Added jupyter notebook profile. Fixes for Achilles Dockerfile and tra…

…efik routing.

Update traefik to 2.11.2.

Set atlasdb to restart unless stopped.

README.md

@@ -150,16 +150,14 @@ docker compose --env-file .env --profile profile1 --profile profile2 ... up -d
 | omop-vocab-pg-load   | <ul><li>Using OMOP Vocab files downloaded from Athena, this can load them into a Postgres instance (can be Broadsea's atlasdb or an external one)</li><li>Rebuilds the CPTs using the CPT jar file from Athena, with UMLS API Key (see .env file Section 9)</li><li>Creates the schema if necessary</li><li>Runs copy command for each vocabulary CSV file</li><li>Creates all necessary Postgres indices</li><li>Once complete, the omop-vocab-load container will finish with an exit status; you can remove this container</li></ul> |
 | phoebe-pg-load       | <ul><li>For Atlas 2.12+, which offers Concept Recommendation options based on the [Phoebe project](https://forums.ohdsi.org/t/phoebe-2-0/17410 "Phoebe Project")</li><li>Loads Phoebe files into an existing OMOP Vocabulary hosted in a Postgres instance (can be Broadsea's atlasdb or an external one)</li><li>Note: your Atlas instance must use this OMOP Vocabulary as its default vocabulary source in order to use this feature</li><li>Once complete, the phoebe-load container will finish with an exit status; you can remove this container</li></ul> |
 | openldap             | <ul><li>For testing security in Atlas, this Open LDAP container can be used to assess security needs</li><li>You can specify a comma separated list of user ids and passwords</li><li>This is not recommended for any production level setup</li></ul> |
-| open-shiny-server    | <ul><li>An open source version of Shiny Server, where you can drop shiny apps into a mounted folder.</li><li>Recommended if your organization does not have a Posit Connect license.</li></ul> |
-| posit-connect        | <ul><li>For sites with commercial Posit Connect licenses,
 
-#### Perseus Profiles
+#### Experimental Profiles
 
-We also offer profiles for Perseus, but please note, **these are EXPERIMENTAL and not guaranteed to work**:
+We also offer profiles for Perseus and other useful services, but please note, **these are EXPERIMENTAL and not guaranteed to work**:
 
 | Profile                 | Description |
 |-------------------------|-------------|
-| perseus                 | <ul><li>Experimental in this version</li><li>Deploys the entire Perseus stack of services, but in the Broadsea network</li><li>Services include:</li><li>Currently, does have overlapping capabilities (e.g. Solr, OMOP Vocab on Postgres)</li></ul> |
+| perseus                 | <ul><li>Deploys the entire Perseus stack of services, but in the Broadsea network</li><li>Currently, does have overlapping capabilities (e.g. Solr, OMOP Vocab on Postgres</li></ul> |
 | perseus-shareddb        | <ul><li>Deploys only the shareddb Postgres backend for Perseus</li></ul> |
 | perseus-files-manager   | <ul><li>Deploys only the files-manager backend for Perseus</li></ul> |
 | perseus-user            | <ul><li>Deploys only the user management system for Perseus</li></ul> |
@@ -174,6 +172,9 @@ We also offer profiles for Perseus, but please note, **these are EXPERIMENTAL an
 | perseus-dqd             | <ul><li>Deploys the DataQualityDashboard instance for Perseus</li></ul> |
 | perseus-swagger         | <ul><li>Deploys the Swagger instance for Perseus</li></ul> |
 | perseus-white-rabbit    | <ul><li>Deploys the White Rabbit instance for Perseus</li></ul> |
+| open-shiny-server    | <ul><li>An open source version of Shiny Server, where you can drop shiny apps into a mounted folder.</li><li>Recommended if your organization does not have a Posit Connect license.</li></ul> |
+| posit-connect        | <ul><li>For sites with commercial Posit Connect licenses
+| jupyter-notebook        | <ul><li>Deploys a simple Jupyter Data Science Notebook with no authentication.</li></ul>
 
 ### Traefik Dashboard
 

achilles/Dockerfile

@@ -10,7 +10,7 @@ apt-get clean
 rm -rf /var/lib/apt/lists/*
 
 # The default GitHub Actions runner has 2 vCPUs (https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners)
-install2.r --error --ncpus 2 \
+install2.r --error --ncpus 2  --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \
     rJava \
     remotes \ 
     ParallelLogger \

docker-compose.yml

@@ -19,11 +19,13 @@ volumes:
     name: perseus-vocabularydb
   perseus-solr:
     name: perseus-solr
+  jupyter-notebook:
+    name: jupyter-notebook
 
 services:
 
   traefik:
-    image: docker.io/library/traefik:v2.10.4
+    image: docker.io/library/traefik:v2.11.2
     container_name: traefik
     restart: unless-stopped
     ipc: none
@@ -117,6 +119,7 @@ services:
     image: ohdsi/broadsea-atlasdb:2.1.0-secret
     container_name: broadsea-atlasdb
     platform: linux/amd64
+    restart: unless-stopped
     cpus: 2
     mem_limit: "2G"
     environment:
@@ -591,6 +594,27 @@ services:
       - perseus-shareddb
       - perseus-files-manager
 
+  broadsea-jupyter-notebook:
+    profiles: [ "jupyter-notebook" ]
+    image: quay.io/jupyter/datascience-notebook:latest
+    platform: ${DOCKER_ARCH}
+    restart: unless-stopped
+    container_name: broadsea-jupyter-notebook
+    environment:
+      JUPYTERHUB_SERVICE_PREFIX: /jupyter/
+      JUPYTERHUB_BASE_URL: ${HTTP_TYPE}://${BROADSEA_HOST}
+    volumes:
+      - jupyter-notebook:/home/jovyan/work:rw
+    command:
+      - jupyter-lab
+      - --ip=*
+      - --NotebookApp.token=
+      - --NotebookApp.password=
+      - --NotebookApp.base_url=/jupyter
+    labels:
+      - "traefik.enable=true"
+
+
 secrets:
   GITHUB_PAT:
     file: ${GITHUB_PAT_SECRET_FILE}

traefik/routers.yml

@@ -121,6 +121,10 @@ http:
         - "broadsea-perseus-strip-prefix"
 
 
+    broadsea-jupyter-notebook:
+      entryPoints: '{{ env "HTTP_TYPE" }}'
+      service: "broadsea-jupyter-notebook"
+      rule: 'Host(`{{ env "BROADSEA_HOST" }}`) && PathPrefix(`/jupyter`)'
 
   middlewares:
 
@@ -135,10 +139,6 @@ http:
           - "/hades"
         forceSlash: false
 
-    broadsea-perseus-add-prefix:
-      addPrefix:
-        prefix: "/perseus"
-
     broadsea-perseus-strip-prefix:
       stripPrefix:
         prefixes: 
@@ -250,4 +250,10 @@ http:
     perseus-athena:
       loadBalancer:
         servers:
-          - url: http://perseus-athena:5002
+          - url: http://perseus-athena:5002
+
+
+    broadsea-jupyter-notebook:
+      loadBalancer:
+        servers:
+          - url: http://broadsea-jupyter-notebook:8888