[ARVADOS] updated: f02f9915ecccc36bc13ad7ae34567be26e55a339
Git user
git at public.curoverse.com
Fri Jul 15 14:11:40 EDT 2016
Summary of changes:
.../app/assets/javascripts/infinite_scroll.js | 3 +-
.../app/controllers/application_controller.rb | 2 +-
.../controllers/container_requests_controller.rb | 5 +
.../app/controllers/containers_controller.rb | 5 +
apps/workbench/app/controllers/jobs_controller.rb | 11 +-
.../app/controllers/projects_controller.rb | 10 +-
apps/workbench/app/models/container_request.rb | 4 +
.../projects/_show_jobs_and_pipelines.html.erb | 5 -
.../_show_pipelines_and_processes.html.erb | 5 +
.../test/controllers/projects_controller_test.rb | 2 +-
.../test/integration/anonymous_access_test.rb | 24 +-
apps/workbench/test/integration/download_test.rb | 6 +-
.../test/integration/pipeline_instances_test.rb | 2 +-
apps/workbench/test/integration/projects_test.rb | 22 +-
build/run-build-packages.sh | 7 +-
build/run-tests.sh | 1 +
crunch_scripts/cwl-runner | 26 +-
doc/api/methods/groups.html.textile.liquid | 2 +
doc/install/install-keepstore.html.textile.liquid | 78 +++-
doc/sdk/cli/install.html.textile.liquid | 32 +-
doc/sdk/python/sdk-python.html.textile.liquid | 6 +-
docker/jobs/Dockerfile | 2 +-
lib/crunchstat/crunchstat.go | 439 ++++++++++++++++++
lib/crunchstat/crunchstat_test.go | 62 +++
sdk/cwl/arvados_cwl/__init__.py | 12 +-
sdk/cwl/arvados_cwl/arvcontainer.py | 28 +-
sdk/cwl/arvados_cwl/arvjob.py | 43 +-
sdk/cwl/arvados_cwl/arvtool.py | 5 +-
sdk/cwl/arvados_cwl/fsaccess.py | 49 +-
sdk/cwl/arvados_cwl/pathmapper.py | 149 +++++-
sdk/cwl/arvados_cwl/runner.py | 42 +-
sdk/cwl/setup.py | 4 +-
sdk/cwl/test_with_arvbox.sh | 13 +-
sdk/cwl/tests/test_submit.py | 46 +-
sdk/cwl/tests/tool/submit_tool.cwl | 4 +-
sdk/cwl/tests/wf/inputs_test.cwl | 10 +-
sdk/cwl/tests/wf/submit_wf.cwl | 6 +-
sdk/go/arvados/client_test.go | 2 +-
sdk/go/arvados/keep_service.go | 9 +
sdk/go/crunchrunner/crunchrunner.go | 37 +-
sdk/go/crunchrunner/crunchrunner_test.go | 40 +-
sdk/go/keepclient/collectionreader.go | 2 +-
sdk/python/arvados/commands/run.py | 1 +
sdk/python/arvados/keep.py | 16 +-
sdk/python/tests/run_test_server.py | 2 +-
.../controllers/arvados/v1/groups_controller.rb | 27 +-
services/api/lib/eventbus.rb | 20 +-
services/api/test/fixtures/container_requests.yml | 33 ++
services/api/test/fixtures/groups.yml | 6 +-
services/api/test/fixtures/jobs.yml | 16 -
services/api/test/fixtures/pipeline_instances.yml | 6 +-
.../arvados/v1/groups_controller_test.rb | 25 +
services/api/test/integration/websocket_test.rb | 4 +-
services/api/test/websocket_runner.rb | 11 +-
.../crunch-dispatch-local/crunch-dispatch-local.go | 2 +-
.../crunch-dispatch-local_test.go | 2 +-
.../crunch-dispatch-slurm/crunch-dispatch-slurm.go | 12 +-
.../crunch-dispatch-slurm_test.go | 4 +-
services/crunch-run/crunchrun.go | 37 +-
services/crunch-run/crunchrun_test.go | 110 +++--
services/crunch-run/logging.go | 50 +-
services/crunch-run/logging_test.go | 6 +-
services/crunchstat/crunchstat.go | 513 +++------------------
services/crunchstat/crunchstat_test.go | 72 +--
services/datamanager/collection/collection.go | 12 +-
services/datamanager/collection/collection_test.go | 14 +-
services/datamanager/keep/keep.go | 20 +-
services/datamanager/keep/keep_test.go | 4 +-
services/datamanager/summary/pull_list_test.go | 50 +-
services/datamanager/summary/summary_test.go | 24 +-
services/datamanager/summary/trash_list.go | 2 +-
services/datamanager/summary/trash_list_test.go | 30 +-
services/keep-balance/balance.go | 42 +-
services/keep-balance/balance_run_test.go | 19 +-
services/keep-balance/balance_test.go | 4 +-
services/keep-balance/integration_test.go | 4 +-
services/keep-balance/main.go | 12 +-
services/keepstore/azure_blob_volume.go | 2 +-
services/keepstore/keepstore.go | 4 +-
services/keepstore/s3_volume.go | 4 +-
services/keepstore/trash_worker.go | 6 +-
services/keepstore/trash_worker_test.go | 2 +-
services/keepstore/volume_generic_test.go | 37 +-
services/keepstore/volume_unix.go | 7 +-
services/keepstore/work_queue_test.go | 2 +-
.../arvnodeman/computenode/driver/__init__.py | 6 +-
.../nodemanager/tests/test_computenode_dispatch.py | 26 ++
tools/arvbox/bin/arvbox | 27 +-
88 files changed, 1622 insertions(+), 975 deletions(-)
delete mode 100644 apps/workbench/app/views/projects/_show_jobs_and_pipelines.html.erb
create mode 100644 apps/workbench/app/views/projects/_show_pipelines_and_processes.html.erb
create mode 100644 lib/crunchstat/crunchstat.go
create mode 100644 lib/crunchstat/crunchstat_test.go
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commit f02f9915ecccc36bc13ad7ae34567be26e55a339
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Jul 15 14:11:37 2016 -0400
9369: Remove cwl install from Python SDK page. Remove "sudo -i" from
pip/python install instructions. Fixup use of ~$ prompt in example
instructions.
diff --git a/doc/sdk/cli/install.html.textile.liquid b/doc/sdk/cli/install.html.textile.liquid
index 53821b5..cf6432d 100644
--- a/doc/sdk/cli/install.html.textile.liquid
+++ b/doc/sdk/cli/install.html.textile.liquid
@@ -16,7 +16,7 @@ Install curl libraries with your system's package manager. For example, on Debia
<notextile>
<pre>
-$ <code class="userinput">sudo apt-get install libcurl3 libcurl3-gnutls libcurl4-openssl-dev</code>
+~$ <code class="userinput">sudo apt-get install libcurl3 libcurl3-gnutls libcurl4-openssl-dev</code>
</pre>
</notextile>
@@ -24,13 +24,13 @@ h3. Option 1: Install from RubyGems and PyPI
<notextile>
<pre>
-arvados/sdk/cli$ <code class="userinput">sudo -i gem install arvados-cli</code>
+~$ <code class="userinput">sudo -i gem install arvados-cli</code>
</pre>
</notextile>
<notextile>
<pre>
-arvados/sdk/cli$ <code class="userinput">sudo -i pip install arvados-python-client arvados-cwl-runner</code>
+~$ <code class="userinput">pip install arvados-python-client arvados-cwl-runner</code>
</pre>
</notextile>
@@ -38,23 +38,13 @@ h3. Option 2: Build and install from source
<notextile>
<pre>
-$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
-$ <code class="userinput">cd arvados/sdk/cli</code>
-$ <code class="userinput">gem build arvados-cli.gemspec</code>
-$ <code class="userinput">sudo -i gem install arvados-cli-*.gem</code>
-</pre>
-</notextile>
-
-<notextile>
-<pre>
-$ <code class="userinput">cd arvados/sdk/python</code>
-$ <code class="userinput">sudo -i python setup.py install</code>
-</pre>
-</notextile>
-
-<notextile>
-<pre>
-$ <code class="userinput">cd arvados/sdk/cwl</code>
-$ <code class="userinput">sudo -i python setup.py install</code>
+~$ <code class="userinput">git clone https://github.com/curoverse/arvados.git</code>
+~$ <code class="userinput">cd arvados/sdk/cli</code>
+~/arvados/sdk/cli$ <code class="userinput">gem build arvados-cli.gemspec</code>
+~/arvados/sdk/cli$ <code class="userinput">sudo -i gem install arvados-cli-*.gem</code>
+~/arvados/sdk/cli$ <code class="userinput">cd ../python</code>
+~/arvados/sdk/python$ <code class="userinput">python setup.py install</code>
+~/arvados/sdk/python$ <code class="userinput">cd ../cwl</code>
+~/arvados/sdk/cwl$ <code class="userinput">python setup.py install</code>
</pre>
</notextile>
diff --git a/doc/sdk/python/sdk-python.html.textile.liquid b/doc/sdk/python/sdk-python.html.textile.liquid
index 8380618..0b0f77d 100644
--- a/doc/sdk/python/sdk-python.html.textile.liquid
+++ b/doc/sdk/python/sdk-python.html.textile.liquid
@@ -58,10 +58,8 @@ Install the @python-setuptools@ package from your distribution. Then run the fo
<notextile>
<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados.git</span>
-~$ <span class="userinput">cd ~/arvados/sdk/python</span>
-~$ <span class="userinput">python2.7 setup.py install</span>
-~$ <span class="userinput">cd ~/arvados/sdk/cwl</span>
-~$ <span class="userinput">python2.7 setup.py install</span>
+~$ <span class="userinput">cd arvados/sdk/python</span>
+~/arvados/sdk/python$ <span class="userinput">python2.7 setup.py install</span>
</code></pre>
</notextile>
commit 3a0aa1db801154916f50b1b299d5100945a3e1df
Merge: f17319c 5cf55ab
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Jul 15 13:11:49 2016 -0400
Merge branch 'master' into 9369-arv-cwl-docs
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