Merge branch 'next'

Author: jennydaman

.gitignore

@@ -1,3 +1,6 @@
 node_modules/
 .vagrant/
 .idea/
+
+.env
+

docker-compose.yml

@@ -17,7 +17,7 @@ services:
       - local
 
   db_migrate:
-    image: ghcr.io/fnndsc/cube:5.0.0
+    image: ghcr.io/fnndsc/cube:6.3.0-beta.7
     command: python manage.py migrate --noinput
     env_file: secrets.env
     volumes:
@@ -30,7 +30,7 @@ services:
 
   chris:
     container_name: chris
-    image: ghcr.io/fnndsc/cube:5.0.0
+    image: ghcr.io/fnndsc/cube:6.3.0-beta.7
     ports:
       - "8000:8000"
     volumes:
@@ -39,7 +39,7 @@ services:
       db_migrate:
         condition: service_completed_successfully
       queue:
-        condition: service_started
+        condition: service_healthy
       cube-nonroot-user-volume-fix:
         condition: service_completed_successfully
     networks:
@@ -49,7 +49,7 @@ services:
       org.chrisproject.role: "ChRIS_ultron_backEnd"
       org.chrisproject.miniChRIS: "miniChRIS"
   worker:
-    image: ghcr.io/fnndsc/cube:5.0.0
+    image: ghcr.io/fnndsc/cube:6.3.0-beta.7
     command: celery -A core worker -c 4 -l info -Q main1,main2
     volumes:
       - chris_files:/data:rw
@@ -58,7 +58,7 @@ services:
       db_migrate:
         condition: service_completed_successfully
       queue:
-        condition: service_started
+        condition: service_healthy
       pfcon:
         condition: service_started
       cube-nonroot-user-volume-fix:
@@ -67,7 +67,7 @@ services:
     networks:
       - local
   worker_periodic:
-    image: ghcr.io/fnndsc/cube:5.0.0
+    image: ghcr.io/fnndsc/cube:6.3.0-beta.7
     command: celery -A core worker -c 2 -l info -Q periodic
     volumes:
       - chris_files:/data:rw
@@ -76,14 +76,14 @@ services:
       db_migrate:
         condition: service_completed_successfully
       queue:
-        condition: service_started
+        condition: service_healthy
       cube-nonroot-user-volume-fix:
         condition: service_completed_successfully
     restart: unless-stopped
     networks:
       - local
   scheduler:
-    image: ghcr.io/fnndsc/cube:5.0.0
+    image: ghcr.io/fnndsc/cube:6.3.0-beta.7
     command: celery -A core beat -l info --scheduler django_celery_beat.schedulers:DatabaseScheduler
     volumes:
       - chris_files:/data:rw
@@ -92,7 +92,7 @@ services:
       db_migrate:
         condition: service_completed_successfully
       queue:
-        condition: service_started
+        condition: service_healthy
       cube-nonroot-user-volume-fix:
         condition: service_completed_successfully
     restart: unless-stopped
@@ -115,19 +115,27 @@ services:
   queue:
     image: docker.io/library/rabbitmq:3
     restart: on-failure
+    ports:
+      - 5672:5672
     networks:
       - local
+    healthcheck:
+      test: rabbitmq-diagnostics -q ping
+      start_period: 20s
+      retries: 3
+      timeout: 10s
+      interval: 5s
 
   pfcon:
     container_name: pfcon
-    image: ghcr.io/fnndsc/pfcon:5.2.2
+    image: ghcr.io/fnndsc/pfcon:5.2.3
     environment:
       COMPUTE_SERVICE_URL: http://pman:5010/api/v1/
       SECRET_KEY: secret
       PFCON_USER: pfcon
       PFCON_PASSWORD: pfcon1234
       PFCON_INNETWORK: "true"
-      STORAGE_ENV: filesystem
+      STORAGE_ENV: fslink
       STOREBASE_MOUNT: /var/local/storeBase
     ports:
       - "5005:5005"
@@ -169,13 +177,27 @@ services:
       org.chrisproject.role: "pman"
 
   chris_ui:
-    image: ghcr.io/fnndsc/chris_ui:20240507.446-767958ca
-    command: sirv --host --single
+    # This image is likely outdated.
+    # Newer tags can be found here --> https://github.com/FNNDSC/ChRIS_ui/pkgs/container/chris_ui
+    image: ghcr.io/fnndsc/chris_ui:staging
     environment:
-      REACT_APP_CHRIS_UI_URL: http://localhost:8000/api/v1/
-      REACT_APP_PFDCM_URL: http://localhost:4005/
+      # https://chrisproject.org/docs/run/chris_ui#environment-variables
+      CHRIS_UI_URL: http://${HOSTNAME:-localhost}:8000/api/v1/
+      PFDCM_URL: http://${HOSTNAME:-localhost}:4005
+      OHIF_URL: http://${HOSTNAME:-localhost}:8042/ohif/
+      SERVER_PORT: "8020"
+      SERVER_LOG_REMOTE_ADDRESS: "true"
+      SERVER_HEALTH: "true"
     ports:
-      - "8020:3000"
+      - "8020:8020"
+    user: "100100:100100"
+    group_add: [ root ]
+    healthcheck:
+      test: ["CMD", "wget", "--spider", "http://127.0.0.1:8020/health"]
+      interval: 5s
+      timeout: 2s
+      retries: 3
+      start_period: 10s
 
   orthanc:
     image: docker.io/jodogne/orthanc-plugins:1.12.3
@@ -212,17 +234,19 @@ services:
         condition: service_completed_successfully
 
   oxidicom:
-    image: ghcr.io/fnndsc/oxidicom:2.0.0
+    image: ghcr.io/fnndsc/oxidicom:pr-3  # https://github.com/FNNDSC/oxidicom/pull/3
     environment:
-      OXIDICOM_DB_CONNECTION: postgresql://chris:chris1234@db:5432/chris
+      # https://chrisproject.org/docs/oxidicom/deployment#environment-variables
       OXIDICOM_FILES_ROOT: /data
+      OXIDICOM_AMQP_ADDRESS: amqp://queue:5672
+      OXIDICOM_NATS_ADDRESS: nats:4222
       OXIDICOM_SCP_AET: ChRIS
-      OXIDICOM_PACS_ADDRESS: '{MINICHRISORTHANC="orthanc:4242"}'
       OXIDICOM_SCP_PROMISCUOUS: "true"
-      OXIDICOM_DB_BATCH_SIZE: 20
       OXIDICOM_LISTENER_THREADS: 32
-      OXIDICOM_VERBOSE: "true"
       OXIDICOM_LISTENER_PORT: 11111
+      RUST_LOG: oxidicom=info
+      OXIDICOM_PROGRESS_INTERVAL: 100ms
+      OXIDICOM_DEV_SLEEP: 150ms  # throttle performance, so that we can see what's going on in ChRIS_ui
     ports:
       - "11111:11111"
     volumes:
@@ -233,9 +257,28 @@ services:
     profiles:
       - pacs
     user: 1001:0
+    stop_signal: SIGKILL
     depends_on:
+      queue:
+        condition: service_healthy
+      nats:
+        condition: service_healthy
       cube-nonroot-user-volume-fix:
         condition: service_completed_successfully
+
+  nats:
+    image: docker.io/library/nats:2.10.20-alpine3.20
+    ports:
+      - "4222:4222"
+    networks:
+      - local
+    healthcheck:
+      test: wget http://localhost:8222/healthz -q -S -O -
+      start_period: 10s
+      retries: 3
+      timeout: 2s
+      interval: 2s
+
   pfbridge:
     image: docker.io/fnndsc/pfbridge:3.7.2
     container_name: pfbridge
@@ -287,7 +330,7 @@ services:
       - pflink
 
   graphql-engine:
-    image: docker.io/hasura/graphql-engine:v2.40.0
+    image: docker.io/hasura/graphql-engine:v2.41.0
     ports:
       - "8090:8080"
     restart: unless-stopped

minichris.sh

@@ -7,7 +7,13 @@ fi
 # change to directory where this script lives
 cd "$(dirname "$(readlink -f "$0")")"
 
-set -ex
+set -x  # print commands before running them
+
+# (optional) set HOSTNAME environment variable
+hn="$(hostname)" && echo "HOSTNAME=$hn" > .env
+
+set -e  # fail on error
+
 docker compose up -d "$@"
 
 # if chris is running, run chrisomatic

scripts/clear_pacsfiles.sh

@@ -12,10 +12,10 @@ docker compose exec chris pip install tqdm
 docker compose exec chris python manage.py shell -c '
 from django.conf import settings
 from core.storage import connect_storage
-from pacsfiles.models import PACSFile
+from pacsfiles.models import PACSSeries
 from tqdm import tqdm
 
-with tqdm(PACSFile.objects.all()) as pbar:
+with tqdm(PACSSeries.objects.all()) as pbar:
     for pacs_file in pbar:
         _ = pacs_file.delete()
 

secrets.env

@@ -1,3 +1,4 @@
+CHRIS_SUPERUSER_PASSWORD=chris1234
 DJANGO_SETTINGS_MODULE=config.settings.production
 CUBE_CELERY_POLL_INTERVAL=5.0
 DJANGO_ALLOWED_HOSTS=*
@@ -11,8 +12,11 @@ DATABASE_PORT=5432
 POSTGRES_DB=chris
 POSTGRES_USER=chris
 POSTGRES_PASSWORD=chris1234
-CHRIS_STORE_URL=https://chrisstore.co/api/v1/
-STORAGE_ENV=filesystem
+CHRIS_STORE_URL=https://cube.chrisproject.org/api/v1/
+STORAGE_ENV=fslink
 MEDIA_ROOT=/data
 CELERY_BROKER_URL=amqp://queue:5672
+PFDCM_ADDRESS=http://pfdcm:4005
+NATS_ADDRESS=nats://nats:4222
 AUTH_LDAP=False
+DISABLE_USER_ACCOUNT_CREATION=false

test.sh

@@ -1,8 +1,10 @@
-#!/bin/bash -x
+#!/usr/bin/env bash
 # run pl-dircopy on the file "LICENSE", that's it
 
 cd $(dirname "$(readlink -f "$0")")
 
+set -x
+
 ok_statuses=(created waiting scheduled started registeringFiles)
 
 function is_ok() {
@@ -31,10 +33,10 @@ token=$(
 )
 
 # upload a file
-curl -s 'http://localhost:8000/api/v1/uploadedfiles/' \
+curl -s 'http://localhost:8000/api/v1/userfiles/' \
   -H 'Accept: application/vnd.collection+json' \
   -H "Authorization: Token $token" \
-  -F 'upload_path=chris/uploads/wow-upload-01/LICENSE' \
+  -F 'upload_path=home/chris/uploads/wow-upload-01/LICENSE' \
   -F "fname=@LICENSE"
 
 # find the plugin ID for pl-dircopy
@@ -50,7 +52,7 @@ feed=$(
     -H "Authorization: Token $token" \
     -H 'Content-Type: application/vnd.collection+json' \
     -H 'Accept: application/json' \
-    --data '{"template":{"data":[{"name":"dir","value":"chris/uploads/wow-upload-01"}]}}'
+    --data '{"template":{"data":[{"name":"dir","value":"home/chris/uploads/wow-upload-01"}]}}'
 )
 
 job_url=$(echo $feed | jq -r .url)
@@ -82,13 +84,28 @@ if [ "$run_status" != "finishedSuccessfully" ]; then
 fi
 
 # download output file
+output_folder_root=$(
+  curl -s "$(echo $job | jq -r .output_folder)" \
+    -H "Authorization: Token $token" \
+    -H 'Accept: application/json'
+)
+output_folder_linkfiles=$(
+  curl -s "$(echo $output_folder_root | jq -r .link_files)" \
+    -H "Authorization: Token $token" \
+    -H 'Accept: application/json'
+)
+linked_folder=$(
+  curl -s "$(echo $output_folder_linkfiles | jq -r '.results[0].linked_folder')" \
+    -H "Authorization: Token $token" \
+    -H 'Accept: application/json'
+)
 output_files=$(
-  curl -s "$(echo $job | jq -r .files)" \
+  curl -s "$(echo $linked_folder | jq -r '.files')" \
     -H "Authorization: Token $token" \
     -H 'Accept: application/json'
 )
 copied_file_url=$(
-  echo $output_files \
+  echo "$output_files" \
     | jq -r '.results | map(select(.fname|endswith("LICENSE")))[0].file_resource'
 )
 

wrapper.js

@@ -8,9 +8,9 @@
  */
 
 
-const fs = require('fs');
-const path = require('path');
-const { execFileSync } = require('child_process');
+const fs = require('node:fs');
+const path = require('node:path');
+const { execFileSync } = require('node:child_process');
 const assert = require('node:assert/strict');