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[MNT] Remove trailing slashes from all paths + rename NB_FAPI_ROOT_PATH #157

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merged 5 commits into from
Feb 12, 2025
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[MNT] Remove trailing slashes from all paths + rename NB_FAPI_ROOT_PATH #157

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afbd580
remove trailing slash from attribute routers
alyssadai Feb 12, 2025
f43fe76
rename environment variable for API root path
alyssadai Feb 12, 2025
913b372
add links to README badges
alyssadai Feb 12, 2025
ae8fee6
update docstrings
alyssadai Feb 12, 2025
b184c06
add test case
alyssadai Feb 12, 2025
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14 changes: 7 additions & 7 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,13 @@

# Federation API

![GitHub branch check runs](https://img.shields.io/github/check-runs/neurobagel/federation-api/main?style=flat-square)
![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/neurobagel/federation-api/test.yaml?branch=main&style=flat-square&label=tests&link=https%3A%2F%2Fgithub.com%2Fneurobagel%2Ffederation-api%2Factions%2Fworkflows%2Ftest.yaml)
![Codecov](https://img.shields.io/codecov/c/github/neurobagel/federation-api?token=B827PI9W1U&style=flat-square&logo=codecov&link=https%3A%2F%2Fcodecov.io%2Fgh%2Fneurobagel%2Ffederation-api)
![Static Badge](https://img.shields.io/badge/python-3.10-blue?style=flat-square&logo=python)
![GitHub License](https://img.shields.io/github/license/neurobagel/federation-api?style=flat-square&color=purple&link=LICENSE)
![Docker Image Version (tag)](https://img.shields.io/docker/v/neurobagel/federation_api/latest?style=flat-square&logo=docker&link=https%3A%2F%2Fhub.docker.com%2Fr%2Fneurobagel%2Ffederation_api%2Ftags)
![Docker Pulls](https://img.shields.io/docker/pulls/neurobagel/federation_api?style=flat-square&logo=docker&link=https%3A%2F%2Fhub.docker.com%2Fr%2Fneurobagel%2Ffederation_api%2Ftags)
[![Main branch check status](https://img.shields.io/github/check-runs/neurobagel/federation-api/main?style=flat-square)](https://github.com/neurobagel/federation-api/actions?query=branch:main)
[![Tests status](https://img.shields.io/github/actions/workflow/status/neurobagel/federation-api/test.yaml?branch=main&style=flat-square&label=tests&link=https%3A%2F%2Fgithub.com%2Fneurobagel%2Ffederation-api%2Factions%2Fworkflows%2Ftest.yaml)](https://github.com/neurobagel/federation-api/actions/workflows/test.yaml)
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[![Python versions static](https://img.shields.io/badge/python-3.10-blue?style=flat-square&logo=python)](https://www.python.org)
[![License](https://img.shields.io/github/license/neurobagel/federation-api?style=flat-square&color=purple&link=LICENSE)](LICENSE)
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[![Docker Pulls](https://img.shields.io/docker/pulls/neurobagel/federation_api?style=flat-square&logo=docker&link=https%3A%2F%2Fhub.docker.com%2Fr%2Fneurobagel%2Ffederation_api%2Ftags)](https://hub.docker.com/r/neurobagel/federation_api/tags)

</div>

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2 changes: 1 addition & 1 deletion app/api/routers/assessments.py
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Expand Up @@ -6,7 +6,7 @@
router = APIRouter(prefix="/assessments", tags=["assessments"])

router.add_api_route(
path="/",
path="",
endpoint=route_factory.create_get_instances_handler(
attributes_base_path="assessments"
),
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2 changes: 1 addition & 1 deletion app/api/routers/diagnoses.py
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Expand Up @@ -6,7 +6,7 @@
router = APIRouter(prefix="/diagnoses", tags=["diagnoses"])

router.add_api_route(
path="/",
path="",
endpoint=route_factory.create_get_instances_handler(
attributes_base_path="diagnoses"
),
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2 changes: 1 addition & 1 deletion app/api/routers/pipelines.py
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Expand Up @@ -8,7 +8,7 @@
router = APIRouter(prefix="/pipelines", tags=["pipelines"])

router.add_api_route(
path="/",
path="",
endpoint=route_factory.create_get_instances_handler(
attributes_base_path="pipelines"
),
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4 changes: 2 additions & 2 deletions app/api/routers/route_factory.py
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Expand Up @@ -12,8 +12,8 @@
# (less relevant for now since there is only one response model).
def create_get_instances_handler(attributes_base_path: str):
"""
Create the handler (path function) for a federated GET request to the root `/` subpath of
a given attribute router, e.g. /assesssments/.
Create the handler (path function) for a federated GET request to the base subpath of
a given attribute router, e.g. /assesssments.
"""

async def get_instances(response: Response):
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2 changes: 1 addition & 1 deletion app/api/utility.py
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Expand Up @@ -15,7 +15,7 @@
EnvVar = namedtuple("EnvVar", ["name", "value"])

ROOT_PATH = EnvVar(
"NB_FAPI_ROOT_PATH", os.environ.get("NB_FAPI_ROOT_PATH", "")
"NB_FAPI_BASE_PATH", os.environ.get("NB_FAPI_BASE_PATH", "")
)
IS_FEDERATE_REMOTE_PUBLIC_NODES = EnvVar(
"NB_FEDERATE_REMOTE_PUBLIC_NODES",
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12 changes: 6 additions & 6 deletions tests/test_attribute_factory_routes.py
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Expand Up @@ -6,7 +6,7 @@ def test_get_instances_with_duplicate_terms_handled(
test_app, monkeypatch, set_valid_test_federation_nodes
):
"""
When multiple nodes return an assessment with the same URI for a request to /assessments/,
When multiple nodes return an assessment with the same URI for a request to /assessments,
the API should return only one instance of that assessment term in the final federated response.
"""

Expand Down Expand Up @@ -42,7 +42,7 @@ async def mock_httpx_get(self, **kwargs):

monkeypatch.setattr(httpx.AsyncClient, "get", mock_httpx_get)

response = test_app.get("/assessments/")
response = test_app.get("/assessments")

response_object = response.json()
found_instances = response_object["responses"]["nb:Assessment"]
Expand All @@ -66,7 +66,7 @@ def test_partially_failed_get_instances_handled_gracefully(
test_app, monkeypatch, set_valid_test_federation_nodes, caplog
):
"""
When some nodes fail while getting term instances for an attribute (/assessments/),
When some nodes fail while getting term instances for an attribute (/assessments),
the overall API get request still succeeds, and the response includes a list of the encountered errors along with the successfully fetched terms.
"""
mocked_node_get_assessments_response = {
Expand Down Expand Up @@ -94,7 +94,7 @@ async def mock_httpx_get(self, **kwargs):

monkeypatch.setattr(httpx.AsyncClient, "get", mock_httpx_get)

response = test_app.get("/assessments/")
response = test_app.get("/assessments")

assert response.status_code == status.HTTP_207_MULTI_STATUS

Expand All @@ -120,14 +120,14 @@ def test_fully_failed_get_instances_handled_gracefully(
caplog,
):
"""
When *all* nodes fail while getting term instances for an attribute (/assessments/),
When *all* nodes fail while getting term instances for an attribute (/assessments),
the overall API get request still succeeds, but includes an overall failure status and all encountered errors in the response.
"""
monkeypatch.setattr(
httpx.AsyncClient, "get", mock_failed_connection_httpx_get
)

response = test_app.get("/assessments/")
response = test_app.get("/assessments")

assert response.status_code == status.HTTP_207_MULTI_STATUS
# We expect several warnings from logging
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8 changes: 7 additions & 1 deletion tests/test_routing.py
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Expand Up @@ -52,7 +52,13 @@ async def mock_httpx_get(self, **kwargs):

@pytest.mark.parametrize(
"invalid_route",
["/query/", "/query/?min_age=20", "/nodes/", "/attributes/nb:SomeClass/"],
[
"/query/",
"/query/?min_age=20",
"/nodes/",
"/attributes/",
"/assessments/",
],
)
def test_request_including_trailing_slash_fails(
test_app, disable_auth, invalid_route
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