questions"] == pytest.approx(question_perc * 4)
editor = UserFactory()
rs.add_reader(editor)
rs.add_editor(editor)
for q in [q1, q2, q3]:
for im in [im1, im2]:
a = AnswerFactory(question=q,
answer="foo",
creator=editor,
is_ground_truth=True)
a.images.add(im)
progress = rs.get_progress_for_user(editor)
assert progress["hangings"] == 0
assert progress["questions"] == 0
for q in [q1, q2, q3]:
for im in [im1, im2]:
a = AnswerFactory(question=q,
answer="foo",
creator=editor,
is_ground_truth=False)
a.images.add(im)
progress = rs.get_progress_for_user(editor)
assert progress["hangings"] == 100.0
assert progress["questions"] == 100.0
def test_answer_update(client):
im1, im2 = ImageFactory(), ImageFactory()
rs = ReaderStudyFactory()
rs.images.add(im1, im2)
rs.save()
reader = UserFactory()
rs.add_reader(reader)
editor = UserFactory()
rs.add_editor(editor)
q = QuestionFactory(reader_study=rs, answer_type=Question.AnswerType.BOOL)
response = get_view_for_user(
viewname="api:reader-studies-answer-list",
user=reader,
client=client,
method=client.post,
data={
"answer": True,
"images": [im1.api_url],
"question": q.api_url
},
content_type="application/json",
)
assert response.status_code == 201
answer = Answer.objects.get(pk=response.data.get("pk"))
assert answer.answer is True
assert answer.images.first() == im1
assert answer.history.count() == 1
response = get_view_for_user(
viewname="api:reader-studies-answer-detail",
reverse_kwargs={"pk": answer.pk},
user=reader,
client=client,
method=client.patch,
data={
"answer": False,
"images": [im2.api_url]
},
content_type="application/json",
)
assert response.status_code == 400
answer.refresh_from_db()
assert response.json() == {
"non_field_errors":
["This reader study does not allow answer modification."]
}
assert answer.answer is True
assert answer.images.first() == im1
assert answer.history.count() == 1
rs.allow_answer_modification = True
rs.save()
response = get_view_for_user(
viewname="api:reader-studies-answer-detail",
reverse_kwargs={"pk": answer.pk},
user=reader,
client=client,
method=client.patch,
data={
"answer": False,
"images": [im2.api_url]
},
content_type="application/json",
)
assert response.status_code == 400
answer.refresh_from_db()
assert response.json() == {
"non_field_errors": ["Only the answer field can be modified."]
}
assert answer.answer is True
assert answer.images.first() == im1
assert answer.history.count() == 1
response = get_view_for_user(
viewname="api:reader-studies-answer-detail",
reverse_kwargs={"pk": answer.pk},
user=reader,
client=client,
method=client.patch,
data={"answer": False},
content_type="application/json",
)
assert response.status_code == 200
answer.refresh_from_db()
assert answer.answer is False
assert answer.images.first() == im1
assert answer.history.count() == 2
response = get_view_for_user(
viewname="api:reader-studies-answer-detail",
reverse_kwargs={"pk": answer.pk},
user=editor,
client=client,
method=client.patch,
data={"answer": False},
content_type="application/json",
)
assert response.status_code == 403
answer.refresh_from_db()
assert answer.answer is False
assert answer.history.count() == 2
def test_progress_for_user(settings, use_display_sets): # noqa: C901
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
rs = ReaderStudyFactory(use_display_sets=use_display_sets)
im1, im2 = ImageFactory(name="im1"), ImageFactory(name="im2")
q1, q2, q3 = [
QuestionFactory(reader_study=rs),
QuestionFactory(reader_study=rs),
QuestionFactory(reader_study=rs),
]
reader = UserFactory()
rs.add_reader(reader)
question_perc = 100 / 6
assert rs.get_progress_for_user(reader) == {
"diff": 0.0,
"hangings": 0.0,
"questions": 0.0,
}
if use_display_sets:
ci = ComponentInterface.objects.get(slug="generic-medical-image")
civ1 = ComponentInterfaceValueFactory(image=im1, interface=ci)
civ2 = ComponentInterfaceValueFactory(image=im2, interface=ci)
ds1, ds2 = DisplaySetFactory(reader_study=rs), DisplaySetFactory(
reader_study=rs)
ds1.values.add(civ1)
ds2.values.add(civ2)
else:
rs.images.set([im1, im2])
rs.hanging_list = [{"main": im1.name}, {"main": im2.name}]
rs.save()
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == 0
a11 = AnswerFactory(question=q1, answer="foo", creator=reader)
if use_display_sets:
a11.display_set = ds1
a11.save()
else:
a11.images.add(im1)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == pytest.approx(question_perc)
a21 = AnswerFactory(question=q1, answer="foo", creator=reader)
if use_display_sets:
a21.display_set = ds2
a21.save()
else:
a21.images.add(im2)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 0
assert progress["questions"] == pytest.approx(question_perc * 2)
a12 = AnswerFactory(question=q2, answer="foo", creator=reader)
a13 = AnswerFactory(question=q3, answer="foo", creator=reader)
if use_display_sets:
a12.display_set = ds1
a12.save()
a13.display_set = ds1
a13.save()
else:
a12.images.add(im1)
a13.images.add(im1)
progress = rs.get_progress_for_user(reader)
assert progress["hangings"] == 50
assert progress["questions"] == pytest.approx(question_perc * 4)
editor = UserFactory()
rs.add_reader(editor)
rs.add_editor(editor)
for q in [q1, q2, q3]:
if use_display_sets:
for ds in [ds1, ds2]:
a = AnswerFactory(
question=q,
answer="foo",
creator=editor,
is_ground_truth=True,
display_set=ds,
)
else:
for im in [im1, im2]:
a = AnswerFactory(
question=q,
answer="foo",
creator=editor,
is_ground_truth=True,
)
a.images.add(im)
progress = rs.get_progress_for_user(editor)
assert progress["hangings"] == 0
assert progress["questions"] == 0
for q in [q1, q2, q3]:
if use_display_sets:
for ds in [ds1, ds2]:
a = AnswerFactory(
question=q,
answer="foo",
creator=editor,
is_ground_truth=False,
display_set=ds,
)
else:
for im in [im1, im2]:
a = AnswerFactory(
question=q,
answer="foo",
creator=editor,
is_ground_truth=False,
)
a.images.add(im)
progress = rs.get_progress_for_user(editor)
assert progress["hangings"] == 100.0
assert progress["questions"] == 100.0
def test_archive_items_to_reader_study_update(client, settings):
settings.task_eager_propagates = (True, )
settings.task_always_eager = (True, )
archive = ArchiveFactory()
rs1 = ReaderStudyFactory(use_display_sets=True)
rs2 = ReaderStudyFactory(use_display_sets=False)
editor, user = UserFactory(), UserFactory()
archive.add_user(user)
archive.add_editor(editor)
rs1.add_editor(editor)
rs2.add_editor(editor)
im1, im2, im3, im4 = ImageFactory.create_batch(4)
overlay = ComponentInterface.objects.get(slug="generic-overlay")
image = ComponentInterface.objects.get(slug="generic-medical-image")
civ1, civ2, civ3, civ4 = (
ComponentInterfaceValueFactory(interface=image, image=im1),
ComponentInterfaceValueFactory(interface=image, image=im2),
ComponentInterfaceValueFactory(interface=overlay, image=im3),
ComponentInterfaceValueFactory(interface=overlay, image=im4),
)
ai1 = ArchiveItemFactory(archive=archive)
ai2 = ArchiveItemFactory(archive=archive)
ai1.values.add(civ1)
ai2.values.add(civ2)
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
reverse_kwargs={"slug": archive.slug},
user=user,
)
assert response.status_code == 200
assert str(rs1.pk) not in response.rendered_content
assert str(rs2.pk) not in response.rendered_content
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
reverse_kwargs={"slug": archive.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert str(rs1.pk) in response.rendered_content
assert str(rs2.pk) not in response.rendered_content
assert im1.name in response.rendered_content
assert im2.name in response.rendered_content
assert im3.name not in response.rendered_content
assert im4.name not in response.rendered_content
ai1.values.add(civ3)
ai2.values.add(civ4)
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
reverse_kwargs={"slug": archive.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert f"{im1.name}, {im3.name}" in response.rendered_content
assert f"{im2.name}, {im4.name}" in response.rendered_content
def test_archive_items_to_reader_study_update_form(client, settings):
settings.task_eager_propagates = (True,)
settings.task_always_eager = (True,)
archive = ArchiveFactory()
rs1, rs2 = ReaderStudyFactory(use_display_sets=True), ReaderStudyFactory(
use_display_sets=False
)
editor, reader = UserFactory(), UserFactory()
archive.editors_group.user_set.add(editor)
rs1.add_editor(editor)
rs1.add_reader(reader)
rs2.add_editor(editor)
im1, im2, im3, im4 = ImageFactory.create_batch(4)
overlay = ComponentInterface.objects.get(slug="generic-overlay")
image = ComponentInterface.objects.get(slug="generic-medical-image")
civ1, civ2, civ3, civ4 = (
ComponentInterfaceValueFactory(interface=image, image=im1),
ComponentInterfaceValueFactory(interface=image, image=im2),
ComponentInterfaceValueFactory(interface=overlay, image=im3),
ComponentInterfaceValueFactory(interface=overlay, image=im4),
)
ai1 = ArchiveItemFactory(archive=archive)
ai2 = ArchiveItemFactory(archive=archive)
ai1.values.add(civ1)
ai2.values.add(civ2)
assert rs1.display_sets.count() == 0
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
method=client.post,
data={"items": [ai1.pk, ai2.pk], "reader_study": rs1.pk},
reverse_kwargs={"slug": archive.slug},
follow=True,
user=reader,
)
assert response.status_code == 403
assert rs1.display_sets.count() == 0
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
method=client.post,
data={"items": [ai1.pk, ai2.pk], "reader_study": rs1.pk},
reverse_kwargs={"slug": archive.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert rs1.display_sets.count() == 2
assert sorted(
list(rs1.display_sets.values_list("values", flat=True))
) == sorted([civ1.pk, civ2.pk])
assert rs2.display_sets.count() == 0
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
method=client.post,
data={"items": [ai1.pk, ai2.pk], "reader_study": rs2.pk},
reverse_kwargs={"slug": archive.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert rs2.display_sets.count() == 0
ai1.values.add(civ3)
ai2.values.add(civ4)
response = get_view_for_user(
viewname="archives:items-reader-study-update",
client=client,
method=client.post,
data={"items": [ai1.pk, ai2.pk], "reader_study": rs1.pk},
reverse_kwargs={"slug": archive.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert rs1.display_sets.count() == 4
assert sorted(
sorted(list(ds.values.values_list("pk", flat=True)))
for ds in rs1.display_sets.all()
) == sorted([[civ1.pk], [civ2.pk], [civ1.pk, civ3.pk], [civ2.pk, civ4.pk]])
def test_example_ground_truth(client, tmpdir):
rs = ReaderStudyFactory()
reader, editor = UserFactory(), UserFactory()
q1, q2, q3 = (
QuestionFactory(
reader_study=rs,
question_text="q1",
answer_type=Question.ANSWER_TYPE_BOOL,
),
QuestionFactory(
reader_study=rs,
question_text="q2",
answer_type=Question.ANSWER_TYPE_CHOICE,
),
QuestionFactory(
reader_study=rs,
question_text="q3",
answer_type=Question.ANSWER_TYPE_SINGLE_LINE_TEXT,
),
)
CategoricalOptionFactory(question=q2, title="option")
im1, im2, im3 = (ImageFactory(), ImageFactory(), ImageFactory())
rs.images.set([im1, im2, im3])
rs.add_reader(reader)
rs.add_editor(editor)
rs.generate_hanging_list()
response = get_view_for_user(
viewname="reader-studies:example-ground-truth",
client=client,
method=client.get,
reverse_kwargs={"slug": rs.slug},
follow=True,
user=reader,
)
assert response.status_code == 403
response = get_view_for_user(
viewname="reader-studies:example-ground-truth",
client=client,
method=client.get,
reverse_kwargs={"slug": rs.slug},
follow=True,
user=editor,
)
assert response.status_code == 200
assert Answer.objects.count() == 0
gt = io.BytesIO()
gt.write(response.content)
gt.seek(0)
response = get_view_for_user(
viewname="reader-studies:add-ground-truth",
client=client,
method=client.post,
reverse_kwargs={"slug": rs.slug},
follow=True,
data={"ground_truth": gt},
user=editor,
)
assert response.status_code == 200
assert Answer.objects.count() == rs.images.count() * rs.questions.count()
for image in [im1, im2, im3]:
for question in [q1, q2, q3]:
assert Answer.objects.filter(images=image,
question=question,
is_ground_truth=True).exists()
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
