[ARVADOS] updated: 1.3.0-526-g57e98dd9a

[Git user]

Summary of changes:
 apps/workbench/app/controllers/container_requests_controller.rb | 2 +-
 apps/workbench/app/helpers/application_helper.rb                | 7 ++++---
 sdk/cwl/arvados_cwl/fsaccess.py                                 | 9 ++++++---
 3 files changed, 11 insertions(+), 7 deletions(-)

       via  57e98dd9ab22e903b06940067433705498aacd2c (commit)
       via  c433ed943db67d41932a4141974e1c1335b9bdc1 (commit)
      from  c63b86e079325b1d6b5a5ae3d9b06c231fad4bae (commit)

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commit 57e98dd9ab22e903b06940067433705498aacd2c
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Mar 13 16:19:37 2019 -0400

    14322: Tweak workbench support from manual testing
    
    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 e241b52d0..46b9a306d 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -497,9 +497,9 @@ module ApplicationHelper
       if attrvalue.is_a? Hash
         display_value = attrvalue[:"http://arvados.org/cwl#collectionUUID"] || attrvalue[:"arv:collection"] || attrvalue[:location]
         re = CollectionsHelper.match_uuid_with_optional_filepath(display_value)
-        locationre = CollectionsHelper.match(attrvalue[:location])
+        locationre = CollectionsHelper.match(attrvalue[:location][5..-1])
         if re
-          if locationre[4]
+          if locationre and locationre[4]
             display_value = "#{Collection.find(re[1]).name} / #{locationre[4][1..-1]}"
           else
             display_value = Collection.find(re[1]).name
diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index 6eb1bf640..252ca57d4 100644
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -70,9 +70,12 @@ class CollectionCache(object):
                 if m:
                     self.cap_cache(int(m.group(2)) * 128)
                 logger.debug("Creating collection reader for %s", locator)
-                cr = arvados.collection.CollectionReader(locator, api_client=self.api_client,
-                                                         keep_client=self.keep_client,
-                                                         num_retries=self.num_retries)
+                try:
+                    cr = arvados.collection.CollectionReader(locator, api_client=self.api_client,
+                                                             keep_client=self.keep_client,
+                                                             num_retries=self.num_retries)
+                except arvados.errors.ApiError as ap:
+                    raise IOError(errno.ENOENT, "Could not access collection '%s': %s" % (locator, str(ap._get_reason())))
                 sz = len(cr.manifest_text()) * 128
                 self.collections[locator] = (cr, sz)
                 self.total += sz

commit c433ed943db67d41932a4141974e1c1335b9bdc1
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Mar 13 15:52:20 2019 -0400

    14322: Update workbench to use new collectionUUID
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/apps/workbench/app/controllers/container_requests_controller.rb b/apps/workbench/app/controllers/container_requests_controller.rb
index 783cafa11..454be448d 100644
--- a/apps/workbench/app/controllers/container_requests_controller.rb
+++ b/apps/workbench/app/controllers/container_requests_controller.rb
@@ -120,7 +120,7 @@ class ContainerRequestsController < ApplicationController
             c = Collection.find(re[1])
             input_obj[param_id] = {"class" => primary_type,
                                    "location" => "keep:#{c.portable_data_hash}#{re[4]}",
-                                   "arv:collection" => input_obj[param_id]}
+                                   "http://arvados.org/cwl#collectionUUID" => re[1]}
           end
         end
       end
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 15bf77fa0..e241b52d0 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -495,11 +495,12 @@ module ApplicationHelper
       chooser_title = "Choose a #{primary_type == 'Directory' ? 'dataset' : 'file'}:"
       selection_param = object.class.to_s.underscore + dn
       if attrvalue.is_a? Hash
-        display_value = attrvalue[:"arv:collection"] || attrvalue[:location]
+        display_value = attrvalue[:"http://arvados.org/cwl#collectionUUID"] || attrvalue[:"arv:collection"] || attrvalue[:location]
         re = CollectionsHelper.match_uuid_with_optional_filepath(display_value)
+        locationre = CollectionsHelper.match(attrvalue[:location])
         if re
-          if re[4]
-            display_value = "#{Collection.find(re[1]).name} / #{re[4][1..-1]}"
+          if locationre[4]
+            display_value = "#{Collection.find(re[1]).name} / #{locationre[4][1..-1]}"
           else
             display_value = Collection.find(re[1]).name
           end

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