[ARVADOS] updated: 9eaccd0367a1101ad9424eff21dff2f1138121b8

git at public.curoverse.com git at public.curoverse.com
Thu Apr 2 10:25:00 EDT 2015


Summary of changes:
 .../app/assets/javascripts/add_repository.js       |  38 +++
 .../views/application/_selection_checkbox.html.erb |   1 +
 .../app/views/collections/_show_files.html.erb     |   1 +
 .../app/views/users/_add_repository_modal.html.erb |  41 ++++
 .../app/views/users/_manage_account.html.erb       |  56 +----
 .../app/views/users/_manage_current_token.html.erb |  12 +
 .../app/views/users/_manage_repositories.html.erb  |  19 +-
 .../app/views/users/_manage_ssh_keys.html.erb      |  17 +-
 .../views/users/_manage_virtual_machines.html.erb  |  12 +-
 .../test/integration/user_manage_account_test.rb   |  10 +
 apps/workbench/test/integration/users_test.rb      |  21 +-
 doc/_includes/_tutorial_submit_job.liquid          |   2 +-
 doc/api/methods/jobs.html.textile.liquid           |  14 +-
 .../schema/PipelineTemplate.html.textile.liquid    |  16 +-
 doc/api/schema/Repository.html.textile.liquid      |   6 +-
 .../topics/tutorial-parallel.html.textile.liquid   |   2 +-
 .../tutorial-submit-job.html.textile.liquid        |   6 +-
 docker/api/.gitolite.rc                            | 191 +++++++++++++++
 docker/api/Dockerfile                              |   1 +
 docker/api/application.yml.in                      |   1 +
 docker/api/setup-gitolite.sh.in                    |   5 +-
 docker/api/setup.sh.in                             |   4 +-
 docker/api/update-gitolite.rb                      | 252 +++++++++++++-------
 docker/arvdock                                     |  43 ++--
 docker/compute/setup.sh.in                         |  20 +-
 sdk/python/arvados/arvfile.py                      |   2 +-
 sdk/python/tests/test_stream.py                    |   2 +-
 .../app/controllers/arvados/v1/users_controller.rb |  21 +-
 services/api/app/models/arvados_model.rb           |   9 +-
 services/api/app/models/commit.rb                  |  28 +--
 services/api/app/models/repository.rb              |  80 ++++++-
 services/api/app/models/user.rb                    |  31 ++-
 services/api/config/application.default.yml        |   5 +
 ...backward_compatibility_for_user_repositories.rb |  89 +++++++
 services/api/db/structure.sql                      |   8 +-
 services/api/script/crunch-dispatch.rb             |  22 +-
 .../api/script/migrate-gitolite-to-uuid-storage.rb | 217 +++++++++++++++++
 .../test/fixtures/api_client_authorizations.yml    |   6 +
 services/api/test/fixtures/jobs.yml                |  30 +--
 services/api/test/fixtures/repositories.yml        |  17 +-
 services/api/test/fixtures/users.yml               |   1 +
 .../arvados/v1/commits_controller_test.rb          |   8 +-
 .../arvados/v1/job_reuse_controller_test.rb        |  56 ++---
 .../functional/arvados/v1/jobs_controller_test.rb  |   4 +-
 .../arvados/v1/repositories_controller_test.rb     |  16 ++
 .../functional/arvados/v1/users_controller_test.rb |  51 ++--
 .../api/test/integration/crunch_dispatch_test.rb   |   2 +-
 .../test/integration/serialized_encoding_test.rb   |   2 +-
 services/api/test/integration/users_test.rb        |  21 +-
 services/api/test/test.git.tar                     | Bin 194560 -> 194560 bytes
 services/api/test/test_helper.rb                   |  19 ++
 services/api/test/unit/job_test.rb                 |   2 +-
 services/api/test/unit/permission_test.rb          |  14 --
 services/api/test/unit/repository_test.rb          | 262 ++++++++++++++++++++-
 services/api/test/unit/user_test.rb                |  68 ++++--
 55 files changed, 1491 insertions(+), 393 deletions(-)
 create mode 100644 apps/workbench/app/assets/javascripts/add_repository.js
 create mode 100644 apps/workbench/app/views/users/_add_repository_modal.html.erb
 create mode 100644 docker/api/.gitolite.rc
 create mode 100644 services/api/db/migrate/20150324152204_backward_compatibility_for_user_repositories.rb
 create mode 100755 services/api/script/migrate-gitolite-to-uuid-storage.rb

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commit 9eaccd0367a1101ad9424eff21dff2f1138121b8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Apr 2 10:24:56 2015 -0400

    4752: Websockets works.  Fix compute node containers to restart correctly.  Fix
    git server hostname.  Arvdock waits for API/workbench to be ready before telling
    the user to go to workbench.

diff --git a/docker/api/application.yml.in b/docker/api/application.yml.in
index 84dc0c3..3cfb5a9 100644
--- a/docker/api/application.yml.in
+++ b/docker/api/application.yml.in
@@ -20,6 +20,7 @@ development:
 
 production:
   host: api.dev.arvados
+  git_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).
diff --git a/docker/api/setup.sh.in b/docker/api/setup.sh.in
index 98bd3bd..2c7da92 100755
--- a/docker/api/setup.sh.in
+++ b/docker/api/setup.sh.in
@@ -18,7 +18,9 @@ while ! arv user current ; do sleep 1 ; done
 
 # Arvados repository object
 all_users_group_uuid="@@API_HOSTNAME@@-j7d0g-fffffffffffffff"
-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"}'`
+
+arv user update --uuid @@API_HOSTNAME@@-tpzed-000000000000000 --user '{"username":"root"}'
+repo_uuid=`arv --format=uuid repository create --repository '{"owner_uuid":"@@API_HOSTNAME@@-tpzed-000000000000000", "name":"arvados"}'`
 echo "Arvados repository uuid is $repo_uuid"
 
 read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"
diff --git a/docker/arvdock b/docker/arvdock
index 4b7509e..788c1b3 100755
--- a/docker/arvdock
+++ b/docker/arvdock
@@ -93,23 +93,6 @@ function start_container {
       echo "Started container: $container"
     fi
 
-    if [[ "$name" == "doc_server" ]]; then
-      echo
-      echo "******************************************************************"
-      echo "You can access the Arvados documentation at http://doc.dev.arvados"
-      echo "******************************************************************"
-      echo
-    fi
-
-    if [[ "$name" == "workbench_server" ]]; then
-      echo
-      echo "********************************************************************"
-      echo "You can access the Arvados workbench at http://workbench.dev.arvados"
-      echo "********************************************************************"
-      echo
-   fi
-
-
 }
 
 # Create a Docker data volume
@@ -324,9 +307,35 @@ EOF
         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 "Then run '$0 start' again"
         echo "******************************************************************"
         echo
+    else
+        while ! curl -L -f http://workbench.dev.arvados >/dev/null 2>/dev/null ; do
+            echo "Waiting for Arvados to be ready."
+            sleep 1
+        done
+
+        `$DOCKER ps |grep -P "doc_server[^/]" -q`
+        if [[ "$?" == "0" ]]; then
+            echo
+            echo "******************************************************************"
+            echo "You can access the Arvados documentation at http://doc.dev.arvados"
+            echo "******************************************************************"
+            echo
+        fi
+
+        `$DOCKER ps |grep -P "workbench_server[^/]" -q`
+        if [[ "$?" == "0" ]]; then
+            echo
+            echo "********************************************************************"
+            echo "You can access the Arvados workbench at http://workbench.dev.arvados"
+            echo "********************************************************************"
+            echo
+        fi
     fi
+
 }
 
 function do_stop {
diff --git a/docker/compute/setup.sh.in b/docker/compute/setup.sh.in
index 6a4e951..efb2c41 100755
--- a/docker/compute/setup.sh.in
+++ b/docker/compute/setup.sh.in
@@ -5,19 +5,23 @@
 export ARVADOS_API_HOST=api
 export ARVADOS_API_HOST_INSECURE=yes
 export ARVADOS_API_TOKEN=@@API_SUPERUSER_SECRET@@
+export HOME=/root
 
 # Wait for API server to come up.
 while ! arv user current ; do sleep 1 ; done
 
-arv node create --node {} > /tmp/node.json
+if ! test -f /root/node.json ; then
+    arv node create --node "{\"hostname\": \"$(hostname)\"}" > /root/node.json
 
-UUID=`grep \"uuid\" /tmp//node.json  |cut -f4 -d\"`
-PING_SECRET=`grep \"ping_secret\" /tmp//node.json  |cut -f4 -d\"`
+    # Make sure /dev/fuse permissions are correct (the device appears after fuse is loaded)
+    chmod 1660 /dev/fuse && chgrp fuse /dev/fuse
+fi
 
-echo "*/5 * * * * root /usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping" > /etc/cron.d/node_ping
+UUID=`grep \"uuid\" /root/node.json  |cut -f4 -d\"`
+PING_SECRET=`grep \"ping_secret\" /root/node.json  |cut -f4 -d\"`
 
-# Send a ping now
-/usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping?ping_secret=$PING_SECRET
+if ! test -f /etc/cron.d/node_ping ; then
+    echo "*/5 * * * * root /usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping" > /etc/cron.d/node_ping
+fi
 
-# Just make sure /dev/fuse permissions are correct (the device appears after fuse is loaded)
-chmod 1660 /dev/fuse && chgrp fuse /dev/fuse
+/usr/bin/curl -k -d ping_secret=$PING_SECRET https://api/arvados/v1/nodes/$UUID/ping?ping_secret=$PING_SECRET

commit 379717415ec5f772ab2f54e263c2c3f44d77f70f
Merge: d318cc5 0b99046
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Apr 1 16:14:19 2015 -0400

    Merge branch '5626-git-server-hostname' into 4752-docker-websockets


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