Add iRODS 4.3.3 and remove iRODS 4.3.0

4.3.3 is the latest release, while 4.3.0 is has broken C API headers, so is not usable by us.
wtsi-npg · Sep 3, 2024 · 6ab21bf · 6ab21bf
1 parent 90cf16d
commit 6ab21bf
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diff --git a/docker/Makefile b/docker/Makefile
@@ -19,24 +19,28 @@ image_names := ub-16.04-base ub-18.04-base ub-22.04-base
 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-4.3.2
+image_names += ub-22.04-irods-4.3.3
 # 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-22.04-irods-clients-dev-4.3.1
 image_names += ub-22.04-irods-clients-dev-4.3.2
+image_names += ub-22.04-irods-clients-dev-4.3.3
 # 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-4.3.2
+image_names += ub-22.04-irods-clients-4.3.3
 # image_names += ub-22.04-irods-clients-4.3-nightly
 
 git_url=$(shell git remote get-url origin)
@@ -129,20 +133,6 @@ ub-18.04-irods-4.2.12.$(TAG): irods/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
 	--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.2.12:$(TAG) --file $< ./irods
 	touch $@
 
-ub-18.04-irods-4.3.0.$(TAG): irods/ubuntu/18.04/Dockerfile ub-18.04-base.$(TAG)
-	docker buildx build $(DOCKER_ARGS) \
-	--load \
-	--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-18.04-base \
-	--build-arg IRODS_VERSION=4.3.0 \
-	--label org.opencontainers.image.title="iRODS 4.3.0 server, Ubuntu 18.04" \
-	--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-18.04-irods-4.3.0:latest \
-	--tag $(DOCKER_PREFIX)/ub-18.04-irods-4.3.0:$(TAG) --file $< ./irods
-	touch $@
-
 ub-22.04-irods-4.3.1.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
@@ -171,6 +161,20 @@ ub-22.04-irods-4.3.2.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
 	--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.2:$(TAG) --file $< ./irods
 	touch $@
 
+ub-22.04-irods-4.3.3.$(TAG): irods/ubuntu/22.04/Dockerfile ub-22.04-base.$(TAG)
+	docker buildx build $(DOCKER_ARGS) \
+	--load \
+	--build-arg BASE_IMAGE=$(DOCKER_PREFIX)/ub-22.04-base \
+	--build-arg IRODS_VERSION=4.3.2 \
+	--label org.opencontainers.image.title="iRODS 4.3.3 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-4.3.3:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-4.3.3:$(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 $(DOCKER_ARGS) \
 	--load \
@@ -193,7 +197,7 @@ ub-16.04-irods-clients-4.2.7.$(TAG): irods_clients/ubuntu/16.04/Dockerfile ub-16
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.2.7 \
-	--build-arg BATON_VERSION=4.2.1 \
+	--build-arg BATON_VERSION=4.2.2 \
 	--build-arg HTSLIB_VERSION=1.20 \
 	--build-arg SAMTOOLS_VERSION=1.20 \
 	--build-arg BCFTOOLS_VERSION=1.20 \
@@ -214,7 +218,7 @@ ub-18.04-irods-clients-4.2.11.$(TAG): irods_clients/ubuntu/18.04/Dockerfile ub-1
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.2.11 \
-	--build-arg BATON_VERSION=4.2.1 \
+	--build-arg BATON_VERSION=4.2.2 \
 	--build-arg HTSLIB_VERSION=1.20 \
 	--build-arg SAMTOOLS_VERSION=1.20 \
 	--build-arg BCFTOOLS_VERSION=1.20 \
@@ -258,7 +262,7 @@ ub-22.04-irods-clients-4.3.1.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
 	--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 BATON_VERSION=4.2.2 \
 	--build-arg HTSLIB_VERSION=1.20 \
 	--build-arg SAMTOOLS_VERSION=1.20 \
 	--build-arg BCFTOOLS_VERSION=1.20 \
@@ -280,7 +284,7 @@ ub-22.04-irods-clients-4.3.2.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.3.2 \
-	--build-arg BATON_VERSION=4.2.1 \
+	--build-arg BATON_VERSION=4.2.2 \
 	--build-arg HTSLIB_VERSION=1.20 \
 	--build-arg SAMTOOLS_VERSION=1.20 \
 	--build-arg BCFTOOLS_VERSION=1.20 \
@@ -293,6 +297,28 @@ ub-22.04-irods-clients-4.3.2.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
 	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.2:$(TAG) --file $< ./irods_clients
 	touch $@
 
+ub-22.04-irods-clients-4.3.3.$(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=$(TAG) \
+	--build-arg IRODS_VERSION=4.3.3 \
+	--build-arg BATON_VERSION=4.2.2 \
+	--build-arg HTSLIB_VERSION=1.20 \
+	--build-arg SAMTOOLS_VERSION=1.20 \
+	--build-arg BCFTOOLS_VERSION=1.20 \
+	--label org.opencontainers.image.title="iRODS 4.3.3 clients, Ubuntu 22.04" \
+	--label org.opencontainers.image.source=$(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-4.3.3:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-4.3.3:$(TAG) --file $< ./irods_clients
+	touch $@
+
 ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile.nightly
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
@@ -302,7 +328,7 @@ ub-22.04-irods-clients-4.3-nightly.$(TAG): irods_clients/ubuntu/22.04/Dockerfile
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
 	--build-arg IRODS_VERSION=4.3-nightly \
-	--build-arg BATON_VERSION=4.2.1 \
+	--build-arg BATON_VERSION=4.2.2 \
 	--build-arg HTSLIB_VERSION=1.20 \
 	--build-arg SAMTOOLS_VERSION=1.20 \
 	--build-arg BCFTOOLS_VERSION=1.20 \
@@ -366,57 +392,58 @@ ub-18.04-irods-clients-dev-4.2.12.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerf
 	--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.$(TAG): irods_clients_dev/ubuntu/18.04/Dockerfile
+ub-22.04-irods-clients-dev-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
 	docker buildx build $(DOCKER_ARGS) \
 	--load \
 	--build-context singularity=../singularity \
-	--build-arg BASE_IMAGE=ubuntu:18.04 \
+	--build-arg DOCKER_PREFIX=$(DOCKER_PREFIX) \
+	--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) \
-	--build-arg IRODS_VERSION=4.3.0 \
-	--label org.opencontainers.image.title="iRODS 4.3.0 client development, Ubuntu 18.04" \
+	--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-18.04-irods-clients-dev-4.3.0:latest \
-	--tag $(DOCKER_PREFIX)/ub-18.04-irods-clients-dev-4.3.0:$(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-4.3.1.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
+ub-22.04-irods-clients-dev-4.3.2.$(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:22.04 \
-	--build-arg IRODS_VERSION=4.3.1 \
+	--build-arg IRODS_VERSION=4.3.2 \
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
-	--label org.opencontainers.image.title="iRODS 4.3.1 client development, Ubuntu 22.04" \
+	--label org.opencontainers.image.title="iRODS 4.3.2 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-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
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.2:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.2:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
-ub-22.04-irods-clients-dev-4.3.2.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile
+ub-22.04-irods-clients-dev-4.3.3.$(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:22.04 \
-	--build-arg IRODS_VERSION=4.3.2 \
+	--build-arg IRODS_VERSION=4.3.3 \
 	--build-arg DOCKER_IMAGE=$(subst .$(TAG),,$@) \
 	--build-arg DOCKER_TAG=$(TAG) \
-	--label org.opencontainers.image.title="iRODS 4.3.2 client development, Ubuntu 22.04" \
+	--label org.opencontainers.image.title="iRODS 4.3.3 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-22.04-irods-clients-dev-4.3.2:latest \
-	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.2:$(TAG) --file $< ./irods_clients_dev
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.3:latest \
+	--tag $(DOCKER_PREFIX)/ub-22.04-irods-clients-dev-4.3.3:$(TAG) --file $< ./irods_clients_dev
 	touch $@
 
 ub-22.04-irods-clients-dev-4.3-nightly.$(TAG): irods_clients_dev/ubuntu/22.04/Dockerfile.nightly

diff --git a/docker/irods/scripts/configure_irods.sh b/docker/irods/scripts/configure_irods.sh
@@ -30,6 +30,12 @@ case "$IRODS_VERSION" in
         python3 /var/lib/irods/scripts/setup_irods.py < /opt/docker/irods/config/4.3.x.setup_irods.py.in
         ;;
     4.3.2)
+        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
+        ;;
+    4.3.3)
+        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
@@ -4,14 +4,15 @@ FROM $BASE_IMAGE
 # This default is the latest usable version
 ARG IRODS_VERSION="4.2.7"
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 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 && \
+RUN apt-get update && \
     apt-get install -q -y --no-install-recommends \
     apt-transport-https \
     ca-certificates \
@@ -29,7 +30,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio
 
 ENV LANG=en_GB.UTF-8 \
     LANGUAGE=en_GB \
-    LC_ALL=en_GB.UTF-8
+    LC_ALL=en_GB.UTF-8 \
+    TZ=/Etc/UTC
 
 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" | \

diff --git a/docker/irods/ubuntu/18.04/Dockerfile b/docker/irods/ubuntu/18.04/Dockerfile
@@ -6,14 +6,15 @@ ARG IRODS_VERSION="4.3.1"
 # This is the Debian package revision number
 ARG IRODS_REVISION="1"
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 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 && \
+RUN apt-get update && \
     apt-get install -q -y --no-install-recommends \
     apt-utils \
     ca-certificates \
@@ -33,7 +34,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio
 
 ENV LANG=en_GB.UTF-8 \
     LANGUAGE=en_GB \
-    LC_ALL=en_GB.UTF-8
+    LC_ALL=en_GB.UTF-8 \
+    TZ=/Etc/UTC
 
 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" | \

diff --git a/docker/irods/ubuntu/22.04/Dockerfile b/docker/irods/ubuntu/22.04/Dockerfile
@@ -6,14 +6,15 @@ ARG IRODS_VERSION="4.3.1"
 # This is the Debian package revision number
 ARG IRODS_REVISION="0"
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 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 && \
+RUN apt-get update && \
     apt-get install -q -y --no-install-recommends \
     apt-utils \
     ca-certificates \
@@ -33,7 +34,8 @@ RUN echo "debconf debconf/frontend select Noninteractive" | debconf-set-selectio
 
 ENV LANG=en_GB.UTF-8 \
     LANGUAGE=en_GB \
-    LC_ALL=en_GB.UTF-8
+    LC_ALL=en_GB.UTF-8 \
+    TZ=/Etc/UTC
 
 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" | \

diff --git a/docker/irods/ubuntu/22.04/Dockerfile.nightly b/docker/irods/ubuntu/22.04/Dockerfile.nightly
@@ -3,14 +3,15 @@ FROM $BASE_IMAGE
 
 ARG IRODS_VERSION="nightly"
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 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 && \
+RUN apt-get update && \
     apt-get install -q -y --no-install-recommends \
     apt-utils \
     ca-certificates \