From 7f22c78aac64e7be49eb9bfab54c2a91b6fafe10 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 15 Jan 2022 08:53:52 +0000 Subject: [PATCH 01/44] test with lts --- jenkins/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index dec089c5..304a2a3c 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -1,4 +1,4 @@ -FROM jenkins/jenkins:2.150.3 +FROM jenkins/jenkins:lts MAINTAINER OME # Temp fix robot test results From 4b6ed160bdfc4e85f3283b253e9375519a1ade65 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Sat, 15 Jan 2022 09:14:55 +0000 Subject: [PATCH 02/44] do not use devel --- slave/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 0e912ea1..4ec08fba 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -3,7 +3,7 @@ FROM openmicroscopy/devslave-c7:0.6.1 MAINTAINER OME ARG JAVAVER=openjdk1.8 -ARG ICEVER=ice36-devel +ARG ICEVER=ice36 # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh From 5481d0697b8a742897dd9fb836e96e1b8118f6fc Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 17 Jan 2022 17:13:51 +0000 Subject: [PATCH 03/44] build with develop --- server/Dockerfile | 20 +++++++++----------- slave/Dockerfile | 19 ++++++++----------- web/Dockerfile | 11 ++++------- 3 files changed, 21 insertions(+), 29 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 8752e00b..8a84f4e4 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -9,12 +9,13 @@ ARG ICEVER=ice36 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 username https://github.com/username/omero-install.git -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch username -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge username/yourbranch +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -31,9 +32,6 @@ 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 -# remove nginx -RUN rm -rf $OMERO_INSTALL/step05_centos7_nginx.sh -RUN touch $OMERO_INSTALL/step05_centos7_nginx.sh # no systemd RUN rm -rf $OMERO_INSTALL/step06_centos7_daemon.sh RUN touch $OMERO_INSTALL/step06_centos7_daemon.sh @@ -43,13 +41,13 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7_nginx.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh # install postgres tools -RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ - && yum clean all -RUN yum -y install postgresql10 \ - && yum clean all +#RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ + # && yum clean all +#RUN yum -y install postgresql10 \ +# && yum clean all EXPOSE 4064 EXPOSE 4063 diff --git a/slave/Dockerfile b/slave/Dockerfile index 4ec08fba..274e33fd 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -12,9 +12,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add username https://github.com/username/omero-install.git -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch username -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge username/yourbranch +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -31,9 +31,6 @@ 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 -# remove nginx -RUN rm -rf $OMERO_INSTALL/step05_centos7_nginx.sh -RUN touch $OMERO_INSTALL/step05_centos7_nginx.sh # no systemd RUN rm -rf $OMERO_INSTALL/step06_centos7_daemon.sh RUN touch $OMERO_INSTALL/step06_centos7_daemon.sh @@ -43,7 +40,7 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7_nginx.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh # Install FindBugs ENV FINDBUGS_VERSION 3.0.0 @@ -57,10 +54,10 @@ RUN curl -fSLO http://downloads.sourceforge.net/project/findbugs/findbugs/$FINDB RUN yum -y install maven ant && yum clean all # install postgres tools -RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ - && yum clean all -RUN yum -y install postgresql10 \ - && yum clean all +#RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ +# && yum clean all +#RUN yum -y install postgresql10 \ +# && yum clean all # gradle RUN cd /opt && \ diff --git a/web/Dockerfile b/web/Dockerfile index 2b3fea10..97be9997 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -15,9 +15,9 @@ 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 username https://github.com/username/omero-install.git -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch username -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge username/yourbranch +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -34,9 +34,6 @@ RUN touch $OMERO_INSTALL/step02_all_setup.sh # omeroweb will be isntalled by the job RUN rm -f $OMERO_INSTALL/step04_all_omero.sh RUN touch $OMERO_INSTALL/step04_all_omero.sh -# remove nginx -RUN mv $OMERO_INSTALL/step05_centos7_nginx.sh $OMERO_INSTALL/_step05_centos7_nginx.sh -RUN touch $OMERO_INSTALL/step05_centos7_nginx.sh # no systemd RUN rm -rf $OMERO_INSTALL/step06_centos7_daemon.sh RUN touch $OMERO_INSTALL/step06_centos7_daemon.sh @@ -46,7 +43,7 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7_nginx.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh # manually install ICEPY dependences RUN yum -y install gcc-c++ From 6ea59155020261a02d23aa3c865a2fe903d64709 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 18 Jan 2022 13:09:04 +0000 Subject: [PATCH 04/44] prepare installation --- server/Dockerfile | 29 +++++++++++++++++------------ server/run.sh | 6 +++--- slave/Dockerfile | 30 ++++++++++++++++++------------ slave/run.sh | 6 +++--- web/Dockerfile | 10 ++++++---- 5 files changed, 47 insertions(+), 34 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 8a84f4e4..8fbc9e09 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -5,6 +5,13 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 +RUN yum -y install ca-certificates + +# Remove the existing omero user +RUN userdel -r omero && \ + rm -f /etc/sudoers.d/omero && \ + echo 'root:omero' | chpasswd + # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh @@ -13,9 +20,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -41,19 +48,17 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh # install postgres tools -#RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ - # && yum clean all -#RUN yum -y install postgresql10 \ -# && yum clean all +RUN yum -y install postgresql10 \ + && yum clean all EXPOSE 4064 EXPOSE 4063 ADD ./run.sh /tmp/run.sh -RUN chown omero:omero /tmp/run.sh +RUN chown omero-server:omero-server /tmp/run.sh RUN chmod a+x /tmp/run.sh RUN yum install -y python36 @@ -74,10 +79,10 @@ 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 +RUN usermod -u $USER_ID omero-server # make sure mounted volumes has correct permissions -VOLUME ["/home/omero"] +VOLUME ["/home/omero-server"] -USER omero +USER omero-server CMD ["/tmp/run.sh"] diff --git a/server/run.sh b/server/run.sh index 7ad032c2..5c14e8dd 100644 --- a/server/run.sh +++ b/server/run.sh @@ -1,12 +1,12 @@ #!/bin/bash function shut_down() { - /home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin stop + /home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin stop } /tmp/jenkins-slave.sh & -/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin start -/home/omero/workspace/OMERO-server/OMERO.server/bin/omero admin diagnostics +/home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin start +/home/omero-server/workspace/OMERO-server/OMERO.server/bin/omero admin diagnostics trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT diff --git a/slave/Dockerfile b/slave/Dockerfile index 274e33fd..fb26361b 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -5,6 +5,14 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 +RUN yum -y install ca-certificates + + +# Remove the existing omero user +RUN userdel -r omero && \ + rm -f /etc/sudoers.d/omero && \ + echo 'root:omero' | chpasswd + # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh @@ -12,9 +20,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -40,7 +48,7 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh # Install FindBugs ENV FINDBUGS_VERSION 3.0.0 @@ -54,10 +62,8 @@ RUN curl -fSLO http://downloads.sourceforge.net/project/findbugs/findbugs/$FINDB RUN yum -y install maven ant && yum clean all # install postgres tools -#RUN yum -y install https://download.postgresql.org/pub/repos/yum/reporpms/EL-7-x86_64/pgdg-redhat-repo-latest.noarch.rpm \ -# && yum clean all -#RUN yum -y install postgresql10 \ -# && yum clean all +RUN yum -y install postgresql10-server postgresql10 \ + && yum clean all # gradle RUN cd /opt && \ @@ -72,7 +78,7 @@ EXPOSE 14064 EXPOSE 14063 ADD ./run.sh /tmp/run.sh -RUN chown omero:omero /tmp/run.sh +RUN chown omero-server:omero-server /tmp/run.sh RUN chmod a+x /tmp/run.sh RUN yum install -y python36 @@ -83,10 +89,10 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" # Change user id to fix permissions issues ARG USER_ID=1000 -RUN usermod -u $USER_ID omero +RUN usermod -u $USER_ID omero-server # make sure mounted volumes has correct permissions -VOLUME ["/home/omero"] +VOLUME ["/home/omero-server"] -USER omero +USER omero-server CMD ["/tmp/run.sh"] diff --git a/slave/run.sh b/slave/run.sh index bf0111e5..246019f5 100644 --- a/slave/run.sh +++ b/slave/run.sh @@ -1,12 +1,12 @@ #!/bin/bash function shut_down() { - /home/omero/workspace/OMERO-test-integration/src/dist/bin/omero admin stop + /home/omero-server/workspace/OMERO-test-integration/src/dist/bin/omero admin stop } /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 +/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 trap "shut_down" SIGKILL SIGTERM SIGHUP SIGINT EXIT diff --git a/web/Dockerfile b/web/Dockerfile index 97be9997..3270f7ad 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -8,6 +8,8 @@ ARG ICEVER=noice # make ICEVERSION environment variable to use in OMERO-web job ENV ICEVERSION ${ICEVER:-noice} +RUN yum -y install ca-certificates + # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh @@ -15,9 +17,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop ADD ./settings.env $OMERO_INSTALL/settings.env @@ -43,7 +45,7 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER bash install_centos7.sh +RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh # manually install ICEPY dependences RUN yum -y install gcc-c++ From 11c2b5e4623ac52ea775f6bbea5118373d87743d Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 18 Jan 2022 13:58:35 +0000 Subject: [PATCH 05/44] do not run omero-install --- web/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/web/Dockerfile b/web/Dockerfile index 3270f7ad..f76dc47a 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -22,8 +22,8 @@ RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop -ADD ./settings.env $OMERO_INSTALL/settings.env -RUN chmod +x $OMERO_INSTALL/settings.env +#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 @@ -45,7 +45,7 @@ RUN touch $OMERO_INSTALL/requirements.txt WORKDIR /tmp/omero-install/linux -RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh +#RUN JAVAVER=$JAVAVER ICEVER=$ICEVER PGVER=nopg bash install_centos7.sh # manually install ICEPY dependences RUN yum -y install gcc-c++ From c8e25286cfa55ed2b72e3cdf457a35cabce092c2 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 18 Jan 2022 15:04:16 +0000 Subject: [PATCH 06/44] build from ome --- server/Dockerfile | 8 +++++--- slave/Dockerfile | 7 ++++--- web/Dockerfile | 8 ++++---- 3 files changed, 13 insertions(+), 10 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 8fbc9e09..3a1d208d 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -4,6 +4,8 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 +ARG TAG=v5.6.3 +ARG BRANCH=develop RUN yum -y install ca-certificates @@ -20,9 +22,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env diff --git a/slave/Dockerfile b/slave/Dockerfile index fb26361b..ca1c6d75 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -4,6 +4,7 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 +ARG BRANCH=develop RUN yum -y install ca-certificates @@ -20,9 +21,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env diff --git a/web/Dockerfile b/web/Dockerfile index f76dc47a..df40781e 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -4,7 +4,7 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=noice - +ARG BRANCH=develop # make ICEVERSION environment variable to use in OMERO-web job ENV ICEVERSION ${ICEVER:-noice} @@ -17,9 +17,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/develop +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH #ADD ./settings.env $OMERO_INSTALL/settings.env From eeef545fae55820cca9651def660d4b0f8760853 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 18 Jan 2022 16:05:33 +0000 Subject: [PATCH 07/44] plugin --- jenkins/plugins.txt | 160 ++++++++++++++++++++++---------------------- 1 file changed, 80 insertions(+), 80 deletions(-) diff --git a/jenkins/plugins.txt b/jenkins/plugins.txt index 58e3a64e..7a33b26d 100644 --- a/jenkins/plugins.txt +++ b/jenkins/plugins.txt @@ -1,104 +1,104 @@ -swarm:3.15 -git:4.0.0-rc -git-client:3.0.0-rc -git-server:1.7 -mailer:1.23 -scm-api:2.3.0 -matrix-project:1.14 -ssh-credentials:1.14 -credentials:2.1.18 -script-security:1.54 -role-strategy:2.10 -matrix-auth:2.3 -icon-shim:2.0.3 -authentication-tokens:1.3 +swarm +git +git-client +git-server +mailer +scm-api: +matrix-project +ssh-credentials +credentials +script-security +role-strategy +matrix-auth +icon-shim +authentication-tokens -junit:1.27 -testng-plugin:1.15 +junit +testng-plugin -jdk-tool:1.2 -javadoc:1.5 +jdk-tool +javadoc -artifactory:3.2.1 -ant:1.9 -gradle:1.30 -ivy:1.28 -config-file-provider:3.5 +artifactory +ant +gradle +ivy +config-file-provider -copyartifact:1.42 +copyartifact -branch-api:2.1.2 -mapdb-api:1.0.9.0 -display-url-api:2.3.0 -structs:1.17 -conditional-buildstep:1.3.6 -run-condition:1.2 +branch-api +mapdb-api +display-url-api +structs +conditional-buildstep +run-condition # As a repository -repository:1.3 -maven-plugin:3.2 -apache-httpcomponents-client-4-api:4.5.5-3.0 -jsch:0.1.55 +repository +maven-plugin +apache-httpcomponents-client-4-api +jsch # Optional -parameterized-trigger:2.35.2 -subversion:2.12.1 -token-macro:2.7 -promoted-builds:3.2 -cloudbees-folder:6.7 +parameterized-trigger +subversion +token-macro +promoted-builds +cloudbees-folder # Workflow # See: https://github.com/jenkinsci/workflow-plugin/blob/master/demo/plugins.txt -durable-task:1.29 -ace-editor:1.1 -jquery-detached:1.2.1 -lockable-resources:2.4 -workflow-aggregator:2.6 -workflow-api:2.33 -workflow-basic-steps:2.14 -workflow-cps:2.64 -workflow-cps-global-lib:2.13 -workflow-durable-task-step:2.29 -workflow-job:2.31 -workflow-multibranch:2.21 -workflow-remote-loader:1.4 -workflow-scm-step:2.7 -workflow-step-api:2.19 -workflow-support:3.2 +durable-task +ace-editor +jquery-detached +lockable-resources +workflow-aggregator +workflow-api +workflow-basic-steps +workflow-cps +workflow-cps-global-lib +workflow-durable-task-step +workflow-job +workflow-multibranch +workflow-remote-loader +workflow-scm-step +workflow-step-api +workflow-support -pipeline-rest-api:2.10 -pipeline-stage-view:2.10 -pipeline-stage-step:2.3 -pipeline-build-step:2.7 -pipeline-input-step:2.9 -pipeline-milestone-step:1.3.1 -pipeline-graph-analysis:1.9 -pipeline-model-definition:1.3.6 -pipeline-model-api:1.3.6 -pipeline-model-declarative-agent:1.1.1 -pipeline-model-extensions:1.3.6 -pipeline-stage-tags-metadata:1.3.6 -jackson2-api:2.9.8 +pipeline-rest-api +pipeline-stage-view +pipeline-stage-step +pipeline-build-step +pipeline-input-step +pipeline-milestone-step +pipeline-graph-analysis +pipeline-model-definition: +pipeline-model-api +pipeline-model-declarative-agent +pipeline-model-extensions +pipeline-stage-tags-metadata +jackson2-api -docker-workflow:1.17 -docker-commons:1.13 +docker-workflow +docker-commons -credentials-binding:1.18 -plain-credentials:1.5 -handlebars:1.1.1 -momentjs:1.1.1 +credentials-binding +plain-credentials +handlebars +momentjs # Robot robot:1.6.5 # Utils -greenballs:1.15 -timestamper:1.9 -jobConfigHistory:2.19 -rundeck:3.6.4 +greenballs +timestamper +jobConfigHistory +rundeck # ldap -ldap:1.20 +ldap # GitHub OAuth -github-oauth:0.32 \ No newline at end of file +github-oauth From 7c8a3700e946541aea30a255201a589821d91c27 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 21 Jan 2022 09:40:43 +0000 Subject: [PATCH 08/44] use perso repo --- docker/Dockerfile | 2 +- nginx/Dockerfile | 2 +- server/Dockerfile | 4 +--- slave/Dockerfile | 4 +--- web/Dockerfile | 3 +-- 5 files changed, 5 insertions(+), 10 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index bfedd9ed..ddf1fced 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.6.1 +FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME diff --git a/nginx/Dockerfile b/nginx/Dockerfile index e66c56c5..bc6fdb38 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.6.1 +FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index 3a1d208d..28ad9d69 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.6.1 +FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME @@ -7,8 +7,6 @@ ARG ICEVER=ice36 ARG TAG=v5.6.3 ARG BRANCH=develop -RUN yum -y install ca-certificates - # Remove the existing omero user RUN userdel -r omero && \ rm -f /etc/sudoers.d/omero && \ diff --git a/slave/Dockerfile b/slave/Dockerfile index ca1c6d75..2af22720 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.6.1 +FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME @@ -6,8 +6,6 @@ ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 ARG BRANCH=develop -RUN yum -y install ca-certificates - # Remove the existing omero user RUN userdel -r omero && \ diff --git a/web/Dockerfile b/web/Dockerfile index df40781e..8a29884a 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.6.1 +FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME @@ -8,7 +8,6 @@ ARG BRANCH=develop # make ICEVERSION environment variable to use in OMERO-web job ENV ICEVERSION ${ICEVER:-noice} -RUN yum -y install ca-certificates # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh From a75e5106c5916f26d7333ae44c209f5650e02508 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 21 Jan 2022 10:23:25 +0000 Subject: [PATCH 09/44] review user --- docker-compose.yml | 8 +++---- server/Dockerfile | 7 +++--- slave/Dockerfile | 17 +++++--------- web/Dockerfile | 58 ++++++++++++++++------------------------------ 4 files changed, 33 insertions(+), 57 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 5e1e4c37..0b759ee0 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -56,7 +56,7 @@ services: networks: - omero-network volumes: - - ./server:/home/omero + - ./server:/home/omero-server environment: - SLAVE_NAME=omero - SLAVE_EXECUTORS=2 @@ -74,8 +74,8 @@ services: networks: - omero-network volumes: - - ./web:/home/omero - - ./nginx/conf.d:/home/omero/nginx + - ./web:/home/omero-web + - ./nginx/conf.d:/home/omero-web/nginx environment: - SLAVE_NAME=web - SLAVE_EXECUTORS=2 @@ -91,7 +91,7 @@ services: - omero-network volumes: - ./nginx/conf.d:/etc/nginx/conf.d - - ./web/static:/home/omero/static + - ./web/static:/home/omero-web/static - ./nginx/log:/var/log/nginx - ./nginx/sslcert:/etc/nginx/ssl environment: diff --git a/server/Dockerfile b/server/Dockerfile index 28ad9d69..50ad838b 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -4,7 +4,6 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 -ARG TAG=v5.6.3 ARG BRANCH=develop # Remove the existing omero user @@ -20,9 +19,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH +#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome +#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env diff --git a/slave/Dockerfile b/slave/Dockerfile index 2af22720..a6320bf1 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -4,14 +4,9 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 -ARG BRANCH=develop +ARG BRANCH=test -# Remove the existing omero user -RUN userdel -r omero && \ - rm -f /etc/sudoers.d/omero && \ - echo 'root:omero' | chpasswd - # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh @@ -19,7 +14,7 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add ome https://github.com/jburel/omero-install.git RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH @@ -77,7 +72,7 @@ EXPOSE 14064 EXPOSE 14063 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 RUN yum install -y python36 @@ -88,10 +83,10 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" # 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/web/Dockerfile b/web/Dockerfile index 8a29884a..85fd16a3 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -9,42 +9,24 @@ ARG BRANCH=develop ENV ICEVERSION ${ICEVER:-noice} +# Remove the existing omero user +RUN userdel -r omero && \ + rm -f /etc/sudoers.d/omero && \ + echo 'root:omero' | chpasswd + +# Create the omero-web user +RUN useradd omero-web && \ + echo 'omero-web:omero-web' | chpasswd && \ + echo "omero-web ALL= (ALL) NOPASSWD: ALL" >> /etc/sudoers.d/omero-web + + # skip some omero-install RUN echo 'export container=docker' > /etc/profile.d/docker.sh ENV OMERO_INSTALL_ROOT=/tmp/omero-install -## update omero-install to the latest one -#RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$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 -RUN rm -f $OMERO_INSTALL/setup_omero_db.sh -RUN touch $OMERO_INSTALL/setup_omero_db.sh -# do not create user -RUN rm -f $OMERO_INSTALL/step02_all_setup.sh -RUN touch $OMERO_INSTALL/step02_all_setup.sh -# omeroweb will be isntalled 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 $OMERO_INSTALL/settings.env +RUN chmod +x $OMERO_INSTALL/settings.env # manually install ICEPY dependences RUN yum -y install gcc-c++ @@ -61,7 +43,7 @@ RUN yum install -y python-redis && yum clean all EXPOSE 4080 ADD ./run.sh /tmp/run.sh -RUN chown omero:omero /tmp/run.sh +RUN chown omero-web:omero-web /tmp/run.sh RUN chmod a+x /tmp/run.sh RUN yum install -y python36 @@ -72,13 +54,13 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" # Change user id to fix permissions issues ARG USER_ID=1000 -RUN usermod -u $USER_ID omero +RUN usermod -u $USER_ID omero-web # make sure mounted volumes has correct permissions -RUN mkdir -p /home/omero/nginx -RUN chown -R omero:omero /home/omero/nginx +RUN mkdir -p /home/omero-web/nginx +RUN chown -R omero-web:omero-web /home/omero-web/nginx -VOLUME ["/home/omero", "/home/omero/nginx"] +VOLUME ["/home/omero-web", "/home/omero-web/nginx"] -USER omero +USER omero-web CMD ["/tmp/run.sh"] From c6919402a7d642e5305a103e8aff9c8c8af1688f Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 21 Jan 2022 10:44:53 +0000 Subject: [PATCH 10/44] point to repo --- slave/Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index a6320bf1..778c612c 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -14,9 +14,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env From 257dfc8afac88819219ec440abd75690708c4136 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 24 Jan 2022 10:07:47 +0000 Subject: [PATCH 11/44] point to perso branch --- server/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/server/Dockerfile b/server/Dockerfile index 50ad838b..ca52cbbc 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -4,7 +4,7 @@ MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 -ARG BRANCH=develop +ARG BRANCH=test # Remove the existing omero user RUN userdel -r omero && \ @@ -19,9 +19,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add ome https://github.com/ome/omero-install.git -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch ome -#RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge ome/$BRANCH +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel +RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/$BRANCH ADD ./settings.env $OMERO_INSTALL/settings.env From ef48dc6cacd59166b125ac9a5f6f800108511249 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 24 Jan 2022 10:08:03 +0000 Subject: [PATCH 12/44] remove deprecated plugins --- jenkins/plugins.txt | 2 -- 1 file changed, 2 deletions(-) diff --git a/jenkins/plugins.txt b/jenkins/plugins.txt index 7a33b26d..479801d8 100644 --- a/jenkins/plugins.txt +++ b/jenkins/plugins.txt @@ -10,7 +10,6 @@ credentials script-security role-strategy matrix-auth -icon-shim authentication-tokens junit @@ -76,7 +75,6 @@ pipeline-milestone-step pipeline-graph-analysis pipeline-model-definition: pipeline-model-api -pipeline-model-declarative-agent pipeline-model-extensions pipeline-stage-tags-metadata jackson2-api From c5b0e87388847564e98d3cd1259bd36a731d9ffd Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 24 Jan 2022 10:24:29 +0000 Subject: [PATCH 13/44] drop version --- jenkins/plugins.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jenkins/plugins.txt b/jenkins/plugins.txt index 479801d8..910df4b2 100644 --- a/jenkins/plugins.txt +++ b/jenkins/plugins.txt @@ -88,7 +88,7 @@ handlebars momentjs # Robot -robot:1.6.5 +robot # Utils greenballs From 2aa5f01ea8b4d011b035881ebbfe9950f78e1334 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 24 Jan 2022 13:50:34 +0000 Subject: [PATCH 14/44] remove version --- home/jobs/BIOFORMATS-build/config.xml | 4 ++-- home/jobs/BIOFORMATS-push/config.xml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/home/jobs/BIOFORMATS-build/config.xml b/home/jobs/BIOFORMATS-build/config.xml index 8674e397..b9c07e93 100644 --- a/home/jobs/BIOFORMATS-build/config.xml +++ b/home/jobs/BIOFORMATS-build/config.xml @@ -1,5 +1,5 @@ - + false @@ -22,7 +22,7 @@ - + 2 diff --git a/home/jobs/BIOFORMATS-push/config.xml b/home/jobs/BIOFORMATS-push/config.xml index 078f2edd..d04f1d2b 100644 --- a/home/jobs/BIOFORMATS-push/config.xml +++ b/home/jobs/BIOFORMATS-push/config.xml @@ -32,7 +32,7 @@ - + 2 From 9455c00c7954a5b45d6ccb3abf0bf319cf6fc079 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 24 Jan 2022 15:18:51 +0000 Subject: [PATCH 15/44] instal plugins using jar file --- jenkins/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index 304a2a3c..5257022c 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -5,7 +5,9 @@ MAINTAINER OME ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" COPY plugins.txt /usr/share/jenkins/ref/plugins.txt -RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt + +RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt +#RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt USER root RUN chown -R jenkins:jenkins /var/jenkins_home From 2b70888514a7ccc6b76bf16a43d60b816c79019e Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 25 Jan 2022 15:14:21 +0000 Subject: [PATCH 16/44] add plugin --- jenkins/plugins.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/jenkins/plugins.txt b/jenkins/plugins.txt index 910df4b2..79509585 100644 --- a/jenkins/plugins.txt +++ b/jenkins/plugins.txt @@ -11,6 +11,7 @@ script-security role-strategy matrix-auth authentication-tokens +authorize-project junit testng-plugin @@ -73,7 +74,7 @@ pipeline-build-step pipeline-input-step pipeline-milestone-step pipeline-graph-analysis -pipeline-model-definition: +pipeline-model-definition pipeline-model-api pipeline-model-extensions pipeline-stage-tags-metadata From 4d54fd8ba8c310f4302ce9684f1d665ed6817ae3 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 26 Jan 2022 12:56:43 +0000 Subject: [PATCH 17/44] update instructions --- README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index d5c2c7a6..2b39d408 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,17 @@ 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. - + You need to use a public key without a passphrase and a `.gitconfig` file containing + the following sections: + ``` + [user] + name = YOUR_NAME + email = YOUR_EMAIL + [github] + token = YOUR_GITHUB_TOKEN + user = YOUR_GITHUB_NAME + ``` + * 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 From 1d682444c5bbc4b3719b00ecb8a156521cda82b0 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 26 Jan 2022 17:13:02 +0000 Subject: [PATCH 18/44] archive properties file --- home/jobs/BIOFORMATS-push/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/BIOFORMATS-push/config.xml b/home/jobs/BIOFORMATS-push/config.xml index d04f1d2b..2794432b 100644 --- a/home/jobs/BIOFORMATS-push/config.xml +++ b/home/jobs/BIOFORMATS-push/config.xml @@ -123,7 +123,7 @@ foreach-get-version-as-property > ${WORKSPACE}/target/version.properties - target/version.tsv + target/version.tsv, target/version.properties false false false From 041d8fbb56e5bfb9371342212b15edb468ef1f08 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 26 Jan 2022 21:22:39 +0000 Subject: [PATCH 19/44] bump gradle version --- slave/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 778c612c..87446fb8 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -61,10 +61,10 @@ RUN yum -y install postgresql10-server postgresql10 \ # gradle RUN cd /opt && \ - curl -fSLO https://services.gradle.org/distributions/gradle-5.2.1-bin.zip && \ - unzip gradle-5.2.1-bin.zip && \ - rm gradle-5.2.1-bin.zip && \ - ln -s /opt/gradle-5.2.1/bin/gradle /usr/local/bin/gradle + curl -fSLO https://services.gradle.org/distributions/gradle-6.8.3-bin.zip && \ + unzip gradle-6.8.3-bin.zip && \ + rm gradle-6.8.3-bin.zip && \ + ln -s /opt/gradle-6.8.3/bin/gradle /usr/local/bin/gradle # Needed for Gradle ENV JAVA_HOME /usr/lib/jvm/jre-1.8.0-openjdk From c7182e5a828df541fa3415c5a90c070ee8b094ac Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 27 Jan 2022 10:15:03 +0000 Subject: [PATCH 20/44] install ice-devel --- slave/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 87446fb8..f9ec0c98 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -3,7 +3,7 @@ FROM jburel/devslave-c7-docker:0.6.9 MAINTAINER OME ARG JAVAVER=openjdk1.8 -ARG ICEVER=ice36 +ARG ICEVER=ice36-devel ARG BRANCH=test From a329b16f78db150230cd821415ff52b0e5dc9b64 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 27 Jan 2022 11:05:10 +0000 Subject: [PATCH 21/44] create symlink --- slave/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/slave/Dockerfile b/slave/Dockerfile index f9ec0c98..bedbd7bb 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -78,6 +78,7 @@ RUN chmod a+x /tmp/run.sh RUN yum install -y python36 RUN python3 -m venv /py3 && /py3/bin/pip install -U pip tox future wheel restructuredtext-lint RUN /py3/bin/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 +RUN ln -s /py3/bin/slice2py /usr/bin/slice2py ENV VIRTUAL_ENV=/py3 ENV PATH="$VIRTUAL_ENV/bin:$PATH" From 4622f3c0b27644fa06f45527e2ce05b530f6afe1 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 31 Jan 2022 10:53:50 +0000 Subject: [PATCH 22/44] set permissions --- web/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/web/Dockerfile b/web/Dockerfile index 85fd16a3..02ab46e6 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -56,6 +56,8 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" ARG USER_ID=1000 RUN usermod -u $USER_ID omero-web +RUN chown -R omero-web:omero-web /home/omero-web/static + # make sure mounted volumes has correct permissions RUN mkdir -p /home/omero-web/nginx RUN chown -R omero-web:omero-web /home/omero-web/nginx From e50984444a7ad27f624451cbcba78f0dc22c85f9 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 1 Feb 2022 10:53:05 +0000 Subject: [PATCH 23/44] update job --- home/jobs/OMERO-build/config.xml | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index 088078e2..ca69176c 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -57,15 +57,27 @@ false + + OMERO-python-superbuild-build + + + + + false + false + - cd src -export OMERO_BRANCH=$MERGE_PUSH_BRANCH + + mv omero-scripts/dist/*.tar.gz . + cd src + export OMERO_BRANCH=$MERGE_PUSH_BRANCH + + virtualenv $WORKSPACE/omero-virtualenv --system-site-packages -virtualenv $WORKSPACE/omero-virtualenv --system-site-packages -source $WORKSPACE/omero-virtualenv/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 -U setuptools 'omero-py>=5.6.0.dev9' -source docs/hudson/OMERO.sh + source $WORKSPACE/omero-virtualenv/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 -U setuptools omero-py + source docs/hudson/OMERO.sh From 67312a54bf0e91024b6dd0f96c35c1906d0f53b3 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 1 Feb 2022 12:12:37 +0000 Subject: [PATCH 24/44] remove optional step. This is required --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2b39d408..f18aff88 100644 --- a/README.md +++ b/README.md @@ -95,6 +95,10 @@ Start and configure: $ docker-compose -p my_project port nginxjenkins 443 +* Create the `maven-internal` Nexus repository: + + $ docker-compose exec nexus /nexus-data/createRepoMavenInternal.sh + * [Optional] Turn on Basic HTTP authentication for Jenkins sudo htpasswd -c jenkins/conf.d/passwdfile nginx @@ -104,10 +108,6 @@ Start and configure: auth_basic "Restricted"; auth_basic_user_file /etc/nginx/conf.d/passwdfile; -* [Optional] Create the `maven-internal` Nexus repository: - - $ docker-compose exec nexus /nexus-data/createRepoMavenInternal.sh - # GitHub OAuth From 14bb27a96ebfcafa36c923cd40fe6af72a09a38d Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 1 Feb 2022 12:15:36 +0000 Subject: [PATCH 25/44] add step --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index f18aff88..0fd8f00b 100644 --- a/README.md +++ b/README.md @@ -128,6 +128,8 @@ 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. + # Job workflow The default deployment initializes a Jenkins server with a [predefined set of From 81d969c73ab7654c408f8871b62ea13dbd1f13d5 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 1 Feb 2022 13:06:20 +0000 Subject: [PATCH 26/44] adjust ownership --- web/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/Dockerfile b/web/Dockerfile index 02ab46e6..7facefa9 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -56,7 +56,7 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH" ARG USER_ID=1000 RUN usermod -u $USER_ID omero-web -RUN chown -R omero-web:omero-web /home/omero-web/static +RUN chown -R omero-web:omero-web /home/omero-web/ # make sure mounted volumes has correct permissions RUN mkdir -p /home/omero-web/nginx From 38c953dd91735ede61f8be7b68744438234dfd34 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 1 Feb 2022 15:27:29 +0000 Subject: [PATCH 27/44] test command --- jenkins/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index 5257022c..b2ad442a 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -6,7 +6,8 @@ ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" COPY plugins.txt /usr/share/jenkins/ref/plugins.txt -RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt +RUN jenkins-plugin-cli --plugin-file /usr/share/jenkins/ref/plugins.txt +#RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt #RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt USER root From a0af274ac7f2c6ffe33fc43b66beb0782e066c6b Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 3 Feb 2022 10:07:10 +0000 Subject: [PATCH 28/44] use official tag --- docker/Dockerfile | 2 +- nginx/Dockerfile | 2 +- server/Dockerfile | 2 +- slave/Dockerfile | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index ddf1fced..55eee582 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7-docker:0.6.9 +FROM openmicroscopy/devslave-c7:0.7.1 MAINTAINER OME diff --git a/nginx/Dockerfile b/nginx/Dockerfile index bc6fdb38..47594875 100644 --- a/nginx/Dockerfile +++ b/nginx/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7-docker:0.6.9 +FROM openmicroscopy/devslave-c7:0.7.1 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index ca52cbbc..1fc53ee2 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7-docker:0.6.9 +FROM openmicroscopy/devslave-c7:0.7.1 MAINTAINER OME diff --git a/slave/Dockerfile b/slave/Dockerfile index bedbd7bb..6d2c09b3 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7-docker:0.6.9 +FROM openmicroscopy/devslave-c7:0.7.1 MAINTAINER OME From abbc12c93dab0c81481bd50a7031f16c7e341507 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 3 Feb 2022 10:54:27 +0000 Subject: [PATCH 29/44] use jar. Previous command failed when deploying on idr1 --- jenkins/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index b2ad442a..5257022c 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -6,8 +6,7 @@ ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" COPY plugins.txt /usr/share/jenkins/ref/plugins.txt -RUN jenkins-plugin-cli --plugin-file /usr/share/jenkins/ref/plugins.txt -#RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt +RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt #RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt USER root From c589c9456b581a81e2d35827e258077bb94103b5 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 3 Feb 2022 14:26:05 +0000 Subject: [PATCH 30/44] use tag --- web/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/Dockerfile b/web/Dockerfile index 7facefa9..16178b92 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,4 +1,4 @@ -FROM jburel/devslave-c7-docker:0.6.9 +FROM openmicroscopy/devslave-c7:0.7.1 MAINTAINER OME From 77c3fb1c74b22cd77d601c0a716b6461152fd3db Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 4 Feb 2022 09:41:29 +0000 Subject: [PATCH 31/44] remove space --- home/jobs/OMERO-build/config.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/home/jobs/OMERO-build/config.xml b/home/jobs/OMERO-build/config.xml index ca69176c..666ca3bc 100644 --- a/home/jobs/OMERO-build/config.xml +++ b/home/jobs/OMERO-build/config.xml @@ -68,16 +68,16 @@ - mv omero-scripts/dist/*.tar.gz . - cd src - export OMERO_BRANCH=$MERGE_PUSH_BRANCH +mv omero-scripts/dist/*.tar.gz . +cd src +export OMERO_BRANCH=$MERGE_PUSH_BRANCH - virtualenv $WORKSPACE/omero-virtualenv --system-site-packages +virtualenv $WORKSPACE/omero-virtualenv --system-site-packages - source $WORKSPACE/omero-virtualenv/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 -U setuptools omero-py - source docs/hudson/OMERO.sh +source $WORKSPACE/omero-virtualenv/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 -U setuptools omero-py +source docs/hudson/OMERO.sh From acdbd34d41e6738f01612c27ee9c2158091ca918 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 8 Feb 2022 08:49:52 +0000 Subject: [PATCH 32/44] cap report lab --- home/jobs/OMERO-server/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index d25296af..9ccfddf0 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -49,7 +49,7 @@ 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 -U pip future pip install markdown -pip install reportlab # For figure +pip install "reportlab<3.6" # For figure pip install omego pip install tables pip install jinja2 From 403941a97b883d9d2096362edaa915d3aa7559cb Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 8 Feb 2022 10:11:36 +0000 Subject: [PATCH 33/44] create static folder as omero-web --- web/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/web/Dockerfile b/web/Dockerfile index 16178b92..c0180dc6 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -61,6 +61,8 @@ RUN chown -R omero-web:omero-web /home/omero-web/ # 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 VOLUME ["/home/omero-web", "/home/omero-web/nginx"] From efdcd081bdfbce28dbdfe3a3dba9f5690ea573fd Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 8 Feb 2022 13:34:59 +0000 Subject: [PATCH 34/44] do not update gradle --- slave/Dockerfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/slave/Dockerfile b/slave/Dockerfile index 6d2c09b3..1a3659dd 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -61,10 +61,10 @@ RUN yum -y install postgresql10-server postgresql10 \ # gradle RUN cd /opt && \ - curl -fSLO https://services.gradle.org/distributions/gradle-6.8.3-bin.zip && \ - unzip gradle-6.8.3-bin.zip && \ - rm gradle-6.8.3-bin.zip && \ - ln -s /opt/gradle-6.8.3/bin/gradle /usr/local/bin/gradle + curl -fSLO https://services.gradle.org/distributions/gradle-5.2.1-bin.zip && \ + unzip gradle-5.2.1-bin.zip && \ + rm gradle-5.2.1-bin.zip && \ + ln -s /opt/gradle-5.2.1/bin/gradle /usr/local/bin/gradle # Needed for Gradle ENV JAVA_HOME /usr/lib/jvm/jre-1.8.0-openjdk From b5b40b9212182568edfbcfc07655f8e56660af9d Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 8 Feb 2022 15:28:07 +0000 Subject: [PATCH 35/44] update instructions --- README.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0fd8f00b..f3629600 100644 --- a/README.md +++ b/README.md @@ -81,9 +81,13 @@ The following instructions explain how to deploy a devspace on a Docker host. Start and configure: +* Build devspace using `docker-compose`: + + $ docker-compose -f docker-compose.yml build + * Start devspace using `docker-compose`: - $ docker-compose 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 From c9c67bf6feb50e4b4b76f05c064df601bb58e524 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 8 Feb 2022 16:25:59 +0000 Subject: [PATCH 36/44] do not check url --- runtest.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/runtest.sh b/runtest.sh index 7ed00e97..6baa73b2 100755 --- a/runtest.sh +++ b/runtest.sh @@ -49,14 +49,14 @@ do done -JENKINS_PORT=$(docker-compose port nginxjenkins 443 | cut -d: -f2) -curl -k -I https://localhost:$JENKINS_PORT +#JENKINS_PORT=$(docker-compose port nginxjenkins 443 | cut -d: -f2) +#curl -k -I https://localhost:$JENKINS_PORT -STATUS=$(curl -k --write-out %{http_code} --silent --output /dev/null https://localhost:$JENKINS_PORT) +#STATUS=$(curl -k --write-out %{http_code} --silent --output /dev/null https://localhost:$JENKINS_PORT) -if [ ! "200" == "$STATUS" ]; then - exit 1 -fi +#if [ ! "200" == "$STATUS" ]; then +# exit 1 +#fi # CLEANUP docker-compose -f docker-compose.yml stop From 42421de9a90d647c248158245d3e3f874c68d540 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 09:04:34 +0000 Subject: [PATCH 37/44] change java version --- home/config.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home/config.xml b/home/config.xml index 1bac5d92..f81cd284 100644 --- a/home/config.xml +++ b/home/config.xml @@ -30,7 +30,7 @@ - jdk-8u192-oth-JPR + jdk-8u221-oth-JPR true From 69c8dce7d5273d566c75d1164b711e647ae8c27c Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 09:16:57 +0000 Subject: [PATCH 38/44] bump version --- home/config.xml | 4 ++-- home/hudson.plugins.git.GitTool.xml | 2 +- home/hudson.tasks.Ant.xml | 2 +- home/org.jenkinsci.plugins.gitclient.JGitTool.xml | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/home/config.xml b/home/config.xml index f81cd284..7d868109 100644 --- a/home/config.xml +++ b/home/config.xml @@ -3,7 +3,7 @@ jenkins.security.s2m.MasterKillSwitchWarning - 2.150.3 + 2.319.2 RESTART 0 NORMAL @@ -29,7 +29,7 @@ - + jdk-8u221-oth-JPR true diff --git a/home/hudson.plugins.git.GitTool.xml b/home/hudson.plugins.git.GitTool.xml index 39ca57a7..382e1ecf 100644 --- a/home/hudson.plugins.git.GitTool.xml +++ b/home/hudson.plugins.git.GitTool.xml @@ -1,5 +1,5 @@ - + Default diff --git a/home/hudson.tasks.Ant.xml b/home/hudson.tasks.Ant.xml index 4fc57d49..434cd8a1 100644 --- a/home/hudson.tasks.Ant.xml +++ b/home/hudson.tasks.Ant.xml @@ -1,5 +1,5 @@ - + Ant 1.9 diff --git a/home/org.jenkinsci.plugins.gitclient.JGitTool.xml b/home/org.jenkinsci.plugins.gitclient.JGitTool.xml index e2da2895..bfbf820c 100644 --- a/home/org.jenkinsci.plugins.gitclient.JGitTool.xml +++ b/home/org.jenkinsci.plugins.gitclient.JGitTool.xml @@ -1,4 +1,4 @@ - + \ No newline at end of file From 05f7d15d8bf2fc732acc80edf7396309630e5fc3 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 09:17:14 +0000 Subject: [PATCH 39/44] add new config --- home/hudson.plugins.copyartifact.CopyArtifactConfigurat | 4 ++++ home/hudson.plugins.gradle.Gradle.xml | 4 ++++ home/org.jenkinsci.plugins.docker.commons.tools.DockerT | 4 ++++ home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml | 4 ++++ 4 files changed, 16 insertions(+) create mode 100644 home/hudson.plugins.copyartifact.CopyArtifactConfigurat create mode 100644 home/hudson.plugins.gradle.Gradle.xml create mode 100644 home/org.jenkinsci.plugins.docker.commons.tools.DockerT create mode 100644 home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml diff --git a/home/hudson.plugins.copyartifact.CopyArtifactConfigurat b/home/hudson.plugins.copyartifact.CopyArtifactConfigurat new file mode 100644 index 00000000..b0c6185c --- /dev/null +++ b/home/hudson.plugins.copyartifact.CopyArtifactConfigurat @@ -0,0 +1,4 @@ + + + PRODUCTION + \ No newline at end of file diff --git a/home/hudson.plugins.gradle.Gradle.xml b/home/hudson.plugins.gradle.Gradle.xml new file mode 100644 index 00000000..be99b58f --- /dev/null +++ b/home/hudson.plugins.gradle.Gradle.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/home/org.jenkinsci.plugins.docker.commons.tools.DockerT b/home/org.jenkinsci.plugins.docker.commons.tools.DockerT new file mode 100644 index 00000000..e1801ee0 --- /dev/null +++ b/home/org.jenkinsci.plugins.docker.commons.tools.DockerT @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml b/home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml new file mode 100644 index 00000000..757ecf27 --- /dev/null +++ b/home/org.jenkinsci.plugins.gitclient.JGitApacheTool.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file From bb14766330404184b36817bea8758ab3a5cef16b Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 10:19:43 +0000 Subject: [PATCH 40/44] install plugins --- jenkins/Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index 5257022c..c323012d 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -2,12 +2,11 @@ FROM jenkins/jenkins:lts MAINTAINER OME # Temp fix robot test results -ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" +ENV JAVA_OPTS "-Dhudson.model.DirectoryBrowserSupport.CSP=" -Djenkins.install.runSetupWizard=false COPY plugins.txt /usr/share/jenkins/ref/plugins.txt -RUN java -jar /opt/jenkins-plugin-manager.jar -f /usr/share/jenkins/ref/plugins.txt -#RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt +RUN /usr/local/bin/install-plugins.sh < /usr/share/jenkins/ref/plugins.txt USER root RUN chown -R jenkins:jenkins /var/jenkins_home From 4a3f57d79c8995f90605cdc113654a7d939f9d3e Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 10:19:56 +0000 Subject: [PATCH 41/44] check url --- runtest.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/runtest.sh b/runtest.sh index 6baa73b2..7ed00e97 100755 --- a/runtest.sh +++ b/runtest.sh @@ -49,14 +49,14 @@ do done -#JENKINS_PORT=$(docker-compose port nginxjenkins 443 | cut -d: -f2) -#curl -k -I https://localhost:$JENKINS_PORT +JENKINS_PORT=$(docker-compose port nginxjenkins 443 | cut -d: -f2) +curl -k -I https://localhost:$JENKINS_PORT -#STATUS=$(curl -k --write-out %{http_code} --silent --output /dev/null https://localhost:$JENKINS_PORT) +STATUS=$(curl -k --write-out %{http_code} --silent --output /dev/null https://localhost:$JENKINS_PORT) -#if [ ! "200" == "$STATUS" ]; then -# exit 1 -#fi +if [ ! "200" == "$STATUS" ]; then + exit 1 +fi # CLEANUP docker-compose -f docker-compose.yml stop From 4e8187530a4c06d54198f4d0f857aa17f079124e Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 9 Feb 2022 13:09:58 +0000 Subject: [PATCH 42/44] remove comments, this leads to a NPE --- home/jobs/OMERO-server/config.xml | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/home/jobs/OMERO-server/config.xml b/home/jobs/OMERO-server/config.xml index 9ccfddf0..345235a4 100644 --- a/home/jobs/OMERO-server/config.xml +++ b/home/jobs/OMERO-server/config.xml @@ -106,7 +106,6 @@ OMERO_DATA_DIR=$DATA_DIR mkdir -p $OMERO_DATA_DIR -# UNZIP SERVER OMERO_DIST=$WORKSPACE/OMERO.server export OMERODIR=$OMERO_DIST @@ -122,7 +121,6 @@ unzip $ZIP rm -f $ZIP mv $WORKSPACE/$DIST $OMERO_DIST -# INSTALL PYTHON PACKAGES source $WORKSPACE/.venv3/bin/activate pip install git+https://github.com/$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 @@ -132,12 +130,7 @@ for x in *.tar.gz; do pip install -U $x # Install marshal, etc. *after* requirements done -## LOAD CONFIG -# LOAD EXTRA CONFIG -#omero load configfile.omero - -# DEFAULT CONFIG omero config set omero.db.name $OMERO_DB_NAME omero config set omero.db.host $OMERO_DB_HOST omero config set omero.db.user $OMERO_DB_USER @@ -147,10 +140,6 @@ omero config set omero.db.poolsize 25 omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts omero config set omero.security.trustStorePassword changeit omero certificates -## END LOAD CONFIG - - -## PURGE if [ "$PURGE_DATA" = "true" ]; then createdb -h $OMERO_DB_HOST -U $OMERO_DB_USER $OMERO_DB_NAME @@ -160,14 +149,11 @@ else omego db -vvv upgrade --serverdir $OMERO_DIST --dbname $OMERO_DB_NAME fi -## END PURGE - export LANG='en_US.UTF-8' export LANGUAGE='en_US:en' export LC_ALL='en_US.UTF-8' BUILD_ID=DONT_KILL_ME omero admin start -# WAIT FOR OMERO TO START UP AND ACCEPT CONNECTIONS omero admin waitup omero admin diagnostics From 5fb96841c1fbbf7bb6592feae2782a099e1e9bfd Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 10 Feb 2022 10:18:47 +0000 Subject: [PATCH 43/44] use explicit version --- jenkins/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jenkins/Dockerfile b/jenkins/Dockerfile index c323012d..f9fcf955 100644 --- a/jenkins/Dockerfile +++ b/jenkins/Dockerfile @@ -1,4 +1,4 @@ -FROM jenkins/jenkins:lts +FROM jenkins/jenkins:2.319.2-lts-jdk11 MAINTAINER OME # Temp fix robot test results From a9f1ddcc49c283f51e0e00e91070ad66069e530f Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 10 Feb 2022 11:30:06 +0000 Subject: [PATCH 44/44] use official image --- docker/Dockerfile | 2 +- server/Dockerfile | 11 ++++++----- slave/Dockerfile | 11 ++++++----- web/Dockerfile | 4 ++-- 4 files changed, 15 insertions(+), 13 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 55eee582..6c88f972 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM openmicroscopy/devslave-c7:0.7.1 +FROM openmicroscopy/devslave-c7:0.7.2 MAINTAINER OME diff --git a/server/Dockerfile b/server/Dockerfile index 1fc53ee2..6861fdbd 100644 --- a/server/Dockerfile +++ b/server/Dockerfile @@ -1,10 +1,11 @@ -FROM openmicroscopy/devslave-c7:0.7.1 +FROM openmicroscopy/devslave-c7:0.7.2 MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36 -ARG BRANCH=test +ARG BRANCH=yourbranch +ARG NAME=yourname # Remove the existing omero user RUN userdel -r omero && \ @@ -19,9 +20,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/$BRANCH +#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 $OMERO_INSTALL/settings.env diff --git a/slave/Dockerfile b/slave/Dockerfile index 1a3659dd..cab063c4 100644 --- a/slave/Dockerfile +++ b/slave/Dockerfile @@ -1,10 +1,11 @@ -FROM openmicroscopy/devslave-c7:0.7.1 +FROM openmicroscopy/devslave-c7:0.7.2 MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=ice36-devel -ARG BRANCH=test +ARG BRANCH=yourbranch +ARG NAME=yourname # skip some omero-install @@ -14,9 +15,9 @@ ENV OMERO_INSTALL_ROOT=/tmp/omero-install ## update omero-install to the latest one #RUN git --git-dir=$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=$OMERO_INSTALL_ROOT remote add jburel https://github.com/jburel/omero-install.git -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT fetch jburel -RUN git --git-dir=$OMERO_INSTALL_ROOT/.git --work-tree=$OMERO_INSTALL_ROOT merge jburel/$BRANCH +#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 diff --git a/web/Dockerfile b/web/Dockerfile index c0180dc6..1df0c372 100644 --- a/web/Dockerfile +++ b/web/Dockerfile @@ -1,10 +1,10 @@ -FROM openmicroscopy/devslave-c7:0.7.1 +FROM openmicroscopy/devslave-c7:0.7.2 MAINTAINER OME ARG JAVAVER=openjdk1.8 ARG ICEVER=noice -ARG BRANCH=develop + # make ICEVERSION environment variable to use in OMERO-web job ENV ICEVERSION ${ICEVER:-noice}