[ARVADOS] updated: 0e6434711ce72cb9f37be8d52f0e1fd039780e7d
Git user
git at public.curoverse.com
Wed Sep 28 11:22:32 EDT 2016
Summary of changes:
.../app/views/work_units/_show_log.html.erb | 8 +-
.../container_requests_controller_test.rb | 17 ++-
crunch_scripts/cwl-runner | 4 +-
.../install-dispatch.html.textile.liquid | 11 +-
.../crunch2-slurm/install-test.html.textile.liquid | 2 +-
sdk/cwl/arvados_cwl/__init__.py | 45 +++++---
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 47 +++++++++
sdk/cwl/arvados_cwl/arvcontainer.py | 8 ++
sdk/cwl/arvados_cwl/arvjob.py | 7 ++
sdk/cwl/arvados_cwl/arvworkflow.py | 83 ++++++++++++++-
sdk/cwl/arvados_cwl/pathmapper.py | 2 +-
sdk/cwl/arvados_cwl/runner.py | 2 +-
sdk/cwl/setup.py | 1 +
sdk/cwl/tests/test_container.py | 8 +-
sdk/cwl/tests/test_job.py | 76 +++++++++++++-
sdk/cwl/tests/wf/scatter2.cwl | 56 ++++++++++
sdk/cwl/tests/wf/scatter2_subwf.cwl | 33 ++++++
sdk/go/arvadosclient/pool.go | 36 ++++---
sdk/go/arvadostest/run_servers.go | 9 ++
sdk/go/config/load.go | 7 +-
services/api/app/models/arvados_model.rb | 2 +-
services/api/config/application.default.yml | 6 ++
.../api/lib/tasks/delete_old_container_logs.rake | 14 +++
services/api/lib/tasks/delete_old_job_logs.rake | 11 +-
services/api/test/fixtures/container_requests.yml | 2 +-
services/api/test/fixtures/containers.yml | 55 +++++++++-
services/api/test/fixtures/logs.yml | 114 +++++++++++++++++++++
.../test/tasks/delete_old_container_logs_test.rb | 50 +++++++++
.../arv-git-httpd.service} | 5 +-
services/arv-git-httpd/auth_handler.go | 28 +++--
services/arv-git-httpd/git_handler.go | 6 +-
services/arv-git-httpd/git_handler_test.go | 2 +-
services/arv-git-httpd/gitolite_test.go | 16 ++-
services/arv-git-httpd/integration_test.go | 25 +++--
services/arv-git-httpd/main.go | 75 ++++++++++----
services/arv-git-httpd/server.go | 4 +-
services/arv-git-httpd/usage.go | 62 +++++++++++
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 53 +++++-----
.../crunch-dispatch-slurm.service | 1 +
.../crunch-dispatch-slurm_test.go | 8 +-
.../dockercleaner/arvados-docker-cleaner.service | 1 +
services/dockercleaner/arvados_docker/cleaner.py | 2 +-
services/fuse/tests/test_mount.py | 50 ++++++---
services/keep-balance/keep-balance.service | 3 +-
services/keep-balance/main.go | 18 ++--
services/keep-balance/main_test.go | 7 +-
services/keep-balance/usage.go | 24 ++---
services/keep-web/doc.go | 28 +++--
services/keep-web/keep-web.service | 1 +
services/keep-web/main.go | 4 +-
services/keep-web/usage.go | 2 +-
services/keepproxy/keepproxy.go | 2 +-
services/keepproxy/keepproxy.service | 1 +
services/keepproxy/usage.go | 2 +-
54 files changed, 937 insertions(+), 209 deletions(-)
create mode 100644 sdk/cwl/arvados_cwl/arv-cwl-schema.yml
create mode 100644 sdk/cwl/tests/wf/scatter2.cwl
create mode 100644 sdk/cwl/tests/wf/scatter2_subwf.cwl
create mode 100644 services/api/lib/tasks/delete_old_container_logs.rake
create mode 100644 services/api/test/tasks/delete_old_container_logs_test.rb
copy services/{crunch-dispatch-slurm/crunch-dispatch-slurm.service => arv-git-httpd/arv-git-httpd.service} (50%)
create mode 100644 services/arv-git-httpd/usage.go
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commit 0e6434711ce72cb9f37be8d52f0e1fd039780e7d
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Sep 28 11:13:40 2016 -0400
9950: 9953: 9954: 9955: 9957: Add AssertPathExists= to unit file to avoid startup until config file exists.
diff --git a/services/arv-git-httpd/arv-git-httpd.service b/services/arv-git-httpd/arv-git-httpd.service
index 8aaf674..f71c2ff 100644
--- a/services/arv-git-httpd/arv-git-httpd.service
+++ b/services/arv-git-httpd/arv-git-httpd.service
@@ -2,6 +2,7 @@
Description=Arvados git server
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/arvados-git-httpd/arvados-git-httpd.yml
[Service]
Type=notify
diff --git a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.service b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.service
index 5b37e3c..34ba80b 100644
--- a/services/crunch-dispatch-slurm/crunch-dispatch-slurm.service
+++ b/services/crunch-dispatch-slurm/crunch-dispatch-slurm.service
@@ -2,6 +2,7 @@
Description=Arvados Crunch Dispatcher for SLURM
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml
[Service]
Type=notify
diff --git a/services/dockercleaner/arvados-docker-cleaner.service b/services/dockercleaner/arvados-docker-cleaner.service
index 43e4ab8..28653ae 100644
--- a/services/dockercleaner/arvados-docker-cleaner.service
+++ b/services/dockercleaner/arvados-docker-cleaner.service
@@ -2,6 +2,7 @@
Description=Arvados Docker Image Cleaner
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/docker-cleaner/docker-cleaner.json
[Service]
Type=simple
diff --git a/services/keep-balance/keep-balance.service b/services/keep-balance/keep-balance.service
index 634b44b..157e42c 100644
--- a/services/keep-balance/keep-balance.service
+++ b/services/keep-balance/keep-balance.service
@@ -2,6 +2,7 @@
Description=Arvados Keep Balance
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/keep-balance/keep-balance.yml
[Service]
Type=simple
diff --git a/services/keep-web/keep-web.service b/services/keep-web/keep-web.service
index da56212..24be771 100644
--- a/services/keep-web/keep-web.service
+++ b/services/keep-web/keep-web.service
@@ -2,6 +2,7 @@
Description=Arvados Keep web gateway
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/keep-web/keep-web.yml
[Service]
Type=notify
diff --git a/services/keepproxy/keepproxy.service b/services/keepproxy/keepproxy.service
index 5bd3036..c340fab 100644
--- a/services/keepproxy/keepproxy.service
+++ b/services/keepproxy/keepproxy.service
@@ -2,6 +2,7 @@
Description=Arvados Keep Proxy
Documentation=https://doc.arvados.org/
After=network.target
+AssertPathExists=/etc/arvados/keepproxy/keepproxy.yml
[Service]
Type=notify
commit e5a158a14552e250a239f8e184e9471289683d25
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Sep 28 11:12:11 2016 -0400
9950: Fix arvados-git-httpd executable path. Update config path to /etc/arvados/git-httpd/.
diff --git a/services/arv-git-httpd/arv-git-httpd.service b/services/arv-git-httpd/arv-git-httpd.service
index 1182a0e..8aaf674 100644
--- a/services/arv-git-httpd/arv-git-httpd.service
+++ b/services/arv-git-httpd/arv-git-httpd.service
@@ -5,7 +5,7 @@ After=network.target
[Service]
Type=notify
-ExecStart=/usr/bin/arv-git-httpd
+ExecStart=/usr/bin/arvados-git-httpd
Restart=always
[Install]
diff --git a/services/arv-git-httpd/main.go b/services/arv-git-httpd/main.go
index 26d2914..dd28136 100644
--- a/services/arv-git-httpd/main.go
+++ b/services/arv-git-httpd/main.go
@@ -35,7 +35,7 @@ func defaultConfig() *Config {
}
func init() {
- const defaultCfgPath = "/etc/arvados/arv-git-httpd/arv-git-httpd.yml"
+ const defaultCfgPath = "/etc/arvados/git-httpd/git-httpd.yml"
const deprecated = " (DEPRECATED -- use config file instead)"
flag.StringVar(&theConfig.Listen, "address", theConfig.Listen,
"Address to listen on, \"host:port\" or \":port\"."+deprecated)
commit 9bcf0f9acc345477668aa25083ecbe3dd4fe44f3
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Sep 28 10:47:36 2016 -0400
9953: Update default config path.
diff --git a/services/dockercleaner/arvados_docker/cleaner.py b/services/dockercleaner/arvados_docker/cleaner.py
index 8b8c772..5ac8100 100755
--- a/services/dockercleaner/arvados_docker/cleaner.py
+++ b/services/dockercleaner/arvados_docker/cleaner.py
@@ -294,7 +294,7 @@ def parse_arguments(arguments):
formatter_class=Formatter,
)
parser.add_argument(
- '--config', action='store', type=str, default='/etc/arvados/docker-cleaner/config.json',
+ '--config', action='store', type=str, default='/etc/arvados/docker-cleaner/docker-cleaner.json',
help="configuration file")
deprecated = " (DEPRECATED -- use config file instead)"
commit dec0d5fbdfff3a13d70afedca2a7b5b36ebb8f2e
Merge: 30fb9bf a5445a2
Author: Tom Clegg <tom at curoverse.com>
Date: Wed Sep 28 10:32:07 2016 -0400
9953: Merge branch 'master' into 9953-dockercleaner-config
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