16831: arvbox: bugfix: fix bundler version issue in documentation.

       Upgrade images to Debian Buster. Clean up whitespace in the
       arvbox command.

Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward@curii.com>

diff --git a/tools/arvbox/bin/arvbox b/tools/arvbox/bin/arvbox
index 279d46c08b4ee98a652d78b88f949f1587453d8a..122e2bec7c5bb1790fe357f33ded44a369b0fc75 100755 (executable)
--- a/tools/arvbox/bin/arvbox
+++ b/tools/arvbox/bin/arvbox
@@ -107,11 +107,11 @@ wait_for_arvbox() {
     while read line ; do
         if [[ $line =~ "ok: down: ready:" ]] ; then
             kill $LOGPID
     while read line ; do
         if [[ $line =~ "ok: down: ready:" ]] ; then
             kill $LOGPID

-           set +e
-           wait $LOGPID 2>/dev/null
-           set -e
-       else
-           echo $line
+            set +e
+            wait $LOGPID 2>/dev/null
+            set -e
+        else
+            echo $line

         fi
     done < $FF
     rm $FF
         fi
     done < $FF
     rm $FF


@@ -125,7 +125,7 @@ wait_for_arvbox() {
 
 docker_run_dev() {
     docker run \
 
 docker_run_dev() {
     docker run \

-          "--volume=$ARVADOS_ROOT:/usr/src/arvados:rw" \
+           "--volume=$ARVADOS_ROOT:/usr/src/arvados:rw" \

            "--volume=$COMPOSER_ROOT:/usr/src/composer:rw" \
            "--volume=$WORKBENCH2_ROOT:/usr/src/workbench2:rw" \
            "--volume=$PG_DATA:/var/lib/postgresql:rw" \
            "--volume=$COMPOSER_ROOT:/usr/src/composer:rw" \
            "--volume=$WORKBENCH2_ROOT:/usr/src/workbench2:rw" \
            "--volume=$PG_DATA:/var/lib/postgresql:rw" \


@@ -136,8 +136,8 @@ docker_run_dev() {
            "--volume=$NPMCACHE:/var/lib/npm:rw" \
            "--volume=$GOSTUFF:/var/lib/gopath:rw" \
            "--volume=$RLIBS:/var/lib/Rlibs:rw" \
            "--volume=$NPMCACHE:/var/lib/npm:rw" \
            "--volume=$GOSTUFF:/var/lib/gopath:rw" \
            "--volume=$RLIBS:/var/lib/Rlibs:rw" \

-          --label "org.arvados.arvbox_config=$CONFIG" \
-          "$@"
+           --label "org.arvados.arvbox_config=$CONFIG" \
+           "$@"

 }
 
 running_config() {
 }
 
 running_config() {


@@ -153,10 +153,10 @@ run() {
     need_setup=1
 
     if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then
     need_setup=1
 
     if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then

-       if [[ $(running_config) != "$CONFIG" ]] ; then
-           echo "Container $ARVBOX_CONTAINER is '$(running_config)' config but requested '$CONFIG'; use restart or reboot"
-           return 1
-       fi
+        if [[ $(running_config) != "$CONFIG" ]] ; then
+            echo "Container $ARVBOX_CONTAINER is '$(running_config)' config but requested '$CONFIG'; use restart or reboot"
+            return 1
+        fi

         if test "$CONFIG" = test -o "$CONFIG" = devenv ; then
             need_setup=0
         else
         if test "$CONFIG" = test -o "$CONFIG" = devenv ; then
             need_setup=0
         else


@@ -175,12 +175,12 @@ run() {
     if test -n "$TAG"
     then
         if test $(echo $TAG | cut -c1-1) != '-' ; then
     if test -n "$TAG"
     then
         if test $(echo $TAG | cut -c1-1) != '-' ; then

-           TAG=":$TAG"
+            TAG=":$TAG"

             shift
         else
             shift
         else

-           if [[ $TAG = '-' ]] ; then
-               shift
-           fi
+            if [[ $TAG = '-' ]] ; then
+                shift
+            fi

             unset TAG
         fi
     fi
             unset TAG
         fi
     fi


@@ -192,7 +192,7 @@ run() {
             defaultdev=$(/sbin/ip route|awk '/default/ { print $5 }')
             localip=$(ip addr show $defaultdev | grep 'inet ' | sed 's/ *inet \(.*\)\/.*/\1/')
         fi
             defaultdev=$(/sbin/ip route|awk '/default/ { print $5 }')
             localip=$(ip addr show $defaultdev | grep 'inet ' | sed 's/ *inet \(.*\)\/.*/\1/')
         fi

-       echo "Public arvbox will use address $localip"
+        echo "Public arvbox will use address $localip"

         iptemp=$(mktemp)
         echo $localip > $iptemp
         chmod og+r $iptemp
         iptemp=$(mktemp)
         echo $localip > $iptemp
         chmod og+r $iptemp


@@ -207,7 +207,7 @@ run() {
               --publish=8001:8001
               --publish=8002:8002
               --publish=4202:4202
               --publish=8001:8001
               --publish=8002:8002
               --publish=4202:4202

-             --publish=45000-45020:45000-45020"
+              --publish=45000-45020:45000-45020"

     else
         PUBLIC=""
     fi
     else
         PUBLIC=""
     fi


@@ -228,7 +228,7 @@ run() {
                --name=$ARVBOX_CONTAINER \
                --privileged \
                --volumes-from $ARVBOX_CONTAINER-data \
                --name=$ARVBOX_CONTAINER \
                --privileged \
                --volumes-from $ARVBOX_CONTAINER-data \

-              --label "org.arvados.arvbox_config=$CONFIG" \
+               --label "org.arvados.arvbox_config=$CONFIG" \

                $PUBLIC \
                arvados/arvbox-demo$TAG
         updateconf
                $PUBLIC \
                arvados/arvbox-demo$TAG
         updateconf


@@ -257,7 +257,7 @@ run() {
                        --detach \
                        --name=$ARVBOX_CONTAINER \
                        --privileged \
                        --detach \
                        --name=$ARVBOX_CONTAINER \
                        --privileged \

-                      "--env=SVDIR=/etc/test-service" \
+                       "--env=SVDIR=/etc/test-service" \

                        arvados/arvbox-dev$TAG
 
                 docker exec -ti \
                        arvados/arvbox-dev$TAG
 
                 docker exec -ti \


@@ -271,10 +271,10 @@ run() {
                        /var/lib/arvbox/service/api/run-service --only-setup
             fi
 
                        /var/lib/arvbox/service/api/run-service --only-setup
             fi
 

-           interactive=""
-           if [[ -z "$@" ]] ; then
-               interactive=--interactive
-           fi
+            interactive=""
+            if [[ -z "$@" ]] ; then
+                interactive=--interactive
+            fi

 
             docker exec -ti \
                    -e LINES=$(tput lines) \
 
             docker exec -ti \
                    -e LINES=$(tput lines) \


@@ -282,32 +282,32 @@ run() {
                    -e TERM=$TERM \
                    -e WORKSPACE=/usr/src/arvados \
                    -e GEM_HOME=/var/lib/gems \
                    -e TERM=$TERM \
                    -e WORKSPACE=/usr/src/arvados \
                    -e GEM_HOME=/var/lib/gems \

-                  -e CONFIGSRC=/var/lib/arvados/run_tests \
+                   -e CONFIGSRC=/var/lib/arvados/run_tests \

                    $ARVBOX_CONTAINER \
                    /usr/local/lib/arvbox/runsu.sh \
                    /usr/src/arvados/build/run-tests.sh \
                    --temp /var/lib/arvados/test \
                    $ARVBOX_CONTAINER \
                    /usr/local/lib/arvbox/runsu.sh \
                    /usr/src/arvados/build/run-tests.sh \
                    --temp /var/lib/arvados/test \

-                  $interactive \
+                   $interactive \

                    "$@"
         elif [[ "$CONFIG" = devenv ]] ; then
                    "$@"
         elif [[ "$CONFIG" = devenv ]] ; then

-           if [[ $need_setup = 1 ]] ; then
-               docker_run_dev \
+            if [[ $need_setup = 1 ]] ; then
+                    docker_run_dev \

                     --detach \
                     --detach \

-                   --name=${ARVBOX_CONTAINER} \
-                   "--env=SVDIR=/etc/devenv-service" \
-                   "--volume=$HOME:$HOME:rw" \
-                   --volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
-                   arvados/arvbox-dev$TAG
-           fi
-           exec docker exec --interactive --tty \
-                -e LINES=$(tput lines) \
-                -e COLUMNS=$(tput cols) \
-                -e TERM=$TERM \
-                -e "ARVBOX_HOME=$HOME" \
-                -e "DISPLAY=$DISPLAY" \
-                --workdir=$PWD \
-                ${ARVBOX_CONTAINER} \
-                /usr/local/lib/arvbox/devenv.sh "$@"
+                    --name=${ARVBOX_CONTAINER} \
+                    "--env=SVDIR=/etc/devenv-service" \
+                        "--volume=$HOME:$HOME:rw" \
+                    --volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
+                        arvados/arvbox-dev$TAG
+            fi
+                exec docker exec --interactive --tty \
+                     -e LINES=$(tput lines) \
+                     -e COLUMNS=$(tput cols) \
+                     -e TERM=$TERM \
+                     -e "ARVBOX_HOME=$HOME" \
+                     -e "DISPLAY=$DISPLAY" \
+                     --workdir=$PWD \
+                 ${ARVBOX_CONTAINER} \
+                     /usr/local/lib/arvbox/devenv.sh "$@"

         elif [[ "$CONFIG" =~ dev$ ]] ; then
             docker_run_dev \
                    --detach \
         elif [[ "$CONFIG" =~ dev$ ]] ; then
             docker_run_dev \
                    --detach \


@@ -318,12 +318,12 @@ run() {
             updateconf
             wait_for_arvbox
             echo "The Arvados source code is checked out at: $ARVADOS_ROOT"
             updateconf
             wait_for_arvbox
             echo "The Arvados source code is checked out at: $ARVADOS_ROOT"

-           echo "The Arvados testing root certificate is $VAR_DATA/root-cert.pem"
-           if [[ "$(listusers)" =~ ^\{\} ]] ; then
-               echo "No users defined, use 'arvbox adduser' to add user logins"
-           else
-               echo "Use 'arvbox listusers' to see user logins"
-           fi
+            echo "The Arvados testing root certificate is $VAR_DATA/root-cert.pem"
+            if [[ "$(listusers)" =~ ^\{\} ]] ; then
+                echo "No users defined, use 'arvbox adduser' to add user logins"
+            else
+                echo "Use 'arvbox listusers' to see user logins"
+            fi

         else
             echo "Unknown configuration '$CONFIG'"
         fi
         else
             echo "Unknown configuration '$CONFIG'"
         fi


@@ -337,7 +337,7 @@ update() {
     if test -n "$TAG"
     then
         if test $(echo $TAG | cut -c1-1) != '-' ; then
     if test -n "$TAG"
     then
         if test $(echo $TAG | cut -c1-1) != '-' ; then

-           TAG=":$TAG"
+            TAG=":$TAG"

             shift
         else
             unset TAG
             shift
         else
             unset TAG


@@ -345,9 +345,9 @@ update() {
     fi
 
     if echo "$CONFIG" | grep 'demo$' ; then
     fi
 
     if echo "$CONFIG" | grep 'demo$' ; then

-       docker pull arvados/arvbox-demo$TAG
+        docker pull arvados/arvbox-demo$TAG

     else
     else

-       docker pull arvados/arvbox-dev$TAG
+        docker pull arvados/arvbox-dev$TAG

     fi
 }
 
     fi
 }
 


@@ -421,22 +421,22 @@ case "$subcmd" in
 
     sh*)
         exec docker exec --interactive --tty \
 
     sh*)
         exec docker exec --interactive --tty \

-              -e LINES=$(tput lines) \
-              -e COLUMNS=$(tput cols) \
-              -e TERM=$TERM \
-              -e GEM_HOME=/var/lib/gems \
-              $ARVBOX_CONTAINER /bin/bash
+               -e LINES=$(tput lines) \
+               -e COLUMNS=$(tput cols) \
+               -e TERM=$TERM \
+               -e GEM_HOME=/var/lib/gems \
+               $ARVBOX_CONTAINER /bin/bash

         ;;
 
     ash*)
         exec docker exec --interactive --tty \
         ;;
 
     ash*)
         exec docker exec --interactive --tty \

-              -e LINES=$(tput lines) \
-              -e COLUMNS=$(tput cols) \
-              -e TERM=$TERM \
-              -e GEM_HOME=/var/lib/gems \
-              -u arvbox \
-              -w /usr/src/arvados \
-              $ARVBOX_CONTAINER /bin/bash --login
+               -e LINES=$(tput lines) \
+               -e COLUMNS=$(tput cols) \
+               -e TERM=$TERM \
+               -e GEM_HOME=/var/lib/gems \
+               -u arvbox \
+               -w /usr/src/arvados \
+               $ARVBOX_CONTAINER /bin/bash --login

         ;;
 
     pipe)
         ;;
 
     pipe)


@@ -463,7 +463,7 @@ case "$subcmd" in
     update)
         check $@
         stop
     update)
         check $@
         stop

-       update $@
+        update $@

         run $@
         ;;
 
         run $@
         ;;
 


@@ -482,7 +482,7 @@ case "$subcmd" in
     status)
         echo "Container: $ARVBOX_CONTAINER"
         if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then
     status)
         echo "Container: $ARVBOX_CONTAINER"
         if docker ps -a --filter "status=running" | grep -E "$ARVBOX_CONTAINER$" -q ; then

-           echo "Cluster id: $(getclusterid)"
+            echo "Cluster id: $(getclusterid)"

             echo "Status: running"
             echo "Container IP: $(getip)"
             echo "Published host: $(gethost)"
             echo "Status: running"
             echo "Container IP: $(getip)"
             echo "Published host: $(gethost)"


@@ -563,17 +563,17 @@ case "$subcmd" in
 
     clone)
         if test -n "$2" ; then
 
     clone)
         if test -n "$2" ; then

-           mkdir -p "$ARVBOX_BASE/$2"
+            mkdir -p "$ARVBOX_BASE/$2"

             cp -a "$ARVBOX_BASE/$1/passenger" \
             cp -a "$ARVBOX_BASE/$1/passenger" \

-              "$ARVBOX_BASE/$1/gems" \
-              "$ARVBOX_BASE/$1/pip" \
-              "$ARVBOX_BASE/$1/npm" \
-              "$ARVBOX_BASE/$1/gopath" \
-              "$ARVBOX_BASE/$1/Rlibs" \
-              "$ARVBOX_BASE/$1/arvados" \
-              "$ARVBOX_BASE/$1/composer" \
-              "$ARVBOX_BASE/$1/workbench2" \
-              "$ARVBOX_BASE/$2"
+               "$ARVBOX_BASE/$1/gems" \
+               "$ARVBOX_BASE/$1/pip" \
+               "$ARVBOX_BASE/$1/npm" \
+               "$ARVBOX_BASE/$1/gopath" \
+               "$ARVBOX_BASE/$1/Rlibs" \
+               "$ARVBOX_BASE/$1/arvados" \
+               "$ARVBOX_BASE/$1/composer" \
+               "$ARVBOX_BASE/$1/workbench2" \
+               "$ARVBOX_BASE/$2"

             echo "Created new arvbox $2"
             echo "export ARVBOX_CONTAINER=$2"
         else
             echo "Created new arvbox $2"
             echo "export ARVBOX_CONTAINER=$2"
         else


@@ -583,28 +583,28 @@ case "$subcmd" in
         ;;
 
     root-cert)
         ;;
 
     root-cert)

-       CERT=$PWD/${ARVBOX_CONTAINER}-root-cert.crt
-       if test -n "$1" ; then
-           CERT="$1"
-       fi
-       docker exec $ARVBOX_CONTAINER cat /var/lib/arvados/root-cert.pem > "$CERT"
-       echo "Certificate copied to $CERT"
-       ;;
+        CERT=$PWD/${ARVBOX_CONTAINER}-root-cert.crt
+        if test -n "$1" ; then
+            CERT="$1"
+        fi
+        docker exec $ARVBOX_CONTAINER cat /var/lib/arvados/root-cert.pem > "$CERT"
+        echo "Certificate copied to $CERT"
+        ;;

 
     psql)
 
     psql)

-       exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec psql --dbname=arvados_development --host=localhost --username=arvados'
-       ;;
+        exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec psql --dbname=arvados_development --host=localhost --username=arvados'
+        ;;

 
     checkpoint)
 
     checkpoint)

-       exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec pg_dump --host=localhost --username=arvados --clean arvados_development > /var/lib/arvados/checkpoint.sql'
-       ;;
+        exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec pg_dump --host=localhost --username=arvados --clean arvados_development > /var/lib/arvados/checkpoint.sql'
+        ;;

 
     restore)
 
     restore)

-       exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec psql --dbname=arvados_development --host=localhost --username=arvados --quiet --file=/var/lib/arvados/checkpoint.sql'
-       ;;
+        exec docker exec -ti $ARVBOX_CONTAINER bash -c 'PGPASSWORD=$(cat /var/lib/arvados/api_database_pw) exec psql --dbname=arvados_development --host=localhost --username=arvados --quiet --file=/var/lib/arvados/checkpoint.sql'
+        ;;

 
     hotreset)
 
     hotreset)

-       exec docker exec -i $ARVBOX_CONTAINER /usr/bin/env GEM_HOME=/var/lib/gems /bin/bash - <<EOF
+        exec docker exec -i $ARVBOX_CONTAINER /usr/bin/env GEM_HOME=/var/lib/gems /bin/bash - <<EOF

 sv stop api
 sv stop controller
 sv stop websockets
 sv stop api
 sv stop controller
 sv stop websockets


@@ -627,21 +627,21 @@ sv restart keepstore0
 sv restart keepstore1
 sv restart keepproxy
 EOF
 sv restart keepstore1
 sv restart keepproxy
 EOF

-       ;;
+        ;;

 
     adduser)
 
     adduser)

-       docker exec -ti $ARVBOX_CONTAINER /usr/local/lib/arvbox/edit_users.py /var/lib/arvados/cluster_config.yml.override $(getclusterid) add $@
-       docker exec $ARVBOX_CONTAINER sv restart controller
-       ;;
+        docker exec -ti $ARVBOX_CONTAINER /usr/local/lib/arvbox/edit_users.py /var/lib/arvados/cluster_config.yml.override $(getclusterid) add $@
+        docker exec $ARVBOX_CONTAINER sv restart controller
+        ;;

 
     removeuser)
 
     removeuser)

-       docker exec -ti $ARVBOX_CONTAINER /usr/local/lib/arvbox/edit_users.py /var/lib/arvados/cluster_config.yml.override $(getclusterid) remove $@
-       docker exec $ARVBOX_CONTAINER sv restart controller
-       ;;
+        docker exec -ti $ARVBOX_CONTAINER /usr/local/lib/arvbox/edit_users.py /var/lib/arvados/cluster_config.yml.override $(getclusterid) remove $@
+        docker exec $ARVBOX_CONTAINER sv restart controller
+        ;;

 
     listusers)
 
     listusers)

-       listusers
-       ;;
+        listusers
+        ;;

 
     *)
         echo "Arvados-in-a-box             https://doc.arvados.org/install/arvbox.html"
 
     *)
         echo "Arvados-in-a-box             https://doc.arvados.org/install/arvbox.html"


@@ -661,9 +661,9 @@ EOF
         echo "build   <config>   build arvbox Docker image"
         echo "reboot  <config>   stop, build arvbox Docker image, run"
         echo "rebuild <config>   build arvbox Docker image, no layer cache"
         echo "build   <config>   build arvbox Docker image"
         echo "reboot  <config>   stop, build arvbox Docker image, run"
         echo "rebuild <config>   build arvbox Docker image, no layer cache"

-       echo "checkpoint         create database backup"
-       echo "restore            restore checkpoint"
-       echo "hotreset           reset database and restart API without restarting container"
+        echo "checkpoint         create database backup"
+        echo "restore            restore checkpoint"
+        echo "hotreset           reset database and restart API without restarting container"

         echo "reset              delete arvbox arvados data (be careful!)"
         echo "destroy            delete all arvbox code and data (be careful!)"
         echo "log <service>      tail log of specified service"
         echo "reset              delete arvbox arvados data (be careful!)"
         echo "destroy            delete all arvbox code and data (be careful!)"
         echo "log <service>      tail log of specified service"


@@ -671,12 +671,12 @@ EOF
         echo "cat <files>        get contents of files inside arvbox"
         echo "pipe               run a bash script piped in from stdin"
         echo "sv <start|stop|restart> <service> "
         echo "cat <files>        get contents of files inside arvbox"
         echo "pipe               run a bash script piped in from stdin"
         echo "sv <start|stop|restart> <service> "

-       echo "                   change state of service inside arvbox"
+        echo "                   change state of service inside arvbox"

         echo "clone <from> <to>  clone dev arvbox"
         echo "clone <from> <to>  clone dev arvbox"

-       echo "adduser <username> <email>"
-       echo "                   add a user login"
-       echo "removeuser <username>"
-       echo "                   remove user login"
-       echo "listusers          list user logins"
+        echo "adduser <username> <email>"
+        echo "                   add a user login"
+        echo "removeuser <username>"
+        echo "                   remove user login"
+        echo "listusers          list user logins"

         ;;
 esac
         ;;
 esac

diff --git a/tools/arvbox/lib/arvbox/docker/Dockerfile.base b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
index 815db22b4ca5f9e983af413dff93e04d3608a949..eb52ca5a780e252873739c45a2e87fa667748024 100644 (file)
--- a/tools/arvbox/lib/arvbox/docker/Dockerfile.base
+++ b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
@@ -2,17 +2,17 @@
 #
 # SPDX-License-Identifier: AGPL-3.0
 
 #
 # SPDX-License-Identifier: AGPL-3.0
 

-FROM debian:9
+FROM debian:10

 
 ENV DEBIAN_FRONTEND noninteractive
 
 RUN apt-get update && \
     apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \
 
 ENV DEBIAN_FRONTEND noninteractive
 
 RUN apt-get update && \
     apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \

-    postgresql-9.6 postgresql-contrib-9.6 git build-essential runit curl libpq-dev \
-    libcurl4-openssl-dev libssl1.0-dev zlib1g-dev libpcre3-dev libpam-dev \
+    postgresql postgresql-contrib git build-essential runit curl libpq-dev \
+    libcurl4-openssl-dev libssl-dev zlib1g-dev libpcre3-dev libpam-dev \

     openssh-server netcat-traditional \
     graphviz bzip2 less sudo virtualenv \
     openssh-server netcat-traditional \
     graphviz bzip2 less sudo virtualenv \

-    libpython-dev fuse libfuse-dev \
+    fuse libfuse-dev \

     pkg-config libattr1-dev \
     libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
     libjson-perl nginx gitolite3 lsof libreadline-dev \
     pkg-config libattr1-dev \
     libwww-perl libio-socket-ssl-perl libcrypt-ssleay-perl \
     libjson-perl nginx gitolite3 lsof libreadline-dev \


@@ -20,14 +20,12 @@ RUN apt-get update && \
     linkchecker python3-virtualenv python3-venv xvfb iceweasel \
     libgnutls28-dev python3-dev vim cadaver cython gnupg dirmngr \
     libsecret-1-dev r-base r-cran-testthat libxml2-dev pandoc \
     linkchecker python3-virtualenv python3-venv xvfb iceweasel \
     libgnutls28-dev python3-dev vim cadaver cython gnupg dirmngr \
     libsecret-1-dev r-base r-cran-testthat libxml2-dev pandoc \

-    python3-setuptools python3-pip openjdk-8-jdk bsdmainutils net-tools \
-    ruby2.3 ruby-dev bundler shellinabox  && \
-    apt-get remove -yq libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev \
-    libpython2.7-minimal libpython2.7-stdlib python2.7-minimal python2.7 && \
+    python3-setuptools python3-pip default-jdk-headless bsdmainutils net-tools \
+    ruby ruby-dev bundler shellinabox  && \

     apt-get clean
 
     apt-get clean
 

-ENV RUBYVERSION_MINOR 2.3
-ENV RUBYVERSION 2.3.5
+ENV RUBYVERSION_MINOR 2.5
+ENV RUBYVERSION 2.5.1

 
 # Install Ruby from source
 # RUN cd /tmp && \
 
 # Install Ruby from source
 # RUN cd /tmp && \


@@ -40,10 +38,9 @@ ENV RUBYVERSION 2.3.5
 #  rm -rf ruby-${RUBYVERSION}
 
 ENV GEM_HOME /var/lib/gems
 #  rm -rf ruby-${RUBYVERSION}
 
 ENV GEM_HOME /var/lib/gems

-ENV GEM_PATH /var/lib/gems

 ENV PATH $PATH:/var/lib/gems/bin
 
 ENV PATH $PATH:/var/lib/gems/bin
 

-ENV GOVERSION 1.13.6
+ENV GOVERSION 1.15.2

 
 # Install golang binary
 RUN curl -f http://storage.googleapis.com/golang/go${GOVERSION}.linux-amd64.tar.gz | \
 
 # Install golang binary
 RUN curl -f http://storage.googleapis.com/golang/go${GOVERSION}.linux-amd64.tar.gz | \


@@ -60,9 +57,9 @@ RUN apt-key add --no-tty /tmp/8D81803C0EBFCD88.asc && \
     rm -f /tmp/8D81803C0EBFCD88.asc
 
 RUN mkdir -p /etc/apt/sources.list.d && \
     rm -f /tmp/8D81803C0EBFCD88.asc
 
 RUN mkdir -p /etc/apt/sources.list.d && \

-    echo deb https://download.docker.com/linux/debian/ stretch stable > /etc/apt/sources.list.d/docker.list && \
+    echo deb https://download.docker.com/linux/debian/ buster stable > /etc/apt/sources.list.d/docker.list && \

     apt-get update && \
     apt-get update && \

-    apt-get -yq --no-install-recommends install docker-ce=17.06.0~ce-0~debian && \
+    apt-get -yq --no-install-recommends install docker-ce=5:19.03.13~3-0~debian-buster && \

     apt-get clean
 
 RUN rm -rf /var/lib/postgresql && mkdir -p /var/lib/postgresql
     apt-get clean
 
 RUN rm -rf /var/lib/postgresql && mkdir -p /var/lib/postgresql


@@ -117,4 +114,4 @@ ADD runit /etc/runit
 # Start the supervisor.
 ENV SVDIR /etc/service
 STOPSIGNAL SIGINT
 # Start the supervisor.
 ENV SVDIR /etc/service
 STOPSIGNAL SIGINT

-CMD ["/sbin/runit"]
+CMD ["/etc/runit/2"]

diff --git a/tools/arvbox/lib/arvbox/docker/common.sh b/tools/arvbox/lib/arvbox/docker/common.sh
index e81e8108e249fc7215c4ca19c4e25a4bb81efbd9..185467cf7de8d7d5b599f714bb4771090e05abb0 100644 (file)
--- a/tools/arvbox/lib/arvbox/docker/common.sh
+++ b/tools/arvbox/lib/arvbox/docker/common.sh
@@ -2,10 +2,9 @@
 #
 # SPDX-License-Identifier: AGPL-3.0
 
 #
 # SPDX-License-Identifier: AGPL-3.0
 

-
+export DEBIAN_FRONTEND=noninteractive

 export PATH=${PATH}:/usr/local/go/bin:/var/lib/gems/bin
 export GEM_HOME=/var/lib/gems
 export PATH=${PATH}:/usr/local/go/bin:/var/lib/gems/bin
 export GEM_HOME=/var/lib/gems

-export GEM_PATH=/var/lib/gems

 export npm_config_cache=/var/lib/npm
 export npm_config_cache_min=Infinity
 export R_LIBS=/var/lib/Rlibs
 export npm_config_cache=/var/lib/npm
 export npm_config_cache_min=Infinity
 export R_LIBS=/var/lib/Rlibs


@@ -60,6 +59,10 @@ fi
 
 run_bundler() {
     if test -f Gemfile.lock ; then
 
 run_bundler() {
     if test -f Gemfile.lock ; then

+        # The 'gem install bundler line below' is cf.
+        # https://bundler.io/blog/2019/05/14/solutions-for-cant-find-gem-bundler-with-executable-bundle.html,
+        # until we get bundler 2.7.10/3.0.0 or higher
+        gem install bundler --no-document -v "$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1|tr -d ' ')"

         frozen=--frozen
     else
         frozen=""
         frozen=--frozen
     else
         frozen=""


@@ -73,8 +76,8 @@ run_bundler() {
     #         flock /var/lib/gems/gems.lock gem install --verbose --no-document bundler --version ${bundleversion}
     #     fi
     # fi
     #         flock /var/lib/gems/gems.lock gem install --verbose --no-document bundler --version ${bundleversion}
     #     fi
     # fi

-    if ! flock /var/lib/gems/gems.lock bundler install --verbose --path $GEM_HOME --local --no-deployment $frozen "$@" ; then
-        flock /var/lib/gems/gems.lock bundler install --verbose --path $GEM_HOME --no-deployment $frozen "$@"
+    if ! flock /var/lib/gems/gems.lock bundler install --verbose --local --no-deployment $frozen "$@" ; then
+        flock /var/lib/gems/gems.lock bundler install --verbose --no-deployment $frozen "$@"

     fi
 }
 
     fi
 }
 

diff --git a/tools/arvbox/lib/arvbox/docker/createusers.sh b/tools/arvbox/lib/arvbox/docker/createusers.sh
index 58fb413582e0a513c1819f66a36ccf47a3f36306..de1e7bba9606696d41fbc309f706a9a944888d49 100755 (executable)
--- a/tools/arvbox/lib/arvbox/docker/createusers.sh
+++ b/tools/arvbox/lib/arvbox/docker/createusers.sh
@@ -46,7 +46,6 @@ if ! grep "^arvbox:" /etc/passwd >/dev/null 2>/dev/null ; then
     cat <<EOF > /etc/profile.d/paths.sh
 export PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/go/bin:/var/lib/gems/bin:$(ls -d /usr/local/node-*)/bin
 export GEM_HOME=/var/lib/gems
     cat <<EOF > /etc/profile.d/paths.sh
 export PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/go/bin:/var/lib/gems/bin:$(ls -d /usr/local/node-*)/bin
 export GEM_HOME=/var/lib/gems

-export GEM_PATH=/var/lib/gems

 export npm_config_cache=/var/lib/npm
 export npm_config_cache_min=Infinity
 export R_LIBS=/var/lib/Rlibs
 export npm_config_cache=/var/lib/npm
 export npm_config_cache_min=Infinity
 export R_LIBS=/var/lib/Rlibs

diff --git a/tools/arvbox/lib/arvbox/docker/service/postgres/run-service b/tools/arvbox/lib/arvbox/docker/service/postgres/run-service
index a0771aa6a04a9ba007b49c85e298f8f44c9cc7d6..f2377a0c2dd7a544cb0a5cf87318bada12b045e1 100755 (executable)
--- a/tools/arvbox/lib/arvbox/docker/service/postgres/run-service
+++ b/tools/arvbox/lib/arvbox/docker/service/postgres/run-service
@@ -6,7 +6,7 @@
 exec 2>&1
 set -eux -o pipefail
 
 exec 2>&1
 set -eux -o pipefail
 

-PGVERSION=9.6
+PGVERSION=11

 
 if ! test -d /var/lib/postgresql/$PGVERSION/main ; then
     /usr/lib/postgresql/$PGVERSION/bin/initdb --locale=en_US.UTF-8 -D /var/lib/postgresql/$PGVERSION/main
 
 if ! test -d /var/lib/postgresql/$PGVERSION/main ; then
     /usr/lib/postgresql/$PGVERSION/bin/initdb --locale=en_US.UTF-8 -D /var/lib/postgresql/$PGVERSION/main

diff --git a/tools/arvbox/lib/arvbox/docker/service/sdk/run-service b/tools/arvbox/lib/arvbox/docker/service/sdk/run-service
index 1ec225ca128c60c2587ebcd950a7661f1ce4aa12..d66bf315b12752338eed263aec2e3eff0218397e 100755 (executable)
--- a/tools/arvbox/lib/arvbox/docker/service/sdk/run-service
+++ b/tools/arvbox/lib/arvbox/docker/service/sdk/run-service
@@ -20,20 +20,6 @@ ln -sf /usr/src/arvados/sdk/cli/binstubs/arv /usr/local/bin/arv
 
 export PYCMD=python3
 
 
 export PYCMD=python3
 

-# Need to install the upstream version of pip because the python-pip package
-# shipped with Debian 9 is patched to change behavior in a way that breaks our
-# use case.
-# See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=876145
-# When a non-root user attempts to install system packages, it makes the
-# --ignore-installed flag the default (and there is no way to turn it off),
-# this has the effect of making it very hard to share dependencies shared among
-# multiple packages, because it will blindly install the latest version of each
-# dependency requested by each package, even if a compatible package version is
-# already installed.
-if ! pip3 install --no-index --find-links /var/lib/pip pip==9.0.3 ; then
-    pip3 install pip==9.0.3
-fi
-

 pip_install wheel
 
 cd /usr/src/arvados/sdk/python
 pip_install wheel
 
 cd /usr/src/arvados/sdk/python