[ARVADOS] updated: 374a802e502d044973fd21ca68d2f6ab707bd770
Git user
git at public.curoverse.com
Tue Sep 6 12:07:59 EDT 2016
Summary of changes:
.../app/controllers/projects_controller.rb | 2 +-
.../app/controllers/workflows_controller.rb | 4 +
apps/workbench/app/models/container_work_unit.rb | 27 +-
apps/workbench/app/models/job.rb | 3 +-
apps/workbench/app/models/proxy_work_unit.rb | 9 +
apps/workbench/app/models/work_unit.rb | 4 +
.../application/_name_and_description.html.erb | 13 +-
.../_object_description.html.erb} | 2 +-
.../app/views/application/_object_name.html.erb | 5 +
.../_name_and_description.html.erb | 21 +
.../projects/_show_pipeline_templates.html.erb | 5 +-
.../app/views/work_units/_show_child.html.erb | 4 +-
.../app/views/work_units/_show_component.html.erb | 64 +--
.../test/integration/anonymous_access_test.rb | 44 +-
.../test/integration/application_layout_test.rb | 74 ---
.../test/integration/container_requests_test.rb | 4 +-
apps/workbench/test/integration/websockets_test.rb | 200 ++++----
apps/workbench/test/integration/work_units_test.rb | 73 +++
apps/workbench/test/integration_helper.rb | 18 +-
apps/workbench/test/test_helper.rb | 8 +-
apps/workbench/test/unit/work_unit_test.rb | 27 +
build/README | 30 ++
build/run-build-docker-jobs-image.sh | 18 +-
build/run-build-packages.sh | 19 +-
doc/sdk/java/index.html.textile.liquid | 8 +-
docker/.gitignore | 2 -
docker/README.md | 81 ---
docker/api/.gitolite.rc | 191 -------
docker/api/Dockerfile | 75 ---
docker/api/apache2_foreground.sh | 7 -
docker/api/apache2_vhost.in | 50 --
docker/api/application.yml.in | 67 ---
docker/api/apt.arvados.org.list | 2 -
docker/api/arvados-clients.yml.in | 6 -
docker/api/config_databases.sh.in | 15 -
docker/api/crunch-dispatch-run.sh | 24 -
docker/api/database.yml.in | 25 -
docker/api/keep_proxy.json | 6 -
docker/api/keep_server_0.json.in | 6 -
docker/api/keep_server_1.json.in | 6 -
docker/api/munge.key | Bin 1024 -> 0 bytes
docker/api/munge.sh | 3 -
docker/api/omniauth.rb.in | 18 -
docker/api/passenger.sh | 7 -
docker/api/setup-gitolite.sh.in | 73 ---
docker/api/setup.sh.in | 82 ---
docker/api/slurm.conf.in | 60 ---
docker/api/superuser_token.in | 1 -
docker/api/supervisor.conf | 43 --
docker/arv-web/Dockerfile | 15 -
docker/arv-web/apache2_foreground.sh | 8 -
docker/arv-web/apache2_vhost | 19 -
docker/arvdock | 559 ---------------------
docker/base/Dockerfile | 43 --
docker/base/apt.arvados.org.list | 2 -
docker/bcbio-nextgen/Dockerfile | 47 --
docker/build.sh | 41 --
docker/build_tools/Makefile | 281 -----------
docker/build_tools/build.rb | 232 ---------
docker/build_tools/config.rb | 74 ---
docker/compute/Dockerfile | 29 --
docker/compute/fuse.conf | 10 -
docker/compute/munge.sh | 3 -
docker/compute/setup.sh.in | 27 -
docker/compute/supervisor.conf | 28 --
docker/compute/wrapdocker | 90 ----
docker/config.yml.example | 91 ----
docker/doc/Dockerfile | 29 --
docker/doc/apache2_foreground.sh | 7 -
docker/doc/apache2_vhost.in | 11 -
docker/install_sdk.sh | 13 -
docker/java-bwa-samtools/Dockerfile | 23 -
docker/keep/Dockerfile | 14 -
docker/keep/keep_signing_secret.in | 1 -
docker/keep/run-keep.in | 11 -
docker/keepproxy/Dockerfile | 12 -
docker/keepproxy/run-keepproxy.in | 15 -
docker/mkimage-debootstrap.sh | 240 ---------
docker/passenger/Dockerfile | 19 -
docker/postgresql/Dockerfile | 35 --
docker/postgresql/pg_hba.conf | 15 -
docker/postgresql/postgresql.conf | 20 -
docker/shell/Dockerfile | 24 -
docker/shell/fuse.conf | 10 -
docker/shell/setup.sh.in | 19 -
docker/shell/superuser_token.in | 1 -
docker/shell/supervisor.conf | 15 -
docker/slurm/Dockerfile | 12 -
docker/slurm/munge.key | Bin 1024 -> 0 bytes
docker/slurm/slurm.conf.in | 60 ---
docker/slurm/supervisor.conf | 7 -
docker/sso/Dockerfile | 32 --
docker/sso/apache2_foreground.sh | 7 -
docker/sso/apache2_vhost.in | 50 --
docker/sso/application.yml.in | 30 --
docker/sso/database.yml.in | 22 -
docker/sso/seeds.rb.in | 9 -
docker/workbench/.gitignore | 3 -
docker/workbench/Dockerfile | 37 --
docker/workbench/apache2_foreground.sh | 7 -
docker/workbench/apache2_vhost.in | 35 --
docker/workbench/application.yml.in | 29 --
docker/workbench/production.rb.in | 91 ----
docker/workbench/secret_token.rb.in | 7 -
docker/workbench/workbench_rails_env.in | 1 -
sdk/cwl/arvados_cwl/fsaccess.py | 4 +-
sdk/cwl/setup.py | 2 +-
sdk/cwl/tests/test_container.py | 2 +
sdk/cwl/tests/test_job.py | 15 +-
sdk/java/ArvadosSDKJavaExample.java | 4 +-
sdk/java/ArvadosSDKJavaExampleWithPrompt.java | 2 +-
.../java/org/arvados/sdk/java/ArvadosTest.java | 5 +-
sdk/java/src/test/resources/first_pipeline.json | 1 -
.../api/app/controllers/application_controller.rb | 8 +-
.../arvados/v1/container_requests_controller.rb | 1 +
.../controllers/arvados/v1/groups_controller.rb | 2 +-
.../app/controllers/arvados/v1/jobs_controller.rb | 166 +-----
services/api/app/models/arvados_model.rb | 85 ++--
services/api/app/models/container.rb | 14 +
services/api/app/models/job.rb | 177 ++++++-
services/api/app/models/log.rb | 18 +
services/api/config/application.default.yml | 6 +
services/api/config/initializers/lograge.rb | 4 +-
...160901210110_repair_script_parameters_digest.rb | 17 +
services/api/db/structure.sql | 4 +-
services/api/lib/eventbus.rb | 2 +-
services/api/lib/simulate_job_log.rb | 3 +
services/api/test/factories/api_client.rb | 2 +-
.../api/test/factories/api_client_authorization.rb | 2 +-
services/api/test/factories/user.rb | 10 +-
services/api/test/fixtures/container_requests.yml | 40 +-
services/api/test/fixtures/containers.yml | 40 +-
services/api/test/fixtures/logs.yml | 4 +-
services/api/test/fixtures/workflows.yml | 2 +-
.../arvados/v1/job_reuse_controller_test.rb | 2 +-
services/api/test/integration/permissions_test.rb | 10 +-
services/api/test/integration/websocket_test.rb | 60 +--
services/api/test/test_helper.rb | 1 +
services/api/test/unit/container_request_test.rb | 6 +
services/api/test/unit/job_test.rb | 6 +
services/api/test/unit/log_test.rb | 3 +-
services/api/test/unit/permission_test.rb | 23 +
services/fuse/tests/test_mount.py | 2 +-
143 files changed, 835 insertions(+), 4028 deletions(-)
copy apps/workbench/app/views/{projects/_show_description.html.erb => application/_object_description.html.erb} (65%)
create mode 100644 apps/workbench/app/views/application/_object_name.html.erb
create mode 100644 apps/workbench/app/views/container_requests/_name_and_description.html.erb
create mode 100644 build/README
delete mode 100644 docker/.gitignore
delete mode 100644 docker/README.md
delete mode 100644 docker/api/.gitolite.rc
delete mode 100644 docker/api/Dockerfile
delete mode 100755 docker/api/apache2_foreground.sh
delete mode 100644 docker/api/apache2_vhost.in
delete mode 100644 docker/api/application.yml.in
delete mode 100644 docker/api/apt.arvados.org.list
delete mode 100644 docker/api/arvados-clients.yml.in
delete mode 100755 docker/api/config_databases.sh.in
delete mode 100755 docker/api/crunch-dispatch-run.sh
delete mode 100644 docker/api/database.yml.in
delete mode 100644 docker/api/keep_proxy.json
delete mode 100644 docker/api/keep_server_0.json.in
delete mode 100644 docker/api/keep_server_1.json.in
delete mode 100644 docker/api/munge.key
delete mode 100755 docker/api/munge.sh
delete mode 100644 docker/api/omniauth.rb.in
delete mode 100755 docker/api/passenger.sh
delete mode 100755 docker/api/setup-gitolite.sh.in
delete mode 100755 docker/api/setup.sh.in
delete mode 100644 docker/api/slurm.conf.in
delete mode 100644 docker/api/superuser_token.in
delete mode 100644 docker/api/supervisor.conf
delete mode 100644 docker/arv-web/Dockerfile
delete mode 100755 docker/arv-web/apache2_foreground.sh
delete mode 100644 docker/arv-web/apache2_vhost
delete mode 100755 docker/arvdock
delete mode 100644 docker/base/Dockerfile
delete mode 100644 docker/base/apt.arvados.org.list
delete mode 100644 docker/bcbio-nextgen/Dockerfile
delete mode 100755 docker/build.sh
delete mode 100644 docker/build_tools/Makefile
delete mode 100755 docker/build_tools/build.rb
delete mode 100755 docker/build_tools/config.rb
delete mode 100644 docker/compute/Dockerfile
delete mode 100644 docker/compute/fuse.conf
delete mode 100755 docker/compute/munge.sh
delete mode 100755 docker/compute/setup.sh.in
delete mode 100644 docker/compute/supervisor.conf
delete mode 100755 docker/compute/wrapdocker
delete mode 100644 docker/config.yml.example
delete mode 100644 docker/doc/Dockerfile
delete mode 100755 docker/doc/apache2_foreground.sh
delete mode 100644 docker/doc/apache2_vhost.in
delete mode 100755 docker/install_sdk.sh
delete mode 100644 docker/java-bwa-samtools/Dockerfile
delete mode 100644 docker/keep/Dockerfile
delete mode 100644 docker/keep/keep_signing_secret.in
delete mode 100755 docker/keep/run-keep.in
delete mode 100644 docker/keepproxy/Dockerfile
delete mode 100755 docker/keepproxy/run-keepproxy.in
delete mode 100755 docker/mkimage-debootstrap.sh
delete mode 100644 docker/passenger/Dockerfile
delete mode 100644 docker/postgresql/Dockerfile
delete mode 100644 docker/postgresql/pg_hba.conf
delete mode 100644 docker/postgresql/postgresql.conf
delete mode 100644 docker/shell/Dockerfile
delete mode 100644 docker/shell/fuse.conf
delete mode 100755 docker/shell/setup.sh.in
delete mode 100644 docker/shell/superuser_token.in
delete mode 100644 docker/shell/supervisor.conf
delete mode 100644 docker/slurm/Dockerfile
delete mode 100644 docker/slurm/munge.key
delete mode 100644 docker/slurm/slurm.conf.in
delete mode 100644 docker/slurm/supervisor.conf
delete mode 100644 docker/sso/Dockerfile
delete mode 100755 docker/sso/apache2_foreground.sh
delete mode 100644 docker/sso/apache2_vhost.in
delete mode 100644 docker/sso/application.yml.in
delete mode 100644 docker/sso/database.yml.in
delete mode 100644 docker/sso/seeds.rb.in
delete mode 100644 docker/workbench/.gitignore
delete mode 100644 docker/workbench/Dockerfile
delete mode 100755 docker/workbench/apache2_foreground.sh
delete mode 100644 docker/workbench/apache2_vhost.in
delete mode 100644 docker/workbench/application.yml.in
delete mode 100644 docker/workbench/production.rb.in
delete mode 100644 docker/workbench/secret_token.rb.in
delete mode 100644 docker/workbench/workbench_rails_env.in
create mode 100644 services/api/db/migrate/20160901210110_repair_script_parameters_digest.rb
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Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit 374a802e502d044973fd21ca68d2f6ab707bd770
Merge: d420221 96cc894
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Sep 6 12:07:51 2016 -0400
Merge branch 'master' into 9766-register-workflow
Conflicts:
build/run-build-packages.sh
sdk/cwl/setup.py
sdk/cwl/tests/test_job.py
diff --cc sdk/cwl/tests/test_container.py
index 6b5c321,7dd14a0..7d941cf
--- a/sdk/cwl/tests/test_container.py
+++ b/sdk/cwl/tests/test_container.py
@@@ -5,8 -5,9 +5,10 @@@ import unittes
import os
import functools
import cwltool.process
+from schema_salad.ref_resolver import Loader
+ from schema_salad.ref_resolver import Loader
+
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
diff --cc sdk/cwl/tests/test_job.py
index 50c4e34,19ae93a..6189a2d
--- a/sdk/cwl/tests/test_job.py
+++ b/sdk/cwl/tests/test_job.py
@@@ -5,8 -5,9 +5,10 @@@ import unittes
import os
import functools
import cwltool.process
+from schema_salad.ref_resolver import Loader
+ from schema_salad.ref_resolver import Loader
+
if not os.getenv('ARVADOS_DEBUG'):
logging.getLogger('arvados.cwl-runner').setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
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