arvados.git
8 years ago8650: test and fixture update
radhika [Wed, 8 Jun 2016 14:31:45 +0000 (10:31 -0400)]
8650: test and fixture update

8 years agoMerge branch 'master' into 8650-container-work-unit
radhika [Wed, 8 Jun 2016 14:25:36 +0000 (10:25 -0400)]
Merge branch 'master' into 8650-container-work-unit

8 years agocloses #8087
radhika [Wed, 8 Jun 2016 14:23:15 +0000 (10:23 -0400)]
closes #8087
Merge branch 'wtsi-hgi-8087-arv-cli-request-body-from-file'

8 years agoMerge branch 'master' into wtsi-hgi-8087-arv-cli-request-body-from-file
radhika [Wed, 8 Jun 2016 11:23:19 +0000 (07:23 -0400)]
Merge branch 'master' into wtsi-hgi-8087-arv-cli-request-body-from-file

8 years agoMerge branch '8087-arv-cli-request-body-from-file' of https://github.com/wtsi-hgi...
radhika [Wed, 8 Jun 2016 11:19:36 +0000 (07:19 -0400)]
Merge branch '8087-arv-cli-request-body-from-file' of https://github.com/wtsi-hgi/arvados into wtsi-hgi-8087-arv-cli-request-body-from-file

8 years agorefs #8876
radhika [Wed, 8 Jun 2016 03:26:15 +0000 (23:26 -0400)]
refs #8876
Merge branch '8876-work-unit'

8 years ago8876: Pass work unit to determine_wallclock_runtime, not the original object.
radhika [Wed, 8 Jun 2016 03:23:43 +0000 (23:23 -0400)]
8876: Pass work unit to determine_wallclock_runtime, not the original object.

8 years agocloses #8876
radhika [Tue, 7 Jun 2016 21:07:04 +0000 (17:07 -0400)]
closes #8876
Merge branch '8876-work-unit'

8 years ago8876: remove show_child_summary and replace it with is_running?
radhika [Tue, 7 Jun 2016 21:00:41 +0000 (17:00 -0400)]
8876: remove show_child_summary and replace it with is_running?

8 years agoBugfix submitting cwl jobs with arvados-cwl-runner refs #9275
Peter Amstutz [Tue, 7 Jun 2016 20:43:19 +0000 (16:43 -0400)]
Bugfix submitting cwl jobs with arvados-cwl-runner refs #9275

8 years agoMerge branch '9275-cwl-runner-creates-jobs' closes #9275
Peter Amstutz [Tue, 7 Jun 2016 20:24:37 +0000 (16:24 -0400)]
Merge branch '9275-cwl-runner-creates-jobs' closes #9275

8 years ago9275: Initial pipeline/job component update from response
Peter Amstutz [Tue, 7 Jun 2016 20:17:49 +0000 (16:17 -0400)]
9275: Initial pipeline/job component update from response

8 years agoMerge branch '8876-work-unit' into 8650-container-work-unit
radhika [Tue, 7 Jun 2016 17:22:50 +0000 (13:22 -0400)]
Merge branch '8876-work-unit' into 8650-container-work-unit

8 years ago8876: when computing cpu and running times, use the work unit's start and finished...
radhika [Tue, 7 Jun 2016 16:55:59 +0000 (12:55 -0400)]
8876: when computing cpu and running times, use the work unit's start and finished times if there are no children.

8 years ago9275: Update the update_pipeline_component method to check if pipeline is null.
radhika [Tue, 7 Jun 2016 02:40:01 +0000 (22:40 -0400)]
9275: Update the update_pipeline_component method to check if pipeline is null.

8 years ago8650: some more methods in ContainerWorkUnit
radhika [Tue, 7 Jun 2016 00:37:01 +0000 (20:37 -0400)]
8650: some more methods in ContainerWorkUnit

8 years agoMerge branch '8876-work-unit' into 8650-container-work-unit
radhika [Tue, 7 Jun 2016 00:29:30 +0000 (20:29 -0400)]
Merge branch '8876-work-unit' into 8650-container-work-unit

8 years ago8876: Use JobWorkUnit for pipeline components and cleanup.
radhika [Tue, 7 Jun 2016 00:28:21 +0000 (20:28 -0400)]
8876: Use JobWorkUnit for pipeline components and cleanup.

8 years ago9275: add record to cwl_runner_job as components
radhika [Mon, 6 Jun 2016 19:50:58 +0000 (15:50 -0400)]
9275: add record to cwl_runner_job as components

8 years agoMerge branch '9187-crunchv2-dispatching' closes #9187
Peter Amstutz [Mon, 6 Jun 2016 19:26:03 +0000 (15:26 -0400)]
Merge branch '9187-crunchv2-dispatching' closes #9187

8 years agoMerge branch 'master' into 9187-crunchv2-dispatching
Peter Amstutz [Mon, 6 Jun 2016 18:46:37 +0000 (14:46 -0400)]
Merge branch 'master' into 9187-crunchv2-dispatching

8 years ago9187: Remove "squeueError" because checkSqueue for a successful squeue run. Refactor...
Peter Amstutz [Mon, 6 Jun 2016 14:44:11 +0000 (10:44 -0400)]
9187: Remove "squeueError" because checkSqueue for a successful squeue run.  Refactor tests a bit and add a test for canceling containers.

8 years agoMerge branch '8876-work-unit' into 8650-container-work-unit
radhika [Sat, 4 Jun 2016 23:09:58 +0000 (19:09 -0400)]
Merge branch '8876-work-unit' into 8650-container-work-unit

Conflicts:
apps/workbench/test/unit/work_unit_test.rb

8 years ago8876: add tests for link_to_log and queuedtime etc.
radhika [Sat, 4 Jun 2016 23:03:32 +0000 (19:03 -0400)]
8876: add tests for link_to_log and queuedtime etc.

8 years ago8876: introduce view helper methods such as link_to_log and queuedtime etc so that...
radhika [Sat, 4 Jun 2016 14:06:09 +0000 (10:06 -0400)]
8876: introduce view helper methods such as link_to_log and queuedtime etc so that the views do not have to do too many decisions based on the state of the work unit.

8 years ago9187: Fix refactoring messup
Peter Amstutz [Fri, 3 Jun 2016 21:57:48 +0000 (17:57 -0400)]
9187: Fix refactoring messup

8 years ago8876: display "no process has been submitted" when a child uuid is not presented.
radhika [Fri, 3 Jun 2016 20:52:06 +0000 (16:52 -0400)]
8876: display "no process has been submitted" when a child uuid is not presented.

8 years agoMerge branch '9272-use-container-auth'
Tom Clegg [Fri, 3 Jun 2016 19:54:05 +0000 (15:54 -0400)]
Merge branch '9272-use-container-auth'

closes #9272

8 years ago9272: Skip slow test when running -short tests.
Tom Clegg [Fri, 27 May 2016 01:25:47 +0000 (21:25 -0400)]
9272: Skip slow test when running -short tests.

8 years ago9272: Simplify json decoding with Unmarshal.
Tom Clegg [Fri, 27 May 2016 01:22:11 +0000 (21:22 -0400)]
9272: Simplify json decoding with Unmarshal.

8 years ago9272: Fix up state transitions:
Tom Clegg [Fri, 27 May 2016 01:17:31 +0000 (21:17 -0400)]
9272: Fix up state transitions:

* Change state to Running only at the last possible moment before
  starting the container.

* When erroring out before Running, change state back to Queued.

* Do not save log/output/exit code when changing state to Cancelled.

Incidental fixes:

* Clean up error handling in Run()

* Don't create a collection for (or try to attach to the container)
  the second "cleanup activities" log that gets opened after closing
  the real container log.

8 years ago9272: Pass container auth info into container if requested.
Tom Clegg [Thu, 26 May 2016 20:48:08 +0000 (16:48 -0400)]
9272: Pass container auth info into container if requested.

8 years ago9272: Get container auth instead of passing the dispatcher token into the container.
Tom Clegg [Thu, 26 May 2016 19:50:21 +0000 (15:50 -0400)]
9272: Get container auth instead of passing the dispatcher token into the container.

8 years ago9275: create pipeline_instance in submit mode as well and add the runner job to it...
radhika [Fri, 3 Jun 2016 17:13:26 +0000 (13:13 -0400)]
9275: create pipeline_instance in submit mode as well and add the runner job to it's components.

8 years ago9187: Fix comment typo
Peter Amstutz [Fri, 3 Jun 2016 02:46:55 +0000 (22:46 -0400)]
9187: Fix comment typo

8 years ago9187: Add documentation comments to Squeue functions.
Peter Amstutz [Fri, 3 Jun 2016 02:18:55 +0000 (22:18 -0400)]
9187: Add documentation comments to Squeue functions.

8 years ago9187: Improve squeue synchronization
Peter Amstutz [Thu, 2 Jun 2016 21:59:20 +0000 (17:59 -0400)]
9187: Improve squeue synchronization

* Put squeue functions into separate file.

* CheckSqueue() now blocks on a condition variable until the next successful
update of squeue, which then wakes up all goroutines waiting on CheckSqueue().

* Never do anything when squeue returns an error.

* Merge submitting, monitoring, and cleanup behaviors into a single goroutine
which updates based on CheckSqueue() instead of a ticker.

* Introduce a lock on squeue, sbatch and scancel operations, so that on next
wakeup the queue is guaranteed to reflect most recent sbatch/scancel
operations.

8 years agoMerge branch '9343-no-env-vars'
Tom Clegg [Thu, 2 Jun 2016 20:51:11 +0000 (16:51 -0400)]
Merge branch '9343-no-env-vars'

refs #9343

8 years ago9343: Do not check env vars when setting up Keep client for pull requests.
Tom Clegg [Thu, 2 Jun 2016 20:38:55 +0000 (16:38 -0400)]
9343: Do not check env vars when setting up Keep client for pull requests.

8 years agoMerge branch '8876-work-unit' into 8650-container-work-unit
radhika [Thu, 2 Jun 2016 19:07:48 +0000 (15:07 -0400)]
Merge branch '8876-work-unit' into 8650-container-work-unit

8 years ago8876: success? includes Canceled as well.
radhika [Thu, 2 Jun 2016 19:07:15 +0000 (15:07 -0400)]
8876: success? includes Canceled as well.

8 years ago8650: add children to container_work_unit
radhika [Thu, 2 Jun 2016 19:04:18 +0000 (15:04 -0400)]
8650: add children to container_work_unit

8 years agoMerge branch '8876-work-unit' into 8650-container-work-unit
radhika [Wed, 1 Jun 2016 23:22:13 +0000 (19:22 -0400)]
Merge branch '8876-work-unit' into 8650-container-work-unit

8 years ago8876: move some methods such as log and output from job_work_unit into proxy_work_uni...
radhika [Wed, 1 Jun 2016 23:20:42 +0000 (19:20 -0400)]
8876: move some methods such as log and output from job_work_unit into proxy_work_unit to aid reusability.

8 years ago8650: add container_work_unit
radhika [Wed, 1 Jun 2016 23:05:37 +0000 (19:05 -0400)]
8650: add container_work_unit

8 years ago8876: child_summary_str checks if total > 0
radhika [Wed, 1 Jun 2016 22:55:37 +0000 (18:55 -0400)]
8876: child_summary_str checks if total > 0

8 years ago9187: Slurm dispatcher improvements around squeue
Peter Amstutz [Wed, 1 Jun 2016 20:06:26 +0000 (16:06 -0400)]
9187: Slurm dispatcher improvements around squeue

* Clarify that status updates are not guaranteed to be delivered on a
heartbeat.
* Refactor slurm dispatcher to monitor the container in squeue in a separate
goroutine.
* Refactor polling squeue to a single goroutine and cache the results so that
monitoring 100 containers doesn't result in 100 calls to squeue.
* No longer set up strigger to cancel job on finish, instead cancel running
jobs not in squeue.
* Test both cases where a job is/is not in squeue.

8 years agoMerge branch 'master' into 8876-work-unit
radhika [Wed, 1 Jun 2016 19:11:39 +0000 (15:11 -0400)]
Merge branch 'master' into 8876-work-unit

8 years agoMerge branch '9309-centos-7-packages-wip'
Brett Smith [Wed, 1 Jun 2016 18:28:24 +0000 (14:28 -0400)]
Merge branch '9309-centos-7-packages-wip'

Refs #9309.  Closes #9313.

8 years ago9309: Add packages and tests for CentOS 7.
Brett Smith [Fri, 27 May 2016 22:34:56 +0000 (18:34 -0400)]
9309: Add packages and tests for CentOS 7.

8 years ago9309: Look for fpm-info in backports/$PACKAGE_NAME.
Brett Smith [Tue, 31 May 2016 21:37:02 +0000 (17:37 -0400)]
9309: Look for fpm-info in backports/$PACKAGE_NAME.

This lets us define additional fpm flags when we build a non-dir
package from a source directory.

8 years ago9242: Restore newer backported versions of Python packages.
Brett Smith [Tue, 31 May 2016 21:36:08 +0000 (17:36 -0400)]
9242: Restore newer backported versions of Python packages.

I accidentally reverted this in 758d39f.
Refs #9242.

8 years ago9242: Update Python module paths for CentOS 6.
Brett Smith [Tue, 31 May 2016 20:35:53 +0000 (16:35 -0400)]
9242: Update Python module paths for CentOS 6.

I am more sure that this is correct, based on multiple data points
from Python 2 and 3 packages across CentOS 6 and 7.
This might be a change that's fallout from
44ceaa474a330f12dd9e00115af107d7258044f2.
Refs #9242.

8 years agoMerge branch '9162-keep-balance'
Tom Clegg [Tue, 31 May 2016 20:23:30 +0000 (16:23 -0400)]
Merge branch '9162-keep-balance'

closes #9162

8 years ago9162: Add replication level histogram
Tom Clegg [Tue, 24 May 2016 14:02:39 +0000 (10:02 -0400)]
9162: Add replication level histogram

Ported from 00a8ece1580a894dbbf9f756685eefc134e4d0d6 by jrandall

8 years ago9162: Add keep-balance
Tom Clegg [Mon, 16 May 2016 21:09:21 +0000 (17:09 -0400)]
9162: Add keep-balance

8 years agoMerge branch '9242-python-backport-prefix-wip'
Brett Smith [Tue, 31 May 2016 20:09:57 +0000 (16:09 -0400)]
Merge branch '9242-python-backport-prefix-wip'

Closes #9242, #9247.

8 years ago9242: Python packages install libraries to the distro path.
Brett Smith [Tue, 31 May 2016 15:13:41 +0000 (11:13 -0400)]
9242: Python packages install libraries to the distro path.

This avoids breaking dependent packages that expect to find files in
the same place.

8 years ago8876: typo in fixture
radhika [Tue, 31 May 2016 17:12:06 +0000 (13:12 -0400)]
8876: typo in fixture

8 years ago8876: correct the job_reader2 fixture
radhika [Tue, 31 May 2016 17:07:09 +0000 (13:07 -0400)]
8876: correct the job_reader2 fixture

8 years ago8876: improve jobs_with_components test to have components that can be un/read
radhika [Tue, 31 May 2016 16:52:35 +0000 (12:52 -0400)]
8876: improve jobs_with_components test to have components that can be un/read

8 years agoMerge branch 'master' into 8876-work-unit
radhika [Tue, 31 May 2016 15:42:42 +0000 (11:42 -0400)]
Merge branch 'master' into 8876-work-unit

8 years ago9242: Refactor Python constant definitions in r-b-p.
Brett Smith [Thu, 19 May 2016 19:41:16 +0000 (15:41 -0400)]
9242: Refactor Python constant definitions in r-b-p.

There are about to be more of them, which will make this a real space
savings.

8 years ago9316: Include documentation in CWL SDK.
Brett Smith [Tue, 31 May 2016 01:32:52 +0000 (21:32 -0400)]
9316: Include documentation in CWL SDK.

This is necessary to make pip distributions installable, since
setup.py tries to open README.rst.  Closes #9316.

8 years ago8876: For jobs also, compute progress from it's children if present; otherwise, use...
radhika [Tue, 31 May 2016 00:41:32 +0000 (20:41 -0400)]
8876: For jobs also, compute progress from it's children if present; otherwise, use task_summary.

8 years agoFix centos6 package build (ruamel.yaml package building arguments for fpm).
Ward Vandewege [Sat, 28 May 2016 13:27:16 +0000 (09:27 -0400)]
Fix centos6 package build (ruamel.yaml package building arguments for fpm).

No issue #

8 years agoUpdate Software Collections package name in Install Guide.
Brett Smith [Fri, 27 May 2016 22:43:38 +0000 (18:43 -0400)]
Update Software Collections package name in Install Guide.

Follows up previous commit.  No issue #.

8 years agoUpdate Software Collections package name in CentOS 6 Dockerfiles.
Brett Smith [Fri, 27 May 2016 22:42:09 +0000 (18:42 -0400)]
Update Software Collections package name in CentOS 6 Dockerfiles.

Why does the name of this package keep changing?
It is a mystery.
No issue #.

8 years ago8959: Remove redundant python-gflags fpm-info.sh.
Brett Smith [Fri, 27 May 2016 22:30:57 +0000 (18:30 -0400)]
8959: Remove redundant python-gflags fpm-info.sh.

I added this file in 495a485ff.  Later, Nico pinned the version in
run-build-packages, in a8bbf6ef, to try to fix #8959.  However, odds
are that #8959 was an ops problem, and not a package building problem:
the gflags 3.0 packages were still published on our repository, and
needed to be removed there.

Having both files causes trouble when you're building backports from
scratch.  We haven't noticed because Jenkins never does that.  But
I'm working on new packages and getting:

    Loading fpm overrides from /arvados/backports/python-gflags/fpm-info.sh

    fpm --maintainer=Ward Vandewege <ward@curoverse.com> -s python -t rpm --exclude=*/dist-packages/tests/* --exclude=*/site-packages/tests/* --verbose --log info -n python-gflags --iteration 1 --python-bin python2.7 --python-easyinstall easy_install-2.7 --python-package-name-prefix python --depends python -v 2.0 python-gflags==2.0

    Error: python-gflags==2.0: Unable to figure out package name from fpm results:

    {:timestamp=>"2016-05-27T22:20:53.045329+0000", :message=>"Setting workdir", :workdir=>"/tmp", :level=>:info} {:timestamp=>"2016-05-27T22:20:53.049435+0000", :message=>"Trying to download", :package=>"python-gflags==2.0", :level=>:info} {:timestamp=>"2016-05-27T22:20:53.122897+0000", :message=>"error: Not a URL, existing file, or requirement spec: 'python-gflags==2.0==2.0'", :level=>:info} {:timestamp=>"2016-05-27T22:20:53.130325+0000", :message=>"Process failed: easy_install-2.7 failed (exit code 1). Full command was:[\"easy_install-2.7\", \"-i\", \"https://pypi.python.org/simple\", \"--editable\", \"-U\", \"--build-directory\", \"/tmp/package-python-build20160527-1643-3sl5ec/python-gflags==2.0\", \"python-gflags==2.0==2.0\"]", :level=>:error}

Refs #8959.

8 years agoAdd dependency for ruamel.yaml to the build list.
Ward Vandewege [Fri, 27 May 2016 21:35:24 +0000 (17:35 -0400)]
Add dependency for ruamel.yaml to the build list.

No issue #

8 years agoFix bug in run-build-packages-one-target.sh: make sure to escape the *
Ward Vandewege [Fri, 27 May 2016 21:34:55 +0000 (17:34 -0400)]
Fix bug in run-build-packages-one-target.sh: make sure to escape the *
passed to find.

No issue #

8 years ago9187: Check LockedByUUID on container updates and terminate status updates if
Peter Amstutz [Fri, 27 May 2016 21:30:07 +0000 (17:30 -0400)]
9187: Check LockedByUUID on container updates and terminate status updates if
not equal to dispatcher token.

8 years ago8876: remove some job specific bits and make them generic
radhika [Fri, 27 May 2016 20:57:31 +0000 (16:57 -0400)]
8876: remove some job specific bits and make them generic

8 years agoMerge branch '9272-test-races'
Tom Clegg [Fri, 27 May 2016 15:35:30 +0000 (11:35 -0400)]
Merge branch '9272-test-races'

refs #9272

8 years ago9272: Fix some race conditions in flaky tests.
Tom Clegg [Thu, 26 May 2016 19:49:49 +0000 (15:49 -0400)]
9272: Fix some race conditions in flaky tests.

8 years agoArvbox installs binaries for go 1.6 instead of golang Debian package
Peter Amstutz [Fri, 27 May 2016 15:25:22 +0000 (11:25 -0400)]
Arvbox installs binaries for go 1.6 instead of golang Debian package
(which is stuck at 1.3) no issue #

8 years ago8876: add an integration with job with components.
radhika [Fri, 27 May 2016 14:50:55 +0000 (10:50 -0400)]
8876: add an integration with job with components.

8 years ago9187: Refactor dispatcher support into common library and update to use Locking API.
Peter Amstutz [Thu, 19 May 2016 18:12:42 +0000 (14:12 -0400)]
9187: Refactor dispatcher support into common library and update to use Locking API.

New dispatcher package in Go SDK provides framework for monitoring list of
queued/locked/running containers.  Try to lock containers in the queue; locked
or running containers are passed to RunContainer goroutine supplied by the
specific dispatcher.  Refactor existing dispatchers (-local and -slurm) to use
this framework.  Dispatchers have crash recovery behavior, can put containers
which are unaccounted in cancelled state.

8 years ago8876: progress bar and strage component display
radhika [Thu, 26 May 2016 19:18:36 +0000 (15:18 -0400)]
8876: progress bar and strage component display

8 years agoPackage ruamel.yaml, which is a new dependency of schema-salad.
Ward Vandewege [Thu, 26 May 2016 15:37:06 +0000 (11:37 -0400)]
Package ruamel.yaml, which is a new dependency of schema-salad.

No issue #

8 years agoMerge branch '9303-actor-dead-dead' refs #9303
Peter Amstutz [Thu, 26 May 2016 14:09:04 +0000 (10:09 -0400)]
Merge branch '9303-actor-dead-dead' refs #9303

8 years ago9303: Fetch arv_node before trying to shut down node, because monitor actor may
Peter Amstutz [Thu, 26 May 2016 13:51:24 +0000 (09:51 -0400)]
9303: Fetch arv_node before trying to shut down node, because monitor actor may
go away once the node has been successfully shut down.  Also handle case of
node_finished_shutdown called after shutdown actor is stopped.

8 years agoLog watchdog exception refs #9303
Peter Amstutz [Wed, 25 May 2016 20:33:49 +0000 (16:33 -0400)]
Log watchdog exception refs #9303

8 years agoMerge branch '9303-kill-nodemanager-on-dead-actor' refs #9303
Peter Amstutz [Wed, 25 May 2016 20:30:10 +0000 (16:30 -0400)]
Merge branch '9303-kill-nodemanager-on-dead-actor' refs #9303

8 years ago9303: Watchdog kill node manager on any error
Peter Amstutz [Wed, 25 May 2016 20:29:30 +0000 (16:29 -0400)]
9303: Watchdog kill node manager on any error

8 years agoBuild distribution packages for the version of python-schema-salad that
Ward Vandewege [Tue, 24 May 2016 19:41:08 +0000 (15:41 -0400)]
Build distribution packages for the version of python-schema-salad that
python-cwltool now depends on.

refs #8653

8 years agoBuild distribution packages for the version of python-cwltool that
Ward Vandewege [Tue, 24 May 2016 17:10:53 +0000 (13:10 -0400)]
Build distribution packages for the version of python-cwltool that
python-arvados-cwl-runner now depends on.

refs #8653

8 years agocloses #8556
radhika [Tue, 24 May 2016 16:41:17 +0000 (12:41 -0400)]
closes #8556
Merge branch '8556-azure-trash'

8 years ago8556: implement trash/untrash for azure volumes.
radhika [Tue, 24 May 2016 16:39:28 +0000 (12:39 -0400)]
8556: implement trash/untrash for azure volumes.

8 years ago8876: work unit views
radhika [Mon, 23 May 2016 20:56:24 +0000 (16:56 -0400)]
8876: work unit views

8 years ago8876: misplaced divs!
radhika [Sat, 21 May 2016 03:57:24 +0000 (23:57 -0400)]
8876: misplaced divs!

8 years ago8876: work_unit views in progress
radhika [Sat, 21 May 2016 03:40:00 +0000 (23:40 -0400)]
8876: work_unit views in progress

8 years agoMerge branch 'wtsi-hgi-9231-rename-redunancy-to-replication-desired'
Tom Clegg [Fri, 20 May 2016 14:01:55 +0000 (10:01 -0400)]
Merge branch 'wtsi-hgi-9231-rename-redunancy-to-replication-desired'

closes #9231

8 years agoMerge branch '8653-cwl-runner-handle-files' closes #8653
Peter Amstutz [Thu, 19 May 2016 20:02:17 +0000 (16:02 -0400)]
Merge branch '8653-cwl-runner-handle-files' closes #8653

8 years ago8653: Fix tests.
Peter Amstutz [Thu, 19 May 2016 19:48:46 +0000 (15:48 -0400)]
8653: Fix tests.

8 years ago8653: Use load_tool.fetch_document() instead of Loader() to read raw document.
Peter Amstutz [Thu, 19 May 2016 17:50:47 +0000 (13:50 -0400)]
8653: Use load_tool.fetch_document() instead of Loader() to read raw document.

8 years ago8653: add cwlVersion so file validate correctly.
Peter Amstutz [Thu, 19 May 2016 15:32:00 +0000 (11:32 -0400)]
8653: add cwlVersion so file validate correctly.

8 years ago8653: Fix pathmapper API
Peter Amstutz [Thu, 19 May 2016 02:08:48 +0000 (22:08 -0400)]
8653: Fix pathmapper API

8 years ago8653: Set basedir for CollectionFsAccess
Peter Amstutz [Thu, 19 May 2016 02:06:19 +0000 (22:06 -0400)]
8653: Set basedir for CollectionFsAccess

8 years ago8653: Update load_tool in cwl-runner crunch script
Peter Amstutz [Thu, 19 May 2016 02:01:15 +0000 (22:01 -0400)]
8653: Update load_tool in cwl-runner crunch script