From c5b081fa719fd175fd165b6b2b2213c848062ed7 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 10:43:35 +0000 Subject: [PATCH 01/80] run web on rocky9 --- web/Dockerfile | 36 +++++++++++++----------------------- 1 file changed, 13 insertions(+), 23 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index b82df1de..98b5cdae 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.7.2 +FROM jburel/devslave-c7:0.8.0 MAINTAINER OME @@ -10,37 +10,29 @@ ENV ICEVERSION ${ICEVER:-noice} # Remove the existing omero user RUN userdel -r omero && \ - rm -f /etc/sudoers.d/omero && \ + sed '%omero/d' /etc/sudoers && \ echo 'root:omero' | chpasswd # Create the omero-web user RUN useradd omero-web && \ echo 'omero-web:omero-web' | chpasswd && \ - echo "omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers.d/omero-web + echo "%omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers -# skip some omero-install -RUN echo 'export container=docker' > /etc/profile.d/docker.sh - -ENV OMERO_INSTALL_ROOT=/tmp/omero-install - -ADD ./settings.env $OMERO_INSTALL/settings.env -RUN chmod +x $OMERO_INSTALL/settings.env - # manually install ICEPY dependences -RUN yum -y install gcc-c++ +RUN dnf -y install gcc-c++ # ant for iviewer, make for nodejs -RUN yum -y install ant make -RUN yum -y install openssl-devel bzip2-devel expat-devel +RUN dnf -y install ant make +RUN dnf -y install openssl-devel bzip2-devel expat-devel RUN curl -sL https://rpm.nodesource.com/setup_16.x | bash -RUN yum install -y nodejs +RUN dnf install -y nodejs # grunt for figure RUN npm install -g grunt -RUN yum install -y python-redis && yum clean all +RUN dnf install -y python-redis && dnf clean all -# manually install java11 -RUN yum -y install java-11-openjdk-devel +# manually install java11 devel +RUN dnf -y install java-11-openjdk-devel # Switch Java version ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk ENV PATH=$JAVA_HOME/bin:$PATH @@ -51,13 +43,11 @@ ADD ./run.sh /tmp/run.sh RUN chown omero-web:omero-web /tmp/run.sh RUN chmod a+x /tmp/run.sh -RUN yum -y install centos-release-scl -RUN yum install -y rh-python38-python +RUN dnf install -y python3 -ENV PATH=/opt/rh/rh-python38/root/usr/bin:$PATH -RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox build future wheel restructuredtext-lint -RUN /py3/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl +RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox future wheel restructuredtext-lint +RUN /py3/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl ENV VIRTUAL_ENV=/py3 ENV PATH="$VIRTUAL_ENV/bin:$PATH" From 29880140dadd83ca03a6b14103887d8f3437f324 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 08:18:42 +0100 Subject: [PATCH 02/80] install python redis from pypi --- web/Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index 98b5cdae..7d903fc9 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -10,7 +10,6 @@ ENV ICEVERSION ${ICEVER:-noice} # Remove the existing omero user RUN userdel -r omero && \ - sed '%omero/d' /etc/sudoers && \ echo 'root:omero' | chpasswd # Create the omero-web user @@ -29,7 +28,6 @@ RUN dnf install -y nodejs # grunt for figure RUN npm install -g grunt -RUN dnf install -y python-redis && dnf clean all # manually install java11 devel RUN dnf -y install java-11-openjdk-devel @@ -45,9 +43,10 @@ RUN chmod a+x /tmp/run.sh RUN dnf install -y python3 - +RUN dnf clean all RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox future wheel restructuredtext-lint RUN /py3/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl +RUN /py3/bin/pip install redis ENV VIRTUAL_ENV=/py3 ENV PATH="$VIRTUAL_ENV/bin:$PATH" From ae61218f1eef7a6902fd1fdc33e3cb447a237cb3 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 09:43:52 +0100 Subject: [PATCH 03/80] java11-devel now installed by default --- web/Dockerfile | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index 7d903fc9..4c724f38 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.0 +FROM jburel/devslave-c7:0.8.1 MAINTAINER OME @@ -29,12 +29,6 @@ RUN dnf install -y nodejs RUN npm install -g grunt -# manually install java11 devel -RUN dnf -y install java-11-openjdk-devel -# Switch Java version -ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk -ENV PATH=$JAVA_HOME/bin:$PATH - EXPOSE 4080 ADD ./run.sh /tmp/run.sh From 4462ab1a74c1d253b545cff183f3876c095dfb38 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 11:12:50 +0100 Subject: [PATCH 04/80] remove py3 env --- web/Dockerfile | 5 ----- 1 file changed, 5 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index 4c724f38..7bb0e92d 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -38,11 +38,6 @@ RUN chmod a+x /tmp/run.sh RUN dnf install -y python3 RUN dnf clean all -RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox future wheel restructuredtext-lint -RUN /py3/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl -RUN /py3/bin/pip install redis -ENV VIRTUAL_ENV=/py3 -ENV PATH="$VIRTUAL_ENV/bin:$PATH" # Change user id to fix permissions issues ARG USER_ID=1000 From b5cf8dd86c081cc04a8bcaad2fe85162fb022e76 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 13:14:50 +0100 Subject: [PATCH 05/80] clean up --- web/Dockerfile | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index 7bb0e92d..76364f1e 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -2,12 +2,6 @@ FROM jburel/devslave-c7:0.8.1 MAINTAINER OME -ARG ICEVER=noice - -# make ICEVERSION environment variable to use in OMERO-web job -ENV ICEVERSION ${ICEVER:-noice} - - # Remove the existing omero user RUN userdel -r omero && \ echo 'root:omero' | chpasswd @@ -18,11 +12,8 @@ RUN useradd omero-web && \ echo "%omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers -# manually install ICEPY dependences -RUN dnf -y install gcc-c++ # ant for iviewer, make for nodejs RUN dnf -y install ant make -RUN dnf -y install openssl-devel bzip2-devel expat-devel RUN curl -sL https://rpm.nodesource.com/setup_16.x | bash RUN dnf install -y nodejs # grunt for figure @@ -35,7 +26,7 @@ ADD ./run.sh /tmp/run.sh RUN chown omero-web:omero-web /tmp/run.sh RUN chmod a+x /tmp/run.sh -RUN dnf install -y python3 +RUN dnf install -y python3 openssl RUN dnf clean all From bcc5490cc829f786a854e12aaa375bd8be471543 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 10:45:18 +0000 Subject: [PATCH 06/80] switch to rocky9 --- server/Dockerfile | 75 ++++++++++++++++------------------------------- 1 file changed, 25 insertions(+), 50 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 1dd90005..72447491 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,62 +1,43 @@ -FROM openmicroscopy/devslave-c7:0.7.2 +FROM jburel/devslave-c7:0.8.1 MAINTAINER OME -ARG JAVAVER=openjdk11-devel -ARG ICEVER=ice36 -ARG BRANCH=scl_c7 -ARG NAME=ome - # Remove the existing omero user RUN userdel -r omero && \ - rm -f /etc/sudoers.d/omero && \ echo 'root:omero' | chpasswd -# skip some omero-install -RUN echo 'export container=docker' > /etc/profile.d/docker.sh - -ENV OMERO_INSTALL_ROOT=/tmp/omero-install +# Create the omero-server user +RUN useradd omero-server && \ + echo 'omero-server:omero-server' | chpasswd && \ + echo "%omero-server ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers -## update omero-install to the latest one -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT config --global user.email "you@example.com" -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT config --global user.name "Your Name" -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add $NAME https://github.com/$NAME/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch $NAME -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge $NAME/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env RUN chmod +x $OMERO_INSTALL/settings.env -# Customize: run particular scripts from omero-install -RUN rm -f $OMERO_INSTALL/setup_centos_selinux.sh -RUN touch $OMERO_INSTALL/setup_centos_selinux.sh -# db will be managed by the job -RUN rm -f $OMERO_INSTALL/setup_omero_db.sh -RUN touch $OMERO_INSTALL/setup_omero_db.sh -RUN rm -f $OMERO_INSTALL/step03_all_postgres.sh -RUN touch $OMERO_INSTALL/step03_all_postgres.sh -# omeroweb will be installed by the job -RUN rm -f $OMERO_INSTALL/step04_all_omero.sh -RUN touch $OMERO_INSTALL/step04_all_omero.sh -# no systemd -RUN rm -rf $OMERO_INSTALL/step06_centos7_daemon.sh -RUN touch $OMERO_INSTALL/step06_centos7_daemon.sh -# no Pillow -RUN rm -rf $OMERO_INSTALL/requirements.txt -RUN touch $OMERO_INSTALL/requirements.txt - WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh -# install postgres tools -RUN yum -y install postgresql13 \ - && yum clean all +RUN dnf install -y python3 -# Switch Java version -ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk -ENV PATH=$JAVA_HOME/bin:$PATH +# Ice dependencies +RUN dnf install -y 'dnf-command(config-manager)' && \ + dnf config-manager --set-enabled crb +RUN dnf install -y openssl libdb-cxx +RUN cd /tmp && \ + wget -q https://github.com/sbesson/zeroc-ice-rockylinux9-x86_64/releases/download/20230720/Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + tar xf Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + mv Ice-3.6.5 /opt/ice-3.6.5 && \ + echo /opt/ice-3.6.5/lib64 > /etc/ld.so.conf.d/ice-x86_64.conf && \ + ldconfig +ENV ICE_HOME=/opt/ice-3.6.5 + +ENV PATH=$ICE_HOME/bin:$PATH + +# install postgres tools +RUN dnf -y install postgresql \ + && dnf clean all EXPOSE 4064 @@ -66,18 +47,12 @@ ADD ./run.sh /tmp/run.sh RUN chown omero-server:omero-server /tmp/run.sh RUN chmod a+x /tmp/run.sh -ENV PATH=/opt/rh/rh-python38/root/usr/bin:$PATH -RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox build future wheel restructuredtext-lint -RUN /py3/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl -ENV VIRTUAL_ENV=/py3 -ENV PATH="$VIRTUAL_ENV/bin:$PATH" # Install mencoder # See https://github.com/ome/prod-playbooks/blob/7d8e59ced0b47a224d6be02907d913c392ef9379/ome-dundeeomero.yml#L48 -RUN yum install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm -RUN yum install -y mencoder +RUN dnf install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm +RUN dnf install -y mencoder -RUN yum install -y openssl RUN localedef -i en_US -f UTF-8 en_US.UTF-8 ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8' From 1eee6def9acfb867992a219b0654d64e70227f89 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 13:33:14 +0100 Subject: [PATCH 07/80] do not install mencoder --- server/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 72447491..a8175679 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -50,8 +50,8 @@ RUN chmod a+x /tmp/run.sh # Install mencoder # See https://github.com/ome/prod-playbooks/blob/7d8e59ced0b47a224d6be02907d913c392ef9379/ome-dundeeomero.yml#L48 -RUN dnf install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm -RUN dnf install -y mencoder +# RUN dnf install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm +# RUN dnf install -y mencoder RUN localedef -i en_US -f UTF-8 en_US.UTF-8 From 5e111785431a3e40c26f025f9ca9db1a180ad9f8 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 13:44:21 +0100 Subject: [PATCH 08/80] comment out line --- server/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/server/Dockerfile b/server/Dockerfile index a8175679..2af30330 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -54,7 +54,7 @@ RUN chmod a+x /tmp/run.sh # RUN dnf install -y mencoder -RUN localedef -i en_US -f UTF-8 en_US.UTF-8 +#RUN localedef -i en_US -f UTF-8 en_US.UTF-8 ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8' # Change user id to fix permissions issues From 037b59562cbed96bc1652614fc03170a7a80f9d1 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 14 Sep 2023 16:42:51 +0100 Subject: [PATCH 09/80] bump version --- server/Dockerfile | 5 +---- web/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 2af30330..99c1cf13 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.1 +FROM jburel/devslave-c7:0.8.3 MAINTAINER OME @@ -54,9 +54,6 @@ RUN chmod a+x /tmp/run.sh # RUN dnf install -y mencoder -#RUN localedef -i en_US -f UTF-8 en_US.UTF-8 -ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8' - # Change user id to fix permissions issues ARG USER_ID=1000 RUN usermod -u $USER_ID omero-server diff --git a/web/Dockerfile b/web/Dockerfile index 76364f1e..a5456443 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.1 +FROM jburel/devslave-c7:0.8.3 MAINTAINER OME From c1d3df05f7ce344177bba3073f80a9c8b45ba159 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 15:36:14 +0100 Subject: [PATCH 10/80] set location of settings.env --- server/Dockerfile | 4 ++-- web/Dockerfile | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 99c1cf13..1637f27d 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -13,8 +13,8 @@ RUN useradd omero-server && \ -ADD ./settings.env $OMERO_INSTALL/settings.env -RUN chmod +x $OMERO_INSTALL/settings.env +ADD ./settings.env /home/settings.env +RUN chmod +x /home/settings.env WORKDIR /tmp/omero-install/linux diff --git a/web/Dockerfile b/web/Dockerfile index a5456443..2cecda7b 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -11,6 +11,8 @@ RUN useradd omero-web && \ echo 'omero-web:omero-web' | chpasswd && \ echo "%omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers +ADD ./settings.env /home/settings.env +RUN chmod +x /home/settings.env # ant for iviewer, make for nodejs RUN dnf -y install ant make From 00cea1d2fc824b73b0949451ae5b41293ec4b2cb Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 10:48:20 +0000 Subject: [PATCH 11/80] update dockerfile to work with rocky9 --- slave/Dockerfile | 70 +++++++++++++++++------------------------------- 1 file changed, 25 insertions(+), 45 deletions(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 7160b2af..c2140841 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,50 +1,29 @@ -FROM openmicroscopy/devslave-c7:0.7.2 +FROM openmicroscopy/devslave-c7:0.8.3 MAINTAINER OME -ARG JAVAVER=openjdk11-devel -ARG ICEVER=ice36-devel -ARG BRANCH=scl_c7 ARG NAME=ome ARG GRADLEVER=6.9.3 -# skip some omero-install -RUN echo 'export container=docker' > /etc/profile.d/docker.sh - -ENV OMERO_INSTALL_ROOT=/tmp/omero-install -## update omero-install to the latest one -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT config --global user.email "you@example.com" -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT config --global user.name "Your Name" -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add $NAME https://github.com/$NAME/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch $NAME -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge $NAME/$BRANCH - - -ADD ./settings.env $OMERO_INSTALL/settings.env -RUN chmod +x $OMERO_INSTALL/settings.env - -# Customize: run particular scripts from omero-install -RUN rm -f $OMERO_INSTALL/setup_centos_selinux.sh -RUN touch $OMERO_INSTALL/setup_centos_selinux.sh -# db will be managed by the job -RUN rm -f $OMERO_INSTALL/setup_omero_db.sh -RUN touch $OMERO_INSTALL/setup_omero_db.sh -RUN rm -f $OMERO_INSTALL/step03_all_postgres.sh -RUN touch $OMERO_INSTALL/step03_all_postgres.sh -# omeroweb will be installed by the job -RUN rm -f $OMERO_INSTALL/step04_all_omero.sh -RUN touch $OMERO_INSTALL/step04_all_omero.sh -# no systemd -RUN rm -rf $OMERO_INSTALL/step06_centos7_daemon.sh -RUN touch $OMERO_INSTALL/step06_centos7_daemon.sh -# no Pillow -RUN rm -rf $OMERO_INSTALL/requirements.txt -RUN touch $OMERO_INSTALL/requirements.txt - -WORKDIR /tmp/omero-install/linux - -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh +ADD ./settings.env /home/settings.env +RUN chmod +x /home/settings.env + + +# Ice dependencies +RUN dnf install -y 'dnf-command(config-manager)' && \ + dnf config-manager --set-enabled crb +RUN dnf install -y openssl libdb-cxx +RUN cd /tmp && \ + wget -q https://github.com/sbesson/zeroc-ice-rockylinux9-x86_64/releases/download/20230720/Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + tar xf Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + mv Ice-3.6.5 /opt/ice-3.6.5 && \ + echo /opt/ice-3.6.5/lib64 > /etc/ld.so.conf.d/ice-x86_64.conf && \ + ldconfig + +ENV ICE_HOME=/opt/ice-3.6.5 + +ENV PATH=$ICE_HOME/bin:$PATH # Install FindBugs ENV FINDBUGS_VERSION 3.0.0 @@ -55,11 +34,11 @@ RUN curl -fSLO http://downloads.sourceforge.net/project/findbugs/findbugs/$FINDB rm findbugs-$FINDBUGS_VERSION.tar.gz # Install build tools from EPEL -RUN yum -y install maven ant && yum clean all +RUN dnf -y install maven ant && dnf clean all # install postgres tools -RUN yum -y install postgresql13-server postgresql13 \ - && yum clean all +RUN dnf -y install postgresql-server postgresql\ + && dnf clean all # gradle RUN cd /opt && \ @@ -68,8 +47,6 @@ RUN cd /opt && \ rm gradle-$GRADLEVER-bin.zip && \ ln -s /opt/gradle-$GRADLEVER/bin/gradle /usr/local/bin/gradle -ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk -ENV PATH=$JAVA_HOME/bin:$PATH EXPOSE 14064 EXPOSE 14063 @@ -78,6 +55,7 @@ ADD ./run.sh /tmp/run.sh RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh +<<<<<<< HEAD ENV PATH=/opt/rh/rh-python38/root/usr/bin:$PATH RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox build future wheel restructuredtext-lint RUN /py3/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl @@ -85,6 +63,8 @@ RUN ln -s /py3/bin/slice2py /usr/bin/slice2py ENV VIRTUAL_ENV=/py3 ENV PATH="$VIRTUAL_ENV/bin:$PATH" +======= +>>>>>>> 9535936 (update dockerfile to work with rocky9) # Change user id to fix permissions issues ARG USER_ID=1000 RUN usermod -u $USER_ID omero From 9cb77097afac6b23b93c1bdf25983e78873b8953 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 15:42:39 +0100 Subject: [PATCH 12/80] use own repo --- slave/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index c2140841..898e8060 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.3 MAINTAINER OME From 225b2222a722bd2e0d919c16b1285b33829414b5 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 15:45:30 +0100 Subject: [PATCH 13/80] switch to rocky9 --- docker/Dockerfile | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 1d846dcf..9e6072fb 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,13 +1,7 @@ -FROM openmicroscopy/devslave-c7:0.7.2 +FROM jburel/devslave-c7:0.8.3 MAINTAINER OME -# manually install java11 -RUN yum -y install java-11-openjdk-devel -# Switch Java version -ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk -ENV PATH=$JAVA_HOME/bin:$PATH - RUN yum -y install -y yum-utils \ device-mapper-persistent-data \ lvm2 From 567d0c791506ceebdbbb5707058fc9471074b3c8 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 16:06:16 +0100 Subject: [PATCH 14/80] use dnf --- docker/Dockerfile | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 9e6072fb..fdeba1a6 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -2,15 +2,17 @@ FROM jburel/devslave-c7:0.8.3 MAINTAINER OME -RUN yum -y install -y yum-utils \ +USER root + + +RUN dnf -y install -y yum-utils \ device-mapper-persistent-data \ lvm2 -RUN yum-config-manager \ - --add-repo \ - https://download.docker.com/linux/centos/docker-ce.repo -RUN yum -y install docker-ce +RUN dnf config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo + +RUN dnf -y install docker-ce # Change user id to fix permissions issues ARG USER_ID=1000 From 43cac60e0d0ef7e2f0594c41785b6919a945c3a6 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 21:27:36 +0100 Subject: [PATCH 15/80] remove installation --- git/Dockerfile | 5 ----- 1 file changed, 5 deletions(-) diff --git a/git/Dockerfile b/git/Dockerfile index 3ad977e1..a3cd7848 100644 --- a/git/Dockerfile +++ b/git/Dockerfile @@ -1,13 +1,8 @@ FROM mini/base MAINTAINER ome-devel@lists.openmicroscopy.org.uk -ENV TAG 5.1.4 RUN apk-install git && \ mkdir /src -RUN time git clone --bare --depth=1 -b v$TAG https://github.com/ome/scripts/ /src/scripts.git -RUN time git clone --bare --depth=1 -b v$TAG https://github.com/ome/openmicroscopy /src/omero.git -RUN time git clone --bare --depth=1 -b v$TAG https://github.com/ome/bioformats /src/bio-formats.git - WORKDIR /src From f16c97c10c27555e6dd667abc2246478beed05ae Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 18 Sep 2023 23:30:41 +0100 Subject: [PATCH 16/80] build as root --- docker-compose.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index 9f555734..ddb98920 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -33,6 +33,7 @@ services: build: context: ./slave dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -55,6 +56,7 @@ services: build: context: ./server dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -73,6 +75,7 @@ services: build: context: ./web dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -157,6 +160,7 @@ services: docker: build: docker + user: root networks: - omero-network volumes: From 69bba9706b20b4bdb46dbda0863d543d429e8599 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 19 Sep 2023 13:24:21 +0100 Subject: [PATCH 17/80] remove OMERO_INSTALL --- home/jobs/OMERO-server/config.xml | 8 ++++---- home/jobs/OMERO-test-integration/config.xml | 6 ++---- home/jobs/OMERO-training/config.xml | 4 ++-- home/jobs/OMERO-web/config.xml | 3 +-- 4 files changed, 9 insertions(+), 12 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 0d150248..da5fd803 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -42,8 +42,8 @@ false - OMERO_INSTALL=/tmp/omero-install/linux -source $OMERO_INSTALL/settings.env + +source /home/settings.env OMERO_DB_NAME=$DB_NAME OMERO_DIST=$WORKSPACE/OMERO.server export OMERODIR=$OMERO_DIST @@ -85,8 +85,8 @@ rm -rf $WORKSPACE/* # Should leave .venv3 false - OMERO_INSTALL=/tmp/omero-install/linux -source $OMERO_INSTALL/settings.env + +source /home/settings.env OMERO_DB_NAME=$DB_NAME OMERO_DATA_DIR=$DATA_DIR diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index 7f52db9a..882172aa 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -33,8 +33,7 @@ pip install omero-py omero-web # Latest in order to stop server. -OMERO_INSTALL=/tmp/omero-install/linux -source $OMERO_INSTALL/settings.env +source /home/settings.env OMERO_DB_NAME=$JOB_NAME SRC=$WORKSPACE/src OMERO_DIST=$SRC/dist @@ -72,8 +71,7 @@ rm -rf $WORKSPACE/* -OMERO_INSTALL=/tmp/omero-install/linux -source $OMERO_INSTALL/settings.env +source /home/settings.env OMERO_DB_NAME=$JOB_NAME OMERO_DATA_DIR=$WORKSPACE/data diff --git a/home/jobs/OMERO-training/config.xml b/home/jobs/OMERO-training/config.xml index 9ab7987d..3c63c3ff 100644 --- a/home/jobs/OMERO-training/config.xml +++ b/home/jobs/OMERO-training/config.xml @@ -48,8 +48,8 @@ rm -rf $WORKSPACE/* false - OMERO_INSTALL=/tmp/omero-install/linux -source $OMERO_INSTALL/settings.env + +source /home/settings.env # UNZIP openmicroscopy OMERO_EXAMPLE_DIST=$WORKSPACE/openmicroscopy diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index 8d9d3155..a76f21bd 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -75,7 +75,6 @@ rm -rf $WORKSPACE/* OMERO_DIST=$WORKSPACE/OMERO.web export OMERODIR=$OMERO_DIST -OMERO_INSTALL=/tmp/omero-install/linux ZIP=$(ls OMERO.server*.zip) if [ ! -z "$OMERO_PY_ZIP_URL" ] @@ -93,7 +92,7 @@ mv $WORKSPACE/$DIST $OMERO_DIST source $WORKSPACE/.venv3/bin/activate -source $OMERO_INSTALL/settings.env +source /home/settings.env # Install omero-py, omero-web etc from OMERO-python-superbuild-build job for x in *.tar.gz; do From b0c3c8c04f13126748a7f2874bbfcc3c998e4bc4 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 19 Sep 2023 13:32:44 +0100 Subject: [PATCH 18/80] install ice Python binding --- home/jobs/OMERO-build/config.xml | 2 +- home/jobs/OMERO-robot/config.xml | 2 +- home/jobs/OMERO-server/config.xml | 2 +- home/jobs/OMERO-test-integration/config.xml | 2 +- home/jobs/OMERO-training/config.xml | 2 +- home/jobs/OMERO-web/config.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index dc0d36c3..0d89304e 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -77,7 +77,7 @@ OMERO_VEN=$WORKSPACE/omero-virtualenv source $HOME/settings.env python3 -m venv $OMERO_VEN -$OMERO_VEN/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl +$OMERO_VEN/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl $OMERO_VEN/bin/pip install -U setuptools omero-py source docs/hudson/OMERO.sh diff --git a/home/jobs/OMERO-robot/config.xml b/home/jobs/OMERO-robot/config.xml index b43e3e73..b564e608 100644 --- a/home/jobs/OMERO-robot/config.xml +++ b/home/jobs/OMERO-robot/config.xml @@ -58,7 +58,7 @@ python -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl +pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future setuptools pip install omero-py omero-web # Latest in order to stop server. diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index da5fd803..9053044a 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -108,7 +108,7 @@ rm -f $ZIP mv $WORKSPACE/$DIST $OMERO_DIST source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl +pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future pip install markdown pip install reportlab # For figure diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index 882172aa..712bd9fd 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -18,7 +18,7 @@ python -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl +pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future setuptools pip install markdown # Avoid installing psutil for now diff --git a/home/jobs/OMERO-training/config.xml b/home/jobs/OMERO-training/config.xml index 3c63c3ff..560ed435 100644 --- a/home/jobs/OMERO-training/config.xml +++ b/home/jobs/OMERO-training/config.xml @@ -18,7 +18,7 @@ python -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl +pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future setuptools pip install markdown # Avoid installing psutil for now diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index a76f21bd..357b4c4f 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -29,7 +29,7 @@ python -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate -pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl +pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future pip install markdown pip install "urllib3<2" # to be removed if/when included in omero-py From 9fd13b265db1290e0578d39e3f43de2ee71f4370 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 20 Sep 2023 15:22:26 +0100 Subject: [PATCH 19/80] Remove root --- docker-compose.yml | 4 ---- nginx/Dockerfile | 16 ++++------------ 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index ddb98920..9f555734 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -33,7 +33,6 @@ services: build: context: ./slave dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -56,7 +55,6 @@ services: build: context: ./server dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -75,7 +73,6 @@ services: build: context: ./web dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -160,7 +157,6 @@ services: docker: build: docker - user: root networks: - omero-network volumes: diff --git a/nginx/Dockerfile b/nginx/Dockerfile index edcc82e0..0ea29840 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,18 +1,10 @@ -FROM openmicroscopy/devslave-c7:0.7.2 +FROM jburel/devslave-c7:0.8.3 MAINTAINER OME -# manually install java11 -RUN yum -y install java-11-openjdk-devel -# Switch Java version -ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk -ENV PATH=$JAVA_HOME/bin:$PATH - -RUN yum -y localinstall http://nginx.org/packages/rhel/7/noarch/RPMS/nginx-release-rhel-7-0.el7.ngx.noarch.rpm \ - && yum clean all -RUN yum -y install nginx --disablerepo=epel \ - && yum clean all -RUN mv /etc/nginx/conf.d/default.conf /etc/nginx/conf.d/default.conf.disabled + +RUN dnf -y install nginx\ + && dnf clean all VOLUME ["/etc/nginx/conf.d", "/var/log/nginx"] From b645f4b811b0d5b02e273a0cbf6d62a9779b4742 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 20 Sep 2023 15:23:19 +0100 Subject: [PATCH 20/80] change label --- docker-compose.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 9f555734..eeeb0a3e 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -41,7 +41,7 @@ services: environment: - SLAVE_NAME=testintegration - SLAVE_EXECUTORS=2 - - SLAVE_PARAMS=-labels centos7 -labels ice36 -labels java11 -disableClientsUniqueId + - SLAVE_PARAMS=-labels rocky9 -labels ice36 -labels java11 -disableClientsUniqueId - JENKINS_MASTER=${JENKINS_BASE}${JENKINS_PREFIX} - WEB_PREFIX - REPO_CONFIG @@ -62,7 +62,7 @@ services: environment: - SLAVE_NAME=omero - SLAVE_EXECUTORS=2 - - SLAVE_PARAMS=-labels centos7 -labels ice36 -labels java11 -disableClientsUniqueId + - SLAVE_PARAMS=-labels rocky9 -labels ice36 -labels java11 -disableClientsUniqueId - JENKINS_MASTER=${JENKINS_BASE}${JENKINS_PREFIX} - WEBHOST=http://nginx${WEB_PREFIX} ports: @@ -81,7 +81,7 @@ services: environment: - SLAVE_NAME=web - SLAVE_EXECUTORS=2 - - SLAVE_PARAMS= -labels centos7 -labels ice36 -labels java11 -disableClientsUniqueId + - SLAVE_PARAMS= -labels rocky9 -labels ice36 -labels java11 -disableClientsUniqueId - JENKINS_MASTER=${JENKINS_BASE}${JENKINS_PREFIX} - WEB_PREFIX @@ -98,7 +98,7 @@ services: - ./nginx/sslcert:/etc/nginx/ssl environment: - SLAVE_NAME=nginx - - SLAVE_PARAMS=-labels centos7 -labels java11 -disableClientsUniqueId + - SLAVE_PARAMS=-labels rocky9 -labels java11 -disableClientsUniqueId - JENKINS_MASTER=${JENKINS_BASE}${JENKINS_PREFIX} ports: - "${NGINX_PORT}80" From 3cb176dbc3e11000004d18b81becad24eba284a8 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 20 Sep 2023 15:35:12 +0100 Subject: [PATCH 21/80] run as root --- docker-compose.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index eeeb0a3e..9c539521 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -33,6 +33,7 @@ services: build: context: ./slave dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -55,6 +56,7 @@ services: build: context: ./server dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -73,6 +75,7 @@ services: build: context: ./web dockerfile: Dockerfile + user: root networks: - omero-network volumes: @@ -157,6 +160,7 @@ services: docker: build: docker + user: root networks: - omero-network volumes: From ffbdfa5fa63d280630af0e59de0d26738b216cf2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 21 Sep 2023 20:16:33 +0100 Subject: [PATCH 22/80] pin nexus to 3.59.0 --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 9c539521..2b173727 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -175,7 +175,7 @@ services: - REPO_CONFIG nexus: - image: sonatype/nexus3 + image: sonatype/nexus3:3.59.0 user: ${USER_ID} networks: - omero-network From 47a58f4fbd8cc776b02c821f3d5517bad72d87ac Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 22 Sep 2023 18:16:25 +0100 Subject: [PATCH 23/80] install setuptools --- slave/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/slave/Dockerfile b/slave/Dockerfile index 898e8060..f18d3542 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -10,6 +10,8 @@ ADD ./settings.env /home/settings.env RUN chmod +x /home/settings.env +# Python job +RUN dnf install -y python3-setuptools # Ice dependencies RUN dnf install -y 'dnf-command(config-manager)' && \ dnf config-manager --set-enabled crb From f1d322bb7c18a00a89dd6d6b3bc7b3c4116c4727 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 22 Sep 2023 20:32:53 +0100 Subject: [PATCH 24/80] update version --- README.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 148d95f1..d4ad7ff2 100644 --- a/README.md +++ b/README.md @@ -185,14 +185,13 @@ Alternatively create a new job in the Jenkins web-interface in the usual way. # Default packages used -| Name | Version | Optional | -| -----------|---------------| -----------------------------------| -| Java | openJDK 1.8 | openJDK 1.8 devel, oracleJDK 1.8 | -| Python | 2.7 | - | -| Ice | 3.6 | 3.5 | -| PostgreSQL | 9.4 | https://hub.docker.com/_/postgres/ | -| Nginx | 1.8 | - | -| Redis | latest | https://hub.docker.com/_/redis/ | +| Name | Version | +| -----------|-------------------| +| Java | openJDK 11-devel | +| Python | 3.9 | +| Ice | 3.6 | +| PostgreSQL | 13 | +| Nginx | 1.23 | # Troubleshooting From 76270180293d20f035919b303f4330f9c66b5445 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 22 Sep 2023 20:33:04 +0100 Subject: [PATCH 25/80] remove scl python from path --- server/settings.env | 1 - slave/settings.env | 3 +-- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/server/settings.env b/server/settings.env index 39484d40..5b39b7d9 100644 --- a/server/settings.env +++ b/server/settings.env @@ -5,4 +5,3 @@ OMERO_ROOT_PASS=omero OMERO_DATA_DIR=/OMERO export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR -export PATH=/opt/rh/rh-python38/root/usr/bin:$PATH diff --git a/slave/settings.env b/slave/settings.env index 39484d40..1c053ac7 100644 --- a/slave/settings.env +++ b/slave/settings.env @@ -4,5 +4,4 @@ OMERO_DB_PASS= OMERO_ROOT_PASS=omero OMERO_DATA_DIR=/OMERO -export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR -export PATH=/opt/rh/rh-python38/root/usr/bin:$PATH +export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR From e7db43012aedbe06f28c3da86e3e1ceb16fdd09a Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 22 Sep 2023 21:02:15 +0100 Subject: [PATCH 26/80] install make, required to build the docs --- slave/Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/slave/Dockerfile b/slave/Dockerfile index f18d3542..62714e12 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -10,6 +10,9 @@ ADD ./settings.env /home/settings.env RUN chmod +x /home/settings.env +# Required for the docs build +RUN dnf install -y make + # Python job RUN dnf install -y python3-setuptools # Ice dependencies From fb1a85ff43f043b562e03229f322073f89a99ddf Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 22 Sep 2023 21:03:46 +0100 Subject: [PATCH 27/80] use python3 --- home/jobs/OMERO-training/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-training/config.xml b/home/jobs/OMERO-training/config.xml index 560ed435..0b5315ba 100644 --- a/home/jobs/OMERO-training/config.xml +++ b/home/jobs/OMERO-training/config.xml @@ -15,7 +15,7 @@ rm -rf $WORKSPACE/.venv3 -python -m venv $WORKSPACE/.venv3 +python3 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl From ee14b0a4baaa17226a4c0b372028e04483693eef Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 23 Sep 2023 08:07:37 +0100 Subject: [PATCH 28/80] update job --- home/jobs/OMERO-server/config.xml | 2 ++ home/jobs/OMERO-test-integration/config.xml | 3 +-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 9053044a..88887f1c 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -56,6 +56,8 @@ if [ -e $OMERO_DIST ]; then deactivate fi +rm -rf $WORKSPACE/.venv3 +python3 -m venv $WORKSPACE/.venv3 if [ "$PURGE_DATA" = "true" ]; then dropdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME || echo "First run or already exists" diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index 712bd9fd..7ead3bd6 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -15,7 +15,7 @@ rm -rf $WORKSPACE/.venv3 -python -m venv $WORKSPACE/.venv3 +python3 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl @@ -27,7 +27,6 @@ pip install mox3 pytest pytest-django 'pytest-xdist<2' pip install tables pip install jinja2 pip install PyYAML -pip install "urllib3<2" # to be removed if/when included in omero-py pip install omero-py omero-web # Latest in order to stop server. From b41900eefccd14d9e2adee43ea1524fe52909d80 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 23 Sep 2023 18:59:39 +0100 Subject: [PATCH 29/80] remove cap --- home/jobs/OMERO-server/config.xml | 1 - home/jobs/OMERO-web/config.xml | 1 - 2 files changed, 2 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 88887f1c..ec4134da 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -117,7 +117,6 @@ pip install reportlab # For figure pip install omego pip install tables pip install jinja2 -pip install "urllib3<2" # to be removed if/when included in omero-py pip install omero-py pip install git+https://github.com/$SPACE_USER/omero-metadata.git@$MERGE_PUSH_BRANCH#egg=omero-metadata diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index 357b4c4f..54e9dbea 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -32,7 +32,6 @@ source $WORKSPACE/.venv3/bin/activate pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future pip install markdown -pip install "urllib3<2" # to be removed if/when included in omero-py pip install omero-py omero-web # Latest in order to stop server. NB: Re-installed from python-superbuild below From d5c6e35351f9038a3adb7876ef18d0400b530853 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 23 Sep 2023 19:00:10 +0100 Subject: [PATCH 30/80] use python3 --- home/jobs/OMERO-web/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index 54e9dbea..e8ac475f 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -26,7 +26,7 @@ rm -rf $WORKSPACE/.venv3 -python -m venv $WORKSPACE/.venv3 +python3 -m venv $WORKSPACE/.venv3 source $WORKSPACE/.venv3/bin/activate pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl From adf93c1d912aa53ba83669b9635529dd0d4eb141 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 23 Sep 2023 19:16:34 +0100 Subject: [PATCH 31/80] remove omero-server and omero-web user. Adding complexity --- docker-compose.yml | 8 ++++---- server/Dockerfile | 18 ++++-------------- server/run.sh | 6 +++--- slave/run.sh | 6 +++--- web/Dockerfile | 27 +++++++++------------------ 5 files changed, 23 insertions(+), 42 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 2b173727..ff65cdc4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -60,7 +60,7 @@ services: networks: - omero-network volumes: - - ./server:/home/omero-server + - ./server:/home/omero environment: - SLAVE_NAME=omero - SLAVE_EXECUTORS=2 @@ -79,8 +79,8 @@ services: networks: - omero-network volumes: - - ./web:/home/omero-web - - ./nginx/conf.d:/home/omero-web/nginx + - ./web:/home/omero + - ./nginx/conf.d:/home/omero/nginx environment: - SLAVE_NAME=web - SLAVE_EXECUTORS=2 @@ -96,7 +96,7 @@ services: - omero-network volumes: - ./nginx/conf.d:/etc/nginx/conf.d - - ./web/static:/home/omero-web/static + - ./web/static:/home/omero/static - ./nginx/log:/var/log/nginx - ./nginx/sslcert:/etc/nginx/ssl environment: diff --git a/server/Dockerfile b/server/Dockerfile index 1637f27d..499384c6 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -2,16 +2,6 @@ FROM jburel/devslave-c7:0.8.3 MAINTAINER OME -# Remove the existing omero user -RUN userdel -r omero && \ - echo 'root:omero' | chpasswd - -# Create the omero-server user -RUN useradd omero-server && \ - echo 'omero-server:omero-server' | chpasswd && \ - echo "%omero-server ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers - - ADD ./settings.env /home/settings.env RUN chmod +x /home/settings.env @@ -44,7 +34,7 @@ EXPOSE 4064 EXPOSE 4063 ADD ./run.sh /tmp/run.sh -RUN chown omero-server:omero-server /tmp/run.sh +RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh @@ -56,10 +46,10 @@ RUN chmod a+x /tmp/run.sh # Change user id to fix permissions issues ARG USER_ID=1000 -RUN usermod -u $USER_ID omero-server +RUN usermod -u $USER_ID omero # make sure mounted volumes has correct permissions -VOLUME ["/home/omero-server"] +VOLUME ["/home/omero"] -USER omero-server +USER omero CMD ["/tmp/run.sh"] diff --git a/server/run.sh b/server/run.sh index 5c14e8dd..7ad032c2 100644 --- a/server/run.sh +++ b/server/run.sh @@ -1,12 +1,12 @@ #!/bin/bash function shut_down() { - /home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin stop + /home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin stop } /tmp/jenkins-slave.sh & -/home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin start -/home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin diagnostics +/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin start +/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin diagnostics trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT diff --git a/slave/run.sh b/slave/run.sh index 246019f5..bf0111e5 100644 --- a/slave/run.sh +++ b/slave/run.sh @@ -1,12 +1,12 @@ #!/bin/bash function shut_down() { - /home/omero-server/workspace/OMERO-test-integration/src/dist/bin/omero admin stop + /home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin stop } /tmp/jenkins-slave.sh & -/home/omero-server/workspace/OMERO-test-integration/src/dist/bin/omero admin start -/home/omero-server/workspace/OMERO-test-integration/src/dist/bin/omero admin diagnostics +/home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin start +/home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin diagnostics trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT diff --git a/web/Dockerfile b/web/Dockerfile index 2cecda7b..1b2b6090 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -2,15 +2,6 @@ FROM jburel/devslave-c7:0.8.3 MAINTAINER OME -# Remove the existing omero user -RUN userdel -r omero && \ - echo 'root:omero' | chpasswd - -# Create the omero-web user -RUN useradd omero-web && \ - echo 'omero-web:omero-web' | chpasswd && \ - echo "%omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers - ADD ./settings.env /home/settings.env RUN chmod +x /home/settings.env @@ -25,7 +16,7 @@ RUN npm install -g grunt EXPOSE 4080 ADD ./run.sh /tmp/run.sh -RUN chown omero-web:omero-web /tmp/run.sh +RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh RUN dnf install -y python3 openssl @@ -34,17 +25,17 @@ RUN dnf clean all # Change user id to fix permissions issues ARG USER_ID=1000 -RUN usermod -u $USER_ID omero-web +RUN usermod -u $USER_ID omero -RUN chown -R omero-web:omero-web /home/omero-web/ +RUN chown -R omero:omero /home/omero/ # make sure mounted volumes has correct permissions -RUN mkdir -p /home/omero-web/nginx -RUN chown -R omero-web:omero-web /home/omero-web/nginx -RUN mkdir -p /home/omero-web/static -RUN chown -R omero-web:omero-web /home/omero-web/static +RUN mkdir -p /home/omero/nginx +RUN chown -R omero:omero /home/omero/nginx +RUN mkdir -p /home/omero/static +RUN chown -R omero:omero /home/omero/static -VOLUME ["/home/omero-web", "/home/omero-web/nginx"] +VOLUME ["/home/omero", "/home/omero/nginx"] -USER omero-web +USER omero CMD ["/tmp/run.sh"] From e01231f25cd448b2a317047ec21a96c4712cd959 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 25 Sep 2023 13:09:05 +0100 Subject: [PATCH 32/80] use new tag --- docker-compose.yml | 4 ---- docker/Dockerfile | 2 +- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- web/Dockerfile | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index ff65cdc4..6972eba2 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -33,7 +33,6 @@ services: build: context: ./slave dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -56,7 +55,6 @@ services: build: context: ./server dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -75,7 +73,6 @@ services: build: context: ./web dockerfile: Dockerfile - user: root networks: - omero-network volumes: @@ -160,7 +157,6 @@ services: docker: build: docker - user: root networks: - omero-network volumes: diff --git a/docker/Dockerfile b/docker/Dockerfile index fdeba1a6..6d586734 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.5 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index 499384c6..e9b0ddb6 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.5 MAINTAINER OME diff --git a/slave/Dockerfile b/slave/Dockerfile index 62714e12..a602b124 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.5 MAINTAINER OME diff --git a/web/Dockerfile b/web/Dockerfile index 1b2b6090..51f0a5fb 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.5 MAINTAINER OME From 832fc3b5442a1fe5c3b5d21cb11f474c2f083c54 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 25 Sep 2023 14:46:33 +0100 Subject: [PATCH 33/80] remove ref to omero-install --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index d4ad7ff2..231d6d25 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,6 @@ Running Devspace requires access to SSH and Git configuration files used for fet Devspace code depends on the following repositories: -* [OMERO install](https://github.com/ome/omero-install/) * [devslave-c7-docker](https://github.com/ome/devslave-c7-docker) # Installation From 99ff87158c273586d43e282a2886170c85382d8b Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 25 Sep 2023 14:57:25 +0100 Subject: [PATCH 34/80] adjust instructions about ssh key --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 231d6d25..575fba22 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,8 @@ The following instructions explain how to deploy a devspace on a Docker host. * Copy the SSH and Git configuration files used for fetching and pushing the Git repositories under `slave/.ssh` and `slave/.gitconfig`. This is usually - your own SSH and Git configuration files. + your own SSH and Git configuration files. Make sure that the permissions of the key are not + too open. If this is the case, change the permissions e.g. ``chmod 400 YOUR_KEY` You need to use a public key without a passphrase and a `.gitconfig` file containing the following sections: ``` @@ -94,6 +95,13 @@ Start and configure: $ docker-compose up -p my_project -d +* Depending on the ssh key, you might have to run the following comment in the ``test_integration`` container. For example: + $ docker exec -it devspace_testintegration_1 bash + $ ssh -T git@github.com + + A message should be returned after running the command: + $ Hi snoopycrimecop! You've successfully authenticated, but GitHub does not provide shell access. + * Retrieve the dynamic port of the Jenkins NGINX container. You can access the Jenkins UI from https://HOST_IP:PORT after accepting the self-signed certificate: From 49748d644447395f1f0b826a578c2edaf906fcad Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 25 Sep 2023 14:58:00 +0100 Subject: [PATCH 35/80] adjust info about rename script --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 575fba22..acec6af0 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ The following instructions explain how to deploy a devspace on a Docker host. topic branches available on origin, use `develop` or one of the main branches: - $ ./rename.py MYTOPIC --user git_user + $ ./rename.py USER MYTOPIC --user git_user * This will also replace the `USER_ID` of the various Dockerfile with the ID of the user who will run the devspace, assumed to be: `id -u`, i.e. the current user. From 9b48ddfa5f57cb6bd3b9d139b1e34900339f8920 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 25 Sep 2023 17:47:31 +0100 Subject: [PATCH 36/80] update web tagging --- home/jobs/OMERO-web/config.xml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index e8ac475f..f2f871ca 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -180,9 +180,16 @@ pip install git+https://github.com/$SPACE_USER/omero-webtest.git@$MERGE_PUSH_BRA omero config append omero.web.apps '"omero_webtest"' # OMERO.omero-webtagging-autotag installation -pip install omero-webtagging-autotag -omero config append omero.web.apps '"omero_webtagging_autotag"' -omero config append omero.web.ui.center_plugins '["Auto Tag", "omero_webtagging_autotag/auto_tag_init.js.html", "auto_tag_panel"]' +pip install omero-autotag +# Add autotag to webclient +omero config append omero.web.apps '"omero_autotag"' +# Add autotag to centre panel +omero config append omero.web.ui.center_plugins '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]' + +pip install omero-tagsearch +# Add tagsearch to webclient +omero config append omero.web.apps '"omero_tagsearch"' + # OMERO.webtagging-tagsearch installation pip install omero-webtagging-tagsearch From fea0687c927ff8772816547ed70defd091637cc2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 28 Sep 2023 11:07:07 +0100 Subject: [PATCH 37/80] bump nginx to 1.24 for nginx_jenkins --- .env | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.env b/.env index 6b5f62c1..e3cf6855 100644 --- a/.env +++ b/.env @@ -25,7 +25,7 @@ REPO_CONFIG=/tmp/config # Variables for controlling external dependencies versions POSTGRES_VERSION=13 -NGINX_VERSION=1.23 +NGINX_VERSION=1.24 # Other variables DOCKER_EXECUTORS=10 From 81b0151f8a6a56357c1c1e0f9f4db092ed11d9e5 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 28 Sep 2023 11:07:36 +0100 Subject: [PATCH 38/80] bump base image version --- nginx/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nginx/Dockerfile b/nginx/Dockerfile index 0ea29840..35f417f9 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.3 +FROM jburel/devslave-c7:0.8.5 MAINTAINER OME From 3a62f5250124bc25af7c21908faf18f16d701d97 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 28 Sep 2023 12:56:02 +0100 Subject: [PATCH 39/80] use official pre-built ice binaries --- server/Dockerfile | 4 ++-- slave/Dockerfile | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index e9b0ddb6..b5b9ac8d 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -16,8 +16,8 @@ RUN dnf install -y 'dnf-command(config-manager)' && \ dnf config-manager --set-enabled crb RUN dnf install -y openssl libdb-cxx RUN cd /tmp && \ - wget -q https://github.com/sbesson/zeroc-ice-rockylinux9-x86_64/releases/download/20230720/Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ - tar xf Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + wget -q https://github.com/glencoesoftware/zeroc-ice-rhel9-x86_64/releases/download/20230928/Ice-3.6.5-rhel9-x86_64.tar.gz && \ + tar xf Ice-3.6.5-rhel9-x86_64.tar.gz && \ mv Ice-3.6.5 /opt/ice-3.6.5 && \ echo /opt/ice-3.6.5/lib64 > /etc/ld.so.conf.d/ice-x86_64.conf && \ ldconfig diff --git a/slave/Dockerfile b/slave/Dockerfile index a602b124..7175db47 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -20,8 +20,8 @@ RUN dnf install -y 'dnf-command(config-manager)' && \ dnf config-manager --set-enabled crb RUN dnf install -y openssl libdb-cxx RUN cd /tmp && \ - wget -q https://github.com/sbesson/zeroc-ice-rockylinux9-x86_64/releases/download/20230720/Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ - tar xf Ice-3.6.5-rockylinux9-x86_64.tar.gz && \ + wget -q https://github.com/glencoesoftware/zeroc-ice-rhel9-x86_64/releases/download/20230928/Ice-3.6.5-rhel9-x86_64.tar.gz && \ + tar xf Ice-3.6.5-rhel9-x86_64.tar.gz && \ mv Ice-3.6.5 /opt/ice-3.6.5 && \ echo /opt/ice-3.6.5/lib64 > /etc/ld.so.conf.d/ice-x86_64.conf && \ ldconfig From a9df7d36e8870c2ee1694bc6434933e80b2a9f42 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 29 Sep 2023 12:36:22 +0100 Subject: [PATCH 40/80] comment out server config --- nginx/Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nginx/Dockerfile b/nginx/Dockerfile index 35f417f9..e552ee87 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -6,6 +6,9 @@ MAINTAINER OME RUN dnf -y install nginx\ && dnf clean all +# comment out default server config in nginx.conf +RUN sed -i "/^\s\s\s\sserver/, /^\s\s\s\s}/ s|^|#|" /etc/nginx/nginx.conf + VOLUME ["/etc/nginx/conf.d", "/var/log/nginx"] WORKDIR /etc/nginx From 9c60358af6571fddacec545708d66179ba9b427e Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 29 Sep 2023 12:40:27 +0100 Subject: [PATCH 41/80] enable to install the latest stable version --- nginx/Dockerfile | 3 +++ nginx/nginx-stable.repo | 7 +++++++ 2 files changed, 10 insertions(+) create mode 100644 nginx/nginx-stable.repo diff --git a/nginx/Dockerfile b/nginx/Dockerfile index e552ee87..5d38c937 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -2,6 +2,9 @@ FROM jburel/devslave-c7:0.8.5 MAINTAINER OME +COPY nginx-stable.repo /etc/yum.repos.d/ +RUN dnf -y install dnf-utils +RUN yum-config-manager --enable nginx-stable RUN dnf -y install nginx\ && dnf clean all diff --git a/nginx/nginx-stable.repo b/nginx/nginx-stable.repo new file mode 100644 index 00000000..b1de61ff --- /dev/null +++ b/nginx/nginx-stable.repo @@ -0,0 +1,7 @@ +[nginx-stable] +name=nginx stable repo +baseurl=http://nginx.org/packages/centos/9/x86_64/ +gpgcheck=1 +enabled=1 +gpgkey=https://nginx.org/keys/nginx_signing.key +module_hotfixes=true From c1b20ce1cfaef547531b4880cd462945eb8af333 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 29 Sep 2023 14:07:05 +0100 Subject: [PATCH 42/80] bump nginx version to 1.24 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index acec6af0..16687bdb 100644 --- a/README.md +++ b/README.md @@ -198,7 +198,7 @@ Alternatively create a new job in the Jenkins web-interface in the usual way. | Python | 3.9 | | Ice | 3.6 | | PostgreSQL | 13 | -| Nginx | 1.23 | +| Nginx | 1.24 | # Troubleshooting From 242c6d835cc6c26547651d9a2b5d5485040e031f Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 29 Sep 2023 14:08:30 +0100 Subject: [PATCH 43/80] remove ref to omero-install --- README.md | 9 --------- 1 file changed, 9 deletions(-) diff --git a/README.md b/README.md index 16687bdb..5fdddc5e 100644 --- a/README.md +++ b/README.md @@ -204,15 +204,6 @@ Alternatively create a new job in the Jenkins web-interface in the usual way. See [Troubleshooting](Troubleshooting.md) -# ADVANCE: extend omero-install - -In order to install additional components or new version of packages e.g. PostgreSQL 10, it is required to: - -* Modify the files in [omero-install](https://github.com/ome/omero-install) -* Create a new image of [devslave-c7-docker](https://github.com/ome/devslave-c7-docker) using the updated omero-install files -* Push the new image to [Docker Hub](https://hub.docker.com/). You will need to your own account -* Modify each Dockerfile of this repository to use the new image - # Upgrade From 2937c5c82314d360c73595b73465c18dad789a63 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sun, 1 Oct 2023 08:37:07 +0100 Subject: [PATCH 44/80] use pg16 --- .env | 2 +- README.md | 2 +- server/Dockerfile | 7 +++++-- slave/Dockerfile | 6 ++++-- 4 files changed, 11 insertions(+), 6 deletions(-) diff --git a/.env b/.env index e3cf6855..6e558d41 100644 --- a/.env +++ b/.env @@ -24,7 +24,7 @@ REPO_CURATED=/tmp/curated REPO_CONFIG=/tmp/config # Variables for controlling external dependencies versions -POSTGRES_VERSION=13 +POSTGRES_VERSION=16 NGINX_VERSION=1.24 # Other variables diff --git a/README.md b/README.md index 5fdddc5e..36367ccb 100644 --- a/README.md +++ b/README.md @@ -197,7 +197,7 @@ Alternatively create a new job in the Jenkins web-interface in the usual way. | Java | openJDK 11-devel | | Python | 3.9 | | Ice | 3.6 | -| PostgreSQL | 13 | +| PostgreSQL | 16 | | Nginx | 1.24 | # Troubleshooting diff --git a/server/Dockerfile b/server/Dockerfile index b5b9ac8d..3211084e 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -25,8 +25,11 @@ ENV ICE_HOME=/opt/ice-3.6.5 ENV PATH=$ICE_HOME/bin:$PATH -# install postgres tools -RUN dnf -y install postgresql \ +# install postgres tools for pg16 (default is 13) +RUN dnf install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-9-x86_64/pgdg-redhat-repo-latest.noarch.rpm +RUN dnf -qy module disable postgresql + +RUN dnf -y install postgresql16 \ && dnf clean all diff --git a/slave/Dockerfile b/slave/Dockerfile index 7175db47..7a2b6464 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -41,8 +41,10 @@ RUN curl -fSLO http://downloads.sourceforge.net/project/findbugs/findbugs/$FINDB # Install build tools from EPEL RUN dnf -y install maven ant && dnf clean all -# install postgres tools -RUN dnf -y install postgresql-server postgresql\ +# install postgres tools for pg16 (default is 13) +RUN dnf install -y https://download.postgresql.org/pub/repos/yum/reporpms/EL-9-x86_64/pgdg-redhat-repo-latest.noarch.rpm +RUN dnf -qy module disable postgresql +RUN dnf -y install postgresql16-server postgresql16\ && dnf clean all # gradle From f69ad4dfb9895f3c2eaacfc95164bd3f662a20e8 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 2 Oct 2023 09:05:26 +0100 Subject: [PATCH 45/80] fix job name --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 36367ccb..6f74b4ab 100644 --- a/README.md +++ b/README.md @@ -141,7 +141,7 @@ After the script has completed you can either leave it in place so it will overr # Job configurations -* When running the OMERO-build job for the first time, select the ``PURGE_DATA`` option to create the database. +* When running the OMERO-server job for the first time, select the ``PURGE_DATA`` option to create the database. # Job workflow From cca27ceb8ec6926718da6688e3d2784d8bbca119 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 25 Jan 2024 13:36:13 +0000 Subject: [PATCH 46/80] bump to nodejs 20 --- web/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/Dockerfile b/web/Dockerfile index 51f0a5fb..ac7c9091 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -7,7 +7,7 @@ RUN chmod +x /home/settings.env # ant for iviewer, make for nodejs RUN dnf -y install ant make -RUN curl -sL https://rpm.nodesource.com/setup_16.x | bash +RUN curl -sL https://rpm.nodesource.com/setup_20.x | bash RUN dnf install -y nodejs # grunt for figure RUN npm install -g grunt From d912839ef6e4cc78ab952732acc2d19f2631f2ee Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 30 Jan 2024 10:32:43 +0000 Subject: [PATCH 47/80] change jenkins version --- jenkins/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index ba95f0e3..3964a0d7 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -1,4 +1,4 @@ -FROM jenkins/jenkins:2.375.1-lts +FROM jenkins/jenkins:2.426.3 MAINTAINER OME # Temp fix robot test results From e6bafeda27224df9329c081c77706fb2a43af9f2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 31 Jan 2024 22:14:47 +0000 Subject: [PATCH 48/80] add check --- server/run.sh | 13 +++++++++---- slave/run.sh | 14 ++++++++++---- 2 files changed, 19 insertions(+), 8 deletions(-) diff --git a/server/run.sh b/server/run.sh index 7ad032c2..514dcbed 100644 --- a/server/run.sh +++ b/server/run.sh @@ -1,12 +1,17 @@ #!/bin/bash +workspace=/home/omero/workspace/OMERO-server function shut_down() { - /home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin stop + if [ -d "$workspace" ]; then + $workspace/OMERO.server/bin/omero admin stop + fi } -/tmp/jenkins-slave.sh & -/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin start -/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin diagnostics +/tmp/jenkins-slave.sh +if [ -d "$workspace" ]; then + $workspace/OMERO.server/bin/omero admin start + $workspace/OMERO.server/bin/omero admin diagnostics +fi trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT diff --git a/slave/run.sh b/slave/run.sh index bf0111e5..45d086a8 100644 --- a/slave/run.sh +++ b/slave/run.sh @@ -1,12 +1,18 @@ #!/bin/bash +workspace=/home/omero/workspace/OMERO-test-integration function shut_down() { - /home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin stop + if [ -d "$workspace" ]; then + $workspace/src/dist/bin/omero admin stop + fi } -/tmp/jenkins-slave.sh & -/home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin start -/home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin diagnostics +/tmp/jenkins-slave.sh +if [ -d "$workspace" ]; then + + $workspace/src/dist/bin/omero admin start + $workspace/src/dist/bin/omero admin diagnostics +fi trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT From 0d5500fa42f5cda783996450f950f16ed1bdea70 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 31 Jan 2024 22:15:37 +0000 Subject: [PATCH 49/80] bump version --- docker/Dockerfile | 2 +- nginx/Dockerfile | 2 +- server/Dockerfile | 10 +++++++++- slave/Dockerfile | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 6d586734..c9145117 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.5 +FROM jburel/devslave-c7:0.8.7 MAINTAINER OME diff --git a/nginx/Dockerfile b/nginx/Dockerfile index 5d38c937..d25553d7 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.5 +FROM jburel/devslave-c7:0.8.7 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index 3211084e..2bcc20f9 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.5 +FROM jburel/devslave-c7:0.8.7 MAINTAINER OME @@ -41,6 +41,12 @@ RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh +cd /home/omero +SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip +wget -q $SERVER -O OMERO.server-ice36.zip +unzip -q OMERO.server* +rm OMERO.server-ice36.zip + # Install mencoder # See https://github.com/ome/prod-playbooks/blob/7d8e59ced0b47a224d6be02907d913c392ef9379/ome-dundeeomero.yml#L48 # RUN dnf install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm @@ -51,6 +57,8 @@ RUN chmod a+x /tmp/run.sh ARG USER_ID=1000 RUN usermod -u $USER_ID omero + + # make sure mounted volumes has correct permissions VOLUME ["/home/omero"] diff --git a/slave/Dockerfile b/slave/Dockerfile index 7a2b6464..f8667495 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.5 +FROM jburel/devslave-c7:0.8.7 MAINTAINER OME From 724ab34cf7a38072354894272cff50f60fa6a5df Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 06:47:43 +0000 Subject: [PATCH 50/80] change permission to start the node: --- server/run.sh | 2 +- slave/run.sh | 2 +- web/run.sh | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/server/run.sh b/server/run.sh index 514dcbed..979e1e6e 100644 --- a/server/run.sh +++ b/server/run.sh @@ -1,5 +1,5 @@ #!/bin/bash - +sudo chmod 777 -R /home/omero workspace=/home/omero/workspace/OMERO-server function shut_down() { if [ -d "$workspace" ]; then diff --git a/slave/run.sh b/slave/run.sh index 45d086a8..32e76d09 100644 --- a/slave/run.sh +++ b/slave/run.sh @@ -1,5 +1,5 @@ #!/bin/bash - +sudo chmod 777 -R /home/omero workspace=/home/omero/workspace/OMERO-test-integration function shut_down() { if [ -d "$workspace" ]; then diff --git a/web/run.sh b/web/run.sh index 76ba7a38..f9437ec0 100644 --- a/web/run.sh +++ b/web/run.sh @@ -1,5 +1,5 @@ #!/bin/bash - +sudo chmod 777 -R /home/omero workspace=/home/omero/workspace/OMERO-web djangopid="$workspace/OMERO.web/var/django.pid" if [ -f $djangopid ]; then From 750296573dbd310277fdd88e3e04132425fdcf01 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 07:14:09 +0000 Subject: [PATCH 51/80] use the branch name --- home/jenkins.model.JenkinsLocationConfiguration.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jenkins.model.JenkinsLocationConfiguration.xml b/home/jenkins.model.JenkinsLocationConfiguration.xml index eb294ca4..2d86ae3f 100644 --- a/home/jenkins.model.JenkinsLocationConfiguration.xml +++ b/home/jenkins.model.JenkinsLocationConfiguration.xml @@ -1,5 +1,5 @@ address not configured yet <nobody@nowhere> - https://SPACENAME-ci.openmicroscopy.org/jenkins/ + https://BRANCH-ci.openmicroscopy.org/jenkins/ From c21ce880aa92dc9d06766c8a2d0ecc9457342b9a Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 07:19:53 +0000 Subject: [PATCH 52/80] replace docker-compose by docker compose --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 6f74b4ab..459998ae 100644 --- a/README.md +++ b/README.md @@ -85,15 +85,15 @@ Start and configure: * Build devspace using `docker-compose`: - $ docker-compose -f docker-compose.yml build + $ docker compose -f docker-compose.yml build * Start devspace using `docker-compose`: - $ docker-compose -f docker-compose.yml up -d + $ docker compose -f docker-compose.yml up -d By default, this will use the name of the directory as the project name. In the case of a shared Docker host, it is possible to override the project name using - $ docker-compose up -p my_project -d + $ docker compose up -p my_project -d * Depending on the ssh key, you might have to run the following comment in the ``test_integration`` container. For example: $ docker exec -it devspace_testintegration_1 bash @@ -106,11 +106,11 @@ Start and configure: the Jenkins UI from https://HOST_IP:PORT after accepting the self-signed certificate: - $ docker-compose -p my_project port nginxjenkins 443 + $ docker compose -p my_project port nginxjenkins 443 * Create the `maven-internal` Nexus repository: - $ docker-compose exec nexus /nexus-data/createRepoMavenInternal.sh + $ docker compose exec nexus /nexus-data/createRepoMavenInternal.sh * [Optional] Turn on Basic HTTP authentication for Jenkins From f7240a2bbecc632d169ef4737078bead4710b425 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 09:33:18 +0000 Subject: [PATCH 53/80] install build --- server/Dockerfile | 3 ++- slave/Dockerfile | 4 +++- web/Dockerfile | 3 ++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 2bcc20f9..dfb9e7a7 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -9,7 +9,8 @@ RUN chmod +x /home/settings.env WORKDIR /tmp/omero-install/linux -RUN dnf install -y python3 +RUN dnf install -y python3 python3-pip +RUN pip install build # Ice dependencies RUN dnf install -y 'dnf-command(config-manager)' && \ diff --git a/slave/Dockerfile b/slave/Dockerfile index f8667495..a135fd10 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -14,7 +14,9 @@ RUN chmod +x /home/settings.env RUN dnf install -y make # Python job -RUN dnf install -y python3-setuptools +RUN dnf install -y python3-setuptools python3-pip +RUN pip install build + # Ice dependencies RUN dnf install -y 'dnf-command(config-manager)' && \ dnf config-manager --set-enabled crb diff --git a/web/Dockerfile b/web/Dockerfile index ac7c9091..2022634e 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -19,7 +19,8 @@ ADD ./run.sh /tmp/run.sh RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh -RUN dnf install -y python3 openssl +RUN dnf install -y python3 openssl python3-pip +RUN pip install build RUN dnf clean all From 15f3df16f34ebe08d8440426bac9d6f1d1581236 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 09:33:37 +0000 Subject: [PATCH 54/80] bump base image version --- web/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/Dockerfile b/web/Dockerfile index 2022634e..5d207035 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.5 +FROM jburel/devslave-c7:0.8.7 MAINTAINER OME From 83b29be191079e6a50cbc872d730fc26bf5d7e93 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 09:46:21 +0000 Subject: [PATCH 55/80] install blosc --- server/Dockerfile | 4 ++++ slave/Dockerfile | 5 +++++ 2 files changed, 9 insertions(+) diff --git a/server/Dockerfile b/server/Dockerfile index dfb9e7a7..a6a1bba1 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -33,6 +33,10 @@ RUN dnf -qy module disable postgresql RUN dnf -y install postgresql16 \ && dnf clean all +# For OME-zarr +RUN dnf -y install epel-release +RUN dnf -y update +RUN dnf -y blosc EXPOSE 4064 EXPOSE 4063 diff --git a/slave/Dockerfile b/slave/Dockerfile index a135fd10..2dd914aa 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -57,6 +57,11 @@ RUN cd /opt && \ ln -s /opt/gradle-$GRADLEVER/bin/gradle /usr/local/bin/gradle +# For OME-zarr +RUN dnf -y install epel-release +RUN dnf -y update +RUN dnf -y blosc + EXPOSE 14064 EXPOSE 14063 From 936c8194946af15e6f2b6cdde2ff619ada54bab1 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 10:57:25 +0000 Subject: [PATCH 56/80] remove all tag search --- home/jobs/OMERO-web/config.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index f2f871ca..618e9a06 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -190,10 +190,6 @@ pip install omero-tagsearch # Add tagsearch to webclient omero config append omero.web.apps '"omero_tagsearch"' - -# OMERO.webtagging-tagsearch installation -pip install omero-webtagging-tagsearch -omero config append omero.web.apps '"omero_webtagging_tagsearch"' omero config append omero.web.ui.top_links '["Tag Search", "tagsearch"]' # omero-web-zarr From b162fee9195fa5f1ebffcbdcb680600ea03faa54 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 20:31:52 +0000 Subject: [PATCH 57/80] fix blosc installation --- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index a6a1bba1..083054ab 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -36,7 +36,7 @@ RUN dnf -y install postgresql16 \ # For OME-zarr RUN dnf -y install epel-release RUN dnf -y update -RUN dnf -y blosc +RUN dnf -y install blosc EXPOSE 4064 EXPOSE 4063 diff --git a/slave/Dockerfile b/slave/Dockerfile index 2dd914aa..879e1344 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -60,7 +60,7 @@ RUN cd /opt && \ # For OME-zarr RUN dnf -y install epel-release RUN dnf -y update -RUN dnf -y blosc +RUN dnf -y install blosc EXPOSE 14064 EXPOSE 14063 From 4813bebc61ea0ccd12ae2c71edcd22fc63386352 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 20:38:40 +0000 Subject: [PATCH 58/80] add env to keep set the hub --- docker-compose.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index 6972eba2..86c4ec06 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -139,6 +139,9 @@ services: - SCREEN_WIDTH=1920 - SCREEN_HEIGHT=1080 - SCREEN_DEPTH=24 + - SE_EVENT_BUS_HOST=seleniumhub + - SE_EVENT_BUS_PUBLISH_PORT=4442 + - SE_EVENT_BUS_SUBSCRIBE_PORT=4443 depends_on: - seleniumhub @@ -152,6 +155,9 @@ services: - SCREEN_WIDTH=1920 - SCREEN_HEIGHT=1080 - SCREEN_DEPTH=24 + - SE_EVENT_BUS_HOST=seleniumhub + - SE_EVENT_BUS_PUBLISH_PORT=4442 + - SE_EVENT_BUS_SUBSCRIBE_PORT=4443 depends_on: - seleniumhub From 9c5372cd3ee09a94599047120d737fae595c3613 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 1 Feb 2024 21:26:05 +0000 Subject: [PATCH 59/80] remove instructions not belonging to file --- server/Dockerfile | 6 ------ 1 file changed, 6 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 083054ab..eaee0ec8 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -46,12 +46,6 @@ RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh -cd /home/omero -SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip -wget -q $SERVER -O OMERO.server-ice36.zip -unzip -q OMERO.server* -rm OMERO.server-ice36.zip - # Install mencoder # See https://github.com/ome/prod-playbooks/blob/7d8e59ced0b47a224d6be02907d913c392ef9379/ome-dundeeomero.yml#L48 # RUN dnf install -y http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-5.el7.nux.noarch.rpm From a449d8cabf1f07119a6f0e6ec0325d5e913be194 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 2 Feb 2024 13:30:20 +0000 Subject: [PATCH 60/80] remove installation of docker-compose. This is now a plugin --- README.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/README.md b/README.md index 459998ae..36dfddcc 100644 --- a/README.md +++ b/README.md @@ -24,12 +24,6 @@ The following instructions explain how to deploy a devspace on a Docker host. * Log into the Docker host using ssh -* Install the prerequisites [Docker engine](https://docs.docker.com/) and - [Docker compose](https://docs.docker.com/compose/) either globally or in - a virtual environment: - - $ pip install docker-compose - * Create a directory ``/data/username`` and change ownership: $ sudo mkdir /data/username From 0acc1ee11865e468f46b298ad243a34744a474c0 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 2 Feb 2024 13:30:51 +0000 Subject: [PATCH 61/80] remove unused git container --- docker-compose.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 86c4ec06..83a3f2d1 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -12,12 +12,6 @@ services: environment: - JENKINS_OPTS= --prefix=${JENKINS_PREFIX} --argumentsRealm.passwd.${JENKINS_USERNAME}=${JENKINS_PASSWORD} --argumentsRealm.roles.${JENKINS_USERNAME}=admin - git: - build: git - volumes: - - /src - command: 'true' - pg: image: postgres:${POSTGRES_VERSION} networks: From 628d24ed4a60c7c31d762c96a1a0e829e4be1cd2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 5 Feb 2024 10:23:29 +0000 Subject: [PATCH 62/80] install libraries for running python tests --- home/jobs/OMERO-test-integration/config.xml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index 7ead3bd6..1466718a 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -21,9 +21,7 @@ source $WORKSPACE/.venv3/bin/activate pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future setuptools pip install markdown -# Avoid installing psutil for now -# https://github.com/pytest-dev/pytest-xdist/issues/585 -pip install mox3 pytest pytest-django 'pytest-xdist<2' +pip install mox3 pytest pytest-django pytest-xdist pytest-mock pip install tables pip install jinja2 pip install PyYAML From 29a9342f611fed82e16f5c972ba92b65efcaa952 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 10:02:50 +0000 Subject: [PATCH 63/80] use org image --- docker/Dockerfile | 2 +- nginx/Dockerfile | 2 +- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- web/Dockerfile | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index c9145117..a0d03763 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.7 +FROM openmicroscopy/devagent:0.8.0 MAINTAINER OME diff --git a/nginx/Dockerfile b/nginx/Dockerfile index d25553d7..ad4cb4cd 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.7 +FROM openmicroscopy/devagent:0.8.0 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index eaee0ec8..c1b016af 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.7 +FROM openmicroscopy/devagent:0.8.0 MAINTAINER OME diff --git a/slave/Dockerfile b/slave/Dockerfile index 879e1344..37700283 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.7 +FROM openmicroscopy/devagent:0.8.0 MAINTAINER OME diff --git a/web/Dockerfile b/web/Dockerfile index 5d207035..32d0e4a4 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7:0.8.7 +FROM openmicroscopy/devagent:0.8.0 MAINTAINER OME From 9c1d0f688956af8c36ddbda6680b4bd739dfd316 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 10:59:45 +0000 Subject: [PATCH 64/80] remove code from rebase --- slave/Dockerfile | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 37700283..5e898dbb 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -69,16 +69,6 @@ ADD ./run.sh /tmp/run.sh RUN chown omero:omero /tmp/run.sh RUN chmod a+x /tmp/run.sh -<<<<<<< HEAD -ENV PATH=/opt/rh/rh-python38/root/usr/bin:$PATH -RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox build future wheel restructuredtext-lint -RUN /py3/bin/pip install https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.3.0/zeroc_ice-3.6.5-cp38-cp38-linux_x86_64.whl -RUN ln -s /py3/bin/slice2py /usr/bin/slice2py -ENV VIRTUAL_ENV=/py3 -ENV PATH="$VIRTUAL_ENV/bin:$PATH" - -======= ->>>>>>> 9535936 (update dockerfile to work with rocky9) # Change user id to fix permissions issues ARG USER_ID=1000 RUN usermod -u $USER_ID omero From 5df5e744dfc3ab4bab33833500abdf74c27babda Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 11:18:52 +0000 Subject: [PATCH 65/80] update to docker compose --- runtest.sh | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/runtest.sh b/runtest.sh index 15b9f465..9873cb99 100755 --- a/runtest.sh +++ b/runtest.sh @@ -5,13 +5,13 @@ set -e -u -x source .env # start docker container -docker-compose -f docker-compose.yml up -d +docker compose -f docker-compose.yml up -d # inspect containers -service_containers=( devspace_pg_1 devspace_redis_1 ) -selenium_containers=( devspace_seleniumhub_1 devspace_seleniumfirefox_1 devspace_seleniumchrome_1 ) -omero_containers=( devspace_omero_1 devspace_web_1 devspace_nginx_1 devspace_testintegration_1 ) -jenkins_containers=( devspace_jenkins_1 devspace_nginxjenkins_1 ) +service_containers=( devspace-pg-1 devspace-redis-1 ) +selenium_containers=( devspace-seleniumhub-1 devspace-seleniumfirefox-1 devspace-seleniumchrome-1 ) +omero_containers=( devspace-omero-1 devspace-web-1 devspace-nginx-1 devspace-testintegration-1 ) +jenkins_containers=( devspace-jenkins-1 devspace-nginxjenkins-1 ) all_containers=( "${service_containers[@]}" "${selenium_containers[@]}" "${omero_containers[@]}" "${jenkins_containers[@]}") for cname in "${all_containers[@]}" @@ -22,11 +22,11 @@ done # check if Jenkins is fully up and running d=10 -while ! docker logs devspace_jenkins_1 2>&1 | grep "Jenkins is fully up and running" +while ! docker logs devspace-jenkins-1 2>&1 | grep "Jenkins is fully up and running" do sleep 10 d=$[$d -1] if [ $d -lt 0 ]; then - docker logs devspace_jenkins_1 + docker logs devspace-jenkins-1 exit 1 fi done @@ -38,11 +38,11 @@ do SLAVE_ADDR=`docker inspect --format '{{ .NetworkSettings.IPAddress }}' $cname` echo "Checking $cname $SLAVE_ADDR is connected to jenkins" d=10 - while ! docker logs devspace_jenkins_1 2>&1 | grep "from /${SLAVE_ADDR}" + while ! docker logs devspace-jenkins-1 2>&1 | grep "from /${SLAVE_ADDR}" do sleep 10 d=$[$d -1] if [ $d -lt 0 ]; then - docker logs devspace_jenkins_1 + docker logs devspace-jenkins-1 docker logs $cname exit 1 fi @@ -50,7 +50,7 @@ do done -JENKINS_PORT=$(docker-compose port nginxjenkins 80 | cut -d: -f2) +JENKINS_PORT=$(docker compose port nginxjenkins 80 | cut -d: -f2) curl -L -k -I http://localhost:$JENKINS_PORT$JENKINS_PREFIX STATUS=$(curl -L -k --write-out %{http_code} --silent --output /dev/null http://localhost:$JENKINS_PORT$JENKINS_PREFIX) @@ -60,5 +60,5 @@ if [ ! "200" == "$STATUS" ]; then fi # CLEANUP -docker-compose -f docker-compose.yml stop -docker-compose -f docker-compose.yml rm -f +docker compose -f docker-compose.yml stop +docker compose -f docker-compose.yml rm -f From 7eecadadcb72a313dacffec3b99573deea14870d Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 11:27:02 +0000 Subject: [PATCH 66/80] update general doc --- README.md | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 36dfddcc..d00bece8 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Running Devspace requires access to SSH and Git configuration files used for fet Devspace code depends on the following repositories: -* [devslave-c7-docker](https://github.com/ome/devslave-c7-docker) +* [devagent-docker](https://github.com/ome/devagent-docker) # Installation @@ -60,7 +60,7 @@ The following instructions explain how to deploy a devspace on a Docker host. * Run `rename.py` to match your topic name. Specify the Git user corresponding to the confguration files used above. If you do not yet have - topic branches available on origin, use `develop` or one of the + topic branches available on origin, use `develop/master` or one of the main branches: $ ./rename.py USER MYTOPIC --user git_user @@ -77,11 +77,11 @@ The following instructions explain how to deploy a devspace on a Docker host. Start and configure: -* Build devspace using `docker-compose`: +* Build devspace using `docker compose`: $ docker compose -f docker-compose.yml build -* Start devspace using `docker-compose`: +* Start devspace using `docker compose`: $ docker compose -f docker-compose.yml up -d @@ -89,8 +89,8 @@ Start and configure: $ docker compose up -p my_project -d -* Depending on the ssh key, you might have to run the following comment in the ``test_integration`` container. For example: - $ docker exec -it devspace_testintegration_1 bash +* Depending on the ssh key, you might have to run the following comment in the ``test-integration`` container. For example: + $ docker exec -it devspace-testintegration-1 bash $ ssh -T git@github.com A message should be returned after running the command: @@ -148,24 +148,24 @@ they are associated with and a short description of the jobs. | Job name | Name | Description | docker name | | -----------------------|-----------------| ------------------------------------------|----------------------------| | Trigger | | Runs all the following jobs in order | | -| BIOFORMATS-push | testintegration | Merges all Bio-Formats PRs | devspace_testintegration_1 | -| BIOFORMATS-build | testintegration | Builds Bio-Formats components | devspace_testintegration_1 | -| BIOFORMATS-image | testintegration | Builds a Docker image of Bio-Formats | devspace_docker_1 | -| OMERO-push | testintegration | Merges all OMERO PRs | devspace_testintegration_1 | -| OMERO-build | testintegration | Builds OMERO artifacts (server, clients) | devspace_testintegration_1 | -| OMERO-server | omero | Deploys an OMERO.server | devspace_omero_1 | -| OMERO-web | web | Deploys an OMERO.web client | devspace_web_1 | -| OMERO-test-integration | testintegration | Runs the OMERO integration tests | devspace_testintegration_1 | -| OMERO-robot | testintegration | Runs the Robot tests | devspace_testintegration_1 | -| nginx | nginx | Reloads the nginx server | devspace_nginx_1 | -| OMERO-docs | testintegration | Builds the OMERO documentation | devspace_testintegration_1 | +| BIOFORMATS-push | testintegration | Merges all Bio-Formats PRs | devspace-testintegration-1 | +| BIOFORMATS-build | testintegration | Builds Bio-Formats components | devspace-testintegration-1 | +| BIOFORMATS-image | testintegration | Builds a Docker image of Bio-Formats | devspace-docker-1 | +| OMERO-push | testintegration | Merges all OMERO PRs | devspace-testintegration-1 | +| OMERO-build | testintegration | Builds OMERO artifacts (server, clients) | devspace-testintegration-1 | +| OMERO-server | omero | Deploys an OMERO.server | devspace-omero-1 | +| OMERO-web | web | Deploys an OMERO.web client | devspace-web-1 | +| OMERO-test-integration | testintegration | Runs the OMERO integration tests | devspace-testintegration-1 | +| OMERO-robot | testintegration | Runs the Robot tests | devspace-testintegration-1 | +| nginx | nginx | Reloads the nginx server | devspace-nginx-1 | +| OMERO-docs | testintegration | Builds the OMERO documentation | devspace-testintegration-1 | This means that by default the following repositories need to be forked to your GitHub account: * [ome/openmiscrocopy](https://github.com/ome/openmicroscopy) -* [ome/ome-documentation](https://github.com/ome/ome-documentation) +* [ome/omero-documentation](https://github.com/ome/omero-documentation) * [ome/bioformats](https://github.com/ome/bioformats) If you do not have some of the repositories forked, you will need to remove the jobs from the list From 22cc432e74dbfaf6cddf06fbcff4ef91a91b2f07 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 11:30:06 +0000 Subject: [PATCH 67/80] remove git dockerfile no longer needed --- git/Dockerfile | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 git/Dockerfile diff --git a/git/Dockerfile b/git/Dockerfile deleted file mode 100644 index a3cd7848..00000000 --- a/git/Dockerfile +++ /dev/null @@ -1,8 +0,0 @@ -FROM mini/base -MAINTAINER ome-devel@lists.openmicroscopy.org.uk - - -RUN apk-install git && \ - mkdir /src - -WORKDIR /src From 634c7e64142a8e8d5a9a1d4e5c31b8ee366c2557 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 8 Feb 2024 20:41:32 +0000 Subject: [PATCH 68/80] Clean to prevent errors stderr: error: Your local changes to the following files would be overwritten by checkout: pom.xml xsd-fu/templates/java/OMEXMLModelObject.template Please commit your changes or stash them before you switch branches. Aborting --- home/jobs/BIOFORMATS-push/config.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/home/jobs/BIOFORMATS-push/config.xml b/home/jobs/BIOFORMATS-push/config.xml index 2794432b..67b1da5e 100644 --- a/home/jobs/BIOFORMATS-push/config.xml +++ b/home/jobs/BIOFORMATS-push/config.xml @@ -58,7 +58,9 @@ false false - + + true + testintegration From e313498ae8f35b82d5f13e8c4b393d0399a9b2ea Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 9 Feb 2024 05:26:45 +0000 Subject: [PATCH 69/80] set variable --- home/jenkins.model.JenkinsLocationConfiguration.xml | 2 +- rename.py | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/home/jenkins.model.JenkinsLocationConfiguration.xml b/home/jenkins.model.JenkinsLocationConfiguration.xml index 2d86ae3f..eaad10b8 100644 --- a/home/jenkins.model.JenkinsLocationConfiguration.xml +++ b/home/jenkins.model.JenkinsLocationConfiguration.xml @@ -1,5 +1,5 @@ address not configured yet <nobody@nowhere> - https://BRANCH-ci.openmicroscopy.org/jenkins/ + https://BRANCHCI.openmicroscopy.org/jenkins/ diff --git a/rename.py b/rename.py index 628022ce..aeed195e 100755 --- a/rename.py +++ b/rename.py @@ -12,6 +12,7 @@ def replace(name, branch, uid, user): cnt = 0 + branch_ci = branch + "-ci" for root, dirs, files in os.walk("."): dirs[:] = list([x for x in dirs if not x in EXCLUDE]) env = list(fnmatch.filter(files, ".env")) @@ -26,6 +27,7 @@ def replace(name, branch, uid, user): regexp = re.compile(r'(SPACE[NAME|BRANCH|USER]|1000)') if regexp.search(line) is not None: cnt += 1 + line = line.replace("BRANCHCI", branch_ci) line = line.replace("SPACENAME", name) line = line.replace("SPACEUSER", user) line = line.replace("1000", str(uid)) From fbe5cddf9ea3bfb0045c614001e97f42666b1ec0 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 9 Feb 2024 12:10:12 +0000 Subject: [PATCH 70/80] configure job to allow injection of PRs --- home/jobs/OMERO-server/config.xml | 65 +++++++++++++++++++------------ 1 file changed, 40 insertions(+), 25 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index ec4134da..bd600688 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -1,7 +1,6 @@ - - + - + false @@ -25,12 +24,11 @@ OMERO_SERVER_ZIP_URL - - false + omero @@ -42,8 +40,7 @@ false - -source /home/settings.env + source /home/settings.env OMERO_DB_NAME=$DB_NAME OMERO_DIST=$WORKSPACE/OMERO.server export OMERODIR=$OMERO_DIST @@ -59,29 +56,42 @@ fi rm -rf $WORKSPACE/.venv3 python3 -m venv $WORKSPACE/.venv3 -if [ "$PURGE_DATA" = "true" ]; then - dropdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME || echo "First run or already exists" +if [ "$PURGE_DATA" = "true" ]; then + dropdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME || echo "First run or already exists" rm -rf $OMERO_DATA_DIR else - echo "Skipping PURGE_DATA:CleanDbAndRepo" + echo "Skipping PURGE_DATA:CleanDbAndRepo" fi rm -rf $WORKSPACE/* # Should leave .venv3 + - + OMERO-build src/target/OMERO.server*zip - - + + false + true false - + OMERO-python-superbuild-build **/*.tar.gz - - + + false + + + true + false + + + OMERO-build-build + + + false + true false @@ -96,9 +106,11 @@ mkdir -p $OMERO_DATA_DIR OMERO_DIST=$WORKSPACE/OMERO.server export OMERODIR=$OMERO_DIST +export ZIP_FILE=$WORKSPACE/omero-blitz-VERSION-python.zip +export VERSION_PROPERTIES=$WORKSPACE/version.properties ZIP=$(ls OMERO.server*.zip) -if [ ! -z "$OMERO_SERVER_ZIP_URL" ] +if [ ! -z "$OMERO_SERVER_ZIP_URL" ] then rm -f $ZIP wget -q $OMERO_SERVER_ZIP_URL @@ -110,6 +122,7 @@ rm -f $ZIP mv $WORKSPACE/$DIST $OMERO_DIST source $WORKSPACE/.venv3/bin/activate + pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl pip install -U pip future pip install markdown @@ -132,33 +145,35 @@ omero config set omero.db.name $OMERO_DB_NAME omero config set omero.db.host $OMERO_DB_HOST omero config set omero.db.user $OMERO_DB_USER omero config set omero.data.dir $OMERO_DATA_DIR -omero config set omero.fs.repo.path "%user%_%userId%/%thread%//%year%-%month%/%day%/%time%" +omero config set omero.fs.repo.path "%user%_%userId%/%thread%//%year%-%month%/%day%/%time%" omero config set omero.db.poolsize 25 omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts omero config set omero.security.trustStorePassword changeit omero certificates -if [ "$PURGE_DATA" = "true" ]; then +if [ "$PURGE_DATA" = "true" ]; then createdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME omego db init --serverdir $OMERO_DIST --dbname $OMERO_DB_NAME else - echo "Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade" + echo "Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade" omego db -vvv upgrade --serverdir $OMERO_DIST --dbname $OMERO_DB_NAME fi -export LANG='en_US.UTF-8' -export LANGUAGE='en_US:en' -export LC_ALL='en_US.UTF-8' +export LANG='en_US.UTF-8' +export LANGUAGE='en_US:en' +export LC_ALL='en_US.UTF-8' BUILD_ID=DONT_KILL_ME omero admin start omero admin waitup omero admin diagnostics -deactivate +deactivate + + - + \ No newline at end of file From 2c52088564d209f9c947853484bf4f2e1e857e43 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 9 Feb 2024 13:57:02 +0000 Subject: [PATCH 71/80] adjust url --- nginx/nginx-stable.repo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nginx/nginx-stable.repo b/nginx/nginx-stable.repo index b1de61ff..3c2d4b16 100644 --- a/nginx/nginx-stable.repo +++ b/nginx/nginx-stable.repo @@ -1,6 +1,6 @@ [nginx-stable] name=nginx stable repo -baseurl=http://nginx.org/packages/centos/9/x86_64/ +baseurl=http://nginx.org/packages/centos/$releasever/$basearch/ gpgcheck=1 enabled=1 gpgkey=https://nginx.org/keys/nginx_signing.key From 929abdd811d618cfbb7f612effcbb1a94bafba3c Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 9 Feb 2024 21:32:09 +0000 Subject: [PATCH 72/80] remove output that do not exist --- home/jobs/OMERO-build/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 0d89304e..90df658c 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -85,7 +85,7 @@ source docs/hudson/OMERO.sh - src/target/*.zip,src/target/*.egg,src/target/*.log,src/target/*INFO,target/version.tsv + src/target/*.zip,src/target/*.log,src/target/*INFO false false false From 0c771cb593faf553af8d2ff9d845786286720dbb Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 12 Feb 2024 14:38:40 +0000 Subject: [PATCH 73/80] Clear workspace to avoid build error Errors will occur if not clean e.g. Your local changes to the following files would be overwritten by checkout: src/loci/formats/in/ZarrReader.java --- home/jobs/BIOFORMATS-build/config.xml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/home/jobs/BIOFORMATS-build/config.xml b/home/jobs/BIOFORMATS-build/config.xml index 03294bbf..74991e48 100644 --- a/home/jobs/BIOFORMATS-build/config.xml +++ b/home/jobs/BIOFORMATS-build/config.xml @@ -48,7 +48,12 @@ false false - + + false + + + true + testintegration From 8182f7af8182a0b1c1e19e0d18e831d84ca2e2d3 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Feb 2024 07:03:55 +0000 Subject: [PATCH 74/80] review configuration to allow injection of PRs --- home/jobs/OMERO-test-integration/config.xml | 16 ++++++++++-- home/jobs/OMERO-training/config.xml | 16 ++++++++++-- home/jobs/OMERO-web/config.xml | 28 +++++++++++++++------ 3 files changed, 49 insertions(+), 11 deletions(-) diff --git a/home/jobs/OMERO-test-integration/config.xml b/home/jobs/OMERO-test-integration/config.xml index 1466718a..dd480de5 100644 --- a/home/jobs/OMERO-test-integration/config.xml +++ b/home/jobs/OMERO-test-integration/config.xml @@ -48,7 +48,7 @@ dropdb -f -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME || echo Already exi rm -rf $WORKSPACE/* - + OMERO-build src/target/openmicroscopy*zip @@ -57,7 +57,7 @@ rm -rf $WORKSPACE/* true false - + OMERO-python-superbuild-build **/*.tar.gz @@ -66,9 +66,21 @@ rm -rf $WORKSPACE/* true false + + OMERO-build-build + + + false + + + true + false + source /home/settings.env +export ZIP_FILE=$WORKSPACE/omero-blitz-VERSION-python.zip +export VERSION_PROPERTIES=$WORKSPACE/version.properties OMERO_DB_NAME=$JOB_NAME OMERO_DATA_DIR=$WORKSPACE/data diff --git a/home/jobs/OMERO-training/config.xml b/home/jobs/OMERO-training/config.xml index 0b5315ba..9e265d4c 100644 --- a/home/jobs/OMERO-training/config.xml +++ b/home/jobs/OMERO-training/config.xml @@ -29,7 +29,7 @@ pip install jinja2 rm -rf $WORKSPACE/* - + OMERO-python-superbuild-build **/*.gz @@ -38,7 +38,7 @@ rm -rf $WORKSPACE/* true false - + OMERO-build src/target/OMERO.server*zip,src/target/openmicroscopy*zip @@ -47,10 +47,22 @@ rm -rf $WORKSPACE/* true false + + OMERO-build-build + + + false + + + true + false + source /home/settings.env +export ZIP_FILE=$WORKSPACE/omero-blitz-VERSION-python.zip +export VERSION_PROPERTIES=$WORKSPACE/version.properties # UNZIP openmicroscopy OMERO_EXAMPLE_DIST=$WORKSPACE/openmicroscopy diff --git a/home/jobs/OMERO-web/config.xml b/home/jobs/OMERO-web/config.xml index 618e9a06..347233a6 100644 --- a/home/jobs/OMERO-web/config.xml +++ b/home/jobs/OMERO-web/config.xml @@ -52,20 +52,32 @@ fi rm -rf $HOME/static/web/ rm -rf $WORKSPACE/* - + OMERO-build src/target/OMERO.server*zip - - + + false + true false - + OMERO-python-superbuild-build - **/*.gz - - + **/*.tar.gz + + false + + + true + false + + + OMERO-build-build + + + false + true false @@ -74,6 +86,8 @@ rm -rf $WORKSPACE/* OMERO_DIST=$WORKSPACE/OMERO.web export OMERODIR=$OMERO_DIST +export ZIP_FILE=$WORKSPACE/omero-blitz-VERSION-python.zip +export VERSION_PROPERTIES=$WORKSPACE/version.properties ZIP=$(ls OMERO.server*.zip) if [ ! -z "$OMERO_PY_ZIP_URL" ] From 68a4e3e5e620857167ac93f1c435fed9fc1e8058 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Feb 2024 11:46:12 +0000 Subject: [PATCH 75/80] Add ulimits. Server startup was very slow without see https://github.com/netdata/netdata/pull/14092/ --- docker-compose.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index 83a3f2d1..75833203 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -44,6 +44,10 @@ services: ports: - "${OMERO_SERVER_TEST_SSL}14064" - "${OMERO_SERVER_TEST_TCP}14063" + ulimits: + nofile: + soft: 8192 + hard: 65536 omero: build: @@ -62,6 +66,10 @@ services: ports: - "${OMERO_SERVER_SSL}4064" - "${OMERO_SERVER_TCP}4063" + ulimits: + nofile: + soft: 8192 + hard: 65536 web: build: From 9873831548ad3f1d9e7b035ba0d500b00a1d76ea Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Feb 2024 13:24:53 +0000 Subject: [PATCH 76/80] add instructions to run test-folder job --- README.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/README.md b/README.md index d00bece8..044ccf4f 100644 --- a/README.md +++ b/README.md @@ -202,3 +202,12 @@ See [Troubleshooting](Troubleshooting.md) # Upgrade See [Changelog](CHANGELOG.md) + +# Run BioFormats jobs + +To run the BioFormats testing the various readers on sample data, you will need to activate the a private +job + +* In the ``devspace``, create a directory ``home/jobs/DATA_REPO_CONFIG-merge/`` +* Download the job configuration from ``config.xml`` in https://github.com/openmicroscopy/management_tools/tree/master/ci/jobs/DATA_REPO_CONFIG-merge (private repository) and place it in the newly created directory +* Comment out the line ``build job: "DATA_REPO_CONFIG-merge"`` in the ``trigger`` job From a3a98291c8c34905393be84803bffcf75b49f248 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 13 Feb 2024 15:57:51 +0000 Subject: [PATCH 77/80] bump devagent to 0.8.1 --- docker/Dockerfile | 2 +- nginx/Dockerfile | 2 +- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- web/Dockerfile | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index a0d03763..4b6d82ae 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devagent:0.8.0 +FROM openmicroscopy/devagent:0.8.1 MAINTAINER OME diff --git a/nginx/Dockerfile b/nginx/Dockerfile index ad4cb4cd..1bbbf2a5 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devagent:0.8.0 +FROM openmicroscopy/devagent:0.8.1 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index c1b016af..01a2fb1e 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devagent:0.8.0 +FROM openmicroscopy/devagent:0.8.1 MAINTAINER OME diff --git a/slave/Dockerfile b/slave/Dockerfile index 5e898dbb..9aa7052d 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devagent:0.8.0 +FROM openmicroscopy/devagent:0.8.1 MAINTAINER OME diff --git a/web/Dockerfile b/web/Dockerfile index 32d0e4a4..daed2cd7 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devagent:0.8.0 +FROM openmicroscopy/devagent:0.8.1 MAINTAINER OME From 7038757d598030a2685dd607e12ddce914231c46 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 27 Feb 2024 18:04:44 +0000 Subject: [PATCH 78/80] install cli-duplicate from snoopy --- home/jobs/OMERO-server/config.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index bd600688..5bb6d308 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -134,6 +134,7 @@ pip install omero-py pip install git+https://github.com/$SPACE_USER/omero-metadata.git@$MERGE_PUSH_BRANCH#egg=omero-metadata pip install git+https://github.com/$SPACE_USER/omero-cli-render.git@$MERGE_PUSH_BRANCH#egg=omero-cli-render +pip install git+https://github.com/$SPACE_USER/omero-cli-duplicate.git@$MERGE_PUSH_BRANCH#egg=omero-cli-duplicate pip install omero-certificates for x in *.tar.gz; do From bfa15205214f3a36ec636309f781975a8531a848 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 27 Feb 2024 18:08:47 +0000 Subject: [PATCH 79/80] add email config --- home/jobs/OMERO-server/config.xml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 5bb6d308..cc436d3f 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -150,6 +150,9 @@ omero config set omero.fs.repo.path "%user%_%userId%/%thread%//%year%-%month%/%d omero config set omero.db.poolsize 25 omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts omero config set omero.security.trustStorePassword changeit +omero config set omero.mail.config true +//omero config set omero.mail.from your_address +//omero config set omero.mail.host your_smtp_server_for_example omero certificates if [ "$PURGE_DATA" = "true" ]; then From 59f9b7ebef924a71dafab4c31137915323de6d99 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 15 Mar 2024 07:40:45 +0000 Subject: [PATCH 80/80] fix comment --- home/jobs/OMERO-server/config.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index cc436d3f..179ccfe8 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -151,8 +151,8 @@ omero config set omero.db.poolsize 25 omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts omero config set omero.security.trustStorePassword changeit omero config set omero.mail.config true -//omero config set omero.mail.from your_address -//omero config set omero.mail.host your_smtp_server_for_example +# omero config set omero.mail.from your_address +# omero config set omero.mail.host your_smtp_server_for_example omero certificates if [ "$PURGE_DATA" = "true" ]; then