merge v0.12.0-1 release

Merge v0.12.0-1 release

CHANGELOG.md

@@ -1,5 +1,14 @@
 # SODAR Docker Compose Changelog
 
-## v0.11.3-1 (2020-08-30)
+## v0.12.0-1 (2022-10-26)
+
+- Release for SODAR v0.12.0
+- Remove dedicated SODAR Taskflow image (#24)
+- Update Taskflow-related environment variables (#24, #27)
+- Fix duplicate lines in lets-encrypt override (#21)
+- Set bridge network name manually (#26)
+- Add SODAR config directories to volumes (#18)
+
+## v0.11.3-1 (2022-08-30)
 
 - First release of sodar-docker-compose, compatible with SODAR v0.11.3

README.md

@@ -60,7 +60,7 @@ Use the provided `init.sh` script for creating the required volumes (directories
 ```bash
 $ bash init.sh
 $ ls volumes/
-irods  postgres  redis  traefik
+irods  postgres  redis  sodar   traefik
 ```
 
 Next, copy the example environment file `env.example` to `.env`.
@@ -128,7 +128,7 @@ For further instruction on using SODAR, please consult the [SODAR Manual](https:
 
 This repository can also be used to run external SODAR components when developing the main `sodar-server` project.
 
-In this case, the SODAR server itself, consisting of `sodar-web`, `sodar-celeryd-default` and `sodar-celerybeat` will be run locally on the development workstation, while the databases, iRODS, Davrods and SODAR Taskflow are run in the Docker Compose network.
+In this case, the SODAR server itself, consisting of `sodar-web`, `sodar-celeryd-default` and `sodar-celerybeat` will be run locally on the development workstation, while the databases, iRODS and Davrods are run in the Docker Compose network.
 
 For full instructions on how to set up the dev environment, see the development section in the [SODAR manual](https://sodar-server.readthedocs.io/en/latest/).
 

docker-compose.dev.yml

@@ -85,44 +85,6 @@ services:
         source: ./volumes/redis/data
         target: /data
 
-  sodar-taskflow:
-    image: ghcr.io/bihealth/sodar-taskflow:${SODAR_TASKFLOW_VERSION}
-    environment:
-      SODAR_TASKFLOW_SETTINGS: /usr/src/app/config/production.py
-      TASKFLOW_IRODS_HOST: ${IRODS_HOST}
-      TASKFLOW_IRODS_PORT: ${IRODS_PORT}
-      TASKFLOW_IRODS_USER: ${IRODS_USER}
-      TASKFLOW_IRODS_PASS: ${IRODS_PASS}
-      TASKFLOW_IRODS_ZONE: ${IRODS_ZONE}
-      TASKFLOW_IRODS_ROOT_PATH: ${IRODS_ROOT_PATH}
-      TASKFLOW_IRODS_ALLOW_CLEANUP: 1
-      TASKFLOW_SODAR_URL: http://host.docker.internal:8000
-      TASKFLOW_REDIS_URL: redis://redis:6379/2
-      TASKFLOW_SODAR_SECRET: ${TASKFLOW_SODAR_SECRET}
-      TASKFLOW_LOG_PATH: /var/log/sodar-taskflow.log
-      TASKFLOW_LOG_LEVEL: ${TASKFLOW_LOG_LEVEL}
-      TASKFLOW_DEBUG: ${TASKFLOW_DEBUG}
-      TASKFLOW_IRODS_ENV_OVERRIDE: ${TASKFLOW_IRODS_ENV_OVERRIDE}
-      TASKFLOW_IRODS_CERT_PATH: ${TASKFLOW_IRODS_CERT_PATH}
-      TASKFLOW_IRODS_TEST_HOST: irods-test
-      TASKFLOW_IRODS_TEST_PORT: 1247
-    ports:
-      - "5005:5005"
-    networks:
-      - sodar
-    extra_hosts:
-      - host.docker.internal:host-gateway
-    restart: unless-stopped
-    depends_on:
-      - redis
-    volumes:
-      - type: bind
-        source: ./config/sodar
-        target: /etc/sodar
-      - type: bind  # Traefik configuration for shared certs
-        source: ./config/traefik/tls
-        target: /etc/traefik/tls
-
   irods:
     <<: *default-irods
     environment:
@@ -210,3 +172,5 @@ services:
 
 networks:
   sodar:
+    driver_opts:
+      com.docker.network.bridge.name: br-sodar-dev

docker-compose.override.yml.irods

@@ -7,7 +7,6 @@ services:
     depends_on:
       - postgres
       - redis
-      - sodar-taskflow
   irods:
     image: ghcr.io/bihealth/irods-docker:${IRODS_VERSION}
     ports:

docker-compose.override.yml.lets-encrypt

@@ -8,8 +8,6 @@ services:
       - "--entrypoints.web.http.redirections.entryPoint.to=websecure"
       - "--entrypoints.web.http.redirections.entryPoint.scheme=https"
       - "--entrypoints.web.http.redirections.entrypoint.permanent=true"
-      - "--entrypoints.web.address=:80"
-      - "--entrypoints.websecure.address=:443"
       - "--certificatesresolvers.le.acme.email=YOUR_EMAIL@YOUR_DOMAIN.com"  # <-- ADJUST
       - "--certificatesresolvers.le.acme.storage=/letsencrypt/acme.json"
       - "--certificatesresolvers.le.acme.tlschallenge=true"

docker-compose.yml

@@ -66,9 +66,8 @@ x-sodar: &default-sodar
     IRODS_WEBDAV_IGV_PROXY: ${SODAR_IRODS_WEBDAV_IGV_PROXY}
     IRODS_SODAR_AUTH: ${IRODS_SODAR_AUTH}
     BASICAUTH_REALM: ${SODAR_BASICAUTH_REALM}
-    TASKFLOW_BACKEND_HOST: http://sodar-taskflow
-    TASKFLOW_BACKEND_PORT: "5005"
-    TASKFLOW_SODAR_SECRET: ${TASKFLOW_SODAR_SECRET}
+    TASKFLOW_LOCK_RETRY_COUNT: ${TASKFLOW_LOCK_RETRY_COUNT}
+    TASKFLOW_LOCK_RETRY_INTERVAL: ${TASKFLOW_LOCK_RETRY_INTERVAL}
     ENABLE_SENTRY: ${SODAR_ENABLE_SENTRY}
     SENTRY_DSN: ${SODAR_SENTRY_DSN}
 
@@ -134,7 +133,6 @@ services:
     depends_on:
       - postgres
       - redis
-      - sodar-taskflow
     labels:
       - "traefik.enable=true"
       - "traefik.http.middlewares.xforward.headers.customrequestheaders.X-Forwarded-Proto=https"
@@ -144,9 +142,12 @@ services:
       - "traefik.http.services.sodar-web.loadbalancer.server.port=8080"
       - "traefik.http.routers.sodar-web.tls=true"
     volumes:
-      - type: bind
-        source: ./config/sodar
-        target: /etc/sodar
+      - type: bind  # Template include dir
+        source: ./config/sodar/templates
+        target: /usr/src/app/sodar/templates/include
+      - type: bind  # Samplesheets config dir
+        source: ./config/sodar/samplesheets
+        target: /usr/src/app/samplesheets/config
       - type: bind  # Traefik configuration for shared certs
         source: ./config/traefik/tls
         target: /etc/traefik/tls
@@ -177,38 +178,7 @@ services:
         source: ./config/sodar
         target: /etc/sodar
 
-  sodar-taskflow:
-    image: ghcr.io/bihealth/sodar-taskflow:${SODAR_TASKFLOW_VERSION}
-    environment:
-      SODAR_TASKFLOW_SETTINGS: /usr/src/app/config/production.py
-      TASKFLOW_IRODS_HOST: ${IRODS_HOST}
-      TASKFLOW_IRODS_PORT: ${IRODS_PORT}
-      TASKFLOW_IRODS_USER: ${IRODS_USER}
-      TASKFLOW_IRODS_PASS: ${IRODS_PASS}
-      TASKFLOW_IRODS_ZONE: ${IRODS_ZONE}
-      TASKFLOW_IRODS_ROOT_PATH: ${IRODS_ROOT_PATH}
-      TASKFLOW_IRODS_ALLOW_CLEANUP: 0
-      TASKFLOW_SODAR_URL: http://sodar-web:8080
-      TASKFLOW_REDIS_URL: redis://redis:6379/2
-      TASKFLOW_SODAR_SECRET: ${TASKFLOW_SODAR_SECRET}
-      TASKFLOW_LOG_PATH: /var/log/sodar-taskflow.log
-      TASKFLOW_LOG_LEVEL: ${TASKFLOW_LOG_LEVEL}
-      TASKFLOW_DEBUG: ${TASKFLOW_DEBUG}
-      TASKFLOW_IRODS_ENV_OVERRIDE: ${TASKFLOW_IRODS_ENV_OVERRIDE}
-      TASKFLOW_IRODS_CERT_PATH: ${TASKFLOW_IRODS_CERT_PATH}
-    networks:
-      - sodar
-    restart: unless-stopped
-    depends_on:
-      - postgres
-      - redis
-    volumes:
-      - type: bind
-        source: ./config/sodar
-        target: /etc/sodar
-      - type: bind  # Traefik configuration for shared certs
-        source: ./config/traefik/tls
-        target: /etc/traefik/tls
-
 networks:
   sodar:
+    driver_opts:
+      com.docker.network.bridge.name: br-sodar

env.example

@@ -15,7 +15,6 @@
 # Image versions
 # NOTE: For the development build, use "dev-0" for SODAR
 SODAR_SERVER_VERSION=0.11.3-0
-SODAR_TASKFLOW_VERSION=0.6.2-0
 IRODS_VERSION=4.2.11-1
 SSSD_VERSION=1.16.5-10
 
@@ -129,14 +128,8 @@ SODAR_BASICAUTH_REALM="Please log in with your SODAR user name and password."
 #
 # SODAR Taskflow settings
 #
-# Taskflow iRODS environment overrides in format "key=val,key2=val"
-TASKFLOW_IRODS_ENV_OVERRIDE=
-# iRODS cert path for Taskflow
-TASKFLOW_IRODS_CERT_PATH=/etc/traefik/tls/server.crt
-# Shared secret with SODAR Taskflow
-TASKFLOW_SODAR_SECRET=not-so-important-with-docker
-TASKFLOW_LOG_LEVEL=WARNING
-TASKFLOW_DEBUG=0
+TASKFLOW_LOCK_RETRY_COUNT=2
+TASKFLOW_LOCK_RETRY_INTERVAL=3
 
 #
 # WebDAV support

env.example.dev

@@ -3,7 +3,6 @@
 # and their settings must be configured in the sodar-server .env file.
 
 # Image versions
-SODAR_TASKFLOW_VERSION=dev-0
 IRODS_VERSION=4.2.11-1
 SSSD_VERSION=1.16.5-10
 
@@ -55,14 +54,8 @@ SODAR_BASICAUTH_REALM="Please log in with your SODAR user name and password."
 #
 # SODAR Taskflow settings
 #
-# Taskflow iRODS environment overrides in format "key=val,key2=val"
-TASKFLOW_IRODS_ENV_OVERRIDE=
-# iRODS cert path for Taskflow
-TASKFLOW_IRODS_CERT_PATH=/etc/traefik/tls/server.crt
-# Shared secret with SODAR Taskflow
-TASKFLOW_SODAR_SECRET=not-so-important-with-docker
-TASKFLOW_LOG_LEVEL=DEBUG
-TASKFLOW_DEBUG=1
+TASKFLOW_LOCK_RETRY_COUNT=2
+TASKFLOW_LOCK_RETRY_INTERVAL=3
 
 #
 # WebDAV support

init.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
 
 mkdir -p volumes/{postgres/data,redis/data,traefik/letsencrypt,irods/{log,vault,vault-test}} \
-    config/irods/{etc,etc-test} config/davrods/theme config/sodar
+    config/irods/{etc,etc-test} config/davrods/theme config/sodar/{samplesheets,templates}
 chown 1000:1000 volumes/irods/*

run.sh

@@ -4,4 +4,5 @@ docker-compose -f docker-compose.yml \
     -f docker-compose.override.yml.irods \
     -f docker-compose.override.yml.davrods \
     -f docker-compose.override.yml.provided-cert \
-    up
+    up \
+    --remove-orphans

run_dev.sh

@@ -4,4 +4,5 @@
 # You can also use the .sssd override if you need to develop with LDAP.
 docker-compose -f docker-compose.dev.yml \
     -f docker-compose.override.yml.provided-cert \
-    up
+    up \
+    --remove-orphans