Parameters

.travis.yml

@@ -16,7 +16,7 @@ env:
 
 before_install:  
   - sudo apt-get update
-  - sudo DEBIAN_FRONTEND=noninteractive apt-get -q -o Dpkg::Options::="--force-confnew" install -y docker-engine
+  - sudo DEBIAN_FRONTEND=noninteractive apt-get install -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" docker-engine
 
 script:
     - cd linux/test && ./docker-build.sh $ENV && docker run -d omero_install_test_$ENV

linux/autogenerate.sh

@@ -12,46 +12,153 @@ set -e -u -x
 source settings.env
 EOF
 
+N=$OS
+if [ $OS = "debian8" ] ; then
+	N="ubuntu1404"
+fi
 echo -en '\n' >> $file
 echo "#start-step01: As root, install dependencies" >> $file
+line=$(sed -n '2,$p' step01_"$N"_init.sh)
+echo "$line" >> $file
+
+# install java
+N=$OS
+if [[ $OS =~ "centos" ]] ; then
+	N="centos"
+fi 
+echo -en '\n' >> $file
+echo "# install Java" >> $file
+number=$(sed -n '/#start-recommended/=' step01_"$N"_java_deps.sh)
+ns=$((number+1))
+number=$(sed -n '/#end-recommended/=' step01_"$N"_java_deps.sh)
+ne=$((number-1))
+line=$(sed -n ''$ns','$ne'p' step01_"$N"_java_deps.sh)
+
+# remove leading whitespace
+line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+
+echo "$line"  >> $file
+echo -en '\n' >> $file
+
+# install ice
+echo "# install Ice" >> $file
+N=$OS
+if [ $OS = "debian8" ] ; then
+	N="ubuntu1404"
+fi 
+number=$(sed -n '/#start-recommended/=' step01_"$N"_ice_deps.sh)
+ns=$((number+1))
+number=$(sed -n '/#end-recommended/=' step01_"$N"_ice_deps.sh)
+ne=$((number-1))
+line=$(sed -n ''$ns','$ne'p' step01_"$N"_ice_deps.sh)
+
+# remove leading whitespace
+line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+
+echo "$line"  >> $file
+echo -en '\n' >> $file
+
+# install dependencies
 if [ $OS = "centos7" ] ; then
-	number=$(sed -n '/#start-workaround/=' step01_"$OS"_deps.sh)
-	number=$((number-1))
-	line=$(sed -n '2,'$number'p' step01_"$OS"_deps.sh)
+	number=$(sed -n '/#start-docker-pip/=' step01_"$OS"_deps.sh)
+	ne=$((number-2))
+	line=$(sed -n '2,'$ne'p' step01_"$OS"_deps.sh)
 	echo "$line" >> $file
-	number=$(sed -n '/#end-workaround/=' step01_"$OS"_deps.sh)
-	number=$((number+1))
-	line=$(sed -n ''$number',$p' step01_"$OS"_deps.sh)
+	# remove leading whitespace
+	number=$(sed -n '/#start-docker-pip/=' step01_"$OS"_deps.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-docker-pip/=' step01_"$OS"_deps.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step01_"$OS"_deps.sh)
+	line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+
+	echo "$line" >> $file
+	ne=$(($ne+3))
+	line=$(sed -n ''$ne',$p' step01_"$OS"_deps.sh)
 else
 	line=$(sed -n '2,$p' step01_"$OS"_deps.sh)
 fi
 echo "$line" >> $file
+# install postgres
+N=$OS
+if [ $OS = "debian8" ] ; then
+	N="ubuntu1404"
+elif [[ $OS =~ "centos6" ]]; then
+	N="centos6"
+fi
+echo -en '\n' >> $file
+echo "# install Postgres" >> $file
+if [ $OS = "centos7" ] ; then
+	number=$(sed -n '/#start-recommended/=' step01_"$N"_pg_deps.sh)
+	nrs=$((number+1))
+	number=$(sed -n '/#end-recommended/=' step01_"$N"_pg_deps.sh)
+	nre=$((number-1))
+	number=$(sed -n ''$nrs','$nre'!d;/#start-workaround/!d;=' step01_"$N"_pg_deps.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$nrs','$ne'p' step01_"$N"_pg_deps.sh)
+	# remove leading whitespace
+	line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+
+	echo "$line" >> $file
+	number=$(sed -n ''$nrs','$nre'!d;/#end-workaround/!d;=' step01_"$N"_pg_deps.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-recommended/=' step01_"$N"_pg_deps.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step01_"$N"_pg_deps.sh)
+else
+	number=$(sed -n '/#start-recommended/=' step01_"$N"_pg_deps.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-recommended/=' step01_"$N"_pg_deps.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step01_"$N"_pg_deps.sh)
+fi
+# remove leading whitespace
+line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+
+echo "$line"  >> $file
+echo -en '\n' >> $file
+
 echo "#end-step01" >> $file
 
-# review the name of the original file.
 if [ $OS = "centos6_py27_ius" ] ; then
 	echo -en '\n' >> $file
 	echo "#start-step01.1: virtual env" >> $file
 	#find from where to start copying
-	start=$(sed -n '/#start-install/=' step03_"$OS"_virtualenv_deps.sh)
+	start=$(sed -n '/#start-install/=' step01_"$OS"_virtualenv_deps.sh)
 	start=$((start+1))
-	number=$(sed -n '/#start-dev/=' step03_"$OS"_virtualenv_deps.sh)
+	number=$(sed -n '/#start-dev/=' step01_"$OS"_virtualenv_deps.sh)
 	number=$((number-1))
-	line=$(sed -n ''$start','$number'p' step03_"$OS"_virtualenv_deps.sh)
+	line=$(sed -n ''$start','$number'p' step01_"$OS"_virtualenv_deps.sh)
 	echo "$line" >> $file
-	number=$(sed -n '/#end-dev/=' step03_"$OS"_virtualenv_deps.sh)
+	number=$(sed -n '/#end-dev/=' step01_"$OS"_virtualenv_deps.sh)
 	number=$((number+1))
-	line=$(sed -n ''$number',$p' step03_"$OS"_virtualenv_deps.sh)
+	line=$(sed -n ''$number',$p' step01_"$OS"_virtualenv_deps.sh)
 	echo "$line" >> $file
 	echo "#end-step01.1" >> $file
 fi
 
 echo -en '\n' >> $file
 echo "#start-step02: As root, create an omero system user and directory for the OMERO repository" >> $file
-if [ $OS = "centos6_py27" ] || [ $OS = "centos6_py27_ius" ] ; then
-	line=$(sed -n '2,$p' step02_"$OS"_setup.sh)
-else 
-	line=$(sed -n '2,$p' step02_all_setup.sh)
+if [[ $OS =~ "centos6_py27" ]] ; then
+	number=$(sed -n '/#start-create-user/=' step02_"$OS"_setup.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-create-user/=' step02_"$OS"_setup.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step02_"$OS"_setup.sh)
+	line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+	echo "$line" >> $file
+	ne=$((number+3))
+	line=$(sed -n ''$ne',$p' step02_"$OS"_setup.sh)
+else
+	number=$(sed -n '/#start-create-user/=' step02_all_setup.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-create-user/=' step02_all_setup.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step02_all_setup.sh)
+	line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+	echo "$line" >> $file
+	ne=$((number+3))
+	line=$(sed -n ''$ne',$p' step02_all_setup.sh)
 fi
 echo "$line" >> $file
 echo "#end-step02" >> $file
@@ -71,19 +178,43 @@ echo "#start-step04: As the omero system user, install the OMERO.server" >> $fil
 if [[ $OS =~ "centos6_py27" ]] ; then
 	var="${OS//_/}"
 	echo "#start-copy-omeroscript" >> $file
-	echo "cp settings.env omero-$var.env step04_$OS_omero.sh ~omero " >> $file
+	echo "cp settings.env omero-$var.env step04_all_omero.sh setup_omero_db.sh ~omero " >> $file
 	echo "#end-copy-omeroscript" >> $file
-	start=$(sed -n '/#start-install/=' step04_"$OS"_omero.sh)
-	start=$((start+1))
-	line=$(sed -n ''$start',$p' step04_"$OS"_omero.sh)
+	number=$(sed -n '/#start-py27-scl/=' step04_all_omero.sh)
+	ns=$((number+1))
+	number=$(sed -n '/#end-py27-scl/=' step04_all_omero.sh)
+	ne=$((number-1))
+	line=$(sed -n ''$ns','$ne'p' step04_all_omero.sh)
+	line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+	echo "$line" >> $file
+	line=$(sed -n ''$start',$p' step04_all_omero.sh)
 else 
 	echo "#start-copy-omeroscript" >> $file
-	echo "cp settings.env step04_all_omero.sh ~omero " >> $file
+	echo "cp settings.env step04_all_omero.sh setup_omero_db.sh ~omero" >> $file
 	echo "#end-copy-omeroscript" >> $file
-	start=$(sed -n '/#start-install/=' step04_all_omero.sh)
-	start=$((start+1))
-	line=$(sed -n ''$start',$p' step04_all_omero.sh)
 fi
+number=$(sed -n '/#start-venv/=' step04_all_omero.sh)
+ns=$((number+1))
+number=$(sed -n '/#end-venv/=' step04_all_omero.sh)
+ne=$((number-1))
+line=$(sed -n ''$ns','$ne'p' step04_all_omero.sh)
+line="$(echo -e "${line}" | sed -e 's/^[[:space:]]*//')"
+echo "$line" >> $file
+number=$(sed -n '/#start-release/=' step04_all_omero.sh)
+ns=$((number+1))
+number=$(sed -n '/#end-release/=' step04_all_omero.sh)
+ne=$((number-1))
+line=$(sed -n ''$ns','$ne'p' step04_all_omero.sh)
+
+line="$(echo -e "${line}" | sed -e 's/$OMEROVER/latest/g')"
+echo "$line" >> $file
+number=$(sed -n '/#configure/=' step04_all_omero.sh)
+ns=$((number+1))
+line=$(sed -n ''$ns',$p' step04_all_omero.sh)
+echo "$line" >> $file
+number=$(sed -n '/#start-config/=' setup_omero_db.sh)
+ns=$((number+1))
+line=$(sed -n ''$ns',$p' setup_omero_db.sh)
 echo "$line" >> $file
 echo "#end-step04" >> $file
 

linux/docker_shutdown_centos6.sh

@@ -1,4 +1,9 @@
 #!/bin/bash
 # All that's needed to get a clean shutdown of the docker container
 
-service postgresql-9.4 stop
+PGVER=${PGVER:-pg94}
+if [ "$PGVER" = "pg94" ]; then
+	service postgresql-9.4 stop
+elif [ "$PGVER" = "pg94" ]; then
+	service postgresql-9.5 stop
+fi

linux/install_centos6_apache22.sh

@@ -2,18 +2,35 @@
 
 set -e -u -x
 
-OMEROVER=${OMEROVER:-omero}
+OMEROVER=${OMEROVER:-latest}
 WEBAPPS=${WEBAPPS:-false}
+PGVER=${PGVER:-pg94}
 
 source settings.env
 
+bash -eux step01_centos6_init.sh
+
+# install java
+bash -eux step01_centos_java_deps.sh
+
 bash -eux step01_centos6_deps.sh
 
+# install ice
+bash -eux step01_centos6_ice_deps.sh
+
+# install Postgres
+bash -eux step01_centos6_pg_deps.sh
+
 bash -eux step02_all_setup.sh
-bash -eux step03_all_postgres.sh
 
-cp settings.env step04_all_$OMEROVER.sh ~omero
-su - omero -c "bash -eux step04_all_$OMEROVER.sh"
+if [[ "$PGVER" =~ ^(pg94|pg95)$ ]]; then
+	bash -eux step03_all_postgres.sh
+fi
+
+cp settings.env step04_all_omero.sh setup_omero_db.sh ~omero
+su - omero -c "OMEROVER=$OMEROVER bash -eux step04_all_omero.sh"
+
+su - omero -c "bash setup_omero_db.sh"
 
 if [ $WEBAPPS = true ]; then
 	PY_ENV=py26 bash -eux step05_1_all_webapps.sh

linux/install_centos6_nginx.sh

@@ -2,19 +2,36 @@
 
 set -e -u -x
 
-OMEROVER=${OMEROVER:-omero}
+OMEROVER=${OMEROVER:-latest}
 WEBAPPS=${WEBAPPS:-false}
+PGVER=${PGVER:-pg94}
 
 source settings.env
 
+bash -eux step01_centos6_init.sh
+
+# install java
+bash -eux step01_centos_java_deps.sh
+
 bash -eux step01_centos6_deps.sh
 
+# install ice
+bash -eux step01_centos6_ice_deps.sh
+
+# install Postgres
+bash -eux step01_centos6_pg_deps.sh
+
 bash -eux step02_all_setup.sh
-bash -eux step03_all_postgres.sh
 
-cp settings.env step04_all_$OMEROVER.sh ~omero
+if [[ "$PGVER" =~ ^(pg94|pg95)$ ]]; then
+	bash -eux step03_all_postgres.sh
+fi
+
+cp settings.env step04_all_omero.sh setup_omero_db.sh ~omero
+
+su - omero -c "OMEROVER=$OMEROVER bash -eux step04_all_omero.sh"
 
-su - omero -c "bash -eux step04_all_$OMEROVER.sh"
+su - omero -c "bash setup_omero_db.sh"
 
 bash -eux step05_centos6_nginx.sh
 

linux/install_centos6_py27_apache24.sh

@@ -2,18 +2,37 @@
 
 set -e -u -x
 
-OMEROVER=${OMEROVER:-omero}
+OMEROVER=${OMEROVER:-latest}
 WEBAPPS=${WEBAPPS:-false}
+PGVER=${PGVER:-pg94}
 
 source settings.env
 
+bash -eux step01_centos6_py27_init.sh
+
+# install java
+bash -eux step01_centos_java_deps.sh
+
 bash -eux step01_centos6_py27_deps.sh
 
+# install ice
+bash -eux step01_centos6_py27_ice_deps.sh
+
+# install Postgres
+bash -eux step01_centos6_pg_deps.sh
+
 bash -eux step02_centos6_py27_setup.sh
-bash -eux step03_all_postgres.sh
 
-cp settings.env omero-centos6py27.env step04_centos6_py27_${OMEROVER}.sh ~omero
-su - omero -c "bash -eux step04_centos6_py27_${OMEROVER}.sh"
+if [[ "$PGVER" =~ ^(pg94|pg95)$ ]]; then
+	bash -eux step03_all_postgres.sh
+fi
+
+cp settings.env omero-centos6py27.env step04_all_omero.sh setup_omero_db.sh ~omero
+
+su - omero -c "OMEROVER=$OMEROVER PY_ENV=py27_scl bash -eux step04_all_omero.sh"
+
+su - omero -c "bash setup_omero_db.sh"
+
 
 if [ $WEBAPPS = true ]; then
 	PY_ENV=py27_scl bash -eux step05_1_all_webapps.sh