def test_delete_search():
# Arrange: create a codelist with searches
owner = UserFactory()
cl = actions.create_codelist(
owner=owner, name="Test Codelist", coding_system_id="snomedct"
)
s1 = actions.create_search(
codelist=cl, term="synchronised", codes=["1068181000000106"]
)
s2 = actions.create_search(
codelist=cl, term="swimming", codes=["1067731000000107", "1068181000000106"]
)
# Act: delete the search for "swimming"
actions.delete_search(search=s2)
# Assert...
# that the codelist has only 1 search
assert cl.searches.count() == 1
# that the codelist has only 1 code
assert cl.codes.count() == 1
# Arrange: recreate the search for "swimming"
actions.create_search(
codelist=cl, term="swimming", codes=["1067731000000107", "1068181000000106"]
)
# Act: delete the search for "synchronised"
actions.delete_search(search=s1)
# Assert...
# that the codelist has only 1 search
assert cl.searches.count() == 1
# that the codelist still has both codes
assert cl.codes.count() == 2
def test_codelistupdate_with_duplicate_name(rf):
project = ProjectFactory()
CodelistFactory(name="Existing Codelist", project=project)
codelist = CodelistFactory(project=project)
data = {
"project": codelist.project.slug,
"name": "Existing Codelist",
"coding_system_id": "snomedct",
"description": "This is a test CHANGED",
"methodology": "This is how we did it",
"reference-TOTAL_FORMS": "0",
"reference-INITIAL_FORMS": "0",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"signoff-TOTAL_FORMS": "0",
"signoff-INITIAL_FORMS": "0",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistUpdate.as_view()(
request, project_slug=codelist.project.slug, codelist_slug=codelist.slug
)
assert response.status_code == 200
# confirm we have errors from the codelist form
assert response.context_data["codelist_form"].errors
def test_versionupdate_success(rf):
version = create_draft_version()
assert version.codelist.versions.count() == 1
csv_data = "code,description\n1068181000000106, Injury whilst synchronised swimming (disorder)"
data = {
"csv_data": csv_builder(csv_data),
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = VersionUpdate.as_view()(
request,
project_slug=version.codelist.project.slug,
codelist_slug=version.codelist.slug,
qualified_version_str=version.qualified_version_str,
)
assert response.status_code == 302
assert (
response.url
== f"/codelist/{version.codelist.project.slug}/{version.codelist.slug}/2020-07-23-draft/"
)
assert version.codelist.versions.count() == 1
def test_codelistcreate_success(rf):
project = ProjectFactory()
signoff_user = UserFactory()
assert project.codelists.count() == 0
csv_data = "code,description\n1067731000000107,Injury whilst swimming (disorder)"
data = {
"name": "Test Codelist",
"coding_system_id": "snomedct",
"description": "This is a test",
"methodology": "This is how we did it",
"csv_data": csv_builder(csv_data),
"reference-TOTAL_FORMS": "1",
"reference-INITIAL_FORMS": "0",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"reference-0-text": "foo",
"reference-0-url": "http://example.com",
"signoff-TOTAL_FORMS": "1",
"signoff-INITIAL_FORMS": "0",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
"signoff-0-user": signoff_user.username,
"signoff-0-date": "2020-01-23",
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistCreate.as_view()(request, project_slug=project.slug)
assert response.status_code == 302
assert response.url == f"/codelist/{project.slug}/test-codelist/"
assert project.codelists.count() == 1
codelist = project.codelists.first()
assert codelist.name == "Test Codelist"
# we should have one reference to example.com
assert codelist.references.count() == 1
ref = codelist.references.first()
assert ref.url == "http://example.com"
# we should have one signoff by signoff user
assert codelist.signoffs.count() == 1
signoff = codelist.signoffs.first()
assert signoff.user == signoff_user
def test_versioncreate_unknown_codelist(rf):
codelist = CodelistFactory()
request = rf.get("/")
request.user = UserFactory()
with pytest.raises(Http404):
VersionCreate.as_view()(
request, project_slug=codelist.project.slug, codelist_slug="test"
)
def test_versionupdate_unknown_version(rf):
codelist = CodelistFactory()
request = rf.get("/")
request.user = UserFactory()
with pytest.raises(Http404):
VersionUpdate.as_view()(
request,
project_slug=codelist.project.slug,
codelist_slug=codelist.slug,
qualified_version_str="test",
)
def test_versionpublish_unknown_version(rf):
codelist = CodelistFactory()
request = rf.post("/")
request.user = UserFactory()
with pytest.raises(Http404):
version_publish(
request,
project_slug=codelist.project.slug,
codelist_slug=codelist.slug,
qualified_version_str="test",
)
def test_versioncreate_missing_field(rf):
codelist = create_published_version().codelist
request = rf.post("/", data={})
request.user = UserFactory()
response = VersionCreate.as_view()(
request, project_slug=codelist.project.slug, codelist_slug=codelist.slug
)
assert response.status_code == 200
assert "form" in response.context_data
assert len(response.context_data["form"].errors) == 1
assert "csv_data" in response.context_data["form"].errors
def test_codelistcreate_invalid_post(rf):
project = ProjectFactory()
signoff_user = UserFactory()
assert project.codelists.count() == 0
csv_data = "code,description\n1067731000000107,Injury whilst swimming (disorder)"
# missing signoff-0-date
data = {
"name": "Test Codelist",
"coding_system_id": "snomedct",
"description": "This is a test",
"methodology": "This is how we did it",
"csv_data": csv_builder(csv_data),
"reference-TOTAL_FORMS": "1",
"reference-INITIAL_FORMS": "0",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"reference-0-text": "foo",
"reference-0-url": "http://example.com",
"signoff-TOTAL_FORMS": "1",
"signoff-INITIAL_FORMS": "0",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
"signoff-0-user": signoff_user.username,
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistCreate.as_view()(request, project_slug=project.slug)
# we're returning an HTML response when there are errors so check we don't
# receive a redirect code
assert response.status_code == 200
# confirm we have errors from the signoff formset
assert response.context_data["signoff_formset"].errors
def test_codelist(client, tennis_elbow_codelist):
owner = UserFactory()
cl = actions.create_codelist(
owner=owner, name="Elbows", coding_system_id="snomedct"
)
search_results = do_search(cl.coding_system, "elbow")
actions.create_search(codelist=cl, term="elbow", codes=search_results["all_codes"])
client.force_login(owner)
rsp = client.get(f"/builder/{owner.username}/{cl.slug}/")
assert rsp.status_code == 200
assert b"Elbows" in rsp.content
def test_create_codelist():
# Arrange: create a user
owner = UserFactory()
# Act: create a codelist
cl = actions.create_codelist(
owner=owner, name="Test Codelist", coding_system_id="snomedct"
)
# Assert...
# that a codelist's attributes have been set
assert cl.owner == owner
assert cl.name == "Test Codelist"
assert cl.slug == "test-codelist"
assert cl.coding_system_id == "snomedct"
def test_versionupdate_form_error(rf):
version = create_published_version()
request = rf.post("/", data={})
request.user = UserFactory()
response = VersionUpdate.as_view()(
request,
project_slug=version.codelist.project.slug,
codelist_slug=version.codelist.slug,
qualified_version_str=version.qualified_version_str,
)
assert response.status_code == 200
assert "form" in response.context_data
assert "csv_data" in response.context_data["form"].errors
def test_versionpublish_success(rf):
version = create_draft_version()
request = rf.post("/")
request.user = UserFactory()
response = version_publish(
request,
project_slug=version.codelist.project.slug,
codelist_slug=version.codelist.slug,
qualified_version_str=version.qualified_version_str,
)
assert response.status_code == 302
version.refresh_from_db()
assert response.url == version.get_absolute_url()
assert not version.is_draft
def test_versionupdate_draft_mismatch(rf):
version = create_published_version()
# set the version string to that of a draft
qualified_version_str = f"{version.qualified_version_str}-draft"
request = rf.get("/")
request.user = UserFactory()
response = VersionUpdate.as_view()(
request,
project_slug=version.codelist.project.slug,
codelist_slug=version.codelist.slug,
qualified_version_str=qualified_version_str,
)
# we should get redirected to the Version page
assert response.status_code == 302
assert response.url == version.get_absolute_url()
def test_codelistcreate_with_duplicate_name(rf):
project = ProjectFactory()
create_codelist(
project=project,
name="Test",
coding_system_id="snomedct",
description="This is a test",
methodology="This is how we did it",
csv_data="code,description\n1067731000000107,Injury whilst swimming (disorder)",
)
assert project.codelists.count() == 1
csv_data = "code,description\n1067731000000107,Injury whilst swimming (disorder)"
data = {
"name": "Test",
"coding_system_id": "snomedct",
"description": "This is a test",
"methodology": "This is how we did it",
"csv_data": csv_builder(csv_data),
"reference-TOTAL_FORMS": "0",
"reference-INITIAL_FORMS": "0",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"signoff-TOTAL_FORMS": "0",
"signoff-INITIAL_FORMS": "0",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistCreate.as_view()(request, project_slug=project.slug)
assert project.codelists.count() == 1
# we're returning an HTML response when there are errors so check we don't
# receive a redirect code
assert response.status_code == 200
# confirm we have errors from the codelist form
assert response.context_data["codelist_form"].errors
def handle(self, path, **kwargs):
if Concept.objects.count() > 0:
raise CommandError("Must be run against empty database")
fixtures_path = Path(settings.BASE_DIR, "coding_systems", "snomedct",
"fixtures")
call_command("loaddata", fixtures_path / "core-model-components.json")
call_command("loaddata", fixtures_path / "tennis-elbow.json")
owner = UserFactory()
cl = actions.create_codelist(owner=owner,
name="Elbows",
coding_system_id="snomedct")
search_results = do_search(cl.coding_system, "elbow")
actions.create_search(codelist=cl,
term="elbow",
codes=search_results["all_codes"])
client = Client()
client.force_login(owner)
rsp = client.get(f"/builder/{owner.username}/{cl.slug}/")
data = {
k: rsp.context[k]
for k in [
"searches",
"filter",
"tables",
"included_codes",
"excluded_codes",
"displayed_codes",
"parent_map",
"child_map",
"is_editable",
"update_url",
"search_url",
]
}
with open(path, "w") as f:
json.dump(data, f, indent=2)
def test_create_search():
# Arrange: create a codelist
owner = UserFactory()
cl = actions.create_codelist(
owner=owner, name="Test Codelist", coding_system_id="snomedct"
)
# Act: create a first search
s = actions.create_search(
codelist=cl, term="swimming", codes=["1067731000000107", "1068181000000106"]
)
# Assert...
# that the search's attributes have been set
assert s.codelist == cl
assert s.term == "swimming"
assert s.slug == "swimming"
# that the newly created search has 2 results
assert s.results.count() == 2
# that the codelist has 1 search
assert cl.searches.count() == 1
# that the codelist has 2 codes
assert cl.codes.count() == 2
# Act: create another search
s = actions.create_search(
codelist=cl, term="synchronised", codes=["1068181000000106"]
)
# Assert...
# that the newly created search has 1 result
assert s.results.count() == 1
# that the codelist has 2 searches
assert cl.searches.count() == 2
# that the codelist still has 2 codes
assert cl.codes.count() == 2
def test_codelistupdate_invalid_post(rf):
codelist = CodelistFactory()
signoff_1 = SignOffFactory(codelist=codelist)
reference_1 = ReferenceFactory(codelist=codelist)
# missing signoff-0-date
data = {
"project": codelist.project.slug,
"name": "Test Codelist",
"coding_system_id": "snomedct",
"description": "This is a test",
"methodology": "This is how we did it",
"reference-TOTAL_FORMS": "1",
"reference-INITIAL_FORMS": "0",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"reference-0-text": reference_1.text,
"reference-0-url": reference_1.url,
"signoff-TOTAL_FORMS": "1",
"signoff-INITIAL_FORMS": "0",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
"signoff-0-user": signoff_1.user.username,
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistUpdate.as_view()(
request, project_slug=codelist.project.slug, codelist_slug=codelist.slug
)
# we're returning an HTML response when there are errors so check we don't
# receive a redirect code
assert response.status_code == 200
# confirm we have errors from the signoff formset
assert response.context_data["signoff_formset"].errors
def test_update_code_statuses(tennis_elbow):
# Arrange: load fixtures and create a codelist with a search
owner = UserFactory()
cl = actions.create_codelist(
owner=owner, name="Test Codelist", coding_system_id="snomedct"
)
# Search results have this structure in hierarchy
#
# 116309007 Finding of elbow region
# 128133004 Disorder of elbow
# 239964003 Soft tissue lesion of elbow region
# 35185008 Enthesopathy of elbow region
# 73583000 Epicondylitis
# 202855006 Lateral epicondylitis
# 429554009 Arthropathy of elbow
# 439656005 Arthritis of elbow
# 202855006 Lateral epicondylitis
# 298869002 Finding of elbow joint
# 298163003 Elbow joint inflamed
# 439656005 Arthritis of elbow
# 202855006 Lateral epicondylitis
# 429554009 Arthropathy of elbow
# 439656005 Arthritis of elbow
# 202855006 Lateral epicondylitis
actions.create_search(
codelist=cl,
term="elbow",
codes=[
"116309007", # Finding of elbow region
"128133004", # Disorder of elbow
"239964003", # Soft tissue lesion of elbow region
"35185008", # Enthesopathy of elbow region
"73583000", # Epicondylitis
"202855006", # Lateral epicondylitis
"429554009", # Arthropathy of elbow
"439656005", # Arthritis of elbow
"298869002", # Finding of elbow joint
"298163003", # Elbow joint inflamed
],
)
# Act: process single update from the client
actions.update_code_statuses(codelist=cl, updates=[("35185008", "+")])
# Assert that results have the expected status
assert dict(cl.codes.values_list("code", "status")) == {
"116309007": "?", # Finding of elbow region
"128133004": "?", # Disorder of elbow
"239964003": "?", # Soft tissue lesion of elbow region
"35185008": "+", # Enthesopathy of elbow region
"73583000": "(+)", # Epicondylitis
"202855006": "(+)", # Lateral epicondylitis
"429554009": "?", # Arthropathy of elbow
"439656005": "?", # Arthritis of elbow
"298869002": "?", # Finding of elbow joint
"298163003": "?", # Elbow joint inflamed
}
# Act: process multiple updates from the client
actions.update_code_statuses(
codelist=cl, updates=[("35185008", "-"), ("116309007", "+"), ("35185008", "?")]
)
# Assert that results have the expected status
assert dict(cl.codes.values_list("code", "status")) == {
"116309007": "+", # Finding of elbow region
"128133004": "(+)", # Disorder of elbow
"239964003": "(+)", # Soft tissue lesion of elbow region
"35185008": "(+)", # Enthesopathy of elbow region
"73583000": "(+)", # Epicondylitis
"202855006": "(+)", # Lateral epicondylitis
"429554009": "(+)", # Arthropathy of elbow
"439656005": "(+)", # Arthritis of elbow
"298869002": "(+)", # Finding of elbow joint
"298163003": "(+)", # Elbow joint inflamed
}
def test_codelistupdate_success(rf):
codelist = CodelistFactory()
signoff_1 = SignOffFactory(codelist=codelist)
signoff_2 = SignOffFactory(codelist=codelist)
reference_1 = ReferenceFactory(codelist=codelist)
reference_2 = ReferenceFactory(codelist=codelist)
assert codelist.references.count() == 2
assert codelist.signoffs.count() == 2
new_signoff_user = UserFactory()
data = {
"project": codelist.project.slug,
"name": "Test Codelist",
"coding_system_id": "snomedct",
"description": "This is a test CHANGED",
"methodology": "This is how we did it",
"reference-TOTAL_FORMS": "3",
"reference-INITIAL_FORMS": "2",
"reference-MIN_NUM_FORMS": "0",
"reference-MAX_NUM_FORMS": "1000",
"reference-0-text": reference_1.text,
"reference-0-url": reference_1.url,
"reference-0-id": reference_1.id,
"reference-0-DELETE": "on",
"reference-1-text": reference_2.text + " CHANGED",
"reference-1-url": reference_2.url,
"reference-1-id": reference_2.id,
"reference-2-text": "This is a new reference",
"reference-2-url": "http://example.com",
"signoff-TOTAL_FORMS": "3",
"signoff-INITIAL_FORMS": "2",
"signoff-MIN_NUM_FORMS": "0",
"signoff-MAX_NUM_FORMS": "1000",
"signoff-0-user": signoff_1.user.username,
"signoff-0-date": signoff_1.date,
"signoff-0-id": signoff_1.id,
"signoff-0-DELETE": "on",
"signoff-1-user": signoff_2.user.username,
"signoff-1-date": signoff_2.date + datetime.timedelta(days=2),
"signoff-1-id": signoff_2.id,
"signoff-2-user": new_signoff_user.username,
"signoff-2-date": "2000-01-01",
}
request = rf.post("/", data=data)
request.user = UserFactory()
response = CodelistUpdate.as_view()(
request, project_slug=codelist.project.slug, codelist_slug=codelist.slug
)
assert response.status_code == 302
assert response.url == f"/codelist/{codelist.project.slug}/{codelist.slug}/"
# we should have still have 2 references but the first should be changed
# while the second is new.
assert codelist.references.count() == 2
assert codelist.references.first().text == reference_2.text + " CHANGED"
assert codelist.references.last().text == "This is a new reference"
# we should have still have 2 signoffs but the first should be changed
# while the second is new.
assert codelist.signoffs.count() == 2
assert codelist.signoffs.first().date == signoff_2.date + datetime.timedelta(days=2)
assert codelist.signoffs.last().user == new_signoff_user