Update to latest hapi-fhir-jpaserver-starter (#769)

* update jpa * update external * updating to latest hapi * compiled ruler with updates, wip * operation migration table in readMe * Update dependency versions * Delete unused code * Update to br-cs-merged code * More dependency cleanup * Update to use MR cache * Whoops, didn't mean to override * More dependency fixes * Update github actions * jacoco * Fix integration tests * Fixing tests * Various test fixes and updates * WIP, fixing tests * Disable extract provider and fix extract tests * Fixing tests * Update to latest jpaserver-starter branch * Remove extract provider * Update the Readme with migration status of operations * Fix cds hooks test --------- Co-authored-by: Justin McKelvy <[email protected]> Co-authored-by: Brenin Rhodes <[email protected]>
cqframework · Apr 4, 2024 · c8d86f4 · c8d86f4
1 parent b4f8b8a
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diff --git a/.github/workflows/check-pr.yaml b/.github/workflows/check-pr.yaml
@@ -2,15 +2,15 @@ name: Check PR
 on: pull_request
 
 jobs:
-  maven:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-      - uses: actions/setup-java@v3
-        with:
-          distribution: temurin
-          java-version: 11
-      - name: Run Checks
-        run: mvn --batch-mode --no-transfer-progress --update-snapshots verify
+   maven:
+      runs-on: ubuntu-latest
+      steps:
+         - uses: actions/checkout@v4
+           with:
+              submodules: true
+         - uses: actions/setup-java@v4
+           with:
+              distribution: temurin
+              java-version: 21
+         - name: Run Checks
+           run: mvn --batch-mode --no-transfer-progress --update-snapshots verify
diff --git a/.github/workflows/publish-snapshot.yml b/.github/workflows/publish-snapshot.yml
@@ -1,46 +1,46 @@
 name: Publish Snapshot
 on:
-  push:
-    branches:
-      - master
+   push:
+      branches:
+         - master
 
 jobs:
-  maven:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Add SHORT_SHA env property with commit short sha
-        run: echo "SHORT_SHA=`echo ${GITHUB_SHA} | cut -c1-8`" >> $GITHUB_ENV
-      - uses: actions/checkout@v3
-        with:
-          submodules: true
-      - uses: actions/setup-java@v3
-        with:
-          distribution: temurin
-          java-version: 11
-          server-id: ossrh
-          server-username: MAVEN_USERNAME
-          server-password: MAVEN_PASSWORD
-      - name: Publish snapshot
-        run: mvn --batch-mode -no-transfer-progress --update-snapshots deploy
-        env:
-          MAVEN_USERNAME: ${{ vars.OSSRH_USERNAME }}
-          MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Login to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ vars.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-      - name: Build and push
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          push: true
-          platforms: linux/amd64,linux/arm64
-          tags: |
-              contentgroup/cqf-ruler:latest
-              alphora/cqf-ruler:latest
-          build-args: COMMIT_HASH=${{ env.SHORT_SHA }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
+   maven:
+      runs-on: ubuntu-latest
+      steps:
+         - name: Add SHORT_SHA env property with commit short sha
+           run: echo "SHORT_SHA=`echo ${GITHUB_SHA} | cut -c1-8`" >> $GITHUB_ENV
+         - uses: actions/checkout@v4
+           with:
+              submodules: true
+         - uses: actions/setup-java@v4
+           with:
+              distribution: temurin
+              java-version: 21
+              server-id: ossrh
+              server-username: MAVEN_USERNAME
+              server-password: MAVEN_PASSWORD
+         - name: Publish snapshot
+           run: mvn --batch-mode -no-transfer-progress --update-snapshots deploy
+           env:
+              MAVEN_USERNAME: ${{ vars.OSSRH_USERNAME }}
+              MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}
+         - name: Set up Docker Buildx
+           uses: docker/setup-buildx-action@v2
+         - name: Login to Docker Hub
+           uses: docker/login-action@v2
+           with:
+              username: ${{ vars.DOCKER_USERNAME }}
+              password: ${{ secrets.DOCKER_PASSWORD }}
+         - name: Build and push
+           uses: docker/build-push-action@v4
+           with:
+              context: .
+              push: true
+              platforms: linux/amd64,linux/arm64
+              tags: |
+                 contentgroup/cqf-ruler:latest
+                 alphora/cqf-ruler:latest
+              build-args: COMMIT_HASH=${{ env.SHORT_SHA }}
+              cache-from: type=gha
+              cache-to: type=gha,mode=max
diff --git a/.gitignore b/.gitignore
@@ -159,3 +159,4 @@ Snap.*
 .flattened-pom.xml
 
 thunder-tests/thunderActivity.json
+.aider*
diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,4 @@
 [submodule "external/hapi-fhir-jpaserver-starter"]
 	path = external/hapi-fhir-jpaserver-starter
 	url = https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
-	branch = 6.6.1-cr-updates
+	branch = br-cs-merged
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -9,9 +9,7 @@
 		"streetsidesoftware.code-spell-checker-scientific-terms",
 		"streetsidesoftware.code-spell-checker-medical-terms",
 		"shengchen.vscode-checkstyle",
-		"sonarsource.sonarlint-vscode",
-		"redhat.fabric8-analytics",
-		"vscjava.vscode-java-test"
+		"sonarsource.sonarlint-vscode"
 	],
 	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
 	"unwantedRecommendations": []

diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -4,8 +4,6 @@
 	// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
 	"version": "0.2.0",
 	"configurations": [
-
-
 		{
 			"type": "java",
 			"name": "Launch Application",
@@ -19,7 +17,7 @@
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false",
 				"-Dspring.main.allow-bean-definition-overriding=true"
-			],
+			]
 		},
 		{
 			"type": "java",
@@ -38,14 +36,11 @@
 				"-Dspring.datasource.url=jdbc:h2:mem:test_mem",
 				"-Dspring.datasource.dataClassName=org.h2.Driver",
 				"-Dspring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect",
-				"-Dhapi.fhir.cdshooks.enabled=true"
-				"-Dhapi.fhir.cr_enabled=true",
+				"-Dhapi.fhir.cdshooks.enabled=true",
+				"-Dhapi.fhir.cr.enabled=true",
 				"-Dspring.main.allow-bean-definition-overriding=true"
 			],
-			"classPaths": [
-				"$Auto",
-				"$Runtime"
-			]
+			"classPaths": ["$Auto", "$Runtime"]
 		},
 		{
 			"type": "java",
@@ -65,10 +60,7 @@
 				"-Dhapi.fhir.bulk_export_enabled=false",
 				"-Dspring.batch.job.enabled=false"
 			],
-			"classPaths": [
-				"$Auto",
-				"$Runtime"
-			]
+			"classPaths": ["$Auto", "$Runtime"]
 		},
 		{
 			"type": "java",
@@ -89,10 +81,7 @@
 				"-Dspring.datasource.dataClassName=org.h2.Driver",
 				"-Dspring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect"
 			],
-			"classPaths": [
-				"$Auto",
-				"$Runtime"
-			]
+			"classPaths": ["$Auto", "$Runtime"]
 		},
 		{
 			"type": "java",
@@ -105,7 +94,7 @@
 			"type": "java",
 			"name": "Launch Current File",
 			"request": "launch",
-			"mainClass": "${file}",
+			"mainClass": "${file}"
 		}
 	]
-}
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -14,26 +14,18 @@
 				"-Ddebug=true",
 				"-Dloader.debug=true"
 			]
-		},
+		}
 	],
 	"java.test.defaultConfig": "test-config",
 	"java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle.xml",
 	"java.checkstyle.version": "9.2.1",
-	"cSpell.enabledLanguageIds": [
-		"java",
-		"json",
-		"xml",
-		"markdown"
-	],
+	"cSpell.enabledLanguageIds": ["java", "json", "xml", "markdown"],
 	"cSpell.ignorePaths": [
 		".git/objects",
 		".vscode",
 		"**/pom.xml",
 		"checkstyle.xml"
 	],
-	"editor.codeActionsOnSave": {
-		"source.organizeImports": true
-	},
 	"cSpell.words": [
 		"Alphora",
 		"autoconfiguration",
@@ -84,9 +76,6 @@
 		"**/.settings": true,
 		"**/.factorypath": true
 	},
-	"files.eol": "\r\n",
-	"editor.formatOnSave": true,
-	"thunder-client.saveToWorkspace": true,
 	"java.jdt.ls.vmargs": "-Xmx2G -XX:+UseG1GC -XX:+UseStringDeduplication",
 	"java.compile.nullAnalysis.mode": "automatic"
 }
diff --git a/README.md b/README.md
@@ -8,8 +8,7 @@
 
 ---
 
-The cqf-ruler is based on the [HAPI FHIR JPA Server Starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) and adds a set of plugins that provide an implementation of FHIR's [Clinical Reasoning Module](
-http://hl7.org/fhir/clinicalreasoning-module.html), serve as a
+The cqf-ruler is based on the [HAPI FHIR JPA Server Starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) and adds a set of plugins that provide an implementation of FHIR's [Clinical Reasoning Module](http://hl7.org/fhir/clinicalreasoning-module.html), serve as a
 knowledge artifact repository, and a [cds-hooks](https://cds-hooks.org/) compatible clinical decision support service. The cqf-ruler provides an [extensibility API](#plugins) to allow adding custom FHIR operations without the need to fork or clone the entire project.
 
 See the [wiki](https://github.com/DBCG/cqf-ruler/wiki/Home) for more information
@@ -30,6 +29,7 @@ The public sandbox is not persistent, has no authentication, and is regularly re
 
 The easiest way to get started with the cqf-ruler is to pull and run the docker image.
 For avoiding to run docker container by default root user permission, the container from this image will run with a user named `cqfruler`
+
 ```bash
 docker pull alphora/cqf-ruler
 docker run -p 8080:8080 alphora/cqf-ruler
@@ -75,8 +75,7 @@ to clean up any unneeded or unused files, use:
 
 #### Java
 
-Go to [http://www.oracle.com/technetwork/java/javase/downloads/](
-http://www.oracle.com/technetwork/java/javase/downloads/) and download the
+Go to [http://www.oracle.com/technetwork/java/javase/downloads/](http://www.oracle.com/technetwork/java/javase/downloads/) and download the
 latest (version 11 or higher) JDK for your platform, and install it.
 
 #### Apache Maven
@@ -123,12 +122,48 @@ Inquires for commercial support can be directed to [[email protected]](info@alpho
 
 [Clinical Quality Language](https://github.com/cqframework/clinical_quality_language) - Tooling in support of the CQL specification, including the CQL verifier/translator used in this project.
 
-[CQL Evaluator](https://github.com/DBCG/cql-evaluator) - Provides the CQL execution environment used by the cqf-ruler.
+[CQF Clinical Reasoning](https://github.com/cqframework/clinical-reasoning) - Provides the CQL and Clinical Reasoning support used by the cqf-ruler.
 
 [CQF Tooling](https://github.com/cqframework/cqf-tooling) - Provides several operations that the cqf-ruler exposes are services, such as $refresh-generated content.
 
 [CQL Support for VS Code](https://marketplace.visualstudio.com/items?itemName=cqframework.cql) - CQL IDE plugin with syntax highlighting, linting, and local CQL evaluation.
 
+## Operation Migration
+
+Several operations that once were built and exposed in the cqf-ruler have since migrated upstream into [Clinical-Reasoning](https://github.com/cqframework/clinical-reasoning)
+and exposed in versions of [Hapi-Fhir](https://github.com/hapifhir/hapi-fhir) & [Hapi-Fhir-JpaServer-Starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter).
+
+This table maintains a current view of what operations have migrated out of this project and which are remaining.
+
+-  Migrated = source code in Clinical-Reasoning
+-  To Do = source code in Cqf-Ruler
+
+| Plugin         | ResourceType          | Operation                    | Status      |
+| -------------- | --------------------- | ---------------------------- | ------------|
+| CR             | Measure               | $evaluate-measure            | migrated    |
+| CR             | Measure               | $submit-data                 | migrated    |
+| CR             | Measure               | $care-gaps                   | migrated    |
+| CR             | Measure               | $data-requirements           | To do       |
+| CR             | Measure               | $collect-data                | To do       |
+| CR             | PlanDefinition        | $apply                       | migrated    |
+| CR             | PlanDefinition        | $package                     | migrated    |
+| CR             | ActivityDefinition    | $apply                       | migrated    |
+| CPG            | N/A                   | $cql                         | migrated    |
+| CPG            | Library               | $evaluate                    | migrated    |
+| SDC            | Questionnaire         | $package                     | migrated    |
+| SDC            | Questionnaire         | $populate                    | migrated    |
+| SDC            | QuestionnaireResponse | $extract                     | migrated    |
+| SDC            | Observation           | $transform                   | dropped<sup>1</sup>  |
+| RA             | Measure               | $davinci-ra.evaluate-measure | dropped<sup>2</sup>   |
+| Case-Reporting | MeasureReport         | $extract-line-list-data      | To do       |
+| Case-Reporting | N/A                   | $process-message-bundle      | To do       |
+| ERSD           | N/A                   | $ersd-v2-to-v1-transform     | To do       |
+| cds-hooks      | N/A                   | discovery and service        | In progress |
+
+<sup>1</sup> This was a provisional operation in the SDC Ig that has been removed
+
+<sup>2</sup> The RA IG has evolved significantly and this operation needs to be reimplemented.
+
 ## License
 
 Copyright 2019+ Dynamic Content Group, LLC (dba Alphora)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -159,3 +159,4 @@ Snap.*
		.flattened-pom.xml

		thunder-tests/thunderActivity.json
		.aider*