[ARVADOS] updated: 1.3.0-543-g90bb5de47

[Git user]

Summary of changes:
 .../controllers/container_requests_controller.rb   |   2 +-
 apps/workbench/app/helpers/application_helper.rb   |  11 +-
 .../{bwa-mem-input.yml => bwa-mem-input-mixed.yml} |  11 ++
 doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml       |  21 ++++
 doc/user/cwl/cwl-runner.html.textile.liquid        |   6 +-
 sdk/cwl/arvados_cwl/__init__.py                    |   2 +-
 sdk/cwl/arvados_cwl/arvcontainer.py                |   2 +
 sdk/cwl/arvados_cwl/executor.py                    |   4 +-
 sdk/cwl/arvados_cwl/fsaccess.py                    |  40 ++++---
 sdk/cwl/arvados_cwl/pathmapper.py                  |   3 +
 sdk/cwl/arvados_cwl/runner.py                      |  89 ++++++++++++--
 sdk/cwl/arvados_cwl/util.py                        |   4 +-
 ...> submit_test_job_with_inconsistent_uuids.json} |   4 +-
 ... => submit_test_job_with_mismatched_uuids.json} |   7 +-
 ...st_job.json => submit_test_job_with_uuids.json} |   6 +-
 sdk/cwl/tests/test_container.py                    |  14 ++-
 sdk/cwl/tests/test_submit.py                       | 132 +++++++++++++++++++--
 17 files changed, 296 insertions(+), 62 deletions(-)
 copy doc/user/cwl/bwa-mem/{bwa-mem-input.yml => bwa-mem-input-mixed.yml} (54%)
 create mode 100755 doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml
 copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_inconsistent_uuids.json} (68%)
 copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_mismatched_uuids.json} (67%)
 copy sdk/cwl/tests/{submit_test_job.json => submit_test_job_with_uuids.json} (63%)

       via  90bb5de474c45e0b786f387ecab2277b593e335d (commit)
       via  4013f2bd35cf76d92aeafc4d3b0b4e2fd7a2dd84 (commit)
       via  45974ce224baf26d0a4c445dd1e9322193f1f64f (commit)
       via  1eb77b5c90ea52a516c3b38b7316425f6d7cf4fd (commit)
       via  ca521bb33e933aa097e855897ec960fc72e4d497 (commit)
       via  3ccaff49c9da5721d7ae5fc6c41ae91413f797c4 (commit)
       via  6844ff128e34898eae1a2cc513d8a0bfa4aed545 (commit)
       via  a2bfb6d9f3d9e8675a644e9cc9a1bbcdc79f71e6 (commit)
       via  1ea2e3c4125cf9340e8fde52f338fa814f46c0b6 (commit)
       via  9ecc3c378f694f9bd222c1efd6b75104affdb6e7 (commit)
       via  069f4a9236364c6a3f3e4b022bbd3266de6abda9 (commit)
       via  360ba4426a6074f394abe107a7989acf580c1947 (commit)
       via  58b12d248ed05f8b75b16cee33b0e153e7be71f6 (commit)
       via  35a42c13bc91d5b3cfa8dfb53a0d51fc2c3def82 (commit)
       via  9e8d0cd4d5663e1901a2553babe3910bf0a12896 (commit)
      from  1c6c860b90c54f1c257ef2016f725176d9cf50c6 (commit)

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 90bb5de474c45e0b786f387ecab2277b593e335d
Merge: 1c6c860b9 4013f2bd3
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Mar 18 14:43:31 2019 -0400

    Merge branch '14322-cwl-uuid-input' refs #14322
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>


commit 4013f2bd35cf76d92aeafc4d3b0b4e2fd7a2dd84
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Mon Mar 18 14:04:19 2019 -0400

    14322: Tweak JSON_KEEP_LOCATOR_REGEXP and comment
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 8c80a646e..4c4b5ff34 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -678,8 +678,8 @@ module ApplicationHelper
     render_runtime duration, use_words, round_to_min
   end
 
-  # Keep locators are expected to be of the form \"...<pdh/file_path>\"
-  JSON_KEEP_LOCATOR_REGEXP = /([0-9a-f]{32}\+\d+[^'"]*?|[a-z0-9]{5}-4zz18-[a-z0-9]{15})(?=['"]|\z|$)/
+  # Keep locators are expected to be of the form \"...<pdh/file_path>\" or \"...<uuid/file_path>\"
+  JSON_KEEP_LOCATOR_REGEXP = /([0-9a-f]{32}\+\d+[^'"]*|[a-z0-9]{5}-4zz18-[a-z0-9]{15}[^'"]*)(?=['"]|\z|$)/
   def keep_locator_in_json str
     # Return a list of all matches
     str.scan(JSON_KEEP_LOCATOR_REGEXP).flatten

-----------------------------------------------------------------------


hooks/post-receive
--