upgrade to irods-docker v4.3.3-wip (#17, #34)

.gitignore

@@ -26,8 +26,6 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
-lib64/
 parts/
 sdist/
 var/

CHANGELOG.md

@@ -1,5 +1,11 @@
 # SODAR Docker Compose Changelog
 
+## Unreleased
+
+- Suppress iRODS postgres transaction warnings (#17)
+- Upgrade to Postgres v16 (#34)
+- Upgrade to ``irods-docker`` v4.3.3-wip (#34)
+
 ## v0.15.1-1 (2024-09-12)
 
 - Release for SODAR v0.15.1

docker-compose.dev.yml

@@ -58,12 +58,13 @@ services:
         read_only: true
 
   postgres:
-    image: postgres:11
+    image: postgres:16
     shm_size: 512mb
     environment:
       POSTGRES_USER: ${POSTGRES_USERNAME}
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
       POSTGRES_DB: sodar
+    command: ["postgres", "-c", "log_min_messages=error"]
     ports:
       - "5432:5432"
     networks:
@@ -107,7 +108,7 @@ services:
         target: /etc/traefik/tls
       - type: bind  # Log files
         source: ./volumes/irods/log
-        target: /var/lib/irods/log
+        target: /var/log/irods
       - type: bind  # File storage
         source: ./volumes/irods/vault
         target: /data/Vault
@@ -142,7 +143,7 @@ services:
       IRODS_ZONE_PORT: 1247
       IRODS_ZONE_NAME: sodarZone
       IRODS_SSL_VERIFY_SERVER: ${IRODS_SSL_VERIFY_SERVER}
-      IRODS_AUTHENTICATION_SCHEME: ${IRODS_AUTHENTICATION_SCHEME}
+      IRODS_AUTHENTICATION_SCHEME: PAM  # ${IRODS_AUTHENTICATION_SCHEME} # TODO: Update Davrods to 4.3
       IRODS_CLIENT_SERVER_NEGOTIATION: ${IRODS_CLIENT_SERVER_NEGOTIATION}
       IRODS_CLIENT_SERVER_POLICY: ${IRODS_CLIENT_SERVER_POLICY}
       IRODS_SSL_CA_CERT_PATH: ${IRODS_CERT_PATH}

docker-compose.override.yml.irods

@@ -45,12 +45,15 @@ services:
       - type: bind  # iRODS configuration
         source: ./config/irods/etc
         target: /etc/irods
+      - type: bind  # iRODS version.json file
+        source: ./config/irods-lib/version.json
+        target: /var/lib/irods/version.json
       - type: bind  # Traefik configuration for shared certs
         source: ./config/traefik/tls
         target: /etc/traefik/tls
       - type: bind  # Log files
         source: ./volumes/irods/log
-        target: /var/lib/irods/log
+        target: /var/log/irods
       - type: bind  # File storage
         source: ./volumes/irods/vault
         target: /data/Vault

docker-compose.yml

@@ -117,12 +117,13 @@ services:
         read_only: true
 
   postgres:
-    image: postgres:11
+    image: postgres:16
     shm_size: 512mb
     environment:
       POSTGRES_USER: ${POSTGRES_USERNAME}
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
       POSTGRES_DB: sodar
+    command: ["postgres", "-c", "log_min_messages=error"]
     networks:
       - sodar
     restart: unless-stopped

env.example

@@ -17,9 +17,10 @@ NETWORK_BRIDGE_NAME=br-sodar
 
 # Image versions
 # NOTE: For the latest SODAR development build, use "dev-0"
-# NOTE: If using the SOPDAR dev build, use the latest dev branch commit of this repository!
 SODAR_SERVER_VERSION=0.15.1-0
-IRODS_VERSION=4.2.11-1
+# NOTE: See the irods-docker repository for valid versions of our iRODS image.
+# https://github.com/bihealth/irods-docker/pkgs/container/irods-docker
+IRODS_VERSION=4.3.3-wip
 SSSD_VERSION=1.16.5-10
 
 # Logging
@@ -127,7 +128,7 @@ IRODS_PASS=rods
 # Path to iRODS server certificate for iRODS client config (optional)
 IRODS_CERT_PATH=/etc/traefik/tls/server.crt
 # iRODS authentication scheme
-IRODS_AUTHENTICATION_SCHEME=PAM
+IRODS_AUTHENTICATION_SCHEME=pam_password
 # iRODS client SSL verification (set to none if self-signed cert)
 IRODS_SSL_VERIFY_SERVER=none
 # Secret keys used by iRODS, CHANGE FOR PRODUCTION
@@ -148,7 +149,7 @@ IRODS_ROOT_PATH=
 # Env overrides for backend iRODS connections (optional)
 IRODS_ENV_BACKEND=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=native
 # Env overrides for iRODS client config in SODAR (optional)
-IRODS_ENV_CLIENT=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=PAM
+IRODS_ENV_CLIENT=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=pam_password
 
 # Set SSSD auth True if you are using SSSD and PAM
 IRODS_SSSD_AUTH=0

env.example.dev

@@ -6,7 +6,7 @@
 NETWORK_BRIDGE_NAME=br-sodar-dev
 
 # Image versions
-IRODS_VERSION=4.2.11-1
+IRODS_VERSION=4.3.3-wip
 SSSD_VERSION=1.16.5-10
 
 #
@@ -22,7 +22,7 @@ IRODS_PASS=rods
 # Path to iRODS server certificate for iRODS client config (optional)
 IRODS_CERT_PATH=/etc/traefik/tls/server.crt
 # iRODS authentication scheme
-IRODS_AUTHENTICATION_SCHEME=PAM
+IRODS_AUTHENTICATION_SCHEME=pam_password
 # iRODS client SSL verification (set to none if self-signed cert)
 IRODS_SSL_VERIFY_SERVER=none
 # Secret keys used by iRODS, CHANGE FOR PRODUCTION
@@ -43,7 +43,7 @@ IRODS_ROOT_PATH=
 # Env overrides for backend iRODS connections (optional)
 IRODS_ENV_BACKEND=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=native
 # Env overrides for iRODS client config in SODAR (optional)
-IRODS_ENV_CLIENT=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=PAM
+IRODS_ENV_CLIENT=irods_client_server_negotiation=off,irods_client_server_policy=CS_NEG_REFUSE,irods_ssl_verify_server=none,irods_authentication_scheme=pam_password
 
 # Set SSSD auth True if you are using SSSD and PAM
 IRODS_SSSD_AUTH=0