Create integration test for the FHIR converter (#826)

.github/workflows/listContainers.yaml

@@ -5,6 +5,8 @@ on:
     outputs:
       containers: 
         value: ${{ jobs.list-containers.outputs.container-dirs }}
+      integration-dirs:
+        value: ${{ jobs.list-integration-test-directories.outputs.integration-dirs }}
 
 jobs:
   list-containers:
@@ -23,4 +25,19 @@ jobs:
         # use jq to produce json output and filter out the empty item caused by final newline
         run: |
           ls -d * | jq -R -s -c 'split("\n")[:-1]'
-          echo "containers=$(ls -d */ | cut -f1 -d'/' | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
+          echo "containers=$(ls -d */ | cut -f1 -d'/' | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT
+  list-integration-test-directories:
+    runs-on: ubuntu-latest
+    outputs:
+      integration-dirs: ${{steps.generate-integration-list.outputs.containers_to_test}}
+    steps:
+      - name: Check Out Changes
+        uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          sudo apt-get install jq
+      - id: generate-integration-list
+        name: Generate list of integration test directories within containers/
+        working-directory: ./containers
+        run: |
+          echo "containers_to_test=$(find . -name "integration" -type d | cut -d "/" -f2 | jq -R -s -c 'split("\n")[:-1]' )" >> $GITHUB_OUTPUT

.github/workflows/test.yaml

@@ -171,4 +171,29 @@ jobs:
           MPI_PERSON_TABLE: person
         working-directory: ./containers/${{matrix.container-to-test}}/tests
         run: |
-          python -m pytest
+          python -m pytest -m "not integration"
+  integration-test-python-containers:
+    needs: list-containers
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        directories-to-test: ${{fromJson(needs.list-containers.outputs.integration-dirs)}}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}}
+          cache: pip
+      - name: Install Pytest
+        run: pip install pytest
+      - name: Install dependencies
+        working-directory: ./containers/${{matrix.directories-to-test}}
+        run: |
+          pwd
+          pip install -r requirements.txt
+      - name: Run integration tests for containers
+        working-directory: ./containers/${{matrix.directories-to-test}}/tests/integration
+        run: |
+          python -m pytest -m "integration"

containers/fhir-converter/requirements.txt

@@ -31,6 +31,7 @@ requests==2.31.0
 six==1.16.0
 sniffio==1.2.0
 starlette==0.27.0
+testcontainers[compose]==3.7.1
 tomli==2.0.1
 typing_extensions==4.3.0
 ujson==5.4.0

containers/fhir-converter/tests/integration/conftest.py

@@ -0,0 +1,22 @@
+import pytest
+import os
+from testcontainers.compose import DockerCompose
+
+
+@pytest.fixture(scope="session")
+def setup(request):
+    print("Setting up tests...")
+    compose_path = os.path.join(os.path.dirname(__file__), "./")
+    compose_file_name = "docker-compose.yaml"
+    fhir_converter = DockerCompose(compose_path, compose_file_name=compose_file_name)
+    converter_url = "http://0.0.0.0:8080"
+
+    fhir_converter.start()
+    fhir_converter.wait_for(converter_url)
+    print("FHIR Converter ready to test!")
+
+    def teardown():
+        print("Tests finished! Tearing down.")
+        fhir_converter.stop()
+
+    request.addfinalizer(teardown)

containers/fhir-converter/tests/integration/docker-compose.yaml

@@ -0,0 +1,8 @@
+version: '3.3'
+
+services:
+  fhir-converter-service:
+    build:
+      context: ../..
+    ports:
+          - "8080:8080"

containers/fhir-converter/tests/integration/test_FHIR-Converter.py

@@ -0,0 +1,84 @@
+import httpx
+import pytest
+from pathlib import Path
+
+CONVERTER_URL = "http://0.0.0.0:8080"
+CONVERT_TO_FHIR = CONVERTER_URL + "/convert-to-fhir"
+
+
+@pytest.mark.integration
+def test_health_check(setup):
+    health_check_response = httpx.get(CONVERTER_URL)
+    assert health_check_response.status_code == 200
+
+
+@pytest.mark.integration
+def test_vxu_conversion(setup):
+    input_data = open(
+        Path(__file__).parent.parent.parent / "assets" / "sample_request.hl7"
+    ).read()
+    request = {
+        "input_data": input_data,
+        "input_type": "vxu",
+        "root_template": "VXU_V04",
+    }
+    vxu_conversion_response = httpx.post(CONVERT_TO_FHIR, json=request)
+
+    assert vxu_conversion_response.status_code == 200
+    assert (
+        vxu_conversion_response.json()["response"]["FhirResource"]["resourceType"]
+        == "Bundle"
+    )
+
+
+@pytest.mark.integration
+def test_ecr_conversion(setup):
+    input_data = open(
+        Path(__file__).parent.parent.parent.parent.parent
+        / "tests"
+        / "assets"
+        / "fhir-converter"
+        / "ccda"
+        / "ccda_sample.xml"
+    ).read()
+    request = {"input_data": input_data, "input_type": "ecr", "root_template": "EICR"}
+    ecr_conversion_response = httpx.post(CONVERT_TO_FHIR, json=request)
+
+    assert ecr_conversion_response.status_code == 200
+    assert (
+        ecr_conversion_response.json()["response"]["FhirResource"]["resourceType"]
+        == "Bundle"
+    )
+
+
+@pytest.mark.integration
+def test_ecr_conversion_with_rr(setup):
+    rr_data = open(
+        Path(__file__).parent.parent.parent.parent.parent
+        / "tests"
+        / "assets"
+        / "fhir-converter"
+        / "rr_extraction"
+        / "CDA_RR.xml"
+    ).read()
+    input_data = open(
+        Path(__file__).parent.parent.parent.parent.parent
+        / "tests"
+        / "assets"
+        / "fhir-converter"
+        / "rr_extraction"
+        / "CDA_eICR.xml"
+    ).read()
+    request = {
+        "input_data": input_data,
+        "input_type": "ecr",
+        "root_template": "EICR",
+        "rr_data": rr_data,
+    }
+    ecr_conversion_response = httpx.post(CONVERT_TO_FHIR, json=request)
+
+    assert ecr_conversion_response.status_code == 200
+    assert (
+        ecr_conversion_response.json()["response"]["FhirResource"]["resourceType"]
+        == "Bundle"
+    )

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    integration : run all integration tests