[ARVADOS] updated: e97d70a1f6c687ce110f40d0e44a9fa385873ad6
git at public.curoverse.com
git at public.curoverse.com
Tue Mar 24 10:29:18 EDT 2015
Summary of changes:
.../app/assets/javascripts/link_to_remote.js | 23 ++++++++++++++++
.../app/assets/javascripts/select_modal.js | 2 +-
apps/workbench/app/helpers/application_helper.rb | 29 ++++++++++++++++++++
.../app/views/application/_show_sharing.html.erb | 6 ++++
.../test/controllers/projects_controller_test.rb | 2 +-
apps/workbench/test/diagnostics/pipeline_test.rb | 2 +-
apps/workbench/test/helpers/share_object_helper.rb | 5 ++--
docker/api/application.yml.in | 11 ++------
docker/api/arvados-clients.yml.in | 2 +-
docker/api/setup-gitolite.sh.in | 5 ++--
docker/api/setup.sh.in | 4 +--
docker/arvdock | 32 ++++++++++++----------
docker/workbench/apache2_foreground.sh | 6 ----
docker/workbench/application.yml.in | 5 ++--
sdk/cli/bin/crunch-job | 8 ++++--
services/keepproxy/keepproxy.go | 25 ++++++++++++-----
16 files changed, 112 insertions(+), 55 deletions(-)
create mode 100644 apps/workbench/app/assets/javascripts/link_to_remote.js
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commit e97d70a1f6c687ce110f40d0e44a9fa385873ad6
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Mar 24 10:32:58 2015 -0400
5539: Require that the user update resolv.conf, and use FQDN (api.dev.arvados,
workbench.dev.arvados) to refer to services more consistently.
diff --git a/docker/api/application.yml.in b/docker/api/application.yml.in
index 7f41985..c6ee58a 100644
--- a/docker/api/application.yml.in
+++ b/docker/api/application.yml.in
@@ -19,6 +19,8 @@ development:
blob_signing_key: ~
production:
+ host: api.dev.arvados
+
# At minimum, you need a nice long randomly generated secret_token here.
# Use a long string of alphanumeric characters (at least 36).
secret_token: @@API_SECRET@@
@@ -42,14 +44,6 @@ production:
# - 127.0.0.1
# - 192.168.1.1
#
- # The version below is suitable for AWS.
- # Uncomment and change <%# to <%= to use it.
- # compute_node_nameservers: <%#
- # require 'net/http'
- # ['local', 'public'].collect do |iface|
- # Net::HTTP.get(URI("http://169.254.169.254/latest/meta-data/#{iface}-ipv4")).match(/^[\d\.]+$/)[0]
- # end << '172.16.0.23'
- # %>
permit_create_collection_with_unsigned_manifest: true
git_repositories_dir: /home/git/repositories
crunch_job_wrapper: :slurm_immediate
@@ -69,4 +63,3 @@ test:
common:
#git_repositories_dir: /var/cache/git
#git_internal_dir: /var/cache/arvados/internal.git
-
diff --git a/docker/api/arvados-clients.yml.in b/docker/api/arvados-clients.yml.in
index 59ff352..f33352f 100644
--- a/docker/api/arvados-clients.yml.in
+++ b/docker/api/arvados-clients.yml.in
@@ -1,5 +1,5 @@
production:
- gitolite_url: 'git at api:gitolite-admin.git'
+ gitolite_url: 'git at api.dev.arvados:gitolite-admin.git'
gitolite_tmp: 'gitolite-tmp'
arvados_api_host: 'api'
arvados_api_token: '@@API_SUPERUSER_SECRET@@'
diff --git a/docker/api/setup-gitolite.sh.in b/docker/api/setup-gitolite.sh.in
index 92014f9..2bd6fc2 100755
--- a/docker/api/setup-gitolite.sh.in
+++ b/docker/api/setup-gitolite.sh.in
@@ -25,9 +25,9 @@ chmod +rx /home/git/repositories/*git -R
# Now set up the gitolite repo(s) we use
mkdir -p /usr/local/arvados/gitolite-tmp/
# Make ssh store the host key
-ssh -o "StrictHostKeyChecking no" git at api info
+ssh -o "StrictHostKeyChecking no" git at api.dev.arvados info
# Now check out the tree
-git clone git at api:gitolite-admin.git /usr/local/arvados/gitolite-tmp/gitolite-admin/
+git clone git at api.dev.arvados:gitolite-admin.git /usr/local/arvados/gitolite-tmp/gitolite-admin/
cd /usr/local/arvados/gitolite-tmp/gitolite-admin
mkdir keydir/arvados
mkdir conf/admin
@@ -74,4 +74,3 @@ export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
echo "PATH=/usr/bin:/bin:/sbin" > /etc/cron.d/arvados-repo-update
echo "*/5 * * * * git cd ~git/repositories/arvados.git; git fetch https://github.com/curoverse/arvados.git master:master" >> /etc/cron.d/arvados-repo-update
-
diff --git a/docker/api/setup.sh.in b/docker/api/setup.sh.in
index 0111595..af9d54d 100755
--- a/docker/api/setup.sh.in
+++ b/docker/api/setup.sh.in
@@ -10,7 +10,7 @@ export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
# Arvados repository object
all_users_group_uuid="$prefix-j7d0g-fffffffffffffff"
-repo_uuid=`arv --format=uuid repository create --repository '{"name":"arvados","fetch_url":"git at api:arvados.git","push_url":"git at api:arvados.git"}'`
+repo_uuid=`arv --format=uuid repository create --repository '{"name":"arvados","fetch_url":"git at api.dev.arvados:arvados.git","push_url":"git at api.dev.arvados:arvados.git"}'`
echo "Arvados repository uuid is $repo_uuid"
read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
@@ -42,7 +42,7 @@ fi
# User repository object
user_uuid=`arv --format=uuid user current`
-repo_uuid=`arv --format=uuid repository create --repository '{"name":"@@ARVADOS_USER_NAME@@","fetch_url":"git at api:@@ARVADOS_USER_NAME@@.git","push_url":"git at api:@@ARVADOS_USER_NAME@@.git"}'`
+repo_uuid=`arv --format=uuid repository create --repository '{"name":"@@ARVADOS_USER_NAME@@","fetch_url":"git at api.dev.arvados:@@ARVADOS_USER_NAME@@.git","push_url":"git at api.dev.arvados:@@ARVADOS_USER_NAME@@.git"}'`
echo "User repository uuid is $repo_uuid"
read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
diff --git a/docker/arvdock b/docker/arvdock
index 2107ff3..494bdda 100755
--- a/docker/arvdock
+++ b/docker/arvdock
@@ -89,17 +89,17 @@ function start_container {
if [[ "$name" == "doc_server" ]]; then
echo
- echo "*****************************************************************"
- echo "You can access the Arvados documentation at http://localhost:${port%:*}"
- echo "*****************************************************************"
+ echo "******************************************************************"
+ echo "You can access the Arvados documentation at http://doc.dev.arvados"
+ echo "******************************************************************"
echo
fi
if [[ "$name" == "workbench_server" ]]; then
echo
- echo "*****************************************************************"
- echo "You can access the Arvados workbench at http://localhost:${port%:*}"
- echo "*****************************************************************"
+ echo "********************************************************************"
+ echo "You can access the Arvados workbench at http://workbench.dev.arvados"
+ echo "********************************************************************"
echo
fi
@@ -236,14 +236,6 @@ function do_start {
echo $DOCKER run -d -v /var/run/docker.sock:/docker.sock --name skydock crosbymichael/skydock -ttl 30 -environment dev -s /docker.sock -domain arvados -name skydns
$DOCKER run -d -v /var/run/docker.sock:/docker.sock --name skydock crosbymichael/skydock -ttl 30 -environment dev -s /docker.sock -domain arvados -name skydns
fi
-
- echo
- echo "*****************************************************************"
- echo "To access Arvados using command line tools on the host we recommend you add"
- echo "the arvados nameserver to the top of your DNS configuration in /etc/resolv.conf:"
- echo "nameserver 172.17.42.1"
- echo "*****************************************************************"
- echo
fi
if [[ $start_sso != false ]]
@@ -318,6 +310,17 @@ EOF
fi
fi
fi
+
+ `cat /etc/resolv.conf |grep -P "nameserver 172\.17\.42\.1" -q`
+ if [[ "$?" == "1" ]]; then
+ echo
+ echo "******************************************************************"
+ echo "To access Arvados you must add the Arvados nameserver to the top"
+ echo "of your DNS configuration in /etc/resolv.conf:"
+ echo "nameserver 172.17.42.1"
+ echo "******************************************************************"
+ echo
+ fi
}
function do_stop {
@@ -474,7 +477,6 @@ case $1 in
shift
do_reset $@
;;
-
*)
usage
exit 1
diff --git a/docker/workbench/apache2_foreground.sh b/docker/workbench/apache2_foreground.sh
index 1a31fb3..fc6028e 100755
--- a/docker/workbench/apache2_foreground.sh
+++ b/docker/workbench/apache2_foreground.sh
@@ -3,11 +3,5 @@
read pid cmd state ppid pgrp session tty_nr tpgid rest < /proc/self/stat
trap "kill -TERM -$pgrp; exit" EXIT TERM KILL SIGKILL SIGTERM SIGQUIT
-# Override the default API server address if necessary.
-if [[ "$API_PORT_443_TCP_ADDR" != "" ]]; then
- sed -i "s/arvados_login_base: '.*'/arvados_login_base: 'https:\/\/$API_PORT_443_TCP_ADDR\/login'/" /usr/src/arvados/apps/workbench/config/application.yml
- sed -i "s/arvados_v1_base: '.*'/arvados_v1_base: 'https:\/\/$API_PORT_443_TCP_ADDR\/arvados\/v1'/" /usr/src/arvados/apps/workbench/config/application.yml
-fi
-
source /etc/apache2/envvars
/usr/sbin/apache2 -D FOREGROUND
diff --git a/docker/workbench/application.yml.in b/docker/workbench/application.yml.in
index 3140188..c517c5c 100644
--- a/docker/workbench/application.yml.in
+++ b/docker/workbench/application.yml.in
@@ -15,8 +15,8 @@ common:
secret_token: @@WORKBENCH_SECRET@@
# You probably also want to point to your API server.
- arvados_login_base: 'https://localhost:9900/login'
- arvados_v1_base: 'https://localhost:9900/arvados/v1'
+ arvados_login_base: 'https://api.dev.arvados/login'
+ arvados_v1_base: 'https://api.dev.arvados/arvados/v1'
arvados_insecure_https: @@WORKBENCH_INSECURE_HTTPS@@
data_import_dir: @@WORKBENCH_DATA_IMPORT_DIR@@
@@ -24,4 +24,3 @@ common:
site_name: @@WORKBENCH_SITE_NAME@@
activation_contact_link: @@WORKBENCH_ACTIVATION_CONTACT_LINK@@
-
commit 70ab42cb727b6a1bd1a8b26e2481de7caa0853d5
Merge: 3f99a8c e809173
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Mar 24 09:30:01 2015 -0400
Merge branch 'master' into 5539-better-docker
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