upgrade to ubuntu 20.04 and python3 (#18, #19, #21)

README.md

@@ -8,10 +8,19 @@ The image contains features specific to our [SODAR](https://github.com/bihealth/
 ## Building
 
 ```bash
-$ cd docker
-$ docker build .
+$ IRODS_PKG_VERSION=x.x.x-x ./build.sh
 ```
 
+## Build Versions and iRODS Compatibility
+
+Images are built and tagged for a specific iRODS release. The most recent build is tested to be compatible with iRODS version `4.3.1-0`.
+
+Releases are tagged by the iRODS apt package version, followed with our own revision number starting from `1`. This means that e.g. the initial release for iRODS `4.3.1-0` will be tagged as ``4.3.1-0-1`. Fixes or improvements to that release would then be published as `4.3.1-0-2`.
+
+Our goal is to keep up with the most recent major release of iRODS. Updates for older major versions will not be made.
+
+**Note:** Images built for iRODS v4.3.x are **not** compatible with iRODS v4.2 or below.
+
 ## Data Persistency
 
 Each container exposes volumes for data persistency. The list of volumes are provided in the table below:
@@ -40,7 +49,7 @@ iRODS can be run in either "provider" mode, which installs an iCAT catalogue ser
 
 | Variable name                    | Default Value                    | Role       |
 |----------------------------------|----------------------------------|------------|
-| IRODS_PKG_VERSION                | 4.2.8-1                          | both       |
+| IRODS_PKG_VERSION                | 4.3.1-0                          | both       |
 | IRODS_ROLE                       | provider                         | both       |
 | IRODS_HOST_NAME                  | localhost                        | both       |
 | IRODS_SERVICE_ACCOUNT_USER       | irods                            | both       |
@@ -78,7 +87,7 @@ iRODS can be run in either "provider" mode, which installs an iCAT catalogue ser
 
 ## SSSD Support
 
-In addition to the base image, we provide the images `${VERSION}-sssd` (e.g., `4.2.11-1-sssd`) which have SSSD installed.
+In addition to the base image, we provide the images `${VERSION}-sssd` (e.g., `4.3.1-0-sssd`) which have SSSD installed.
 You will have to share `/var/lib/sss` between the SSSD container and iRODS so both containers can communicate.
 
 In our installations, we run [bihealth/sssd-docker](https://github.com/bihealth/sssd-docker) in a second container.

docker/Dockerfile

@@ -1,15 +1,15 @@
 #
 # Stage: first / main
 #
-FROM ubuntu:18.04 as main
+FROM ubuntu:20.04 as main
 
 LABEL org.opencontainers.image.authors="Manuel Holtgrewe <[email protected]>, Mikko Nieminen <[email protected]>"
 LABEL org.opencontainers.image.source https://github.com/bihealth/irods-docker
 
 ARG DEBIAN_FRONTEND=noninteractive
 
 # Environment variables for container runtime
-ENV IRODS_PKG_VERSION=4.3.0-1 \
+ENV IRODS_PKG_VERSION=4.3.1-0 \
     IRODS_ROLE=provider \
     IRODS_HOST_NAME=localhost \
     IRODS_SERVICE_ACCOUNT_USER=irods \
@@ -52,21 +52,22 @@ RUN chmod +x /usr/local/bin/wait
 
 # Install general dependencies
 RUN apt-get update && apt-get install -y apt-utils
-RUN apt-get install -y python python-pip python-dev python3-distro sudo vim wget netcat lsb-release
+RUN apt-get install -y python3 python3-dev python3-distro python3-pip sudo vim wget netcat rsyslog
+# lsb-release g++ gnupg2
 
 # Install database dependencies
 RUN apt-get install -y unixodbc unixodbc-dev odbc-postgresql
 
 # Install iRODS Python dependencies
-RUN pip install pyodbc
+RUN pip3 install pyodbc
 
 # Install iRODS
 RUN wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add - \
-  && echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list \
+  && echo "deb [arch=amd64] https://packages.irods.org/apt/ focal main" | sudo tee /etc/apt/sources.list.d/renci-irods.list \
   && apt-get update
-RUN apt-get install -y irods-server=${IRODS_PKG_VERSION}~bionic \
-    irods-database-plugin-postgres=${IRODS_PKG_VERSION}~bionic \
-    irods-dev=${IRODS_PKG_VERSION}~bionic \
+RUN apt-get install -y irods-server=${IRODS_PKG_VERSION}~focal \
+    irods-database-plugin-postgres=${IRODS_PKG_VERSION}~focal \
+    irods-dev=${IRODS_PKG_VERSION}~focal \
     irods-rule-engine-plugin-python
 RUN useradd -d /var/lib/irods ${IRODS_SERVICE_ACCOUNT_USER}
 
@@ -75,11 +76,11 @@ COPY files/irods_python-re_installer.py /
 RUN chmod +x /irods_python-re_installer.py
 
 # Install j2cli for templating
-RUN apt-get install -y python-jinja2 python-yaml
-RUN pip install j2cli
+RUN apt-get install -y python3-jinja2 python3-yaml
+RUN pip3 install j2cli
 
 # Install Python PAM support
-RUN apt-get install libpam-python pamtester
+RUN apt-get install -y libpam-python pamtester
 
 # Copy scripts and templates
 COPY docker-entrypoint.sh files/irods_login.sh \

docker/docker-entrypoint.sh

@@ -61,7 +61,7 @@ if [[ "$1" == "irods-start" ]]; then
         # Enable the python rule engine
         if [ -f /irods_python-re_installer.py ]; then
             echo "Enable python rule engine"
-            ./irods_python-re_installer.py
+            python3 ./irods_python-re_installer.py
         fi
 
         touch /etc/irods/.provisioned