[ARVADOS] created: b5d3273b5aa503b22fdbeab7f8979e720e30c119
Git user
git at public.curoverse.com
Mon Nov 28 21:28:59 EST 2016
at b5d3273b5aa503b22fdbeab7f8979e720e30c119 (commit)
commit b5d3273b5aa503b22fdbeab7f8979e720e30c119
Author: radhika <radhika at curoverse.com>
Date: Mon Nov 28 21:27:32 2016 -0500
10518: update API groups_controller.contents method to exclude classes with index disabled and update user guide to use "Run a process" instead of "Run a pipeline"
diff --git a/doc/images/upload-using-workbench.png b/doc/images/upload-using-workbench.png
index de8dc9e..3d67577 100644
Binary files a/doc/images/upload-using-workbench.png and b/doc/images/upload-using-workbench.png differ
diff --git a/doc/images/workbench-dashboard.png b/doc/images/workbench-dashboard.png
index 76df32c..3cdf1e4 100644
Binary files a/doc/images/workbench-dashboard.png and b/doc/images/workbench-dashboard.png differ
diff --git a/doc/images/workbench-move-selected.png b/doc/images/workbench-move-selected.png
index 5ed1ef5..bba1a1c 100644
Binary files a/doc/images/workbench-move-selected.png and b/doc/images/workbench-move-selected.png differ
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index 573e2b9..3006990 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -143,7 +143,7 @@ If you reference a local file which is not in @arv-mount@, then @arvados-cwl-run
h2. Registering a workflow to use in Workbench
-Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button on the Workbench Dashboard.
+Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard.
<notextile>
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl</span>
diff --git a/doc/user/getting_started/workbench.html.textile.liquid b/doc/user/getting_started/workbench.html.textile.liquid
index 6e334ba..a64727f 100644
--- a/doc/user/getting_started/workbench.html.textile.liquid
+++ b/doc/user/getting_started/workbench.html.textile.liquid
@@ -14,4 +14,4 @@ You may be asked to log in using a Google account. Arvados uses only your name
Once your account is active, logging in to the Workbench will present you with the Dashboard. This gives a summary of your projects and recent activity in the Arvados instance. "You are now ready to run your first pipeline.":{{ site.baseurl }}/user/tutorials/tutorial-pipeline-workbench.html
-!{{ site.baseurl }}/images/workbench-dashboard.png!
+!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/workbench-dashboard.png!
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 6537fda..37a575c 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -21,7 +21,7 @@ notextile. <div class="spaced-out">
h3. Steps
# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
-# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
+# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
# In the search box, type in *Tutorial align using bwa mem*.
# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will create a new pipeline in your *Home* project and will open it. You can now supply the inputs for the pipeline.
# The first input parameter to the pipeline is *"reference_collection" parameter for run-command script in bwa-mem component*. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header. This will open a dialog box titled *Choose a dataset for "reference_collection" parameter for run-command script in bwa-mem component*.
diff --git a/services/api/app/controllers/arvados/v1/groups_controller.rb b/services/api/app/controllers/arvados/v1/groups_controller.rb
index d6adbf0..5d91a81 100644
--- a/services/api/app/controllers/arvados/v1/groups_controller.rb
+++ b/services/api/app/controllers/arvados/v1/groups_controller.rb
@@ -68,9 +68,14 @@ class Arvados::V1::GroupsController < ApplicationController
Collection,
Human, Specimen, Trait]
- table_names = klasses.map(&:table_name)
+ table_names = Hash[klasses.collect { |k| [k, k.table_name] }]
+
+ disabled_methods = Rails.configuration.disable_api_methods
+ avail_klasses = table_names.select{|k, t| !disabled_methods.include?(t+'.index')}
+ klasses = avail_klasses.keys
+
request_filters.each do |col, op, val|
- if col.index('.') && !table_names.include?(col.split('.', 2)[0])
+ if col.index('.') && !table_names.values.include?(col.split('.', 2)[0])
raise ArgumentError.new("Invalid attribute '#{col}' in filter")
end
end
diff --git a/services/api/test/functional/arvados/v1/groups_controller_test.rb b/services/api/test/functional/arvados/v1/groups_controller_test.rb
index 10534a7..e9abf9d 100644
--- a/services/api/test/functional/arvados/v1/groups_controller_test.rb
+++ b/services/api/test/functional/arvados/v1/groups_controller_test.rb
@@ -55,12 +55,12 @@ class Arvados::V1::GroupsControllerTest < ActionController::TestCase
assert_equal 0, json_response['items_available']
end
- def check_project_contents_response
+ def check_project_contents_response disabled_kinds=[]
assert_response :success
assert_operator 2, :<=, json_response['items_available']
assert_operator 2, :<=, json_response['items'].count
kinds = json_response['items'].collect { |i| i['kind'] }.uniq
- expect_kinds = %w'arvados#group arvados#specimen arvados#pipelineTemplate arvados#job'
+ expect_kinds = %w'arvados#group arvados#specimen arvados#pipelineTemplate arvados#job' - disabled_kinds
assert_equal expect_kinds, (expect_kinds & kinds)
json_response['items'].each do |i|
@@ -69,6 +69,10 @@ class Arvados::V1::GroupsControllerTest < ActionController::TestCase
"group#contents returned a non-project group")
end
end
+
+ disabled_kinds.each do |d|
+ assert_equal true, !kinds.include?(d)
+ end
end
test 'get group-owned objects' do
@@ -448,4 +452,15 @@ class Arvados::V1::GroupsControllerTest < ActionController::TestCase
end
end
end
+
+ test 'get contents with jobs and pipeline instances disabled' do
+ Rails.configuration.disable_api_methods = ['jobs.index', 'pipeline_instances.index']
+
+ authorize_with :active
+ get :contents, {
+ id: groups(:aproject).uuid,
+ format: :json,
+ }
+ check_project_contents_response %w'arvados#pipelineInstance arvados#job'
+ end
end
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