[ARVADOS] updated: 9daf42fbdb868939653c6e3ca8a4fffd1cf94e31
git at public.curoverse.com
git at public.curoverse.com
Wed Apr 8 19:49:24 EDT 2015
Summary of changes:
.../app/controllers/application_controller.rb | 33 ++++++++++++++++++++++
apps/workbench/app/helpers/application_helper.rb | 8 +++---
apps/workbench/app/models/arvados_base.rb | 4 +++
apps/workbench/app/models/arvados_resource_list.rb | 6 ++++
.../pipeline_instances/_running_component.html.erb | 7 +----
.../_show_components_running.html.erb | 1 +
services/api/test/fixtures/pipeline_instances.yml | 8 ++----
7 files changed, 51 insertions(+), 16 deletions(-)
via 9daf42fbdb868939653c6e3ca8a4fffd1cf94e31 (commit)
from 15fef38119793831a6717a98762c60aacb5d0264 (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 9daf42fbdb868939653c6e3ca8a4fffd1cf94e31
Author: Radhika Chippada <radhika at curoverse.com>
Date: Wed Apr 8 19:48:13 2015 -0400
5365: add @distinct handling to workbench select queries and use this to preload portable_data_hashes as well.
diff --git a/apps/workbench/app/controllers/application_controller.rb b/apps/workbench/app/controllers/application_controller.rb
index 1b59c57..4f89f26 100644
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@ -1068,6 +1068,39 @@ class ApplicationController < ActionController::Base
@all_log_collections_for
end
+ # Helper method to get one collection for the given portable_data_hash
+ # This is used to determine if a pdh is readable by the current_user
+ helper_method :collection_for_pdh
+ def collection_for_pdh pdh
+ raise ArgumentError, 'No input argument' unless pdh
+ preload_for_pdhs([pdh])
+ @all_pdhs_for[pdh] ||= []
+ end
+
+ # Helper method to preload one collection each for the given pdhs
+ # This is used to determine if a pdh is readable by the current_user
+ helper_method :preload_for_pdhs
+ def preload_for_pdhs pdhs
+ @all_pdhs_for ||= {}
+
+ raise ArgumentError, 'Argument is not an array' unless pdhs.is_a? Array
+ return @all_pdhs_for if pdhs.empty?
+
+ # if already preloaded for all of these pdhs, return
+ if not pdhs.select { |x| @all_pdhs_for[x].nil? }.any?
+ return @all_pdhs_for
+ end
+
+ pdhs.each do |x|
+ @all_pdhs_for[x] = []
+ end
+ # TODO: make sure we get every page of results from API server
+ Collection.select(%w(portable_data_hash)).where(portable_data_hash: pdhs).distinct().each do |collection|
+ @all_pdhs_for[collection.portable_data_hash] << collection
+ end
+ @all_pdhs_for
+ end
+
# helper method to get object of a given dataclass and uuid
helper_method :object_for_dataclass
def object_for_dataclass dataclass, uuid
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 449d823..b145fdd 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -177,15 +177,15 @@ module ApplicationHelper
end
end
- def link_to_arvados_object_if_readable(attrvalue, link_text, link_text_if_not_readable, use_friendly_name=false, resource_class=nil)
- resource_class = resource_class_for_uuid(attrvalue) if !resource_class
+ def link_to_arvados_object_if_readable(attrvalue, link_text, link_text_if_not_readable, use_friendly_name=false)
+ resource_class = resource_class_for_uuid(attrvalue)
if !resource_class
return link_text_if_not_readable
end
- if resource_class.andand.to_s == 'Collection'
+ if resource_class.to_s == 'Collection'
if CollectionsHelper.match(attrvalue)
- readable = Collection.find? attrvalue # portable_data_hash
+ readable = collection_for_pdh(attrvalue).any?
else
readable = collections_for_object(attrvalue).any?
end
diff --git a/apps/workbench/app/models/arvados_base.rb b/apps/workbench/app/models/arvados_base.rb
index f19d474..2fca11e 100644
--- a/apps/workbench/app/models/arvados_base.rb
+++ b/apps/workbench/app/models/arvados_base.rb
@@ -135,6 +135,10 @@ class ArvadosBase < ActiveRecord::Base
ArvadosResourceList.new(self).select(*args)
end
+ def self.distinct(*args)
+ ArvadosResourceList.new(self).distinct(*args)
+ end
+
def self.eager(*args)
ArvadosResourceList.new(self).eager(*args)
end
diff --git a/apps/workbench/app/models/arvados_resource_list.rb b/apps/workbench/app/models/arvados_resource_list.rb
index d989715..9f66d39 100644
--- a/apps/workbench/app/models/arvados_resource_list.rb
+++ b/apps/workbench/app/models/arvados_resource_list.rb
@@ -16,6 +16,11 @@ class ArvadosResourceList
self
end
+ def distinct(bool=true)
+ @distinct = bool
+ self
+ end
+
def limit(max_results)
if not max_results.nil? and not max_results.is_a? Integer
raise ArgumentError("argument to limit() must be an Integer or nil")
@@ -178,6 +183,7 @@ class ArvadosResourceList
api_params[:select] = @select if @select
api_params[:order] = @orderby_spec if @orderby_spec
api_params[:filters] = @filters if @filters
+ api_params[:distinct] = @distinct if @distinct
item_count = 0
diff --git a/apps/workbench/app/views/pipeline_instances/_running_component.html.erb b/apps/workbench/app/views/pipeline_instances/_running_component.html.erb
index 09d6ab7..d0959f2 100644
--- a/apps/workbench/app/views/pipeline_instances/_running_component.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_running_component.html.erb
@@ -148,12 +148,7 @@
</td>
<td>
<% if k == :uuid %>
- <% resource_class = resource_class_for_uuid(current_component[k]) %>
- <% if resource_class.andand.to_s == 'Job' %>
- <%= link_to_arvados_object_if_readable(current_component[k], current_component[k], current_component[k], false, resource_class) %>
- <% else %>
- <%= link_to_if_arvados_object current_component[k], link_text: current_component[k] %>
- <% end %>
+ <%= link_to_arvados_object_if_readable(current_component[k], current_component[k], current_component[k], false) %>
<% elsif k.to_s.end_with? 'uuid' %>
<%= link_to_if_arvados_object current_component[k], friendly_name: true %>
<% elsif k.to_s.end_with? '_at' %>
diff --git a/apps/workbench/app/views/pipeline_instances/_show_components_running.html.erb b/apps/workbench/app/views/pipeline_instances/_show_components_running.html.erb
index d9814a0..dcbdb1d 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_components_running.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_components_running.html.erb
@@ -92,6 +92,7 @@
job_output_pdhs = job_outputs.select {|x| !(m = CollectionsHelper.match(x)).nil?}.compact
job_output_uuids = job_outputs - job_output_pdhs
preload_collections_for_objects job_output_uuids if job_output_uuids.any?
+ preload_for_pdhs job_output_pdhs if job_output_pdhs.any?
%>
<% pipeline_jobs.each_with_index do |pj, i| %>
diff --git a/services/api/test/fixtures/pipeline_instances.yml b/services/api/test/fixtures/pipeline_instances.yml
index c1ec917..bb06dac 100644
--- a/services/api/test/fixtures/pipeline_instances.yml
+++ b/services/api/test/fixtures/pipeline_instances.yml
@@ -272,9 +272,7 @@ pipeline_in_publicly_accessible_project:
script: foo
script_version: master
script_parameters:
- input:
- dataclass: Collection
- title: foo instance input
+ input: zzzzz-4zz18-4en62shvi99lxd4
log: zzzzz-4zz18-4en62shvi99lxd4
output: b519d9cb706a29fc7ea24dbea2f05851+93
state: Complete
@@ -301,9 +299,7 @@ pipeline_in_publicly_accessible_project_but_other_objects_elsewhere:
script: foo
script_version: master
script_parameters:
- input:
- dataclass: Collection
- title: foo instance input
+ input: zzzzz-4zz18-bv31uwvy3neko21
log: zzzzz-4zz18-bv31uwvy3neko21
output: zzzzz-4zz18-bv31uwvy3neko21
state: Complete
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list