[ARVADOS] updated: ff7803d40cbfbf47a348d4e4eec7d6e48742bbeb
git at public.curoverse.com
git at public.curoverse.com
Thu Mar 6 17:09:08 EST 2014
Summary of changes:
apps/admin/setup-new-user.rb | 6 ++--
apps/workbench/app/assets/javascripts/selection.js | 9 +-----
.../app/assets/stylesheets/application.css.scss | 2 +-
.../app/controllers/actions_controller.rb | 12 +++++++++
apps/workbench/app/helpers/provenance_helper.rb | 8 ++++--
apps/workbench/app/views/users/_tables.html.erb | 25 ++++++++++++++++++-
doc/Rakefile | 2 +-
doc/_config.yml | 11 +++++++-
doc/_includes/_navbar_top.liquid | 10 ++++----
doc/_includes/_parallel_hash_script_py.liquid | 2 +-
doc/install/install-api-server.html.md.liquid | 12 +++++----
.../install-crunch-dispatch.html.textile.liquid | 8 ++++++
doc/sdk/python/sdk-python.html.textile.liquid | 2 +-
.../check-environment.html.textile.liquid | 6 ++--
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
doc/user/reference/sdk-cli.html.textile.liquid | 6 +++-
.../running-external-program.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 7 ++++-
...rial-gatk-variantfiltration.html.textile.liquid | 4 +-
.../tutorial-job-debug.html.textile.liquid | 2 +-
.../tutorials/tutorial-job1.html.textile.liquid | 4 +-
.../tutorials/tutorial-keep.html.textile.liquid | 2 +-
.../tutorial-new-pipeline.html.textile.liquid | 8 +++---
.../tutorial-parallel.html.textile.liquid | 5 +++-
.../tutorial-trait-search.html.textile.liquid | 2 +-
sdk/cli/bin/crunch-job | 26 ++++++++++---------
sdk/python/arvados/fuse.py | 1 -
sdk/python/bin/arv-mount | 3 +-
sdk/ruby/Gemfile.lock | 8 +++---
.../app/controllers/arvados/v1/jobs_controller.rb | 1 +
.../api/test/integration/collections_api_test.rb | 4 ---
services/api/test/integration/jobs_api_test.rb | 23 +++++++++++++++++
services/api/test/test_helper.rb | 6 ++++
33 files changed, 158 insertions(+), 73 deletions(-)
create mode 100644 services/api/test/integration/jobs_api_test.rb
via ff7803d40cbfbf47a348d4e4eec7d6e48742bbeb (commit)
via 9ba66dcc4f4c166fa08512ce0c75e324f26c7b0d (commit)
via 51f56533f4a1dd871551c4c85720a435b874c87f (commit)
via 2133a90a7c31358a025a4ce68385a38954750c3f (commit)
via 45741702d88801640ca6c59269edb610dc2b6071 (commit)
via cad44d1dbfdd2cbadba521a88c0817b144dd1d6b (commit)
via 7722719387453c7ab5f9326536daa2655cad60c9 (commit)
via 198d4c115e1958e1d9779e58548b8276cae244a8 (commit)
via 63511ce5f1dc6d6e38cfafe240f0c907ad11748e (commit)
via 9c3dd1f301b78d556b9d06c81a01c4b4446803ff (commit)
via 6c2b15626cff7c94b0727ab6f3eac7dfde56b6ed (commit)
via e60990e8ccc42495fb8ec1afe53bb47b1b604866 (commit)
via 2bf9aeb2508a6f61518bf838390e31e07e9fe0e1 (commit)
via d1b3c09b51e11a26ac7e735805b79fa4668bbaff (commit)
via 94eca7452812a90d68dd29dc62fe2ac5c5157568 (commit)
via 9a124cfd453548bb447df9513f72809a1fba0433 (commit)
via f96533820a514a36c618c8343d4b6320c7c31cf6 (commit)
via 2abf7fca110acf699645f45025b62608d287bdd4 (commit)
via 06362e4d206c4765567e0a6b5585197ce0c9d30f (commit)
via 342f1555625580dc945766a48bb7be3625af2deb (commit)
via 4f6d03f8329ec63704f6830c56b95be939b38d30 (commit)
via 1b8615efd89707d02ea9de1d95e9e2a26b0436cc (commit)
from 38b9c64d051ebf0d1e430c498249caf608dcce2f (commit)
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commit ff7803d40cbfbf47a348d4e4eec7d6e48742bbeb
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 6 17:10:22 2014 -0500
Fixed bug when selection list was cleared.
Fixed rendering collections in provenance graph.
diff --git a/apps/workbench/app/assets/javascripts/selection.js b/apps/workbench/app/assets/javascripts/selection.js
index ef1c592..c94a557 100644
--- a/apps/workbench/app/assets/javascripts/selection.js
+++ b/apps/workbench/app/assets/javascripts/selection.js
@@ -48,18 +48,14 @@ jQuery(function($){
update_count();
}
- var combine_selected_files_into_collection = function () {
-
- }
-
var update_count = function(e) {
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>');
+
for (var i = 0; i < lst.length; i++) {
$('#selection-form-content > li > table').append("<tr>"
+ "<td>"
@@ -77,7 +73,7 @@ jQuery(function($){
+ "</tr>");
}
} else {
- $('#persistent-selection-list').html("<li class='notification empty'>No selections.</li>");
+ $('#selection-form-content').html("<li class='notification empty'>No selections.</li>");
}
var checkboxes = $('.persistent-selection:checkbox');
@@ -95,7 +91,6 @@ jQuery(function($){
$('.remove-selection').on('click', remove_selection_click);
$('#clear_selections_button').on('click', clear_selections);
- $('#combine_selected_files_into_collection').on('click', combine_selected_files_into_collection);
};
$(document).
diff --git a/apps/workbench/app/controllers/actions_controller.rb b/apps/workbench/app/controllers/actions_controller.rb
index 6f5ed60..c443c21 100644
--- a/apps/workbench/app/controllers/actions_controller.rb
+++ b/apps/workbench/app/controllers/actions_controller.rb
@@ -71,6 +71,18 @@ class ActionsController < ApplicationController
newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
newc.save!
+ chash.each do |k,v|
+ l = Link.new({
+ tail_kind: "arvados#Collection",
+ tail_uuid: k,
+ head_kind: "arvados#Collection",
+ head_uuid: newuuid,
+ link_class: "provenance",
+ name: "provided"
+ })
+ l.save!
+ end
+
'/collections/' + newc.uuid
end
diff --git a/apps/workbench/app/helpers/provenance_helper.rb b/apps/workbench/app/helpers/provenance_helper.rb
index 8278d37..fced9da 100644
--- a/apps/workbench/app/helpers/provenance_helper.rb
+++ b/apps/workbench/app/helpers/provenance_helper.rb
@@ -11,9 +11,11 @@ module ProvenanceHelper
def self.collection_uuid(uuid)
m = CollectionsHelper.match(uuid)
if m
- #if m[2]
- return m[1]
- #else
+ if m[2]
+ return m[1]+m[2]
+ else
+ return m[1]
+ end
# Collection.where(uuid: ['contains', m[1]]).each do |u|
# puts "fixup #{uuid} to #{u.uuid}"
# return u.uuid
commit 9ba66dcc4f4c166fa08512ce0c75e324f26c7b0d
Merge: 38b9c64 51f5653
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Mar 6 15:55:19 2014 -0500
Merge remote-tracking branch 'origin/master' into 2042-new-collection-from-selected-files
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