[ARVADOS] updated: 976f560ab04bf570ed58664d97b8b6069b314941
git at public.curoverse.com
git at public.curoverse.com
Tue Apr 14 15:34:36 EDT 2015
Summary of changes:
apps/workbench/Gemfile | 2 +-
apps/workbench/Gemfile.lock | 4 +-
apps/workbench/app/assets/images/mouse-move.gif | Bin 0 -> 26082 bytes
.../app/assets/images/pipeline-running.gif | Bin 0 -> 114564 bytes
.../app/assets/javascripts/modal_pager.js | 44 +++
.../app/assets/javascripts/pipeline_instances.js | 15 +-
.../app/assets/stylesheets/application.css.scss | 4 +
.../app/controllers/actions_controller.rb | 202 ++++++------
.../controllers/pipeline_instances_controller.rb | 54 ++++
apps/workbench/app/helpers/application_helper.rb | 29 +-
.../views/application/_title_and_buttons.html.erb | 24 +-
.../_getting_started_popup.html.erb | 179 +++++++++++
apps/workbench/app/views/layouts/body.html.erb | 34 +-
.../pipeline_instances/_show_components.html.erb | 6 +
.../_show_components_editable.html.erb | 20 --
.../views/pipeline_instances/_show_inputs.html.erb | 6 +
apps/workbench/app/views/users/profile.html.erb | 13 +-
apps/workbench/config/application.default.yml | 1 +
.../test/controllers/actions_controller_test.rb | 69 ++--
.../test/integration/application_layout_test.rb | 60 +++-
.../test/integration/report_issue_test.rb | 3 +-
.../test/integration/user_profile_test.rb | 24 +-
doc/_config.yml | 20 +-
doc/_includes/_navbar_top.liquid | 6 +-
doc/_layouts/default.html.liquid | 2 +-
doc/index.html.liquid | 32 +-
doc/user/index.html.textile.liquid | 4 +-
docker/mkimage-debootstrap.sh | 2 +-
sdk/cli/bin/crunch-job | 5 +-
sdk/go/keepclient/keepclient.go | 347 ++++++++++-----------
sdk/go/keepclient/keepclient_test.go | 269 ++++++++++++----
sdk/go/keepclient/root_sorter.go | 12 +-
sdk/go/keepclient/root_sorter_test.go | 9 +-
sdk/go/keepclient/support.go | 46 +--
sdk/python/arvados/arvfile.py | 23 +-
sdk/python/arvados/collection.py | 77 ++++-
sdk/python/arvados/keep.py | 103 ++++--
sdk/python/tests/arvados_testutil.py | 5 +-
sdk/python/tests/test_arvfile.py | 54 +++-
sdk/python/tests/test_collections.py | 59 ++--
sdk/python/tests/test_keep_client.py | 67 +++-
sdk/ruby/lib/arvados/collection.rb | 55 +++-
sdk/ruby/test/test_collection.rb | 87 +++++-
.../{zz_load_config.rb => load_config.rb} | 10 +
...preload_all_models.rb => preload_all_models.rb} | 7 +-
.../test/fixtures/api_client_authorizations.yml | 10 +-
services/api/test/fixtures/users.yml | 27 +-
.../functional/arvados/v1/users_controller_test.rb | 6 +-
services/keepproxy/keepproxy.go | 220 ++++++-------
services/keepproxy/keepproxy_test.go | 10 +-
services/keepstore/keepstore.go | 2 +-
services/keepstore/pull_worker.go | 8 +-
services/keepstore/pull_worker_integration_test.go | 10 +-
services/keepstore/pull_worker_test.go | 2 +-
54 files changed, 1638 insertions(+), 751 deletions(-)
create mode 100644 apps/workbench/app/assets/images/mouse-move.gif
create mode 100644 apps/workbench/app/assets/images/pipeline-running.gif
create mode 100644 apps/workbench/app/assets/javascripts/modal_pager.js
create mode 100644 apps/workbench/app/views/getting_started/_getting_started_popup.html.erb
rename services/api/config/initializers/{zz_load_config.rb => load_config.rb} (80%)
rename services/api/config/initializers/{zz_preload_all_models.rb => preload_all_models.rb} (55%)
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commit 976f560ab04bf570ed58664d97b8b6069b314941
Author: Radhika Chippada <radhika at curoverse.com>
Date: Tue Apr 14 15:33:32 2015 -0400
5417: add "unreadable inputs provided" visual cue for an editable pipeline instance.
diff --git a/apps/workbench/app/assets/javascripts/pipeline_instances.js b/apps/workbench/app/assets/javascripts/pipeline_instances.js
index e820ba9..a928d44 100644
--- a/apps/workbench/app/assets/javascripts/pipeline_instances.js
+++ b/apps/workbench/app/assets/javascripts/pipeline_instances.js
@@ -1,6 +1,6 @@
function run_pipeline_button_state() {
var a = $('a.editable.required.editable-empty,input.form-control.required[value=""]');
- if (a.length > 0) {
+ if ((a.length > 0) || ($('.unreadable-inputs-present').length)) {
$(".run-pipeline-button").addClass("disabled");
}
else {
@@ -35,7 +35,7 @@ $(document).on('editable:success', function(event, tag, response, newValue) {
$(document).on('ready ajax:complete', function() {
$('a.editable.required').each(function() {
var $tag = $(this);
- if ($tag.hasClass("editable-empty")) {
+ if ($tag.hasClass("unreadable-input")) {
$tag.parent().css("background-color", "#ffdddd");
$tag.parent().prev().css("background-color", "#ffdddd");
}
@@ -44,6 +44,17 @@ $(document).on('ready ajax:complete', function() {
$tag.parent().prev().css("background-color", "");
}
});
+ $('input.required').each(function() {
+ var $tag = $(this);
+ if ($tag.hasClass("editable-empty") || $tag.hasClass("unreadable-input")) {
+ $tag.parent().parent().css("background-color", "#ffdddd");
+ $tag.parent().parent().prev().css("background-color", "#ffdddd");
+ }
+ else {
+ $tag.parent().css("background-color", "");
+ $tag.parent().prev().css("background-color", "");
+ }
+ });
run_pipeline_button_state();
});
diff --git a/apps/workbench/app/controllers/pipeline_instances_controller.rb b/apps/workbench/app/controllers/pipeline_instances_controller.rb
index b4cce9b..e84d990 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -284,6 +284,60 @@ class PipelineInstancesController < ApplicationController
%w(Compare Graph)
end
+ helper_method :unreadable_inputs_present?
+ def unreadable_inputs_present?
+ unless @unreadable_inputs_present.nil?
+ @unreadable_inputs_present
+ end
+
+ input_uuids = []
+ input_pdhs = []
+ @object.components.each do |k, component|
+ next if !component
+ component[:script_parameters].andand.each do |p, tv|
+ if (tv.is_a? Hash) and (tv[:dataclass] == "Collection")
+ if tv[:value]
+ value = tv[:value]
+ elsif tv[:default]
+ value = tv[:default]
+ end
+ if value
+ split = value.split '/'
+ if CollectionsHelper.match(split[0])
+ input_pdhs << split[0]
+ else
+ input_uuids << split[0]
+ end
+ end
+ end
+ end
+ end
+
+ input_pdhs = input_pdhs.uniq
+ input_uuids = input_uuids.uniq
+
+ preload_collections_for_objects input_uuids if input_uuids.any?
+ preload_for_pdhs input_pdhs if input_pdhs.any?
+
+ @unreadable_inputs_present = false
+ input_uuids.each do |uuid|
+ if !collections_for_object(uuid).any?
+ @unreadable_inputs_present = true
+ break
+ end
+ end
+ if !@unreadable_inputs_present
+ input_pdhs.each do |pdh|
+ if !collection_for_pdh(pdh).any?
+ @unreadable_inputs_present = true
+ break
+ end
+ end
+ end
+
+ @unreadable_inputs_present
+ end
+
protected
def for_comparison v
if v.is_a? Hash or v.is_a? Array
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 72f961f..8d92b47 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -183,20 +183,26 @@ module ApplicationHelper
return link_to_if_arvados_object attrvalue, opts
end
+ readable = object_readable attrvalue, resource_class
+ if readable
+ link_to_if_arvados_object attrvalue, opts
+ else
+ link_text_if_not_readable
+ end
+ end
+
+ def object_readable attrvalue, resource_class=nil
+ resource_class = resource_class_for_uuid(attrvalue)
+ return if resource_class.nil?
+
if resource_class.to_s == 'Collection'
if CollectionsHelper.match(attrvalue)
- readable = collection_for_pdh(attrvalue).any?
+ collection_for_pdh(attrvalue).any?
else
- readable = collections_for_object(attrvalue).any?
+ collections_for_object(attrvalue).any?
end
else
- readable = object_for_dataclass(resource_class, attrvalue)
- end
-
- if readable
- link_to_if_arvados_object attrvalue, opts
- else
- link_text_if_not_readable
+ object_for_dataclass(resource_class, attrvalue)
end
end
@@ -346,10 +352,11 @@ module ApplicationHelper
success: 'page-refresh'
}.to_json,
})
+ is_readable_input = object_readable attrvalue.split('/')[0] unless attrvalue.andand.empty?
return content_tag('div', :class => 'input-group') do
html = text_field_tag(dn, display_value,
:class =>
- "form-control #{'required' if required}")
+ "form-control #{'required' if required} #{'unreadable-input' if !attrvalue.andand.empty? and !is_readable_input}")
html + content_tag('span', :class => 'input-group-btn') do
link_to('Choose',
modal_path,
diff --git a/apps/workbench/app/views/pipeline_instances/_show_components.html.erb b/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
index 7735997..a2dbada 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
@@ -13,6 +13,12 @@
<% else %>
<%# state is either New or Ready %>
+ <% if controller.class.name.eql?('PipelineInstancesController') and unreadable_inputs_present? %>
+ <div class="unreadable-inputs-present">
+ <p style="color:#ff6666"> One or more inputs provided are not readable by you. Please correct these before you can run the pipeline.</p>
+ </div>
+ <% end %>
+
<p><i>Here are all of the pipeline's components (jobs that will need to run in order to complete the pipeline). If you know what you're doing (or you're experimenting) you can modify these parameters before starting the pipeline. Usually, you only need to edit the settings presented on the "Inputs" tab above.</i></p>
<%= render_pipeline_components("editable", :json, editable: true) %>
diff --git a/apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb b/apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb
index 51fe8d4..f6c9e85 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_components_editable.html.erb
@@ -1,23 +1,3 @@
-<%
- input_uuids = []
- input_pdhs = []
- @object.components.each do |k, component|
- next if !component
- component[:script_parameters].andand.each do |p, tv|
- if tv.is_a? Hash and !tv[:value].nil? and (tv[:dataclass] == "Collection")
- if CollectionsHelper.match(tv[:value])
- input_pdhs << tv[:value]
- else
- input_uuids << tv[:value]
- end
- end
- end
- end
-
- preload_collections_for_objects input_uuids if input_uuids.any?
- preload_for_pdhs input_pdhs if input_pdhs.any?
-%>
-
<table class="table pipeline-components-table" style="margin-top: -.1em">
<colgroup>
<col style="width: 20%" />
diff --git a/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb b/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
index e6b7ef2..67afba1 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
@@ -32,6 +32,12 @@
<% if n_inputs == 0 %>
<p>This pipeline does not need any further inputs specified. You can start it by clicking the "Run" button whenever you're ready. (It's not too late to change existing settings, though.)</p>
<% else %>
+ <% if controller.class.name.eql?('PipelineInstancesController') and unreadable_inputs_present? %>
+ <div class="unreadable-inputs-present">
+ <p style="color:#ff6666"> One or more inputs provided are not readable by you. Please correct these before you can run the pipeline.</p>
+ </div>
+ <% end %>
+
<p><i>Provide <%= n_inputs > 1 ? 'values' : 'a value' %> for the following <%= n_inputs > 1 ? 'parameters' : 'parameter' %>, then click the "Run" button to start the pipeline.</i></p>
<% if @object.editable? %>
<%= content_for :pi_input_form %>
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