ci: add full stack NLP regression test

This is overdue. We want to make sure that any NLP changes are not suprises. Questions that we now have PR-time answers for: - Does our Dockerfile build? (was only checked after merge before) - Does our built Docker work even a little bit? - Do the current NLP dependent images work even a little bit? - Are there unexpected regressions in our NLP pipeline? There might still be errors that could creep up in our NLP that this quick smoketest don't uncover. But it's a lot better than nothing!
smart-on-fhir · Jan 11, 2024 · 86e1e71 · 86e1e71
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -14,78 +14,116 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  unittest:
-    name: unit tests
-    runs-on: ubuntu-22.04
-    strategy:
-      matrix:
-        # while we are still private, don't go crazy with the Python versions as they eat up CI minutes
-        python-version: ["3.10"]
+#  unittest:
+#    name: unit tests
+#    runs-on: ubuntu-22.04
+#    strategy:
+#      matrix:
+#        # while we are still private, don't go crazy with the Python versions as they eat up CI minutes
+#        python-version: ["3.10"]
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#
+#      - name: Set up Python ${{ matrix.python-version }}
+#        uses: actions/setup-python@v4
+#        with:
+#          python-version: ${{ matrix.python-version }}
+#
+#      - name: Install dependencies
+#        run: |
+#          python -m pip install --upgrade pip
+#          pip install pytest
+#          pip install .[tests]
+#
+#      - name: Check out MS tool
+#        uses: actions/checkout@v4
+#        with:
+#          repository: microsoft/Tools-for-Health-Data-Anonymization
+#          path: mstool
+#
+#      - name: Build MS tool
+#        run: |
+#          sudo apt-get update
+#          sudo apt-get install dotnet6
+#          dotnet publish \
+#            --runtime=linux-x64 \
+#            --configuration=Release \
+#            -p:PublishSingleFile=true \
+#            --output=$HOME/.local/bin \
+#            mstool/FHIR/src/Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool
+#
+#      - name: Test with pytest
+#        run: |
+#          python -m pytest
 
+  nlp-regression:
+    runs-on: ubuntu-latest
+    env:
+      UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install pytest
-          pip install .[tests]
+      - name: Install Docker
+        uses: docker/setup-buildx-action@v3
 
-      - name: Check out MS tool
-        uses: actions/checkout@v3
+      - name: Build ETL image
+        uses: docker/build-push-action@v5
         with:
-          repository: microsoft/Tools-for-Health-Data-Anonymization
-          path: mstool
+          load: true  # just build, no push
+          tags: smartonfhir/cumulus-etl:latest
 
-      - name: Build MS tool
-        run: |
-          sudo apt-get update
-          sudo apt-get install dotnet6
-          dotnet publish \
-            --runtime=linux-x64 \
-            --configuration=Release \
-            -p:PublishSingleFile=true \
-            --output=$HOME/.local/bin \
-            mstool/FHIR/src/Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool
+      - name: Download NLP images
+        run: docker compose --profile covid-symptom up -d --quiet-pull
 
-      - name: Test with pytest
+      - name: Run NLP
         run: |
-          python -m pytest
+          export DATADIR=$(realpath tests/data/nlp-regression)
 
-  lint:
-    runs-on: ubuntu-22.04
-    steps:
-      - uses: actions/checkout@v3
+          # Run the NLP task
+          docker compose run --rm \
+            --volume $DATADIR:/in \
+            cumulus-etl \
+            /in/input \
+            /in/run-output \
+            /in/phi \
+            --output-format=ndjson \
+            --task covid_symptom__nlp_results
 
-      - name: Install linters
-        # black is synced with the .pre-commit-hooks version
-        run: |
-          python -m pip install --upgrade pip
-          pip install bandit[toml] pycodestyle pylint black==23.11.0
+          # Compare results
+          export OUTDIR=$DATADIR/run-output/covid_symptom__nlp_results
+          sudo sed -i 's/"generated_on": "[^"]*", //g' $OUTDIR/*.ndjson
+          diff -upr $DATADIR/expected-output $OUTDIR
 
-      - name: Run pycodestyle
-        # E203: pycodestyle is a little too rigid about slices & whitespace
-        #  See https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#slices
-        # W503: a default ignore that we are restoring
-        run: |
-          pycodestyle --max-line-length=120 --ignore=E203,W503 .
-
-      - name: Run pylint
-        if: success() || failure() # still run pylint if above checks fail
-        run: |
-          pylint cumulus_etl tests
-
-      - name: Run bandit
-        if: success() || failure() # still run bandit if above checks fail
-        run: |
-          bandit -c pyproject.toml -r .
-
-      - name: Run black
-        if: success() || failure() # still run black if above checks fails
-        run: |
-          black --check --verbose --line-length 120 .
+#  lint:
+#    runs-on: ubuntu-22.04
+#    steps:
+#      - uses: actions/checkout@v4
+#
+#      - name: Install linters
+#        # black is synced with the .pre-commit-hooks version
+#        run: |
+#          python -m pip install --upgrade pip
+#          pip install bandit[toml] pycodestyle pylint black==23.11.0
+#
+#      - name: Run pycodestyle
+#        # E203: pycodestyle is a little too rigid about slices & whitespace
+#        #  See https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#slices
+#        # W503: a default ignore that we are restoring
+#        run: |
+#          pycodestyle --max-line-length=120 --ignore=E203,W503 .
+#
+#      - name: Run pylint
+#        if: success() || failure() # still run pylint if above checks fail
+#        run: |
+#          pylint cumulus_etl tests
+#
+#      - name: Run bandit
+#        if: success() || failure() # still run bandit if above checks fail
+#        run: |
+#          bandit -c pyproject.toml -r .
+#
+#      - name: Run black
+#        if: success() || failure() # still run black if above checks fails
+#        run: |
+#          black --check --verbose --line-length 120 .
diff --git a/.github/workflows/docker-hub.yaml b/.github/workflows/docker-hub.yaml
@@ -13,23 +13,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Get Docker metadata
         id: meta
-        uses: docker/metadata-action@v4
+        uses: docker/metadata-action@v5
         with:
           flavor: latest=true
           images: smartonfhir/cumulus-etl
 
       - name: Log in to Docker Hub
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push image to Docker Hub
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5
         with:
           push: true
           platforms: |

diff --git a/compose.yaml b/compose.yaml
@@ -39,7 +39,7 @@ services:
   ctakes-covid-base:
     image: smartonfhir/ctakes-covid:1.1.0
     environment:
-      - ctakes_umlsuser=umls_api_key 
+      - ctakes_umlsuser=umls_api_key
       - ctakes_umlspw=$UMLS_API_KEY
     networks:
       - cumulus-etl

diff --git a/cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py b/cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py
@@ -73,7 +73,12 @@ async def covid_symptoms_extract(
     def is_covid_match(m: ctakesclient.typesystem.MatchText):
         return bool(covid_symptom_cuis.intersection({attr.cui for attr in m.conceptAttributes}))
 
-    matches = list(filter(is_covid_match, matches))
+    matches = filter(is_covid_match, matches)
+
+    # For better reliability when regression/unit testing, sort matches by begin / first code.
+    # (With stable sorting, we want the primary sort to be done last.)
+    matches = sorted(matches, key=lambda x: x.conceptAttributes and x.conceptAttributes[0].code)
+    matches = sorted(matches, key=lambda x: x.begin)
 
     # OK we have cTAKES symptoms. But let's also filter through cNLP transformers to remove any that are negated
     # there too. We have found this to yield better results than cTAKES alone.

diff --git a/tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.meta b/tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.meta
@@ -0,0 +1,8 @@
+{
+  "groups": [
+    "032b2ff6af8c883760d5a44e32ff80454d69551de6438c46be64604ddc744156",
+    "05d0686aec0a65069a1e5b1a4937f5196b75ae336b7fbe10300882184523f95e",
+    "13e748c21a7c50f6c59fc4613683cd5d7f76bd5d68fda20f4e81ccce74ea7930",
+    "36ecd07bc327bba4e5ea36e34e66ca7f4f54360aef5bbcafc745c9f144aa87f8"
+  ]
+}
diff --git a/tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.ndjson b/tests/data/nlp-regression/expected-output/covid_symptom__nlp_results.000.ndjson
@@ -0,0 +1,16 @@
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