[ARVADOS] updated: 1.3.0-529-ged046e660

Git user git at public.curoverse.com
Wed Mar 13 17:28:53 EDT 2019

Summary of changes:
 apps/workbench/app/helpers/application_helper.rb | 2 +-
 doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml     | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

       via  ed046e66027ba2641e0c3ee259f9f6efd2703a0b (commit)
       via  71aa520ab4769d223a432b96c9c6fa070a07942c (commit)
      from  708b39f720d49119b022e9e6afddf173be8583df (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 ed046e66027ba2641e0c3ee259f9f6efd2703a0b
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Mar 13 17:26:07 2019 -0400

    14322: Workbench links collection uuids in workflow inputs
    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 46b9a306d..8c80a646e 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -679,7 +679,7 @@ module ApplicationHelper
   # Keep locators are expected to be of the form \"...<pdh/file_path>\"
-  JSON_KEEP_LOCATOR_REGEXP = /([0-9a-f]{32}\+\d+[^'"]*?)(?=['"]|\z|$)/
+  JSON_KEEP_LOCATOR_REGEXP = /([0-9a-f]{32}\+\d+[^'"]*?|[a-z0-9]{5}-4zz18-[a-z0-9]{15})(?=['"]|\z|$)/
   def keep_locator_in_json str
     # Return a list of all matches

commit 71aa520ab4769d223a432b96c9c6fa070a07942c
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Mar 13 17:20:22 2019 -0400

    14322: Update comment on bwa-mem-input-mixed.yml
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml
index 8863cba34..73bd9f599 100755
--- a/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml
+++ b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml
@@ -3,8 +3,10 @@
 # SPDX-License-Identifier: CC-BY-SA-3.0
-# Example input file using UUIDs to reference input collections. These
-# will be resolved to content addresses before running the workflow.
+# Example input file providing both content addresses and UUIDs.  The
+# collections identified by 'collectionUUID' will be checked that the
+# current content of the collection record matches the content address
+# in the 'location' field.
   arv: 'http://arvados.org/cwl#'



More information about the arvados-commits mailing list