[ARVADOS] updated: c494f4c398457c5edbd9b2c3f1a439bf041c7ed2
Git user
git at public.curoverse.com
Tue Dec 6 10:45:21 EST 2016
Summary of changes:
apps/workbench/Gemfile | 6 +-
apps/workbench/Gemfile.lock | 16 +-
.../app/controllers/application_controller.rb | 10 +-
apps/workbench/app/models/container_work_unit.rb | 13 +-
.../views/container_requests/_show_inputs.html.erb | 36 ++--
.../test/controllers/projects_controller_test.rb | 21 +-
.../test/integration/application_layout_test.rb | 4 +-
.../test/integration/container_requests_test.rb | 13 ++
build/README | 6 +-
build/build-dev-docker-jobs-image.sh | 63 ++++++
build/run-build-packages.sh | 17 +-
build/run-tests.sh | 6 +
doc/_config.yml | 2 +-
doc/_includes/_arvados_cwl_runner.liquid | 2 +-
.../methods/container_requests.html.textile.liquid | 2 +
doc/user/cwl/cwl-runner.html.textile.liquid | 2 +-
...utorial-workflow-workbench.html.textile.liquid} | 2 +-
sdk/cwl/arvados_cwl/__init__.py | 34 ++-
sdk/cwl/arvados_cwl/arvcontainer.py | 65 +++---
sdk/cwl/arvados_cwl/arvjob.py | 8 +-
sdk/cwl/arvados_cwl/arvworkflow.py | 4 +-
sdk/cwl/arvados_cwl/done.py | 3 +
sdk/cwl/arvados_cwl/runner.py | 19 +-
sdk/cwl/tests/test_container.py | 71 ++----
sdk/cwl/tests/test_submit.py | 58 ++++-
sdk/dev-jobs.dockerfile | 38 ++++
services/api/Gemfile | 19 +-
services/api/Gemfile.lock | 239 +++++++++++----------
.../api/app/controllers/application_controller.rb | 18 +-
.../arvados/v1/collections_controller.rb | 4 +-
.../controllers/arvados/v1/schema_controller.rb | 22 +-
.../arvados/v1/user_agreements_controller.rb | 3 +-
.../app/controllers/arvados/v1/users_controller.rb | 2 +-
.../arvados/v1/virtual_machines_controller.rb | 2 +-
.../api/app/controllers/database_controller.rb | 2 +-
services/api/app/middlewares/arvados_api_token.rb | 2 +-
services/api/app/models/arvados_model.rb | 9 +-
services/api/app/models/blob.rb | 4 +-
services/api/app/models/collection.rb | 15 +-
services/api/app/models/commit_ancestor.rb | 6 +-
services/api/app/models/job.rb | 42 ++--
services/api/app/models/link.rb | 1 -
services/api/app/models/log.rb | 1 -
services/api/app/models/node.rb | 6 +-
services/api/app/models/repository.rb | 2 +-
services/api/app/models/user.rb | 4 +-
services/api/config/boot.rb | 2 +-
services/api/config/initializers/inflections.rb | 8 +-
services/api/config/initializers/load_config.rb | 4 +-
.../api/config/initializers/preload_all_models.rb | 2 +-
services/api/lib/crunch_dispatch.rb | 10 +-
services/api/lib/current_api_client.rb | 10 +-
services/api/lib/eventbus.rb | 35 +--
services/api/lib/load_param.rb | 4 +-
services/api/lib/salvage_collection.rb | 2 +-
services/api/script/arvados-git-sync.rb | 4 +-
.../api/script/migrate-gitolite-to-uuid-storage.rb | 4 +-
services/api/test/factories/user.rb | 2 +-
services/api/test/fixtures/container_requests.yml | 2 +
.../api_client_authorizations_controller_test.rb | 2 +-
.../arvados/v1/collections_controller_test.rb | 8 +-
.../api/test/functional/arvados/v1/filters_test.rb | 6 +-
.../functional/arvados/v1/jobs_controller_test.rb | 2 +-
.../functional/arvados/v1/links_controller_test.rb | 4 +-
.../arvados/v1/repositories_controller_test.rb | 13 +-
.../arvados/v1/schema_controller_test.rb | 2 +-
.../functional/arvados/v1/users_controller_test.rb | 4 +-
.../arvados/v1/virtual_machines_controller_test.rb | 1 -
services/api/test/helpers/users_test_helper.rb | 2 +-
.../api/test/integration/collections_api_test.rb | 14 +-
.../integration/collections_performance_test.rb | 6 +-
services/api/test/integration/cross_origin_test.rb | 2 +-
.../api/test/integration/database_reset_test.rb | 9 +-
.../api/test/integration/user_sessions_test.rb | 2 +-
services/api/test/integration/websocket_test.rb | 136 ++++++++----
services/api/test/test_helper.rb | 32 ++-
services/api/test/unit/app_version_test.rb | 7 +-
services/api/test/unit/authorized_key_test.rb | 2 +-
.../api/test/unit/collection_performance_test.rb | 5 +-
services/api/test/unit/collection_test.rb | 16 +-
services/api/test/unit/commit_test.rb | 18 +-
services/api/test/unit/container_test.rb | 55 +++--
services/api/test/unit/fail_jobs_test.rb | 4 +-
services/api/test/unit/job_test.rb | 6 +-
services/api/test/unit/log_test.rb | 2 +-
services/api/test/unit/node_test.rb | 2 +-
services/api/test/unit/owner_test.rb | 3 +-
services/api/test/unit/permission_test.rb | 14 +-
services/api/test/unit/pipeline_instance_test.rb | 1 -
services/api/test/unit/salvage_collection_test.rb | 12 +-
services/api/test/unit/user_test.rb | 1 -
services/api/test/websocket_runner.rb | 53 -----
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 14 +-
.../crunch-dispatch-slurm_test.go | 5 +-
services/crunch-dispatch-slurm/squeue.go | 42 +++-
services/crunch-run/crunchrun.go | 3 +
services/keep-balance/balance.go | 2 +-
tools/arvbash/arvbash.sh | 124 +++++++++++
.../lib/arvbox/docker/service/api/run-service | 4 +-
99 files changed, 1030 insertions(+), 623 deletions(-)
create mode 100755 build/build-dev-docker-jobs-image.sh
rename doc/user/tutorials/{tutorial-pipeline-workbench.html.textile.liquid => tutorial-workflow-workbench.html.textile.liquid} (98%)
create mode 100644 sdk/dev-jobs.dockerfile
delete mode 100644 services/api/test/websocket_runner.rb
create mode 100755 tools/arvbash/arvbash.sh
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commit c494f4c398457c5edbd9b2c3f1a439bf041c7ed2
Author: radhika <radhika at curoverse.com>
Date: Tue Dec 6 10:44:41 2016 -0500
10604: rename tutorial-pipeline-workbench.html as tutorial-workbench-workbench.html
diff --git a/doc/_config.yml b/doc/_config.yml
index fdd57c5..30df754 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -30,7 +30,7 @@ navbar:
- user/getting_started/community.html.textile.liquid
- Run a workflow using Workbench:
- user/getting_started/workbench.html.textile.liquid
- - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+ - user/tutorials/tutorial-workflow-workbench.html.textile.liquid
- Access an Arvados virtual machine:
- user/getting_started/vm-login-with-webshell.html.textile.liquid
- user/getting_started/ssh-access-unix.html.textile.liquid
diff --git a/doc/_includes/_arvados_cwl_runner.liquid b/doc/_includes/_arvados_cwl_runner.liquid
index 72c95dd..9a10bab 100644
--- a/doc/_includes/_arvados_cwl_runner.liquid
+++ b/doc/_includes/_arvados_cwl_runner.liquid
@@ -26,7 +26,7 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
h3. Submit a workflow with no waiting
-To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the uuid of the job that was submitted to standard output, and exit.
+To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the UUID of the job that was submitted to standard output, and exit.
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml</span>
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index fc0c6b0..ecff47f 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -8,7 +8,7 @@ title: Using Common Workflow Language
{% include 'tutorial_expectations' %}
-h2. Preparing to work with Arvados cwl runner
+h2. Preparing to work with Arvados CWL runner
h3. arvados-cwl-runner
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
similarity index 98%
rename from doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
rename to doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
index 11746bf..445ce75 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-workflow-workbench.html.textile.liquid
@@ -17,7 +17,7 @@ h3. Steps
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline or workflow to run*.
# In the search box, type in *Tutorial bwa mem cwl*.
-# Select *<i class="fa fa-fw fa-gear"></i> Tutorial bwa mem cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are pupulated with default values and you can change them if you prefer.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial bwa mem cwl* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new process in your *Home* project and will open it. You can now supply the inputs for the process. Please note that all required inputs are populated with default values and you can change them if you prefer.
# For example, let's see how to change *"reference" parameter* for this workflow. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath the *"reference" parameter* header. This will open a dialog box titled *Choose a dataset for "reference" parameter for cwl-runner in bwa-mem.cwl component*.
# Open the *Home <span class="caret"></span>* menu and select *All Projects*. Search for and select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference*. You will then see a list of files. Select *<i class="fa fa-fw fa-file"></i> 19-fasta.bwt* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
# Repeat the previous two steps to set the *"read_p1" parameter for cwl-runner script in bwa-mem.cwl component* and *"read_p2" parameter for cwl-runner script in bwa-mem.cwl component* parameters.
commit 0f361d9a0748e2b470ed5bc73351cb2eaf3e02e3
Merge: 6b2481a 0936c2e
Author: radhika <radhika at curoverse.com>
Date: Tue Dec 6 10:31:50 2016 -0500
Merge branch 'master' into 10604-crunch2-user-guide
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