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added blank line #57

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merged 4 commits into from
Dec 7, 2024
Merged

added blank line #57

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b4462bc
added blank line
fcollman Dec 7, 2024
e545493
updating cache action
fcollman Dec 7, 2024
f41ea76
trying to fix coverage
fcollman Dec 7, 2024
53773c0
adding manual trigger
fcollman Dec 7, 2024
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5 changes: 3 additions & 2 deletions .github/workflows/annotationengine.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ on:
- "tests/**"
pull_request:
branches: [master]
workflow_dispatch:

jobs:
test:
Expand All @@ -35,7 +36,7 @@ jobs:
uses: actions/setup-python@v2
with:
python-version: 3.9
- uses: actions/cache@v2
- uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/test_requirements.txt') }}
Expand Down Expand Up @@ -70,4 +71,4 @@ jobs:
- name: Upload coverage to codecov
uses: codecov/codecov-action@v5
with:
use_oidc: true
token: {{ secrets.CODECOV_TOKEN }}
68 changes: 28 additions & 40 deletions test/test_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

aligned_volume_name = "test_aligned_volume"


class TestHealthEndpoint:
def test_health_endpoint(self, client):
url = "annotation/api/versions"
Expand Down Expand Up @@ -47,12 +48,12 @@ def test_post_table(self, client):
assert response.json is None

def test_put_table(self, client, modify_g):
'''
"""
These tests have to be run in sequential order, so instead of trusting
the testing framework to run independent tests in the intended order,
simply package them into a single function.
'''
"""

# Alter the description and populate the notice_text
logging.info("TEST")
data = {
Expand All @@ -77,9 +78,9 @@ def test_put_table(self, client, modify_g):
follow_redirects=True,
)
logging.info(response)
assert response.json['description'] == "Altered test description"
assert response.json['notice_text'] == "Notice"
assert response.json["description"] == "Altered test description"
assert response.json["notice_text"] == "Notice"

# ================================================================================
# Test that notice_text is erased
logging.info("TEST")
Expand All @@ -103,7 +104,7 @@ def test_put_table(self, client, modify_g):
follow_redirects=True,
)
logging.info(response)
assert response.json['notice_text'] is None
assert response.json["notice_text"] is None

# ================================================================================
# Repopulate notice_text
Expand All @@ -128,8 +129,8 @@ def test_put_table(self, client, modify_g):
follow_redirects=True,
)
logging.info(response)
assert response.json['notice_text'] == "Notice2"
assert response.json["notice_text"] == "Notice2"

# ================================================================================
# Test that notice_text is erased
logging.info("TEST")
Expand All @@ -153,7 +154,7 @@ def test_put_table(self, client, modify_g):
follow_redirects=True,
)
logging.info(response)
assert response.json['notice_text'] is None
assert response.json["notice_text"] is None

def test_post_table_to_be_deleted(self, client):
logging.info(client)
Expand Down Expand Up @@ -191,17 +192,15 @@ def test_get_tables(self, client):
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name
response = client.get(
url, content_type="application/json",
follow_redirects=False
url, content_type="application/json", follow_redirects=False
)
logging.info(response)

assert response.json == ["test_table", "test_table_to_delete"]


class TestAnnotationTableEndpoints:
def test_get_table_metadata(self, client):

url = (
f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table"
)
Expand All @@ -211,9 +210,7 @@ def test_get_table_metadata(self, client):
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name

response = client.get(url,
follow_redirects=False
)
response = client.get(url, follow_redirects=False)
logging.info(response.json)

metadata = {
Expand All @@ -234,22 +231,19 @@ def test_get_table_metadata(self, client):
"write_permission": "PRIVATE",
}
response_json = response.json
del response_json['created']
del response_json['last_modified']
del response_json["created"]
del response_json["last_modified"]
assert response_json == metadata

def test_mark_table_to_delete(self, client, modify_g):

url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table_to_delete"

with mock.patch(
"annotationengine.api.check_aligned_volume"
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name

response = client.delete(url,
follow_redirects=False
)
response = client.delete(url, follow_redirects=False)
logging.info(response.json)
assert response.json is True

Expand All @@ -261,16 +255,13 @@ def test_get_row_count(self, client):
"annotationengine.api.check_aligned_volume"
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name
response = client.get(url,
follow_redirects=False
)
response = client.get(url, follow_redirects=False)
logging.info(response.json)
assert response.json == 0


class TestAnnotationsEndpoints:
def test_post_annotations(self, client, modify_g):

url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
data = {
"annotations": [
Expand All @@ -294,7 +285,7 @@ def test_post_annotations(self, client, modify_g):
"annotationengine.api.trigger_supervoxel_lookup",
) as mock_trigger_supervoxel_lookup:
mock_trigger_supervoxel_lookup.return_value = None

response = client.post(
url,
data=json.dumps(data),
Expand All @@ -311,9 +302,7 @@ def test_get_annotations(self, client):
"annotationengine.api.check_aligned_volume"
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name
response = client.get(url, query_string=data,
follow_redirects=False
)
response = client.get(url, query_string=data, follow_redirects=False)
logging.info(response)
logging.info(response.json)
logging.info(response.json[0])
Expand All @@ -323,7 +312,7 @@ def test_get_annotations(self, client):
assert response.json[0]["post_pt_position"] == [33, 33, 0]
assert response.json[0]["valid"] == True
assert response.json[0]["superceded_id"] == None
assert response.json[0]["deleted"] == 'None'
assert response.json[0]["deleted"] == "None"

def test_update_annotations(self, client):
url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
Expand All @@ -346,11 +335,11 @@ def test_update_annotations(self, client):
"annotationengine.api.trigger_supervoxel_lookup",
) as mock_trigger_supervoxel_lookup:
mock_trigger_supervoxel_lookup.return_value = None
response = client.put(url, data=json.dumps(data),
follow_redirects=False
)
response = client.put(
url, data=json.dumps(data), follow_redirects=False
)
logging.info(response)
assert response.json == {'1': 2}
assert response.json == {"1": 2}

def test_delete_annotations(self, client):
url = f"/annotation/api/v2/aligned_volume/{aligned_volume_name}/table/test_table/annotations"
Expand All @@ -360,8 +349,7 @@ def test_delete_annotations(self, client):
"annotationengine.api.check_aligned_volume"
) as mock_aligned_volumes:
mock_aligned_volumes.return_value = aligned_volume_name
response = client.delete(url, data=json.dumps(data),
follow_redirects=False
)
response = client.delete(url, data=json.dumps(data), follow_redirects=False)
logging.info(response)

assert response.json == [2]