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fix: Multiple Slim issues regarding ANN visualization (#306)
* Improve logging * Extract func for report generation * Lint * Add spacing * Only add thumbnail if required to volumes * Add link section * lINT * Lint * Typo * Add zoom to roi for annotation groups * Update create slide to follow constructor * Update dockerfile * Update actions * Lint * Address deep source issues * Add healthchecks * Update healthchecks * Add debug step * Remove wait * Improve wait * Add debug steps * Update workflow * Update workflow * Add logs * Add db healthcheck * Add debug steps * Add debug steps * Add debug steps * Add consistent intervals * Revert dcm4chee custmizations * Add retry * Add retry debug * Add waits * Add waits * add more logs * Add more wait * Add more wait * Add more wait * Wait ldap * add logs * Test pwd * Add ldap file * Add wildly logs * Print always * Fix container get * Use fixed name * Log vars * Always log vars * Copy default ldap config * Simplify docker compose * Update ldap version * Bump dmv
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‎.github/workflows/container-tests.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4.1.4
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uses: actions/checkout@v4.2.2
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- name: Setup Node
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uses: actions/setup-node@v4.0.2
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uses: actions/setup-node@v4.4.0
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with:
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node-version: 20.8.1
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run: |
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sleep 20
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curl -sI http://localhost:8008/dcm4chee-arc/aets/DCM4CHEE/rs/studies | grep -o '204 No Content'
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- name: Wildfly internal server.log
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if: always()
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run: |
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docker cp dcm4chee-arc:/opt/wildfly/standalone/log/server.log ./server.log || echo "Log not found"
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cat ./server.log || echo "Log not found"

‎.github/workflows/deploy-to-firebase.yml‎

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if: "${{ github.event.pull_request.head.repo.full_name == github.repository }}"
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4.1.4
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- name: Checkout to repository
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uses: actions/checkout@v4.2.2
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- name: Setup Node
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uses: actions/setup-node@v4.0.2
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uses: actions/setup-node@v4.4.0
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with:
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node-version: 20.8.1
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‎.github/workflows/deploy-to-github-pages.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout to repository
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uses: actions/checkout@v4.1.4
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uses: actions/checkout@v4.2.2
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- name: Setup Node
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uses: actions/setup-node@v4.0.2
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uses: actions/setup-node@v4.4.0
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with:
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node-version: 20.8.1
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‎.github/workflows/release.yml‎

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name: "Bump version and cut a release"
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4.1.4
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- name: Checkout to repository
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uses: actions/checkout@v4.2.2
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with:
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ref: master
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persist-credentials: false
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- name: Setup node
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uses: actions/setup-node@v4.0.2
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- name: Setup Node
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uses: actions/setup-node@v4.4.0
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with:
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node-version: 20.8.1
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‎.github/workflows/unit-tests.yml‎

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name: "Build and run unit tests"
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4.1.4
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- name: Checkout to repository
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uses: actions/checkout@v4.2.2
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- name: Setup Node
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uses: actions/setup-node@v4.0.2
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uses: actions/setup-node@v4.4.0
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with:
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node-version: 20.8.1
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‎README.md‎

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- [Google Cloud Platform](#google-cloud-platform)
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- [OAuth 2.0 configuration](#oauth-20-configuration)
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- [Development](#development)
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- [Linking Slim to a Local dicom-microscopy-viewer Library](#linking-slim-to-a-local-dicom-microscopy-viewer-library)
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- [Citation](#citation)
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- [Acknowledgments](#acknowledgments)
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- [DICOM Conformance Statement](#dicom-conformance-statement)
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REACT_APP_CONFIG=local yarn start
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```
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## Linking Slim to a Local dicom-microscopy-viewer Library
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If you are developing features or fixing bugs that require changes in both Slim and the underlying [`dicom-microscopy-viewer`](https://github.com/ImagingDataCommons/dicom-microscopy-viewer) library, you can use `yarn link` to connect your local Slim project to a local clone of `dicom-microscopy-viewer`. This allows Slim to immediately use the latest local changes from the library without publishing to npm.
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### Steps
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1. **Clone dicom-microscopy-viewer**
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If you haven't already, clone the `dicom-microscopy-viewer` repository to your machine.
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2. **Set up yarn link in dicom-microscopy-viewer**
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In the root directory of your local `dicom-microscopy-viewer` repository, run:
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```sh
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yarn link
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```
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3. **Link dicom-microscopy-viewer in Slim**
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In the root directory of your Slim project, run:
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```sh
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yarn link dicom-microscopy-viewer
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```
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4. **Enable live rebuilding in dicom-microscopy-viewer**
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To automatically rebuild `dicom-microscopy-viewer` when you make changes, run the following command in the `dicom-microscopy-viewer` directory:
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```sh
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yarn webpack:dynamic-import:watch
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```
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This will watch for file changes and rebuild the library, so Slim can immediately use the updated code.
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5. **Run Slim as usual**
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In the Slim directory, start the development server:
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```sh
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yarn start
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```
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Slim will now use your locally linked version of `dicom-microscopy-viewer`.
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### Notes
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- If you want to unlink and return to the npm-published version, run `yarn unlink dicom-microscopy-viewer` and `yarn install --force` in the Slim directory.
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- Make sure both projects use compatible Node and Yarn versions to avoid dependency issues.
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## Citation
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For more information about the motivation, design, and capabilities of Slim, please see the following article:

‎docker-compose.env‎

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POSTGRES_DB=pacsdb
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POSTGRES_USER=pacs
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POSTGRES_PASSWORD=pacs
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LDAP_INIT_CONFIG="default-config.ldif modify-dcmRemapRetrieveURL.ldif modify-dcmWebServicePath.ldif"
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LDAP_INIT_CONFIG="default-config.ldif modify-dcmRemapRetrieveURL.ldif modify-dcmWebServicePath.ldif"

‎docker-compose.yml‎

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version: "3.7"
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volumes:
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db_data: {}
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arc_data: {}
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ldap:
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image: dcm4che/slapd-dcm4chee:2.6.0-26.0
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# image: dcm4che/slapd-dcm4chee:2.6.8-34.1
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logging:
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driver: json-file
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options:
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- ./etc/openldap/data/modify-dcmWebServicePath.ldif:/etc/openldap/data/modify-dcmWebServicePath.ldif:ro
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db:
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image: dcm4che/postgres-dcm4chee:14.2-26
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image: dcm4che/postgres-dcm4chee:11.22-34
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driver: json-file
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- db_data:/var/lib/postgresql/data
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arc:
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image: dcm4che/dcm4chee-arc-psql:5.26.0
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container_name: dcm4chee-arc
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image: dcm4che/dcm4chee-arc-psql:5.34.0
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logging:
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driver: json-file
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options:
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max-size: "10m"
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expose:
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- 8080
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- 8443
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- 9990
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- 9993
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- 11112
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- 2762
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- 2575
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- 12575
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ports:
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- "8080:8080"
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- "8443:8443"
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- "9990:9990"
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- "9993:9993"
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- "11112:11112"
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- "2762:2762"
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- "2575:2575"
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- "12575:12575"
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env_file: docker-compose.env
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environment:
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# Used to set the initial and maximal Java heap size to avoid
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- ldap
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- db
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volumes:
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- arc_data:/storage
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- arc_data:/storage

‎package.json‎

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"craco-less": "^2.0.0",
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"dcmjs": "^0.35.0",
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"detect-browser": "^5.2.1",
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"dicom-microscopy-viewer": "^0.48.3",
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"dicom-microscopy-viewer": "^0.48.4",
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"dicomweb-client": "^0.10.3",
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"gh-pages": "^5.0.0",
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"oidc-client": "^1.11.5",

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