Merge pull request #83 from kjsanger/feature/irods-4.3.1

Add iRODS 4.3.1 official release
wtsi-npg · Nov 1, 2023 · c4177bc · c4177bc
2 parents 7a6fa4f + c6ef1bf
commit c4177bc
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diff --git a/docker/Makefile b/docker/Makefile
@@ -20,18 +20,20 @@ image_names += ub-16.04-irods-4.2.7
 image_names += ub-18.04-irods-4.2.11
 image_names += ub-18.04-irods-4.2.12
 image_names += ub-18.04-irods-4.3.0
+image_names += ub-22.04-irods-4.3.1
 image_names += ub-22.04-irods-4.3-nightly
 
 image_names += ub-16.04-irods-clients-dev-4.2.7
 image_names += ub-18.04-irods-clients-dev-4.2.11
 image_names += ub-18.04-irods-clients-dev-4.2.12
 image_names += ub-18.04-irods-clients-dev-4.3.0
-image_names += ub-20.04-irods-clients-dev-4.3.0
+image_names += ub-22.04-irods-clients-dev-4.3.1
 image_names += ub-22.04-irods-clients-dev-4.3-nightly
 
 image_names += ub-16.04-irods-clients-4.2.7
 image_names += ub-18.04-irods-clients-4.2.11
 image_names += ub-18.04-irods-clients-4.2.12
+image_names += ub-22.04-irods-clients-4.3.1
 image_names += ub-22.04-irods-clients-4.3-nightly
 
 git_url=$(shell git remote get-url origin)
@@ -138,7 +140,21 @@ ub-18.04-irods-4.3.0.$(TAG): irods/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.3.0:$(TAG) --file $< ./irods
 	touch $@
 
-ub-22.04-irods-4.3-nightly.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
+ub-22.04-irods-4.3.1.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
+	docker buildx build $(DOCKER_ARGS) \
+	--load \
+	--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
+	--build-arg IRODS_VERSION=4.3.1 \
+	--label org.opencontainers.image.title="iRODS 4.3.1 server, Ubuntu 22.04" \
+	--label org.opencontainers.image.source=$(git_url) \
+	--label org.opencontainers.image.revision=$(git_commit) \
+	--label org.opencontainers.image.version=$(TAG) \
+	--label org.opencontainers.image.created=$(NOW) \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.1:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.1:$(TAG) --file $< ./irods
+	touch $@
+
+ub-22.04-irods-4.3-nightly.$(TAG): irods/ubuntu/22.04/Dockerfile.nightly ub-22.04-base.$(TAG)
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
@@ -173,7 +189,7 @@ ub-16.04-irods-clients-4.2.7.$(TAG): irods_clients/ubuntu/16.04/Dockerfile ub-16
 	--tag $(DOCKER_PREFIX)/ub-16.04-irods-clients-4.2.7:$(TAG) --file $< ./irods_clients
 	touch $@
 
-ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-base.$(TAG)
+ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
@@ -194,7 +210,7 @@ ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-b
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-4.2.11:$(TAG) --file $< ./irods_clients
 	touch $@
 
-ub-18.04-irods-clients-4.2.12.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-base.$(TAG)
+ub-18.04-irods-clients-4.2.12.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
@@ -216,7 +232,29 @@ ub-18.04-irods-clients-4.2.12.$(TAG): irods_clients/ubuntu/Dockerfile ub-18.04-b
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-4.2.12:$(TAG) --file $< ./irods_clients
 	touch $@
 
-ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
+ub-22.04-irods-clients-4.3.1.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
+	docker buildx build $(DOCKER_ARGS) \
+	--load \
+	--build-context singularity=../singularity \
+	--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
+	--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
+	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
+	--build-arg DOCKER_TAG=$(TAG) \
+	--build-arg IRODS_VERSION=4.3.1 \
+	--build-arg BATON_VERSION=4.2.1 \
+	--build-arg HTSLIB_VERSION=1.18 \
+	--build-arg SAMTOOLS_VERSION=1.18 \
+	--build-arg BCFTOOLS_VERSION=1.18 \
+	--label org.opencontainers.image.title="iRODS 4.3.1 clients, Ubuntu 22.04" \
+	--label org.opencontainers.image.source=$(git_url) \
+	--label org.opencontainers.image.revision=$(git_commit) \
+	--label org.opencontainers.image.version=$(TAG) \
+	--label org.opencontainers.image.created=$(NOW) \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.1:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.1:$(TAG) --file $< ./irods_clients
+	touch $@
+
+ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile.nightly
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
@@ -255,7 +293,7 @@ ub-16.04-irods-clients-dev-4.2.7.$(TAG): irods_clients_dev/ubuntu/16.04/Dockerfi
 	--tag $(DOCKER_PREFIX)/ub-16.04-irods-clients-dev-4.2.7:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-18.04-irods-clients-dev-4.2.11.$(TAG): irods_clients_dev/ubuntu/Dockerfile
+ub-18.04-irods-clients-dev-4.2.11.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerfile
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
@@ -272,11 +310,11 @@ ub-18.04-irods-clients-dev-4.2.11.$(TAG): irods_clients_dev/ubuntu/Dockerfile
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.2.11:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-18.04-irods-clients-dev-4.2.12.$(TAG): irods_clients_dev/ubuntu/Dockerfile
+ub-18.04-irods-clients-dev-4.2.12.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerfile
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
-	--build-arg BASE_IMAGE=ubuntu:bionic \
+	--build-arg BASE_IMAGE=ubuntu:18.04 \
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.2.12 \
@@ -289,11 +327,11 @@ ub-18.04-irods-clients-dev-4.2.12.$(TAG): irods_clients_dev/ubuntu/Dockerfile
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.2.12:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-18.04-irods-clients-dev-4.3.0.$(TAG): irods_clients_dev/ubuntu/Dockerfile
+ub-18.04-irods-clients-dev-4.3.0.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerfile
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
-	--build-arg BASE_IMAGE=ubuntu:bionic \
+	--build-arg BASE_IMAGE=ubuntu:18.04 \
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.3.0 \
@@ -306,25 +344,25 @@ ub-18.04-irods-clients-dev-4.3.0.$(TAG): irods_clients_dev/ubuntu/Dockerfile
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.3.0:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-20.04-irods-clients-dev-4.3.0.$(TAG): irods_clients_dev/ubuntu/Dockerfile
+ub-22.04-irods-clients-dev-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
 	--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
-	--build-arg BASE_IMAGE=ubuntu:20.04 \
-	--build-arg IRODS_VERSION=4.3.0 \
+	--build-arg BASE_IMAGE=ubuntu:22.04 \
+	--build-arg IRODS_VERSION=4.3.1 \
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
-	--label org.opencontainers.image.title="iRODS 4.3.0 client development, Ubuntu 20.04" \
+	--label org.opencontainers.image.title="iRODS 4.3.1 client development, Ubuntu 22.04" \
 	--label org.opencontainers.image.source=$(git_url) \
 	--label org.opencontainers.image.revision=$(git_commit) \
 	--label org.opencontainers.image.version=$(TAG) \
 	--label org.opencontainers.image.created=$(NOW) \
-	--tag $(DOCKER_PREFIX)/ub-20.04-irods-clients-dev-4.3.0:latest \
-	--tag $(DOCKER_PREFIX)/ub-20.04-irods-clients-dev-4.3.0:$(TAG) --file $< ./irods_clients_dev
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.1:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-22.04-irods-clients-dev-4.3-nightly.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
+ub-22.04-irods-clients-dev-4.3-nightly.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile.nightly
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \

diff --git a/docker/irods/scripts/configure_irods.sh b/docker/irods/scripts/configure_irods.sh
@@ -19,9 +19,14 @@ case "$IRODS_VERSION" in
         patch /var/lib/irods/scripts/irods/lib.py /opt/docker/irods/patches/patch_lib.diff
         python /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/setup_irods.py.in
         ;;
-    4.3.*)
+    4.3.0)
         patch /var/lib/irods/scripts/irods/controller.py /opt/docker/irods/patches/patch_controller.diff
-        sudo python3 /var/lib/irods/scripts/setup_rsyslog_and_logrotate.py # automatic setup for these has been removed
+        sudo python3 /var/lib/irods/scripts/setup_rsyslog_and_logrotate.py # Automatic setup for these has been removed.
+        python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
+        ;;
+    4.3.1)
+        patch /var/lib/irods/scripts/irods/controller.py /opt/docker/irods/patches/patch_controller.diff
+        # Logging has been changed to use rsyslog. A potential enhancement is to configure that here.
         python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
         ;;
     *)

diff --git a/docker/irods/ubuntu/16.04/Dockerfile b/docker/irods/ubuntu/16.04/Dockerfile
@@ -1,6 +1,7 @@
 ARG BASE_IMAGE=16.04-base
 FROM $BASE_IMAGE
 
+# This default is the latest usable version
 ARG IRODS_VERSION="4.2.7"
 
 WORKDIR /opt/docker/irods

diff --git a/docker/irods/ubuntu/18.04/Dockerfile b/docker/irods/ubuntu/18.04/Dockerfile
@@ -1,7 +1,10 @@
 ARG BASE_IMAGE=ub-18.04-base
 FROM $BASE_IMAGE
 
-ARG IRODS_VERSION="4.3.0"
+# The default is the latest usable version
+ARG IRODS_VERSION="4.3.1"
+# This is the Debian package revision number
+ARG IRODS_REVISION="1"
 
 WORKDIR /opt/docker/irods
 
@@ -37,11 +40,11 @@ RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - &
     tee /etc/apt/sources.list.d/renci-irods.list && \
     apt-get update && \
     apt-get install -q -y --no-install-recommends \
-    irods-server="${IRODS_VERSION}-1~$(lsb_release -sc)" \
-    irods-runtime="${IRODS_VERSION}-1~$(lsb_release -sc)" \
-    irods-database-plugin-postgres="${IRODS_VERSION}-1~$(lsb_release -sc)" \
-    irods-icommands="${IRODS_VERSION}-1~$(lsb_release -sc)" \
-    irods-dev="${IRODS_VERSION}-1~$(lsb_release -sc)" && \
+    irods-server="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-runtime="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-database-plugin-postgres="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-dev="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
     apt-get install -q -y -f && \
     unattended-upgrade -v && \
     apt-get remove -q -y unattended-upgrades && \

diff --git a/docker/irods/ubuntu/22.04/Dockerfile b/docker/irods/ubuntu/22.04/Dockerfile
@@ -1,7 +1,10 @@
 ARG BASE_IMAGE=ub-22.04-base
 FROM $BASE_IMAGE
 
-ARG IRODS_VERSION="nightly"
+# The default is the latest usable version
+ARG IRODS_VERSION="4.3.1"
+# This is the Debian package revision number
+ARG IRODS_REVISION="0"
 
 WORKDIR /opt/docker/irods
 
@@ -32,22 +35,22 @@ ENV LANG=en_GB.UTF-8 \
     LANGUAGE=en_GB \
     LC_ALL=en_GB.UTF-8
 
-# Required to get the externals packages
 RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
     echo "deb [arch=amd64] https://packages.irods.org/apt $(lsb_release -sc) main" | \
     tee /etc/apt/sources.list.d/renci-irods.list && \
-    apt-get update
-
-ENV NIGHTLY_URL_BASE=https://github.com/wtsi-npg/irods_development_environment/releases/download/nightly/
-
-RUN curl -sSL \
-    -O ${NIGHTLY_URL_BASE}irods-database-plugin-postgres_4.3.1-0.jammy_amd64.deb \
-    -O ${NIGHTLY_URL_BASE}irods-dev_4.3.1-0.jammy_amd64.deb \
-    -O ${NIGHTLY_URL_BASE}irods-runtime_4.3.1-0.jammy_amd64.deb \
-    -O ${NIGHTLY_URL_BASE}irods-server_4.3.1-0.jammy_amd64.deb \
-    -O ${NIGHTLY_URL_BASE}irods-icommands_4.3.1-0.jammy_amd64.deb
-
-RUN ls -l && apt-get install -y ./*.deb
+    apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    irods-server="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-runtime="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-database-plugin-postgres="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-icommands="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" \
+    irods-dev="${IRODS_VERSION}-${IRODS_REVISION}~$(lsb_release -sc)" && \
+    apt-get install -q -y -f && \
+    unattended-upgrade -v && \
+    apt-get remove -q -y unattended-upgrades && \
+    apt-get autoremove -q -y && \
+    apt-get clean -q -y && \
+    rm -rf /var/lib/apt/lists/*
 
 RUN /opt/docker/irods/scripts/create_database.sh && \
     /opt/docker/irods/scripts/configure_irods.sh

diff --git a/docker/irods/ubuntu/22.04/Dockerfile.nightly b/docker/irods/ubuntu/22.04/Dockerfile.nightly
@@ -0,0 +1,60 @@
+ARG BASE_IMAGE=ub-22.04-base
+FROM $BASE_IMAGE
+
+ARG IRODS_VERSION="nightly"
+
+WORKDIR /opt/docker/irods
+
+COPY ./scripts/*.sh ./scripts/
+COPY ./config/* ./config/
+COPY ./patches/* ./patches/
+
+RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selections && \
+    apt-get update && \
+    apt-get install -q -y --no-install-recommends \
+    apt-utils \
+    ca-certificates \
+    curl \
+    gpg \
+    gpg-agent \
+    lsb-release \
+    jq \
+    netcat \
+    patch \
+    postgresql \
+    rsyslog \
+    unattended-upgrades \
+    locales && \
+    locale-gen en_GB en_GB.UTF-8 && \
+    localedef -i en_GB -c -f UTF-8 -A /usr/share/locale/locale.alias en_GB.UTF-8
+
+ENV LANG=en_GB.UTF-8 \
+    LANGUAGE=en_GB \
+    LC_ALL=en_GB.UTF-8
+
+# Required to get the externals packages
+RUN curl -sSL https://packages.irods.org/irods-signing-key.asc | apt-key add - && \
+    echo "deb [arch=amd64] https://packages.irods.org/apt $(lsb_release -sc) main" | \
+    tee /etc/apt/sources.list.d/renci-irods.list && \
+    apt-get update
+
+ENV NIGHTLY_URL_BASE=https://github.com/wtsi-npg/irods_development_environment/releases/download/nightly/
+
+RUN curl -sSL \
+    -O ${NIGHTLY_URL_BASE}irods-database-plugin-postgres_4.3.1-0.jammy_amd64.deb \
+    -O ${NIGHTLY_URL_BASE}irods-dev_4.3.1-0.jammy_amd64.deb \
+    -O ${NIGHTLY_URL_BASE}irods-runtime_4.3.1-0.jammy_amd64.deb \
+    -O ${NIGHTLY_URL_BASE}irods-server_4.3.1-0.jammy_amd64.deb \
+    -O ${NIGHTLY_URL_BASE}irods-icommands_4.3.1-0.jammy_amd64.deb
+
+RUN ls -l && apt-get update && apt-get install -y ./*.deb
+
+RUN /opt/docker/irods/scripts/create_database.sh && \
+    /opt/docker/irods/scripts/configure_irods.sh
+
+EXPOSE 1247
+
+HEALTHCHECK --interval=10s --timeout=30s --start-period=5s --retries=3 CMD [ "nc", "-v", "-z", "localhost", "1247" ]
+
+ENTRYPOINT []
+CMD ["/opt/docker/irods/scripts/start_irods.sh"]
diff --git a/docker/irods/ubuntu/22.04/README.md b/docker/irods/ubuntu/22.04/README.md
@@ -12,7 +12,7 @@ The iRODS server starts with a single user 'irods' configured.
 
 To run the container (with iCAT port binding to the host machine):
 
-`docker run -d --name irods -p 1247:1247 wtsi-npg/ub-18.04-irods-[VERSION]:latest`
+`docker run -d --name irods -p 1247:1247 wtsi-npg/ub-22.04-irods-[VERSION]:latest`
 
 where [VERSION] is the required release e.g. 4.3.0
 

diff --git a/docker/irods_clients/ubuntu/16.04/Dockerfile b/docker/irods_clients/ubuntu/16.04/Dockerfile
@@ -1,18 +1,27 @@
 # syntax=docker/dockerfile:1
 
-ARG BASE_IMAGE=ubuntu:16.04
-FROM $BASE_IMAGE as installer
+# Set defaults for all build stages
 
-# This default is the latest usable version
+# The latest usable version
 ARG IRODS_VERSION="4.2.7"
 
-# These defaults are the latest usable versions
+# The latest usable versions
 ARG BATON_VERSION="4.2.1"
 ARG HTSLIB_VERSION="1.18"
 ARG SAMTOOLS_VERSION="1.18"
 ARG BCFTOOLS_VERSION="1.18"
 ARG HTSLIB_PLUGINS_VERSION="201712"
 
+ARG BASE_IMAGE=ubuntu:16.04
+FROM $BASE_IMAGE as installer
+
+ARG IRODS_VERSION
+ARG BATON_VERSION
+ARG HTSLIB_VERSION
+ARG SAMTOOLS_VERSION
+ARG BCFTOOLS_VERSION
+ARG HTSLIB_PLUGINS_VERSION
+
 COPY . /opt/docker/irods_clients
 
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
@@ -105,7 +114,7 @@ FROM $BASE_IMAGE
 
 ARG DOCKER_IMAGE
 ARG DOCKER_TAG
-ARG IRODS_VERSION="4.2.7"
+ARG IRODS_VERSION
 
 RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections && \
     apt-get update && \