Add R5 Support

.dockerignore

@@ -1,3 +1,7 @@
 .git
 .github
-logs
+coverage
+html_summaries
+json_results
+logs
+tmp

.github/workflows/ci.yml → .github/workflows/ci-r4.yml

@@ -1,4 +1,4 @@
-name: CI
+name: CI R4
 
 on:
   workflow_dispatch:

.github/workflows/ci-r5.yml

@@ -0,0 +1,160 @@
+name: CI R5
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'master'
+  pull_request:
+
+jobs:
+  build:
+    if: github.repository == 'incendilabs/plan-executor'
+
+    runs-on: ubuntu-24.04
+    steps:
+      -
+        name: Checkout plan-executor
+        uses: actions/checkout@v7
+      -
+        name: Build plan-executor Docker image
+        run: docker build -t incendi/plan_executor:latest .
+      -
+        name: Checkout Spark
+        uses: actions/checkout@v7
+        with:
+          repository: FirelyTeam/spark
+          ref: master
+          path: spark
+      -
+        name: Record Spark revision
+        run: |
+          git -C spark rev-parse HEAD | tee spark-revision.txt
+      -
+        name: Build Spark R5 Docker image
+        run: |
+          docker build spark \
+            --file spark/.docker/linux/Spark.R5.Dockerfile \
+            --tag sparkfhir/spark:r5-latest
+      -
+        name: Build Mongo R5 Docker image
+        run: |
+          docker build spark \
+            --file spark/.docker/linux/Mongo.R5.Dockerfile \
+            --tag sparkfhir/mongo:r5-latest
+      -
+        name: Start Spark
+        run: |
+          mkdir -p logs html_summaries json_results
+          docker compose -f docker-compose.yml -f docker-compose-r5.yml up -d spark
+      -
+        name: Wait for and validate R5 metadata
+        run: |
+          set -e
+          for attempt in $(seq 1 30); do
+            if docker compose -f docker-compose.yml -f docker-compose-r5.yml run --rm --no-deps plan_executor \
+              bundle exec ruby -rnet/http -e '
+                require "fhir_client"
+
+                response = Net::HTTP.get_response(URI("http://spark:8080/fhir/metadata"))
+                abort "metadata request returned #{response.code}" unless response.is_a?(Net::HTTPSuccess)
+
+                capability = FHIR::R5::Json.from_json(response.body)
+                abort "unexpected CapabilityStatement fhirVersion #{capability.fhirVersion.inspect}" unless capability.fhirVersion == "5.0.0"
+              '; then
+              exit 0
+            fi
+
+            echo "Waiting for Spark R5 metadata (attempt ${attempt}/30)"
+            sleep 5
+          done
+
+          echo 'Spark R5 metadata did not become ready in time' >&2
+          exit 1
+      -
+        name: Run R5 tests
+        id: suite
+        run: |
+          set +e
+          docker compose -f docker-compose.yml -f docker-compose-r5.yml run --rm --no-deps plan_executor \
+            ./execute_all.sh 'http://spark:8080/fhir' r5 'html|json|stdout'
+          suite_status=$?
+          printf '%s\n' "$suite_status" > suite-exit-status
+          echo "suite_status=$suite_status" >> "$GITHUB_OUTPUT"
+          exit 0
+      -
+        name: Capture service logs
+        if: ${{ always() }}
+        run: |
+          mkdir -p logs
+          cp spark-revision.txt logs/spark-revision.txt 2>/dev/null || true
+          docker compose -f docker-compose.yml -f docker-compose-r5.yml logs spark > logs/spark.log 2>&1 || true
+          docker compose -f docker-compose.yml -f docker-compose-r5.yml logs mongodb > logs/mongodb.log 2>&1 || true
+      -
+        name: Combine test results
+        if: ${{ always() }}
+        run: |
+          set +e
+          ./combine-test-results.sh json_results annotations.json
+          combine_status=$?
+          printf '%s\n' "$combine_status" > combine-exit-status
+          exit 0
+      -
+        name: Attach test results
+        if: ${{ always() && github.event_name != 'pull_request' }}
+        uses: yuzutech/annotations-action@v0.6.0
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          input: annotations.json
+      -
+        name: Archive logs
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          name: logs-r5-${{ github.sha }}
+          path: logs/*.log*
+      -
+        name: Archive test reports
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          name: html_summaries-r5-${{ github.sha }}
+          path: html_summaries/**/*.html
+      -
+        name: Archive JSON results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          name: json_results-r5-${{ github.sha }}
+          path: json_results/**/*.json
+      -
+        name: Archive annotations file
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v7
+        with:
+          name: annotations-r5-${{ github.sha }}
+          path: annotations.json
+      -
+        name: Evaluate suite status
+        if: ${{ always() }}
+        run: |
+          if [ ! -f suite-exit-status ]; then
+            echo 'R5 suite did not produce an exit status' >&2
+            exit 1
+          fi
+
+          suite_status=$(cat suite-exit-status)
+          combine_status=$(cat combine-exit-status 2>/dev/null || printf '1')
+          if [ "$suite_status" -ne 0 ]; then
+            echo "R5 suite exited with status $suite_status" >&2
+            exit "$suite_status"
+          fi
+
+          if [ "$combine_status" -ne 0 ]; then
+            echo "R5 result combination exited with status $combine_status" >&2
+            exit "$combine_status"
+          fi
+      -
+        name: Cleanup
+        if: ${{ always() }}
+        run: docker compose -f docker-compose.yml -f docker-compose-r5.yml down

Gemfile

@@ -1,7 +1,7 @@
 source "https://rubygems.org"
 
-gem 'fhir_dstu2_models', git: 'https://github.com/incendilabs/fhir_dstu2_models.git'
-gem 'fhir_stu3_models', git: 'https://github.com/incendilabs/fhir_stu3_models.git'
+gem 'fhir_dstu2_models', git: 'https://github.com/incendilabs/fhir_dstu2_models.git', branch: 'master'
+gem 'fhir_stu3_models', git: 'https://github.com/incendilabs/fhir_stu3_models.git', branch: 'master'
 gem 'fhir_client', git: 'https://github.com/incendilabs/fhir_client.git', branch: 'master'
 gem 'fhir_models', git: 'https://github.com/incendilabs/fhir_models.git', branch: 'master'
 gem 'activesupport', '>= 6'

Gemfile.lock

@@ -1,23 +1,24 @@
 GIT
   remote: https://github.com/incendilabs/fhir_client.git
-  revision: 79026641f9b2ac7cf30bc27a3528e505d34c67e8
+  revision: e32abec25f8d6ca1b6997d159c263bb70f54abfd
   branch: master
   specs:
-    fhir_client (5.0.0)
+    fhir_client (5.1.0)
       activesupport (>= 3)
       addressable (>= 2.9.0)
       fhir_dstu2_models (>= 1.0.10)
-      fhir_models (>= 4.0.2)
+      fhir_models (>= 5.0.0)
       fhir_stu3_models (>= 3.0.1)
       nokogiri (>= 1.10.4)
-      oauth2 (~> 1.1)
+      oauth2 (>= 2.0, < 3.0)
       rack (>= 1.5)
       rest-client (~> 2.0)
       tilt (>= 1.1)
 
 GIT
   remote: https://github.com/incendilabs/fhir_dstu2_models.git
-  revision: 66c58438d323f634116dc937446d42d9b4356687
+  revision: 4f8b32300c2991d2803b888adff5c097bbfb018e
+  branch: master
   specs:
     fhir_dstu2_models (1.0.10)
       bcp47 (>= 0.3)
@@ -27,18 +28,19 @@ GIT
 
 GIT
   remote: https://github.com/incendilabs/fhir_models.git
-  revision: a143d2e21d0253b33fdaeb17e2d152ad656c9a3e
+  revision: 19ed4a6070f08a18b3f839b6b74aba51a7240c67
   branch: master
   specs:
-    fhir_models (4.1.0)
+    fhir_models (5.0.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
       nokogiri (>= 1.10.4)
 
 GIT
   remote: https://github.com/incendilabs/fhir_stu3_models.git
-  revision: 71db01196b6cafe2310498135849cae356fe6f44
+  revision: e37cfa7b49518b918727d093c41954be1f1406aa
+  branch: master
   specs:
     fhir_stu3_models (3.0.1)
       bcp47 (>= 0.3)
@@ -63,29 +65,33 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.2.3.1)
+    activesupport (8.1.3.1)
       base64
-      benchmark (>= 0.3)
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.3.1)
       connection_pool (>= 2.2.5)
       drb
       i18n (>= 1.6, < 2)
+      json
       logger (>= 1.4.2)
-      minitest (>= 5.1, < 6)
+      minitest (>= 5.1)
       securerandom (>= 0.3)
       tzinfo (~> 2.0, >= 2.0.5)
+      uri (>= 0.13.1)
     addressable (2.9.0)
       public_suffix (>= 2.0.2, < 8.0)
+    anonymous_loader (0.1.3)
+      version_gem (~> 1.1, >= 1.1.14)
     ansi (1.5.0)
+    auth-sanitizer (0.2.3)
+      version_gem (~> 1.1, >= 1.1.14)
     awesome_print (1.9.2)
     base64 (0.3.0)
     bcp47 (0.3.3)
       i18n
-    benchmark (0.5.0)
-    bigdecimal (4.1.1)
+    bigdecimal (4.1.2)
     coderay (1.1.3)
-    concurrent-ruby (1.3.7)
+    concurrent-ruby (1.3.8)
     connection_pool (3.0.2)
     coolline (0.5.0)
       unicode_utils (~> 1.4)
@@ -103,26 +109,31 @@ GEM
     faraday-net_http (3.4.4)
       net-http (~> 0.5)
     hashdiff (1.2.1)
+    hashie (5.1.0)
+      logger
     http-accept (1.7.0)
-    http-cookie (1.1.4)
+    http-cookie (1.1.6)
       domain_name (~> 0.5)
-    i18n (1.14.8)
+    i18n (1.15.2)
       concurrent-ruby (~> 1.0)
-    json (2.20.0)
+    json (2.21.2)
     jsonpath (1.1.5)
       multi_json
-    jwt (2.10.3)
+    jwt (3.2.0)
       base64
     logger (1.7.0)
     method_source (1.1.0)
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2026.0407)
+    mime-types-data (3.2026.0701)
     mini_portile2 (2.8.9)
-    minitest (5.27.0)
-    multi_json (1.19.1)
-    multi_xml (0.6.0)
+    minitest (6.0.6)
+      drb (~> 2.0)
+      prism (~> 1.5)
+    multi_json (1.21.1)
+    multi_xml (0.9.1)
+      bigdecimal (>= 3.1, < 5)
     net-http (0.9.1)
       uri (>= 0.11.1)
     netrc (0.11.0)
@@ -134,20 +145,25 @@ GEM
     nokogiri-diff (0.3.0)
       nokogiri (~> 1.5)
       tdiff (~> 0.4)
-    oauth2 (1.4.11)
-      faraday (>= 0.17.3, < 3.0)
-      jwt (>= 1.0, < 3.0)
-      multi_json (~> 1.3)
+    oauth2 (2.0.25)
+      anonymous_loader (~> 0.1, >= 0.1.3)
+      auth-sanitizer (~> 0.2, >= 0.2.3)
+      faraday (>= 0.17.3, < 4.0)
+      jwt (>= 1.0, < 4.0)
+      logger (~> 1.2)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 4)
+      snaky_hash (~> 2.0, >= 2.0.7)
+      version_gem (~> 1.1, >= 1.1.14)
     power_assert (3.0.1)
+    prism (1.9.0)
     pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     pry-coolline (0.2.6)
       coolline (~> 0.5)
       pry (~> 0.13)
-    public_suffix (6.0.2)
+    public_suffix (7.0.5)
     racc (1.8.1)
     rack (3.2.6)
     rake (13.3.1)
@@ -164,16 +180,20 @@ GEM
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.13.2)
     simplecov_json_formatter (0.1.4)
+    snaky_hash (2.0.7)
+      hashie (>= 0.1.0, < 6)
+      version_gem (~> 1.1, >= 1.1.14)
     tdiff (0.4.0)
     test-unit (3.7.7)
       power_assert
-    tilt (2.7.0)
+    tilt (2.8.0)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     tzinfo-data (1.2026.1)
       tzinfo (>= 1.0.0)
     unicode_utils (1.4.0)
     uri (1.1.1)
+    version_gem (1.1.14)
     webmock (3.26.2)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)