[ARVADOS] updated: 7df2da959b583d3646b9fde606f9e74d598d4bb9
git at public.curoverse.com
git at public.curoverse.com
Thu Jun 5 11:18:37 EDT 2014
Summary of changes:
.gitignore | 3 +
.../app/assets/javascripts/pipeline_instances.js | 22 ++--
.../app/assets/stylesheets/application.css.scss | 3 +
.../workbench/app/assets/stylesheets/jobs.css.scss | 13 ++-
.../app/controllers/application_controller.rb | 6 +-
.../app/controllers/folders_controller.rb | 2 +
.../controllers/pipeline_instances_controller.rb | 1 +
apps/workbench/app/helpers/application_helper.rb | 8 +-
apps/workbench/app/models/authorized_key.rb | 2 +-
apps/workbench/app/models/collection.rb | 2 +
apps/workbench/app/models/pipeline_instance.rb | 6 +-
apps/workbench/app/models/user.rb | 2 +-
apps/workbench/app/models/virtual_machine.rb | 2 +-
.../views/application/_show_object_button.html.erb | 7 +-
.../app/views/application/_svg_div.html.erb | 2 +-
.../app/views/collections/_choose_rows.html.erb | 26 +++--
.../app/views/collections/_index_tbody.html.erb | 4 +-
.../app/views/collections/_show_recent.html.erb | 4 +-
.../app/views/folders/_show_contents_rows.html.erb | 6 +-
.../pipeline_instances/_show_compare.html.erb | 5 +-
.../pipeline_instances/_show_components.html.erb | 3 +-
.../views/pipeline_instances/_show_inputs.html.erb | 3 +-
.../app/views/pipeline_instances/compare.html.erb | 14 +++
.../test/integration/pipeline_instances_test.rb | 4 +
apps/workbench/test/integration/users_test.rb | 8 +-
doc/api/methods/users.html.textile.liquid | 4 -
...rial-gatk-variantfiltration.html.textile.liquid | 42 +------
doc/user/topics/tutorial-job1.html.textile.liquid | 12 +-
docker/api/secret_token.rb.in | 5 +
docker/build_tools/Makefile | 3 +-
docker/config.yml.example | 4 +
docker/jobs/Dockerfile | 2 +
sdk/cli/bin/arv | 2 -
sdk/cli/bin/crunch-job | 31 +++--
sdk/python/arvados/commands/put.py | 20 ++--
sdk/python/test_cmdline.py | 81 -------------
.../tests/{test_arv-put.py => test_arv_put.py} | 103 ++++++++++++++++-
services/api/Gemfile | 1 -
services/api/Gemfile.lock | 2 -
.../controllers/arvados/v1/job_tasks_controller.rb | 1 +
.../app/controllers/arvados/v1/jobs_controller.rb | 45 --------
.../arvados/v1/pipeline_instances_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 39 +------
services/api/app/mailers/admin_notifier.rb | 52 +++++----
services/api/app/models/job.rb | 19 ----
services/api/app/models/pipeline_instance.rb | 71 ++----------
services/api/app/models/user.rb | 10 +-
.../admin_notifier/after_create_user.text.erb | 7 --
.../admin_notifier/new_inactive_user.text.erb | 13 +++
.../api/app/views/admin_notifier/new_user.text.erb | 16 +++
.../app/views/pipeline_instances/index.html.erb | 4 +-
services/api/config/application.default.yml | 2 +
services/api/config/routes.rb | 2 -
...e_active_and_success_from_pipeline_instances.rb | 42 +++++++
services/api/db/schema.rb | 8 +-
.../test/integration/serialized_encoding_test.rb | 62 ++++++----
services/api/test/unit/pipeline_instance_test.rb | 43 +------
services/api/test/unit/user_test.rb | 105 +++++++++++++----
services/fuse/tests/test_mount.py | 7 +-
services/keep/src/keep/keep.go | 53 +++------
services/keep/src/keep/volume_unix.go | 14 +--
services/keep/tools/traffic_test.py | 126 +++++++++++++++++++++
62 files changed, 658 insertions(+), 555 deletions(-)
delete mode 100644 sdk/python/test_cmdline.py
rename sdk/python/tests/{test_arv-put.py => test_arv_put.py} (78%)
delete mode 100644 services/api/app/views/admin_notifier/after_create_user.text.erb
create mode 100644 services/api/app/views/admin_notifier/new_inactive_user.text.erb
create mode 100644 services/api/app/views/admin_notifier/new_user.text.erb
create mode 100644 services/api/db/migrate/20140602143352_remove_active_and_success_from_pipeline_instances.rb
create mode 100755 services/keep/tools/traffic_test.py
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commit 7df2da959b583d3646b9fde606f9e74d598d4bb9
Merge: 80ab788 20ffc96
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jun 5 11:17:59 2014 -0400
2872: Merge branch 'master' into 2872-folder-nav
Conflicts:
apps/workbench/app/controllers/application_controller.rb
apps/workbench/app/helpers/application_helper.rb
apps/workbench/app/models/authorized_key.rb
apps/workbench/app/models/job.rb
apps/workbench/app/models/pipeline_instance.rb
apps/workbench/app/models/user.rb
apps/workbench/app/models/virtual_machine.rb
diff --cc apps/workbench/app/assets/stylesheets/application.css.scss
index 75080a0,64c5098..8f377be
--- a/apps/workbench/app/assets/stylesheets/application.css.scss
+++ b/apps/workbench/app/assets/stylesheets/application.css.scss
@@@ -175,23 -171,26 +175,26 @@@ table.table-fixed-header-row tbody
z-index:1055;
}
-.navbar-nav.side-nav {
- box-shadow: inset -1px 0 #e7e7e7;
+/* Do not leave space for left-nav */
+div#wrapper {
+ padding-left: 0;
}
-.navbar-nav.side-nav > li:first-child {
- margin-top: 5px; /* keep "hover" bg below top nav bottom border */
+
+.arv-description-as-subtitle {
+ padding-bottom: 1em;
}
-.navbar-nav.side-nav > li > a {
- padding-top: 10px;
- padding-bottom: 10px;
+.arv-description-in-table {
+ max-height: 3.5em;
+ overflow-x: hidden;
+ overflow-y: hidden;
}
-.navbar-nav.side-nav > li.dropdown > ul.dropdown-menu > li > a {
- padding-top: 5px;
- padding-bottom: 5px;
+.arv-description-in-table:hover {
+ overflow-y: scroll;
}
-.navbar-nav.side-nav a.active,
-.navbar-nav.side-nav a:hover,
-.navbar-nav.side-nav a:focus {
- border-right: 1px solid #ffffff;
- background: #ffffff;
+
+.btn.btn-nodecorate {
+ border: none;
}
+ svg text {
+ font-size: 6pt;
-}
++}
commit 80ab788943653194282c6a61cebc871f7944958f
Author: Tom Clegg <tom at curoverse.com>
Date: Thu Jun 5 11:15:02 2014 -0400
2872: Make Show button say Show again. Fix links on collections index.
diff --git a/apps/workbench/app/views/application/_show_object_button.html.erb b/apps/workbench/app/views/application/_show_object_button.html.erb
index 4f6eb7e..762ff7c 100644
--- a/apps/workbench/app/views/application/_show_object_button.html.erb
+++ b/apps/workbench/app/views/application/_show_object_button.html.erb
@@ -1,13 +1,13 @@
<% htmloptions = {class: ''}.merge(htmloptions || {})
htmloptions[:class] += " btn-#{size}" rescue nil %>
<%= link_to_if_arvados_object object, {
- link_text: raw('<i class="fa fa-fw ' + fa_icon_class_for_object(object) + '"></i>'),
+ link_text: raw('<i class="fa fa-fw ' + fa_icon_class_for_object(object) + '"></i> Show'),
name_link: (defined?(name_link) && name_link && name_link.uuid) ? name_link : nil
}, {
data: {
toggle: 'tooltip',
placement: 'top'
},
- title: 'show',
- class: 'btn btn-default btn-nodecorate ' + htmloptions[:class],
+ title: 'show ' + object.class_for_display.downcase,
+ class: 'btn btn-default ' + htmloptions[:class],
} %>
diff --git a/apps/workbench/app/views/collections/_index_tbody.html.erb b/apps/workbench/app/views/collections/_index_tbody.html.erb
index 207ae13..deba78e 100644
--- a/apps/workbench/app/views/collections/_index_tbody.html.erb
+++ b/apps/workbench/app/views/collections/_index_tbody.html.erb
@@ -7,9 +7,11 @@
<% friendly_name += raw(" <span class='label label-info'>#{tag_link.name}</span>") %>
<% end %>
<%= render :partial => "selection_checkbox", :locals => {:object => c, :friendly_name => friendly_name} %>
+
+ <%= render :partial => "show_object_button", :locals => {object: c, size: 'xs'} %>
</td>
<td>
- <%= link_to_if_arvados_object c.uuid, {:no_tags => true } %>
+ <%= c.uuid %>
</td>
<td>
<% i = 0 %>
diff --git a/apps/workbench/app/views/collections/_show_recent.html.erb b/apps/workbench/app/views/collections/_show_recent.html.erb
index 2f4ab64..80640ad 100644
--- a/apps/workbench/app/views/collections/_show_recent.html.erb
+++ b/apps/workbench/app/views/collections/_show_recent.html.erb
@@ -21,10 +21,10 @@
<table id="collections-index" class="topalign table table-condensed table-fixedlayout"> <!-- table-fixed-header-row -->
<colgroup>
- <col width="4%" />
+ <col width="8%" />
<col width="10%" />
<col width="34%" />
- <col width="15%" />
+ <col width="11%" />
<col width="12%" />
<col width="29%" />
</colgroup>
diff --git a/apps/workbench/test/integration/users_test.rb b/apps/workbench/test/integration/users_test.rb
index b7bb49a..f5f66ec 100644
--- a/apps/workbench/test/integration/users_test.rb
+++ b/apps/workbench/test/integration/users_test.rb
@@ -25,7 +25,7 @@ class UsersTest < ActionDispatch::IntegrationTest
end
find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
- find('a[data-original-title=show]').
+ find('a', text: 'Show').
click
assert page.has_text? 'Attributes'
assert page.has_text? 'Metadata'
@@ -80,7 +80,7 @@ class UsersTest < ActionDispatch::IntegrationTest
# go to the new user's page
find('tr', text: new_user_uuid).
- find('a[data-original-title=show]').
+ find('a', text: 'Show').
click
assert page.has_text? 'modified_by_user_uuid'
@@ -107,7 +107,7 @@ class UsersTest < ActionDispatch::IntegrationTest
# click on active user
find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
- find('a[data-original-title=show]').
+ find('a', text: 'Show').
click
# Setup user
@@ -167,7 +167,7 @@ class UsersTest < ActionDispatch::IntegrationTest
# click on active user
find('tr', text: 'zzzzz-tpzed-xurymjxw79nv3jz').
- find('a[data-original-title=show]').
+ find('a', text: 'Show').
click
# Verify that is_active is set
commit 3792301ffcc75954caa41d5cc90abed465fbaf86
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 16:21:32 2014 -0400
2872: Fix breadcrumbs on pipeline instance compare page.
diff --git a/apps/workbench/app/controllers/pipeline_instances_controller.rb b/apps/workbench/app/controllers/pipeline_instances_controller.rb
index 4275410..076f4aa 100644
--- a/apps/workbench/app/controllers/pipeline_instances_controller.rb
+++ b/apps/workbench/app/controllers/pipeline_instances_controller.rb
@@ -175,6 +175,7 @@ class PipelineInstancesController < ApplicationController
:combine_jobs => :script_and_version,
:script_version_nodes => true,
:pips => pips }
+ @object = @objects.first
end
def show_pane_list
diff --git a/apps/workbench/app/views/pipeline_instances/_show_compare.html.erb b/apps/workbench/app/views/pipeline_instances/_show_compare.html.erb
index 53cd6b3..018384b 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_compare.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_compare.html.erb
@@ -20,9 +20,10 @@
</div>
<% @objects.each do |object| %>
<div class="col-sm-<%= pi_span %>" style="overflow-x: hidden; text-overflow: ellipsis;">
- <%= link_to_if_arvados_object object, friendly_name: true %>
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'sm' } %>
+ <%= object.name || "unnamed #{object.class_for_display.downcase}" %>
<br />
- Template: <%= link_to_if_arvados_object object.pipeline_template_uuid, friendly_name: true %>
+ <span class="deemphasize">Template:</span> <%= link_to_if_arvados_object object.pipeline_template_uuid, friendly_name: true %>
</div>
<% end %>
</div>
diff --git a/apps/workbench/app/views/pipeline_instances/compare.html.erb b/apps/workbench/app/views/pipeline_instances/compare.html.erb
index 9e8d1e5..953c098 100644
--- a/apps/workbench/app/views/pipeline_instances/compare.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/compare.html.erb
@@ -1 +1,15 @@
+<% if (o = Group.find?(@objects.first.owner_uuid)) %>
+ <% content_for :breadcrumbs do %>
+ <li class="nav-separator"><span class="glyphicon glyphicon-arrow-right"></span></li>
+ <li>
+ <%= link_to(o.name, folder_path(o.uuid)) %>
+ </li>
+ <li class="nav-separator">
+ <span class="glyphicon glyphicon-arrow-right"></span>
+ </li>
+ <li>
+ <%= link_to '#' do %>compare pipelines<% end %>
+ </li>
+ <% end %>
+<% end %>
<%= render partial: 'content', layout: 'content_layout', locals: {pane_list: controller.compare_pane_list } %>
commit 7f1e9f495fd2e335af08d7be54fb71eee6324421
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 16:08:49 2014 -0400
2872: Fix links to collections from folder view.
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 2d7995e..e23376b 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -124,7 +124,7 @@ module ApplicationHelper
if opts[:no_link]
raw(link_name)
else
- link_to raw(link_name), { controller: resource_class.to_s.tableize, action: 'show', id: link_uuid }, style_opts
+ link_to raw(link_name), { controller: resource_class.to_s.tableize, action: 'show', id: ((opts[:name_link].andand.uuid) || link_uuid) }, style_opts
end
else
# just return attrvalue if it is not recognizable as an Arvados object or uuid.
diff --git a/apps/workbench/app/views/application/_show_object_button.html.erb b/apps/workbench/app/views/application/_show_object_button.html.erb
index 17e9737..4f6eb7e 100644
--- a/apps/workbench/app/views/application/_show_object_button.html.erb
+++ b/apps/workbench/app/views/application/_show_object_button.html.erb
@@ -1,12 +1,13 @@
<% htmloptions = {class: ''}.merge(htmloptions || {})
htmloptions[:class] += " btn-#{size}" rescue nil %>
<%= link_to_if_arvados_object object, {
- link_text: raw('<i class="fa fa-fw ' + fa_icon_class_for_object(object) + '"></i>')
+ link_text: raw('<i class="fa fa-fw ' + fa_icon_class_for_object(object) + '"></i>'),
+ name_link: (defined?(name_link) && name_link && name_link.uuid) ? name_link : nil
}, {
data: {
toggle: 'tooltip',
placement: 'top'
},
title: 'show',
- class: 'btn btn-default btn-nodecorate ' + htmloptions[:class]
+ class: 'btn btn-default btn-nodecorate ' + htmloptions[:class],
} %>
diff --git a/apps/workbench/app/views/folders/_show_contents_rows.html.erb b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
index 68fe048..3c64b53 100644
--- a/apps/workbench/app/views/folders/_show_contents_rows.html.erb
+++ b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
@@ -15,7 +15,7 @@
<i class="fa fa-fw"></i><%# placeholder %>
<% end %>
- <%= render :partial => "show_object_button", :locals => {object: object, size: 'sm'} %>
+ <%= render :partial => "show_object_button", :locals => {object: object, size: 'sm', name_link: name_link} %>
<%= render_editable_attribute (name_link || object), 'name', nil, {btnplacement: :left, tiptitle: 'rename'} %>
</td>
commit a78b72118fba71b880194f04ed06007fdfb58743
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 15:13:32 2014 -0400
2872: Do not try to add name links for objects that have their own names
diff --git a/apps/workbench/app/controllers/folders_controller.rb b/apps/workbench/app/controllers/folders_controller.rb
index 000cbc9..ab7dcec 100644
--- a/apps/workbench/app/controllers/folders_controller.rb
+++ b/apps/workbench/app/controllers/folders_controller.rb
@@ -102,6 +102,8 @@ class FoldersController < ApplicationController
name_links.each do |name_link|
@objects_and_names << [object, name_link]
end
+ elsif object.respond_to? :name
+ @objects_and_names << [object, object]
else
@objects_and_names << [object,
Link.new(owner_uuid: @object.uuid,
commit 918cf0b4e26b6149510bf72194be19b40121437d
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 15:12:50 2014 -0400
2872: Fix syntax
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 016cd1a..354ebd2 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
@@ -8,8 +8,8 @@
<% component[:script_parameters].andand.each do |pname, pvalue_spec| %>
<% if pvalue_spec.is_a? Hash %>
<% if (pvalue_spec[:description] or
- ((pvalue_spec[:required] or pvalue_spec[:optional] == false)
- and not pvalue_spec[:value])) %>
+ ((pvalue_spec[:required] or pvalue_spec[:optional] == false) and
+ not pvalue_spec[:value])) %>
<% n_inputs += 1 %>
<label for="<% "#{cname}-#{pname}" %>">
<%= pvalue_spec[:title] ||
commit 4a3301617ae09e6b28c7b6fd79923ccd60b6b5e9
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 14:43:48 2014 -0400
2872: Fix up log message display on pipeline instance page.
diff --git a/apps/workbench/app/assets/javascripts/pipeline_instances.js b/apps/workbench/app/assets/javascripts/pipeline_instances.js
index 614f45f..4b17b4e 100644
--- a/apps/workbench/app/assets/javascripts/pipeline_instances.js
+++ b/apps/workbench/app/assets/javascripts/pipeline_instances.js
@@ -57,20 +57,26 @@ $(document).on('ajax:complete ready', function() {
});
$(document).on('arv-log-event', '.arv-log-event-handler-append-logs', function(event, eventData){
- parsedData = JSON.parse(eventData);
+ var wasatbottom = ($(this).scrollTop() + $(this).height() >=
+ this.scrollHeight);
+ var parsedData = JSON.parse(eventData);
+ var propertyText = undefined;
+ var properties = parsedData.properties;
- propertyText = undefined
-
- properties = parsedData.properties;
if (properties !== null) {
- propertyText = properties.text;
+ propertyText = properties.text;
}
-
if (propertyText !== undefined) {
- $(this).append(propertyText + "<br/>");
+ $(this).append(propertyText + "<br/>");
} else {
- $(this).append(parsedData.summary + "<br/>");
+ $(this).append(parsedData.summary + "<br/>");
}
+ if (wasatbottom)
+ this.scrollTop = this.scrollHeight;
+}).on('ready ajax:complete', function(){
+ $('.arv-log-event-handler-append-logs').each(function() {
+ this.scrollTop = this.scrollHeight;
+ });
});
var showhide_compare = function() {
diff --git a/apps/workbench/app/assets/stylesheets/jobs.css.scss b/apps/workbench/app/assets/stylesheets/jobs.css.scss
index e485745..14f8699 100644
--- a/apps/workbench/app/assets/stylesheets/jobs.css.scss
+++ b/apps/workbench/app/assets/stylesheets/jobs.css.scss
@@ -1,3 +1,10 @@
-// Place all the styles related to the Jobs controller here.
-// They will automatically be included in application.css.
-// You can use Sass (SCSS) here: http://sass-lang.com/
+.arv-job-log-window {
+ height: 20em;
+ white-space: nowrap;
+ overflow: scroll;
+ background: black;
+ color: white;
+ font-family: monospace;
+ font-size: .8em;
+ border: 2px solid black;
+}
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 efd36d2..d0fcbc9 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_components.html.erb
@@ -121,12 +121,11 @@
<% if !pipeline_job_uuids.empty? %>
<h4>Log messages from running jobs</h4>
<% log_history = pipeline_log_history(pipeline_job_uuids) %>
- <div id="pipeline_event_log_history_div">
+ <div class="arv-log-event-listener arv-log-event-handler-append-logs arv-job-log-window" id="pipeline_event_log_div" data-object-uuids="<%=pipeline_job_uuids.join(" ")%>">
<% log_history.each do |entry| %>
<%=entry%><br/>
<% end %>
</div>
- <div class="arv-log-event-listener arv-log-event-handler-append-logs" id="pipeline_event_log_div" data-object-uuids="<%=pipeline_job_uuids.join(" ")%>"/>
<% end %>
<% end %>
commit 25b1840819d60ed2cb6cb669921a6c3d9eba3f10
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 14:40:19 2014 -0400
2872: Check "optional" flag too when looking for required inputs.
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 5a86728..016cd1a 100644
--- a/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
+++ b/apps/workbench/app/views/pipeline_instances/_show_inputs.html.erb
@@ -8,7 +8,8 @@
<% component[:script_parameters].andand.each do |pname, pvalue_spec| %>
<% if pvalue_spec.is_a? Hash %>
<% if (pvalue_spec[:description] or
- (pvalue_spec[:required] and not pvalue_spec[:value])) %>
+ ((pvalue_spec[:required] or pvalue_spec[:optional] == false)
+ and not pvalue_spec[:value])) %>
<% n_inputs += 1 %>
<label for="<% "#{cname}-#{pname}" %>">
<%= pvalue_spec[:title] ||
commit 72b85b3144ca23e2c3337e38960dec9a0aec0ff8
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 13:18:41 2014 -0400
2872: Fix empty name placeholders.
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 9921775..2d7995e 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -137,7 +137,9 @@ module ApplicationHelper
if !object.attribute_editable?(attr, :ever) or
(!object.editable? and
!object.owner_uuid.in?(my_folders.collect(&:uuid)))
- return attrvalue
+ return ((attrvalue && attrvalue.length > 0 && attrvalue) ||
+ (attr == 'name' and object.andand.default_name) ||
+ '(none)')
end
input_type = 'text'
diff --git a/apps/workbench/app/views/folders/_show_contents_rows.html.erb b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
index 8ecf8d3..68fe048 100644
--- a/apps/workbench/app/views/folders/_show_contents_rows.html.erb
+++ b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
@@ -17,7 +17,7 @@
<%= render :partial => "show_object_button", :locals => {object: object, size: 'sm'} %>
- <%= render_editable_attribute name_object, 'name', nil, {btnplacement: :left, tiptitle: 'rename'} %>
+ <%= render_editable_attribute (name_link || object), 'name', nil, {btnplacement: :left, tiptitle: 'rename'} %>
</td>
<td class="arv-description-in-table">
<%= render_controller_partial(
commit 811beeab989c5b8704ba78bcd365e7caf71bc615
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 11:14:39 2014 -0400
2872: Fix crash on missing object.
diff --git a/apps/workbench/app/views/collections/_choose_rows.html.erb b/apps/workbench/app/views/collections/_choose_rows.html.erb
index d488743..650a8c8 100644
--- a/apps/workbench/app/views/collections/_choose_rows.html.erb
+++ b/apps/workbench/app/views/collections/_choose_rows.html.erb
@@ -1,15 +1,17 @@
<% @name_links.each do |name_link| %>
- <div class="row filterable selectable <%= 'multiple' if multiple %>" data-object-uuid="<%= name_link.uuid %>">
- <div class="col-sm-12" style="overflow-x:hidden">
- <i class="fa fa-fw fa-archive"></i>
- <%= name_link.name %>
+ <% if (object = get_object(name_link.head_uuid)) %>
+ <div class="row filterable selectable <%= 'multiple' if multiple %>" data-object-uuid="<%= name_link.uuid %>">
+ <div class="col-sm-12" style="overflow-x:hidden">
+ <i class="fa fa-fw fa-archive"></i>
+ <%= name_link.name %>
+ </div>
+ <div class="col-sm-11 col-sm-push-1" style="overflow-x: hidden">
+ <%= render_controller_partial(
+ 'show_object_description_cell.html',
+ controller_name: 'collections',
+ locals: {object: object})
+ %>
+ </div>
</div>
- <div class="col-sm-11 col-sm-push-1" style="overflow-x: hidden">
- <%= render_controller_partial(
- 'show_object_description_cell.html',
- controller_name: 'collections',
- locals: {object: get_object(name_link.head_uuid)})
- %>
- </div>
- </div>
+ <% end %>
<% end %>
commit 5abef879fabdff46472e8f34def5d3b0cd332e99
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 11:09:11 2014 -0400
2872: Fix total_bytes returning nil.
diff --git a/apps/workbench/app/models/collection.rb b/apps/workbench/app/models/collection.rb
index 4f4a790..2825618 100644
--- a/apps/workbench/app/models/collection.rb
+++ b/apps/workbench/app/models/collection.rb
@@ -21,6 +21,8 @@ class Collection < ArvadosBase
tot += file[2]
end
tot
+ else
+ 0
end
end
commit a35f886c9a2ca73b55fcb21ca37bf1fa2a3a6fc2
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 10:18:54 2014 -0400
2872: Treat HEAD same as GET in case we are behind a proxy.
diff --git a/apps/workbench/app/controllers/application_controller.rb b/apps/workbench/app/controllers/application_controller.rb
index 1fcfc3a..a5034fd 100644
--- a/apps/workbench/app/controllers/application_controller.rb
+++ b/apps/workbench/app/controllers/application_controller.rb
@@ -118,7 +118,7 @@ class ApplicationController < ActionController::Base
respond_to do |f|
f.json { render json: @object.attributes.merge(href: url_for(@object)) }
f.html {
- if request.method == 'GET'
+ if request.method.in? ['GET', 'HEAD']
render
else
redirect_to params[:return_to] || @object
@@ -255,7 +255,7 @@ class ApplicationController < ActionController::Base
def redirect_to_login
respond_to do |f|
f.html {
- if request.method == 'GET'
+ if request.method.in? ['GET', 'HEAD']
redirect_to arvados_api_client.arvados_login_url(return_to: request.url)
else
flash[:error] = "Either you are not logged in, or your session has timed out. I can't automatically log you in and re-attempt this request."
@@ -325,7 +325,7 @@ class ApplicationController < ActionController::Base
# call to verify its authenticity.
if verify_api_token
session[:arvados_api_token] = params[:api_token]
- if !request.format.json? and request.method == 'GET'
+ if !request.format.json? and request.method.in? ['GET', 'HEAD']
# Repeat this request with api_token in the (new) session
# cookie instead of the query string. This prevents API
# tokens from appearing in (and being inadvisedly copied
commit 70d7acb63d1f66fdde384e4bc7bfe439fe8abc35
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 05:01:20 2014 -0400
2872: Filter by tail instead of owner in case api server rule is not in yet.
diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index 5eed7f8..9921775 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -254,7 +254,7 @@ module ApplicationHelper
end
modal_path = choose_collections_path \
({ title: 'Choose a dataset:',
- filters: [['owner_uuid', '=', object.owner_uuid]].to_json,
+ filters: [['tail_uuid', '=', object.owner_uuid]].to_json,
action_name: 'OK',
action_href: pipeline_instance_path(id: object.uuid),
action_method: 'patch',
commit d9814c9f51b177b15345bf4429baa2ce3b986a57
Author: Tom Clegg <tom at curoverse.com>
Date: Tue Jun 3 04:51:28 2014 -0400
2872: Ensure friendly_name is always a string.
diff --git a/apps/workbench/app/views/folders/_show_contents_rows.html.erb b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
index 1cdd48f..8ecf8d3 100644
--- a/apps/workbench/app/views/folders/_show_contents_rows.html.erb
+++ b/apps/workbench/app/views/folders/_show_contents_rows.html.erb
@@ -5,7 +5,7 @@
data-kind="<%= object.kind %>"
>
<td>
- <%= render partial: 'selection_checkbox', locals: {object: object, friendly_name: (name_object.name rescue nil)} %>
+ <%= render partial: 'selection_checkbox', locals: {object: object, friendly_name: ((name_object.name rescue '') || '')} %>
<% if folder.editable? %>
<%= link_to({action: 'remove_item', id: folder.uuid, item_uuid: ((name_link && name_link.uuid) || object.uuid)}, method: :delete, remote: true, data: {confirm: "Remove #{object.class_for_display.downcase} #{name_object.name rescue object.uuid} from this folder?", toggle: 'tooltip', placement: 'top'}, class: 'btn btn-sm btn-default btn-nodecorate', title: 'remove') do %>
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