ci: added job to sync chart to central chart repo (#52)

.github/workflows/helm-lint.yaml

@@ -37,6 +37,8 @@ jobs:
 
       - name: Install Task
         uses: arduino/setup-task@d665c6beebae46ff3f699d7b2fd3f1959de7153c # tag=1.0.2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Add helm repos and update deps
         run: |

.github/workflows/release.yaml

@@ -29,6 +29,8 @@ jobs:
 
       - name: Install Task
         uses: arduino/setup-task@d665c6beebae46ff3f699d7b2fd3f1959de7153c # tag=1.0.2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install Cosign
         uses: sigstore/cosign-installer@9becc617647dfa20ae7b1151972e9b3a2c338a2b # tag=v2.8.1
@@ -38,7 +40,6 @@ jobs:
           task helm-add-repos
           helm dep build charts/recruit
 
-      # TODO: maybe create a PR to miracum/charts with just the one folder's changes.
       # TODO: maybe replace image tags in values.yaml with digests before packaging
       - name: Package, upload, and sign Helm chart
         run: |
@@ -57,6 +58,39 @@ jobs:
           path: |
             recruit-helm-chart.tgz
 
+  sync-helm-chart-to-central-chart-repo:
+    name: sync helm chart to central chart repo
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b # tag=v3.0.2
+        with:
+          path: recruit
+
+      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b # tag=v3.0.2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          repository: miracum/charts
+          path: miracum-charts
+
+      - name: copy local helm chart to charts repo
+        run: |
+          cp -r recruit/charts/recruit miracum-charts/charts/
+
+      - name: get chart version
+        id: chart-version
+        run: |
+          CHART_VERSION=$(yq .version charts/recruit/Chart.yaml)
+          echo "version=${CHART_VERSION}" >> "$GITHUB_OUTPUT"
+
+      - uses: peter-evans/create-pull-request@2b011faafdcbc9ceb11414d64d0573f37c774b04 # tag=v4.2.3
+        with:
+          token: ${{ secrets.MIRACUM_BOT_SEMANTIC_RELEASE_TOKEN }}
+          path: miracum-charts
+          title: "chore(deps): updated recruit chart to ${{ steps.chart-version.outputs.version }}"
+          branch: sync-recruit-chart-from-source-repo
+
   prepare-artifacts:
     name: prepare artifacts
     runs-on: ubuntu-22.04

.github/workflows/test-k8s-installation.yaml

@@ -70,6 +70,8 @@ jobs:
 
       - name: Install Task
         uses: arduino/setup-task@d665c6beebae46ff3f699d7b2fd3f1959de7153c # tag=1.0.2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Add helm repos and update deps of recruit chart
         run: |

.gitleaks.toml

@@ -0,0 +1,5 @@
+[allowlist]
+description = "allow the keycloak aio export"
+paths = [
+  '''aio-export.json'''
+]

.mega-linter.yml

@@ -12,12 +12,10 @@ DISABLE_LINTERS:
   - REPOSITORY_DEVSKIM
   - SPELL_PROSELINT
   - SPELL_CSPELL
-  - REPOSITORY_GITLEAKS
   - JAVASCRIPT_STANDARD
   - SQL_TSQLLINT
   - PYTHON_PYLINT
   - JAVA_PMD
-  - JAVA_CHECKSTYLE
   - PYTHON_PYRIGHT
   # error - python package "--hash" is available for public registration. /github/workspace/src/query/tests/e2e/requirements.txt
   - REPOSITORY_DUSTILOCK

docker-compose/.staging.env

@@ -24,5 +24,5 @@ OMOP_JDBCURL=jdbc:postgresql://omopdb:5432/ohdsi
 OMOP_PASSWORD=postgres
 OMOP_RESULTSSCHEMA=cds_results
 OMOP_USERNAME=postgres
-QUERY_SCHEDULE_UNIXCRON=*/5 * * * *
+QUERY_SCHEDULE_UNIXCRON="*/5 * * * *"
 QUERY_SELECTOR_MATCHLABELS=UC1,Test

docs/development/contributing.md

@@ -2,17 +2,74 @@
 
 All contributions are welcome!
 
-Development and issue tracking is currently happening in the internal MIRACUM GitLab instance,
-but all internal recruIT repositories are mirrored to the MIRACUM GitHub organization:
-
-| recruIT module                              | GitLab Repository                                       | GitHub Repository                                              |
-| ------------------------------------------- | ------------------------------------------------------- | -------------------------------------------------------------- |
-| Documentation and Docker Compose deployment | _deprecated in favor of GitHub_                         | <https://github.com/miracum/recruit>                           |
-| Helm chart                                  | _deprecated in favor of GitHub_                         | <https://github.com/miracum/charts/tree/master/charts/recruit> |
-| Screening List                              | <https://gitlab.miracum.org/miracum/uc1/recruit/list>   | <https://github.com/miracum/recruit-list>                      |
-| Query                                       | <https://gitlab.miracum.org/miracum/uc1/recruit/query>  | <https://github.com/miracum/recruit-query>                     |
-| Notify                                      | <https://gitlab.miracum.org/miracum/uc1/recruit/notify> | <https://github.com/miracum/recruit-notify>                    |
-
-If you want to provide an external contribution, or report a bug or feature request,
-please first create an issue on the corresponding GitHub repository (or the <https://github.com/miracum/recruit> repository)
-and we can assist and discuss further.
+## Setup for local development
+
+From the `/src` directory:
+
+```sh
+docker compose -f hack/docker-compose.yaml up
+```
+
+This will start all development dependencies:
+
+- OHDSI WebAPI
+- OHDSI ATLAS
+- Broadsea Atlasdb - a pre-filled OMOP database
+- Traefik
+- HAPI FHIR JPA Server
+- Jaeger
+- MailDev
+
+If you want to start any of the recruIT modules as containers, you can specify the corresponding `--profile` switch.
+For example, when working on the query module, it might be useful to run the screening list and the notify module
+for debugging. The following will start all development dependencies as well as build and run the list and notify containers:
+
+```sh
+docker compose -f hack/docker-compose.yaml --profile=notify --profile=list up
+```
+
+You can then start the query module via gradle by running
+
+```sh
+./gradlew :query:bootRun
+```
+
+## Building Container Images
+
+### notify & query
+
+Both the notify and query module are Java applications that can be build using Gradle.
+Therefore, they also share the same Dockerfile for building the container and can optionally
+also be built using [jib](https://github.com/GoogleContainerTools/jib).
+
+#### Using Dockerfile
+
+From the `/src` directory, run
+
+```sh
+export MODULE_NAME=query
+docker build -t "ghcr.io/miracum/recruit/${MODULE_NAME}:local" --build-arg=MODULE_NAME=${MODULE_NAME} .
+```
+
+The `--build-arg` `MODULE_NAME` must be either `notify` or `query` (default).
+
+#### Using jib
+
+You can also build the container images using [jib](https://github.com/GoogleContainerTools/jib) via gradle:
+
+```sh
+export MODULE_NAME=query
+./gradlew :${MODULE_NAME}:jibDockerBuild --image="ghcr.io/miracum/recruit/${MODULE_NAME}:local"
+```
+
+Using `jibDockerBuild` will build the image against the local docker daemon. Running just `./gradlew :query:jib`
+will attempt to push the image to the remote registry.
+
+### list
+
+The list module is a NodeJS app with a Vue frontend and can be built via Dockerfile.
+From the `/src/list` directory, run:
+
+```sh
+docker build -t ghcr.io/miracum/recruit/list:local .
+```

src/README.md

@@ -0,0 +1,4 @@
+# Development
+
+See <https://miracum.github.io/recruit/development/contributing/> for
+detailed instructions on working with the source code in this folder.

src/buildSrc/src/main/groovy/org.miracum.recruit.java-application-conventions.gradle

@@ -109,8 +109,8 @@ spotless {
 }
 
 checkstyle {
-    toolVersion '10.3.3'
-    // configFile = file('../.checkstyle/checkstyle.xml')
+    toolVersion '10.6.0'
+    configFile = file('../config/checkstyle/checkstyle.xml')
 }
 
 jib {