workflows: Set up CI tp run full integration test suite

This runs our full integration test suite to verify that the changes are
sane before pulling them in.

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'master'
+  pull_request:
+
+jobs:
+  build:
+    if: github.repository == 'incendilabs/plan-executor'
+
+    runs-on: ubuntu-24.04
+    steps:
+      -
+        name: Checkout repo
+        uses: actions/checkout@v4
+      -
+        name: Build docker image
+        run: docker build -t incendi/plan-executor:latest .
+      -
+        name: Run tests
+        run: |
+          mkdir -p logs html_summaries json_results
+          docker compose up -d spark
+          docker compose run --rm --no-deps plan_executor ./execute_all.sh 'http://spark:8080/fhir' r4 'html|json|stdout'
+          docker compose logs spark > logs/backend.log
+      -
+        name: Combine test results
+        if: ${{ always() }}
+        run: ./combine-test-results.sh json_results annotations.json
+      -
+        name: Attach test results
+        if: github.event_name != 'pull_request'
+        uses: yuzutech/[email protected]
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          input: annotations.json
+      -
+        name: Archive logs
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: logs-r4-${{ github.sha }}
+          path: logs/*.log*
+      -
+        name: Archive test reports
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: html_summaries-r4-${{ github.sha }}
+          path: html_summaries/**/*.html
+      -
+        name: Archive JSON results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: json_results-r4-${{ github.sha }}
+          path: json_results/**/*.json
+      -
+        name: Archive annotations file
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: annotations-r4-${{ github.sha }}
+          path: annotations.json
+      -
+        name: Cleanup
+        if: ${{ always() }}
+        run: cd tests/integration-tests && docker compose down

combine-test-results.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+
+set -e
+
+JSON_PATH=$1
+ANNOTATIONS_FILE=$2
+
+function usage() {
+  me=`basename "$0"`
+  if [ ! -z "$1" ]; then
+    echo $1
+  fi
+  echo "Usage: ./${me} path/to/input/json_results path/to/output/annotations.json"
+  exit 1
+}
+
+[ $# -eq 2 ] || usage
+
+[ ! -z "${JSON_PATH}" ] || usage
+
+[ -d "${JSON_PATH}" ] || usage "${JSON_PATH} must be a directory"
+
+touch $ANNOTATIONS_FILE || "$ANNOTATIONS_FILE is not writable"
+
+DIR=$(pwd)
+
+cd ${JSON_PATH}
+
+# Output summary to stdout
+
+ls _summary*.json | xargs jq -r '. | "PASS: \(.pass // 0)
+FAIL: \(.fail // 0)
+ERROR: \(.error // 0)
+SKIP: \(.skip // 0)"
+'
+
+# Have to use warning annotation level, notice isn't working anymore (but could be in future).
+
+SUMMARY=$(ls _summary*.json | xargs jq '[ .
+  | { "file": ".github/workflow/integration_tests.yml",  "line": 1, "message": ("PASS: \(.pass // 0)\nFAIL: \(.fail // 0)\nERROR: \(.error // 0)\nSKIP: \(.skip // 0)"), "annotation_level": "warning" }
+]')
+
+FAILURES=$(ls -I '_summary*.json' | xargs -I '{}' jq '[ .[]
+    | select(((.status == "skip") and (.message | contains("TODO") | not))
+        or .status == "fail"
+        or .status == "error")
+    | .id as $id
+    | .status as $status
+    | .message as $message
+    | .description as $description
+    | .test_method as $method
+    | input_filename as $file
+    | { "file": ".github/workflow/integration_tests.yml",  "line": 1, "message": ($id + ": " + $message), "annotation_level": "failure" }
+]' '{}')
+
+cd $DIR
+
+jq 'reduce inputs as $i (.; . += $i)' <(echo "${SUMMARY}") <(echo "${FAILURES}") > ${ANNOTATIONS_FILE}

docker-compose.yml

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+version: "3"
+services:
+  spark:
+    container_name: spark
+    restart: always
+    image: sparkfhir/spark:r4-latest
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:secret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://spark:8080/fhir
+      - ASPNETCORE_URLS=http://+:8080
+      - ASPNETCORE_HTTP_PORT=8080
+    ports:
+      - "8000:8080"
+      - "8001:8081"
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: sparkfhir/mongo:r4-latest
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: secret
+    ports:
+      - "17017:27017"
+  plan_executor:
+    container_name: plan_executor
+    image: incendi/plan_executor:latest
+    depends_on:
+      - spark
+    volumes:
+      - ./logs:/app/logs:rw
+      - ./html_summaries:/app/html_summaries:rw
+      - ./json_results:/app/json_results:rw