Merge pull request #274 from jburel/rocky

Rocky linux 9

.github/workflows/main.yml

@@ -12,14 +12,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        os: [debian10, ubuntu1804, ubuntu2004, ubuntu2204]
+        os: [rockylinux9, debian10, ubuntu1804, ubuntu2004, ubuntu2204]
         pg: [pg13, pg14]
         exclude:
           - os: ubuntu2204
             pg: pg13
     steps:
       - name: Checkout
-        uses: actions/checkout@v1
+        uses: actions/checkout@v2
       - name: Install shunit2
         run: sudo apt-get install -y shunit2
       - name: Build walkthroughs
@@ -30,7 +30,7 @@ jobs:
         run: |
           cd linux/test
           PGVER=$PGVER ./docker-build.sh $ENV
-          ./test_services.sh
+          ./test_services.sh 
         env:
           ENV: ${{ matrix.os }}
           PGVER: ${{ matrix.pg }}

linux/autogenerate.sh

@@ -7,14 +7,14 @@ dir=`dirname $0`
 remove_docker_workaround () {
 l="$(echo -e "${@}" | sed -e 's/^[[:space:]]*//')"
 l="$(echo -e "${l}" | sed -e 's/^if.*!.*then//' )"
-l="$(echo -e "${l}" | sed -e '/^if.*container.*then/,/else/d' )"
+l="$(echo -e "${l}" | sed -e '/^if.*docker.*then/,/else/d' )"
 l="$(echo -e "${l}" | sed -e 's/^fi//')"
 echo "${l}"
 }
 
 #generate the walkthrough for all supported os
 function generate_all() {
-	values=(centos7 debian10 ubuntu1804 ubuntu2004 ubuntu2204)
+	values=(centos7 debian10 ubuntu1804 ubuntu2004 ubuntu2204 rocky9)
 	for os in "${values[@]}"; do
   		echo "${os}"
   		 generate ${os}
@@ -36,6 +36,8 @@ EOF
 N=$OS
 if [[ $OS =~ "debian" ]] || [[ $OS =~ "ubuntu" ]] ; then
 	N="ubuntu"
+elif [[ $OS =~ "rocky" ]]  ; then
+    N="centos7"
 elif [[ $OS =~ "centos" ]]  ; then
     N="centos7"
 fi
@@ -48,6 +50,8 @@ echo "$line" >> $file
 N=$OS
 if [[ $OS =~ "centos" ]] ; then
 	N="centos"
+elif [[ $OS =~ "rocky" ]]  ; then
+	N="centos"
 elif [[ $OS =~ "ubuntu1804" ]]  ; then
 	N="ubuntu1804"
 elif [[ $OS =~ "ubuntu" ]]  ; then
@@ -70,6 +74,8 @@ echo "# install dependencies" >> $file
 N=$OS
 if [[ $OS =~ "ubuntu" ]]  ; then
     N="ubuntu1804"
+elif [[ $OS =~ "rocky" ]]  ; then
+	N="centos7"
 fi
 
 line=$(sed -n '2,$p' $dir/step01_"$N"_deps.sh)
@@ -95,23 +101,26 @@ echo -en '\n' >> $file
 
 # install postgres
 N=$OS
+if [[ $OS =~ "rocky" ]]  ; then
+	N="centos"
+fi
 echo -en '\n' >> $file
 echo "# install Postgres" >> $file
-if [[ $OS =~ "centos" ]] ; then
-    number=$(sed -n '/#start-postgresql-installation-general/=' $dir/step01_"$N"_pg_deps.sh)
+if [[ $N =~ "centos" ]] ; then
+    number=$(sed -n '/#start-postgresql-installation-general/=' $dir/step01_"$OS"_pg_deps.sh)
     nrs=$((number+1))
-    number=$(sed -n '/#end-postgresql-installation-general/=' $dir/step01_"$N"_pg_deps.sh)
+    number=$(sed -n '/#end-postgresql-installation-general/=' $dir/step01_"$OS"_pg_deps.sh)
     nre=$((number-1))
-    line=$(sed -n ''$nrs','$nre'p' $dir/step01_"$N"_pg_deps.sh)
+    line=$(sed -n ''$nrs','$nre'p' $dir/step01_"$OS"_pg_deps.sh)
     line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
 
     echo "$line"  >> $file
 
-	number=$(sed -n '/#start-recommended/=' $dir/step01_"$N"_pg_deps.sh)
+	number=$(sed -n '/#start-recommended/=' $dir/step01_"$OS"_pg_deps.sh)
 	nrs=$((number+1))
-	number=$(sed -n '/#end-recommended/=' $dir/step01_"$N"_pg_deps.sh)
+	number=$(sed -n '/#end-recommended/=' $dir/step01_"$OS"_pg_deps.sh)
 	nre=$((number-1))
-	line=$(sed -n ''$nrs','$nre'p' $dir/step01_"$N"_pg_deps.sh)
+	line=$(sed -n ''$nrs','$nre'p' $dir/step01_"$OS"_pg_deps.sh)
 	# remove docker conditional
 	line=`remove_docker_workaround "${line}"`
 else
@@ -121,6 +130,7 @@ else
 	ne=$((number-1))
 	line=$(sed -n ''$ns','$ne'p' $dir/step01_"$N"_pg_deps.sh)
 fi
+N=$OS
 # remove leading whitespace
 line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
 

linux/install_rocky9.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -e -u -x
+
+OMEROVER=${OMEROVER:-latest}
+
+. `dirname $0`/settings.env
+
+bash -eux step01_centos7_init.sh
+
+bash -eux step01_centos7_deps.sh
+
+# install java
+bash -eux step01_centos_java_deps.sh
+
+# install ice
+bash -eux step01_rocky9_ice_deps.sh
+
+# install Postgres
+bash -eux step01_rocky9_pg_deps.sh
+
+bash -eux step02_all_setup.sh
+
+bash -eux step03_all_postgres.sh
+
+bash -eux step01_rocky9_ice_venv.sh
+
+# Those steps are valid if an omero-server user exists
+# This might not be the case when used in the context of devspace
+if [ "$(getent passwd omero-server)" ]; then
+    cp settings.env step04_all_omero.sh setup_omero_db.sh ~omero-server
+
+    OMEROVER=$OMEROVER bash -eux step04_all_omero_install.sh
+
+    su - omero-server -c " bash -eux step04_all_omero.sh"
+
+    su - omero-server -c "bash setup_omero_db.sh"
+fi
+
+
+#If you don't want to use the systemd scripts you can start OMERO manually:
+#su - omero-server -c ". /home/omero-server/settings.env omero admin start"
+
+bash -eux step06_centos7_daemon.sh

linux/settings.env

@@ -17,4 +17,6 @@ export OMERODIR=/opt/omero/server/OMERO.server
 # Location of the virtual environment for omero-py
 VENV_SERVER=/opt/omero/server/venv3
 
-export PATH=$VENV_SERVER/bin:$PATH
+export ICE_HOME=/opt/ice-3.6.5		
+
+export PATH=$ICE_HOME/bin:$VENV_SERVER/bin:$PATH

linux/step01_rocky9_ice_deps.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+#start-recommended
+dnf config-manager --set-enabled crb
+yum -y install bzip2 expat libdb-cxx
+
+cd /tmp
+wget https://github.com/sbesson/zeroc-ice-rockylinux9-x86_64/releases/download/202307018/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
+#end-recommended

linux/step01_rocky9_ice_venv.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -e -u -x
+
+VENV_SERVER=${VENV_SERVER:-/opt/omero/server/venv3}
+#start-ice-py
+# Create a virtual env
+python3 -mvenv $VENV_SERVER
+
+# Upgrade pip
+$VENV_SERVER/bin/pip install --upgrade pip
+
+# Install the Ice Python binding
+$VENV_SERVER/bin/pip install https://github.com/sbesson/zeroc-ice-py-rockylinux9-x86_64/releases/download/20230719/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl
+
+# Install server dependencies
+$VENV_SERVER/bin/pip install omero-server
+#end-ice-py

linux/step01_rocky9_pg_deps.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+PGVER=${PGVER:-pg13} # pg 13 is installed by default
+
+#start-postgresql-installation-general
+
+#end-postgresql-installation-general
+#start-recommended
+yum -y install postgresql-server postgresql
+
+if [ -f /.dockerenv ]; then
+    su - postgres -c "/usr/bin/initdb -D /var/lib/pgsql/data --encoding=UTF8"
+    echo "listen_addresses='*'" >> /var/lib/pgsql/data/postgresql.conf
+else
+    PGSETUP_INITDB_OPTIONS=--encoding=UTF8 /usr/bin/postgresql-setup --initdb
+fi
+sed -i.bak -re 's/^(host.*)ident/\1md5/' /var/lib/pgsql/data/pg_hba.conf
+
+if [ -f /.dockerenv ]; then
+    su - postgres -c "/usr/bin/pg_ctl start -D /var/lib/pgsql/data -w"
+else
+    systemctl start postgresql
+fi
+    systemctl enable postgresql
+
+sed -i 's/ ident/ trust/g' /var/lib/pgsql/data/pg_hba.conf
+
+#end-recommended

linux/step04_all_omero_install.sh

@@ -1,23 +1,20 @@
 #!/bin/bash
 OMEROVER=${OMEROVER:-latest}
-ICEVER=${ICEVER:-ice36}
 
 set -eux
 
 . `dirname $0`/settings.env
 
 
 #start-install
-if [ "$ICEVER" = "ice36" ] || [ "$ICEVER" = "ice36-devel" ]; then
-	if [ $OMEROVER == "latest" ]; then
-		#start-release-ice36
-		cd /opt/omero/server
-		SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip
-		wget -q $SERVER -O OMERO.server-ice36.zip
-		unzip -q OMERO.server*
-		#end-release-ice36
-		rm OMERO.server-ice36.zip
-	fi
+if [ $OMEROVER == "latest" ]; then
+	#start-release-ice36
+	cd /opt/omero/server
+	SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip
+	wget -q $SERVER -O OMERO.server-ice36.zip
+	unzip -q OMERO.server*
+	#end-release-ice36
+	rm OMERO.server-ice36.zip
 fi
 
 #start-link

linux/step06_centos7_daemon.sh

@@ -2,7 +2,7 @@
 
 #start-recommended
 cp omero-server-systemd.service /etc/systemd/system/omero-server.service
-if [ ! "${container:-}" = docker ]; then
+if [ ! -f /.dockerenv ]; then
     systemctl daemon-reload
 fi
 systemctl enable omero-server.service

linux/test/rockylinux9/Dockerfile

@@ -0,0 +1,21 @@
+# Dockerfile for testing the OMERO Linux installation instructions
+# Not intended for production use
+FROM rockylinux:9
+MAINTAINER [email protected]
+
+ARG OMEROVER=latest
+ARG JAVAVER=openjdk11
+ARG ICEVER=ice36
+ARG PGVER=pg13
+
+RUN touch /.dockerenv
+ADD omero-install-test.zip /
+RUN dnf -y install unzip && unzip omero-install-test.zip
+
+RUN cd omero-install-test && \
+	bash install_rocky9.sh
+
+ADD run.sh /home/omero-server/run.sh
+
+EXPOSE 80 4063 4064
+CMD ["/bin/bash", "-e", "/home/omero-server/run.sh"]

linux/test/rockylinux9/run.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+su - postgres -c "/usr/bin/pg_ctl start -D /var/lib/pgsql/data -w"
+
+#service crond start # Doesn't work in Docker
+su - omero-server -c ". /home/omero-server/settings.env && omero admin start"
+if [ -t 1 ] ; then
+    exec bash
+else
+    exec tail -F /opt/omero/server/OMERO.server/var/log/*
+fi

linux/test/test_services.sh

@@ -39,9 +39,6 @@ docker exec $CNAME /bin/bash -c 'd=10; \
         done;  \
     echo "Entry found"; exit'
 
-#check OMERO.server service status
-docker exec $CNAME /bin/bash -c "service omero-server status -l --no-pager"
-
 docker exec $CNAME /bin/bash -c "su - omero-server -c \". ${SETTINGS} && omero admin diagnostics\""
 
 # Log in to OMERO.server