test new way of wiring up tests

.github/workflows/core.yaml

@@ -38,33 +38,42 @@ jobs:
         run: poetry build
       - name: Run pytest
         run: poetry run pytest
-  ci-make:
+  ci-test-with-api:
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.11"]
         poetry-version: ["1.4.2"]
-        # NOTE - WE DO NOT TEST ON MAC/WINDOWS!!
-        # The current tests dockerize the test runner, so there is not much point on testing across platforms
-        # TODO: we want to change this to more closely follow how users actually run tests (setting up API first, then running tests)
-        # Ticket: https://app.clickup.com/t/8697kxtgx
+        # Note we do not test on windows or mac. Currently, github mac runners do not support nested virtualization, so we cannot run docker on them (since mac docker virtualises linux)
+        # See https://docs.github.com/en/actions/using-github-hosted-runners/using-github-hosted-runners/about-github-hosted-runners#limitations-for-arm64-macos-runners
         os: [ubuntu-20.04] 
         project:
           [
             bia-export,
           ]
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        working-directory: ${{ matrix.project }}
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1 # Set up Docker Buildx for building and pushing Docker images
-      - name: Cache Docker layers
-        uses: actions/cache@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Run poetry image
+        uses: abatilo/actions-poetry@v2
         with:
-          path: /tmp/.buildx-cache
-          key: ${{ runner.os }}-buildx-${{ github.sha }}
-          restore-keys: |
-            ${{ runner.os }}-buildx-
-      - name: run makefile
-        run: make ${{matrix.project}}.test
+          poetry-version: ${{ matrix.poetry-version }}
+      - name: Run docker
+        run:  make -C ../ api.up
+      - name: set up poetry
+        run: |
+          poetry env use python
+          poetry install
+      - name: Run pytest
+        run: poetry run pytest
+      # Always cleanup - even for cancelled jobs
+      - name: Docker Compose Down
+        run:  make -C ../ api.down
+        if: ${{ always() }}
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: api.version client.generate bia-export.test
+.PHONY: api.version client.generate api.up api.down
 
 api.version:
 	@echo $(shell grep '^version =' api/pyproject.toml | awk -F\" '{print $$2}')
@@ -12,7 +12,8 @@ client.generate:
 client.examples:
 	docker compose --profile client_examples up --build --force-recreate --remove-orphans --abort-on-container-exit
 
+api.up:
+	docker compose up -d --build --wait
 
-# Note that the github CI is set up to expect Make commands for testing of the form: make ${{matrix.project}}.test
-bia-export.test:
-	docker compose --profile export_test up --build --force-recreate --remove-orphans --abort-on-container-exit
+api.down:
+	docker compose down

bia-export/bia_export/cli.py

@@ -27,6 +27,11 @@
 app.add_typer(website, name="website")
 
 
+DEFAULT_WEBSITE_STUDY_FILE_NAME = "bia-study-metadata.json"
+DEFAULT_WEBSITE_IMAGE_FILE_NAME = "bia-image-metadata.json"
+DEFAULT_WEBSITE_DATASET_FOR_IMAGE_FILE_NAME = "bia-dataset-metadata-for-images.json"
+
+
 @website.command("all")
 def generate_all(
     id_list: Annotated[
@@ -47,18 +52,25 @@ def generate_all(
             "-c",
         ),
     ] = None,
+    output_directory: Annotated[
+        Optional[Path],
+        typer.Option(
+            "--out_dir",
+            "-o",
+        ),
+    ] = None,
 ):
     settings = Settings()
 
     if not id_list:
         id_list = get_study_ids(root_directory)
 
     logger.info("Exporting study pages")
-    website_study(id_list=id_list, root_directory=root_directory, cache=cache)
+    website_study(id_list=id_list, root_directory=root_directory, cache=cache, output_filename=(output_directory / DEFAULT_WEBSITE_STUDY_FILE_NAME if output_directory else None))
     logger.info("Exporting image pages")
-    website_image(id_list=id_list, root_directory=root_directory)
+    website_image(id_list=id_list, root_directory=root_directory, output_filename=(output_directory / DEFAULT_WEBSITE_IMAGE_FILE_NAME if output_directory else None))
     logger.info("Exporting datasets for study pages")
-    datasets_for_website_image(id_list=id_list, root_directory=root_directory)
+    datasets_for_website_image(id_list=id_list, root_directory=root_directory, output_filename=(output_directory / DEFAULT_WEBSITE_DATASET_FOR_IMAGE_FILE_NAME if output_directory else None))
 
 
 @website.command("study")
@@ -72,7 +84,7 @@ def website_study(
             "--out_file",
             "-o",
         ),
-    ] = Path("bia-study-metadata.json"),
+    ] = Path(DEFAULT_WEBSITE_STUDY_FILE_NAME),
     root_directory: Annotated[
         Optional[Path],
         typer.Option(
@@ -117,7 +129,7 @@ def website_image(
             "--out_file",
             "-o",
         ),
-    ] = Path("bia-image-metadata.json"),
+    ] = Path(DEFAULT_WEBSITE_IMAGE_FILE_NAME),
     root_directory: Annotated[
         Optional[Path],
         typer.Option(
@@ -151,7 +163,7 @@ def datasets_for_website_image(
             "--out_file",
             "-o",
         ),
-    ] = Path("bia-dataset-metadata-for-images.json"),
+    ] = Path(DEFAULT_WEBSITE_DATASET_FOR_IMAGE_FILE_NAME),
     root_directory: Annotated[
         Optional[Path],
         typer.Option(

bia-export/test/conftest.py

@@ -1,17 +1,16 @@
-from dotenv import load_dotenv
 from pathlib import Path
 import pytest
-from bia_test_data.data_to_api import add_objects_to_api
+from bia_test_data.data_to_api import add_objects_to_api, get_object_creation_client
 from bia_export.settings import Settings
+from bia_shared_datamodels.uuid_creation import create_study_uuid
 from pathlib import Path
 import json
 import os
 from glob import glob
 
 
 def pytest_configure(config: pytest.Config):
-    if not os.environ.get("API_BASE_URL", None):
-        os.environ.setdefault("API_BASE_URL", "http://localhost:8080")
+    os.environ.setdefault("API_BASE_URL", "http://localhost:8080")
 
 
 @pytest.fixture(scope="session")
@@ -28,4 +27,58 @@ def data_in_api():
                 json_dict = json.load(object_file)
                 object_list.append(json_dict)
 
-    add_objects_to_api(setttings.api_base_url, object_list)
+
+    private_client = get_object_creation_client(setttings.api_base_url)
+
+    add_objects_to_api(private_client, object_list)
+
+
+
+
+@pytest.fixture(scope="session")
+def api_studies_in_expected_order():
+    setttings = Settings()
+
+    base_study = Path(__file__).parent / "input_data" / "study" / "S-BIADTEST" / "a2fdbd58-ee11-4cd9-bc6a-f3d3da7fff71.json"
+
+    with open(base_study, "r") as object_file:
+        base_study_dict: dict = json.load(object_file)
+
+    object_list = []
+
+    study_1 = base_study_dict.copy() | {
+            "accession_id": "S-BIADTEST1",
+            "uuid": str(create_study_uuid("S-BIADTEST111")),
+            "release_date": "2024-01-01"
+        }
+    object_list.append(study_1)
+
+    study_2 = base_study_dict.copy() | {
+            "accession_id": "S-BIADTEST22",
+            "uuid": str(create_study_uuid("S-BIADTEST22")),
+            "release_date": "2024-01-01"
+        }
+    object_list.append(study_2)
+
+    study_3 = base_study_dict.copy() | {
+            "accession_id": "S-BIADTEST333",
+            "uuid": str(create_study_uuid("S-BIADTEST333")),
+            "release_date": "2024-01-03"
+        }
+    object_list.append(study_3)
+
+
+    study_4 = base_study_dict.copy() | {
+        "accession_id": "S-BIADTEST4444",
+        "uuid": str(create_study_uuid("S-BIADTEST4444")),
+        "release_date": "2024-01-02"
+    }
+    object_list.append(study_4)
+
+    private_client = get_object_creation_client(setttings.api_base_url)
+
+    add_objects_to_api(private_client, object_list)
+
+    expected_order_of_studies = [study_3, study_4, study_2, study_1]
+
+    return expected_order_of_studies

bia-export/test/test_api_export.py

@@ -1,11 +1,66 @@
 from typer.testing import CliRunner
 from pathlib import Path
-from bia_export.cli import app
+import pytest
+from bia_export.cli import (
+    app,
+    DEFAULT_WEBSITE_STUDY_FILE_NAME,
+    DEFAULT_WEBSITE_IMAGE_FILE_NAME,
+    DEFAULT_WEBSITE_DATASET_FOR_IMAGE_FILE_NAME,
+)
 import json
+import os
 
 runner = CliRunner()
 
 
+# Note that pytest fixture data_in_api is unused in test code,
+# but requested in order to guarentee that data is in the test api before running the test
+def test_cli_export_export_all_data_contains_at_least_expected_objects(
+    tmp_path: Path, data_in_api
+):
+
+    outpath = tmp_path.resolve()
+
+    result = runner.invoke(
+        app,
+        [
+            "website",
+            "all",
+            "-o",
+            outpath,
+        ],
+    )
+
+    assert result.exit_code == 0
+    assert len(os.listdir(tmp_path)) == 3
+
+    def check_file_contains_expected_object(outfile: Path, expected_output: Path):
+        with open(outfile, "r") as f:
+            json_result = json.load(f)
+
+        with open(expected_output) as f:
+            json_expected = json.load(f)
+
+        for key, value in json_expected.items():
+            assert key in json_result
+            assert value == json_result[key]
+
+    check_file_contains_expected_object(
+        outpath.joinpath(DEFAULT_WEBSITE_STUDY_FILE_NAME),
+        Path(__file__).parent.joinpath("output_data/bia-study-metadata.json"),
+    )
+
+    check_file_contains_expected_object(
+        outpath.joinpath(DEFAULT_WEBSITE_IMAGE_FILE_NAME),
+        Path(__file__).parent.joinpath("output_data/bia-image-metadata.json"),
+    )
+
+    check_file_contains_expected_object(
+        outpath.joinpath(DEFAULT_WEBSITE_DATASET_FOR_IMAGE_FILE_NAME),
+        Path(__file__).parent.joinpath("output_data/bia-dataset-metadata-for-images.json"),
+    )
+
+
 # Note that pytest fixture data_in_api is unused in test code,
 # but requested in order to guarentee that data is in the test api before running the test
 def test_cli_export_website_studies(tmp_path: Path, data_in_api):
@@ -79,3 +134,28 @@ def test_cli_export_dataset_for_website_images(tmp_path: Path, data_in_api):
         json_expected = json.load(f)
 
     assert json_result == json_expected
+
+
+
+def test_cli_export_study_ordering(tmp_path: Path, api_studies_in_expected_order: list[dict]):
+    outfile = tmp_path.joinpath("bia-dataset-metadata.json").resolve()
+
+    result = runner.invoke(
+        app,
+        [
+            "website",
+            "study",
+            "-o",
+            outfile,
+        ],
+    )
+
+    assert result.exit_code == 0
+
+    expected_study_acc_id_order = [study["accession_id"] for study in api_studies_in_expected_order]
+
+    with open(outfile, "r") as f:
+        json_result: dict = json.load(f)
+
+    it = iter(json_result.keys()) 
+    assert all(acc_id in it for acc_id in expected_study_acc_id_order)

bia-test-data/bia_test_data/data_to_api.py

@@ -1,4 +1,6 @@
 from pathlib import Path
+from time import sleep
+from urllib3.exceptions import MaxRetryError
 from dotenv import dotenv_values
 from bia_integrator_api.api import PrivateApi
 from bia_integrator_api import Configuration, ApiClient, exceptions
@@ -207,9 +209,7 @@ def order_object_for_api(object_list: list[dict]):
     return ordered_object_list
 
 
-def add_objects_to_api(api_base_url, object_list: list[dict]):
-    private_client = get_object_creation_client(api_base_url)
-
+def add_objects_to_api(private_client, object_list: list[dict]):
     ordered_object_list = order_object_for_api(object_list)
 
     for bia_object_dict in ordered_object_list:

docker-compose.yml

@@ -59,16 +59,4 @@ services:
     volumes:
       - ./clients/python:/mnt/share
     profiles:
-      - client_examples
-  export-test:
-    depends_on:
-      bia-integrator-api:
-        condition: service_healthy
-    environment:
-      - API_BASE_URL=http://api:8080
-    container_name: export_test
-    image: bia-integrator-api
-    command: bash -c "echo $PWD && poetry install && poetry run pytest -vv"
-    working_dir: /bia-integrator/bia-export
-    profiles:
-      - export_test
+      - client_examples