[ARVADOS] updated: 5420797c32e73347a79b5ecd8cdfbd212fd8aae8
git at public.curoverse.com
git at public.curoverse.com
Fri Mar 7 13:33:02 EST 2014
Summary of changes:
apps/workbench/app/assets/javascripts/editable.js | 8 +++
apps/workbench/app/assets/javascripts/selection.js | 15 ++++--
.../app/assets/stylesheets/application.css.scss | 7 ---
.../app/controllers/actions_controller.rb | 13 +++--
.../app/controllers/application_controller.rb | 2 +-
.../app/controllers/collections_controller.rb | 12 ++++-
apps/workbench/app/controllers/jobs_controller.rb | 5 ++-
.../controllers/pipeline_instances_controller.rb | 2 +
apps/workbench/app/helpers/provenance_helper.rb | 42 +++++++++++----
apps/workbench/app/models/collection.rb | 18 -------
.../app/views/collections/_show_files.html.erb | 54 +++++++++++---------
11 files changed, 104 insertions(+), 74 deletions(-)
via 5420797c32e73347a79b5ecd8cdfbd212fd8aae8 (commit)
via 239cbf3997a084ae388ad89bdd7577f21d829251 (commit)
from ff7803d40cbfbf47a348d4e4eec7d6e48742bbeb (commit)
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commit 5420797c32e73347a79b5ecd8cdfbd212fd8aae8
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Mar 7 13:34:24 2014 -0500
Fixed styling of selection dropdown menu.
Menu no longer dismisses when clicking a checkbox to remove an item.
Selected files no longer have /./ in the middle.
Fixed nil error when non-file or non-collection items are in the selection list.
Fixed head_kind and tail_kind.
Made a comment about inline x-editable.
diff --git a/apps/workbench/app/assets/javascripts/editable.js b/apps/workbench/app/assets/javascripts/editable.js
index a743586..79bad15 100644
--- a/apps/workbench/app/assets/javascripts/editable.js
+++ b/apps/workbench/app/assets/javascripts/editable.js
@@ -1,6 +1,14 @@
$.fn.editable.defaults.ajaxOptions = {type: 'put', dataType: 'json'};
$.fn.editable.defaults.send = 'always';
+
+// Default for editing is popup. I experimented with inline which is a little
+// nicer in that it shows up right under the mouse instead of nearby. However,
+// the inline box is taller than the regular content, which causes the page
+// layout to shift unless we make the table rows tall, which leaves a lot of
+// wasted space when not editing. Also inline can get cut off if the page is
+// too narrow, when the popup box will just move to do the right thing.
//$.fn.editable.defaults.mode = 'inline';
+
$.fn.editable.defaults.params = function (params) {
var a = {};
var key = params.pk.key;
diff --git a/apps/workbench/app/assets/javascripts/selection.js b/apps/workbench/app/assets/javascripts/selection.js
index c94a557..27d63d1 100644
--- a/apps/workbench/app/assets/javascripts/selection.js
+++ b/apps/workbench/app/assets/javascripts/selection.js
@@ -52,14 +52,17 @@ jQuery(function($){
var lst = get_selection_list();
$("#persistent-selection-count").text(lst.length);
if (lst.length > 0) {
- $('#selection-form-content').html('<li><input type="submit" name="combine_selected_files_into_collection" id="combine_selected_files_into_collection" value="Combine selected collections and files into a new collection"/></li>'
- + '<li><a href="#" id="clear_selections_button">Clear selections</a></li>'
- + '<li class="notification"><table style="width: 100%"></table></li>');
+ $('#selection-form-content').html(
+ '<li><a href="#" id="clear_selections_button">Clear selections</a></li>'
+ + '<li><input type="submit" name="combine_selected_files_into_collection" '
+ + ' id="combine_selected_files_into_collection" '
+ + ' value="Combine selected collections and files into a new collection" /></li>'
+ + '<li class="notification"><table style="width: 100%"></table></li>');
for (var i = 0; i < lst.length; i++) {
$('#selection-form-content > li > table').append("<tr>"
+ "<td>"
- + "<input class='remove-selection' name='selection[]' type='checkbox' value='" + lst[i].uuid + "' checked='true'></input>"
+ + "<input class='remove-selection' name='selection[]' type='checkbox' value='" + lst[i].uuid + "' checked='true' data-stoppropagation='true' />"
+ "</td>"
+ "<td>"
@@ -109,6 +112,10 @@ jQuery(function($){
$(window).on('load storage', update_count);
+
+ $('#selection-form-content').on("click", function(e) {
+ e.stopPropagation();
+ });
});
add_form_selection_sources = null;
diff --git a/apps/workbench/app/assets/stylesheets/application.css.scss b/apps/workbench/app/assets/stylesheets/application.css.scss
index 7a26c70..6a57f9e 100644
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@ -185,10 +185,3 @@ table.table-fixed-header-row tbody {
overflow-y: auto;
}
-#persistent-selection-list {
- width: 500px;
-}
-
-#persistent-selection-list li table tr {
- border-top: 1px solid rgb(221, 221, 221);
-}
diff --git a/apps/workbench/app/controllers/actions_controller.rb b/apps/workbench/app/controllers/actions_controller.rb
index c443c21..74e5831 100644
--- a/apps/workbench/app/controllers/actions_controller.rb
+++ b/apps/workbench/app/controllers/actions_controller.rb
@@ -1,10 +1,13 @@
class ActionsController < ApplicationController
+
+ skip_before_filter :find_object_by_uuid, only: :post
+
def combine_selected_files_into_collection
lst = []
files = []
params["selection"].each do |s|
m = CollectionsHelper.match(s)
- if m[1] and m[2]
+ if m and m[1] and m[2]
lst.append(m[1] + m[2])
files.append(m)
end
@@ -73,9 +76,9 @@ class ActionsController < ApplicationController
chash.each do |k,v|
l = Link.new({
- tail_kind: "arvados#Collection",
+ tail_kind: "arvados#collection",
tail_uuid: k,
- head_kind: "arvados#Collection",
+ head_kind: "arvados#collection",
head_uuid: newuuid,
link_class: "provenance",
name: "provided"
@@ -83,12 +86,12 @@ class ActionsController < ApplicationController
l.save!
end
- '/collections/' + newc.uuid
+ redirect_to controller: 'collections', action: :show, id: newc.uuid
end
def post
if params["combine_selected_files_into_collection"]
- redirect_to combine_selected_files_into_collection
+ combine_selected_files_into_collection
else
redirect_to :back
end
diff --git a/apps/workbench/app/controllers/application_controller.rb b/apps/workbench/app/controllers/application_controller.rb
index 2790f96..412f86c 100644
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@ -4,7 +4,7 @@ class ApplicationController < ActionController::Base
around_filter :thread_clear
around_filter :thread_with_mandatory_api_token, :except => [:render_exception, :render_not_found]
around_filter :thread_with_optional_api_token
- before_filter :find_object_by_uuid, :except => [:index, :post, :render_exception, :render_not_found]
+ before_filter :find_object_by_uuid, :except => [:index, :render_exception, :render_not_found]
before_filter :check_user_agreements, :except => [:render_exception, :render_not_found]
before_filter :check_user_notifications, :except => [:render_exception, :render_not_found]
theme :select_theme
diff --git a/apps/workbench/app/models/collection.rb b/apps/workbench/app/models/collection.rb
index fd6b4e4..6bc55bd 100644
--- a/apps/workbench/app/models/collection.rb
+++ b/apps/workbench/app/models/collection.rb
@@ -26,22 +26,4 @@ class Collection < ArvadosBase
$arvados_api_client.api "collections/#{self.uuid}/", "used_by"
end
- # def selection_label
- # name = ''
- # i = 0
- # if self.files.length > 3
- # m = 3
- # else
- # m = self.files.length
- # end
- # while i < m
- # name += "#{self.files[i][1]}"
- # i += 1
- # name += ", " if i < m
- # end
- # if i < self.files.length
- # name += "&ellip;"
- # end
- # name
- # end
end
diff --git a/apps/workbench/app/views/collections/_show_files.html.erb b/apps/workbench/app/views/collections/_show_files.html.erb
index 6600a40..956958e 100644
--- a/apps/workbench/app/views/collections/_show_files.html.erb
+++ b/apps/workbench/app/views/collections/_show_files.html.erb
@@ -16,34 +16,38 @@
</tr>
</thead><tbody>
<% if @object then @object.files.sort_by{|f|[f[0],f[1]]}.each do |file| %>
- <% file_path = "#{file[0]}/#{file[1]}" %>
- <tr>
- <td>
- <%= check_box_tag 'uuids[]', @object.uuid+'/'+file_path, false, {
- :class => 'persistent-selection',
- :friendly_type => "File",
- :friendly_name => "#{@object.uuid}/#{file_path}",
- :href => "#{url_for controller: 'collections', action: 'show', id: @object.uuid }/#{file_path}"
- } %>
- </td>
- <td>
- <%= file[0] %>
- </td>
+ <% f0 = file[0] %>
+ <% f0 = '' if f0 == '.' %>
+ <% f0 = f0[2..-1] if f0[0..1] == './' %>
+ <% f0 += '/' if not f0.empty? %>
+ <% file_path = "#{f0}#{file[1]}" %>
+ <tr>
+ <td>
+ <%= check_box_tag 'uuids[]', @object.uuid+'/'+file_path, false, {
+ :class => 'persistent-selection',
+ :friendly_type => "File",
+ :friendly_name => "#{@object.uuid}/#{file_path}",
+ :href => "#{url_for controller: 'collections', action: 'show', id: @object.uuid }/#{file_path}"
+ } %>
+ </td>
+ <td>
+ <%= file[0] %>
+ </td>
- <td>
- <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
- </td>
+ <td>
+ <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
+ </td>
- <td style="text-align:right">
- <%= raw(human_readable_bytes_html(file[2])) %>
- </td>
+ <td style="text-align:right">
+ <%= raw(human_readable_bytes_html(file[2])) %>
+ </td>
- <td>
- <div style="display:inline-block">
- <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
- </div>
- </td>
- </tr>
+ <td>
+ <div style="display:inline-block">
+ <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
+ </div>
+ </td>
+ </tr>
<% end; end %>
</tbody>
</table>
commit 239cbf3997a084ae388ad89bdd7577f21d829251
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Mar 7 10:16:56 2014 -0500
Provenance graphing bugfixes
diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb
index b6997b9..737583a 100644
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -102,8 +102,16 @@ class CollectionsController < ApplicationController
end
Collection.where(uuid: @object.uuid).each do |u|
- @prov_svg = ProvenanceHelper::create_provenance_graph u.provenance, "provenance_svg", {:direction => :top_down, :combine_jobs => :script_only} rescue nil
- @used_by_svg = ProvenanceHelper::create_provenance_graph u.used_by, "used_by_svg", {:direction => :top_down, :combine_jobs => :script_only, :pdata_only => true} rescue nil
+ puts request
+ @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only}) rescue nil
+ @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
+ {:request => request,
+ :direction => :top_down,
+ :combine_jobs => :script_only,
+ :pdata_only => true}) rescue nil
end
end
diff --git a/apps/workbench/app/controllers/jobs_controller.rb b/apps/workbench/app/controllers/jobs_controller.rb
index d302bff..4705bb5 100644
--- a/apps/workbench/app/controllers/jobs_controller.rb
+++ b/apps/workbench/app/controllers/jobs_controller.rb
@@ -14,7 +14,10 @@ class JobsController < ApplicationController
nodes << c
end
- @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {:all_script_parameters => true, :script_version_nodes => true}
+ @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :script_version_nodes => true}
end
def index
diff --git a/apps/workbench/app/controllers/pipeline_instances_controller.rb b/apps/workbench/app/controllers/pipeline_instances_controller.rb
index 12db3c3..66772da 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -88,6 +88,7 @@ class PipelineInstancesController < ApplicationController
provenance, pips = graph(@pipelines)
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
@@ -159,6 +160,7 @@ class PipelineInstancesController < ApplicationController
@pipelines = @objects
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
diff --git a/apps/workbench/app/helpers/provenance_helper.rb b/apps/workbench/app/helpers/provenance_helper.rb
index fced9da..c0b2fd3 100644
--- a/apps/workbench/app/helpers/provenance_helper.rb
+++ b/apps/workbench/app/helpers/provenance_helper.rb
@@ -7,7 +7,7 @@ module ProvenanceHelper
@visited = {}
@jobs = {}
end
-
+
def self.collection_uuid(uuid)
m = CollectionsHelper.match(uuid)
if m
@@ -32,11 +32,16 @@ module ProvenanceHelper
end
def describe_node(uuid)
+ uuid = uuid.to_sym
bgcolor = determine_fillcolor @opts[:pips][uuid] if @opts[:pips]
rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
if rsc
- href = "/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => rsc.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s,
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
#"\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{href}\"];\n"
if rsc == Collection
@@ -46,11 +51,12 @@ module ProvenanceHelper
#puts "empty!"
return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
end
+ puts "#{uuid.class} #{@pdata[uuid]}"
if @pdata[uuid]
#puts @pdata[uuid]
if @pdata[uuid][:name]
return "\"#{uuid}\" [label=\"#{@pdata[uuid][:name]}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
- else
+ else
files = nil
if @pdata[uuid].respond_to? :files
files = @pdata[uuid].files
@@ -69,6 +75,7 @@ module ProvenanceHelper
if i < files.length
label += "\\n⋮"
end
+ #puts "#{uuid} #{label} #{files}"
return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
end
end
@@ -101,7 +108,7 @@ module ProvenanceHelper
gr = "\"#{head}\" -> \"#{tail}\""
end
if extra.length > 0
- gr += "["
+ gr += " ["
extra.each do |k, v|
gr += "#{k}=\"#{v}\","
end
@@ -211,6 +218,8 @@ module ProvenanceHelper
gr += edge(job_uuid(job), job[:script_version], {:label => "script_version"})
end
end
+ elsif rsc == Link
+ # do nothing
else
gr += describe_node(uuid)
end
@@ -218,8 +227,14 @@ module ProvenanceHelper
@pdata.each do |k, link|
if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => Link.to_s.tableize,
+ :action => :show,
+ :id => link[:uuid],
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
+
gr += describe_node(link[:tail_uuid])
- gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => "/links/#{link[:uuid]}"})
+ gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => href})
gr += generate_provenance_edges(link[:tail_uuid])
end
end
@@ -232,7 +247,12 @@ module ProvenanceHelper
def describe_jobs
gr = ""
@jobs.each do |k, v|
- gr += "\"#{k}\" [href=\"/jobs?"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => Job.to_s.tableize,
+ :action => :index,
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
+
+ gr += "\"#{k}\" [href=\"#{href}?"
n = 0
v.each do |u|
@@ -243,11 +263,11 @@ module ProvenanceHelper
gr += "\",label=\""
if @opts[:combine_jobs] == :script_only
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}"
elsif @opts[:combine_jobs] == :script_and_version
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}" # Just show the name but the nodes will be distinct
else
- gr += uuid = "#{v[0][:script]}\\n#{v[0][:finished_at]}"
+ gr += "#{v[0][:script]}\\n#{v[0][:finished_at]}"
end
gr += "\",#{determine_fillcolor n}];\n"
end
@@ -291,8 +311,8 @@ edge [fontsize=10];
gr += "}"
svg = ""
- #puts gr
-
+ puts gr
+
require 'open3'
Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
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