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Merge staging for release
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@jvendetti
jvendetti committed Sep 13, 2018
2 parents 5aff0e1 + 5c5a230 commit 263be71
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Showing 83 changed files with 2,518 additions and 3,327 deletions.
9 changes: 4 additions & 5 deletions Gemfile
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@@ -1,7 +1,7 @@
source 'https://rubygems.org'

# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '4.2.6'
gem 'rails', '4.2.10'

gem 'sass-rails', '~> 5.0'
gem 'coffee-rails', '~> 4.1.0'
Expand All @@ -12,8 +12,7 @@ gem 'uglifier', '>= 1.0.3'

gem 'jquery-ui-rails'
gem 'jquery-rails'
gem 'bootstrap-sass', '~> 3.3.7'
gem 'font-awesome-sass', '~> 4.7.0'
gem 'bootstrap', '~> 4.1.0'
gem 'chart-js-rails'
gem 'select2-rails'

Expand All @@ -30,7 +29,7 @@ gem "pry"
gem "iconv"
gem "recaptcha", "= 0.4.0"
gem "rest-client", "~> 1.8.0"
gem "mysql", "~> 2.9.1"
gem "mysql2", "~> 0.4.0"
gem "i18n", "~> 0"
gem "haml", "~> 4.0.0"
gem "will_paginate", "~> 3.0"
Expand Down Expand Up @@ -70,5 +69,5 @@ group :development do
# passenger reload
gem 'capistrano-passenger', require: false
gem 'html2haml'
gem 'i18n-debug'
# gem 'i18n-debug'
end
125 changes: 60 additions & 65 deletions Gemfile.lock
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Expand Up @@ -24,49 +24,49 @@ GIT
GEM
remote: https://rubygems.org/
specs:
actionmailer (4.2.6)
actionpack (= 4.2.6)
actionview (= 4.2.6)
activejob (= 4.2.6)
actionmailer (4.2.10)
actionpack (= 4.2.10)
actionview (= 4.2.10)
activejob (= 4.2.10)
mail (~> 2.5, >= 2.5.4)
rails-dom-testing (~> 1.0, >= 1.0.5)
actionpack (4.2.6)
actionview (= 4.2.6)
activesupport (= 4.2.6)
actionpack (4.2.10)
actionview (= 4.2.10)
activesupport (= 4.2.10)
rack (~> 1.6)
rack-test (~> 0.6.2)
rails-dom-testing (~> 1.0, >= 1.0.5)
rails-html-sanitizer (~> 1.0, >= 1.0.2)
actionview (4.2.6)
activesupport (= 4.2.6)
actionview (4.2.10)
activesupport (= 4.2.10)
builder (~> 3.1)
erubis (~> 2.7.0)
rails-dom-testing (~> 1.0, >= 1.0.5)
rails-html-sanitizer (~> 1.0, >= 1.0.2)
activejob (4.2.6)
activesupport (= 4.2.6)
rails-html-sanitizer (~> 1.0, >= 1.0.3)
activejob (4.2.10)
activesupport (= 4.2.10)
globalid (>= 0.3.0)
activemodel (4.2.6)
activesupport (= 4.2.6)
activemodel (4.2.10)
activesupport (= 4.2.10)
builder (~> 3.1)
activerecord (4.2.6)
activemodel (= 4.2.6)
activesupport (= 4.2.6)
activerecord (4.2.10)
activemodel (= 4.2.10)
activesupport (= 4.2.10)
arel (~> 6.0)
activesupport (4.2.6)
activesupport (4.2.10)
i18n (~> 0.7)
json (~> 1.7, >= 1.7.7)
minitest (~> 5.1)
thread_safe (~> 0.3, >= 0.3.4)
tzinfo (~> 1.1)
airbrussh (1.3.0)
sshkit (>= 1.6.1, != 1.7.0)
arel (6.0.4)
autoprefixer-rails (8.3.0)
autoprefixer-rails (9.1.4)
execjs
bootstrap-sass (3.3.7)
autoprefixer-rails (>= 5.2.1)
sass (>= 3.3.4)
bootstrap (4.1.3)
autoprefixer-rails (>= 6.0.3)
popper_js (>= 1.12.9, < 2)
sass (>= 3.5.2)
builder (3.2.3)
capistrano (3.8.2)
airbrussh (>= 1.0.0)
Expand All @@ -83,7 +83,7 @@ GEM
capistrano-rails (1.1.8)
capistrano (~> 3.1)
capistrano-bundler (~> 1.1)
chart-js-rails (0.1.4)
chart-js-rails (0.1.6)
railties (> 3.1)
coderay (1.1.2)
coffee-rails (4.1.1)
Expand All @@ -98,18 +98,16 @@ GEM
cube-ruby (0.0.3)
daemons (1.2.6)
dalli (2.7.8)
domain_name (0.5.20170404)
domain_name (0.5.20180417)
unf (>= 0.0.5, < 1.0.0)
erubis (2.7.0)
eventmachine (1.2.5)
eventmachine (1.2.7)
excon (0.62.0)
execjs (2.7.0)
faraday (0.14.0)
faraday (0.15.2)
multipart-post (>= 1.2, < 3)
ffi (1.9.23)
ffi (1.9.25)
flamegraph (0.9.5)
font-awesome-sass (4.7.0)
sass (>= 3.2)
globalid (0.4.1)
activesupport (>= 4.2.0)
haml (4.0.7)
Expand All @@ -123,16 +121,13 @@ GEM
domain_name (~> 0.5)
i18n (0.9.5)
concurrent-ruby (~> 1.0)
i18n-debug (1.1.1)
i18n (< 2)
iconv (1.0.5)
jquery-rails (4.3.1)
jquery-rails (4.3.3)
rails-dom-testing (>= 1, < 3)
railties (>= 4.2.0)
thor (>= 0.14, < 2.0)
jquery-ui-rails (6.0.1)
railties (>= 3.2.16)
json (1.8.6)
logstash-event (1.1.5)
logstash-logger (0.3.0)
logstash-event
Expand All @@ -144,39 +139,40 @@ GEM
mini_mime (>= 0.1.1)
method_source (0.9.0)
mime-types (2.99.3)
mini_mime (1.0.0)
mini_mime (1.0.1)
mini_portile2 (2.3.0)
minitest (5.11.3)
multi_json (1.13.1)
multipart-post (2.0.0)
mysql (2.9.1)
mysql2 (0.4.10)
net-scp (1.2.1)
net-ssh (>= 2.6.5)
net-ssh (4.2.0)
net-ssh (5.0.2)
netrc (0.11.0)
newrelic_rpm (5.0.0.342)
nokogiri (1.8.2)
newrelic_rpm (5.4.0.347)
nokogiri (1.8.4)
mini_portile2 (~> 2.3.0)
oj (3.5.1)
oj (3.6.10)
open_uri_redirections (0.2.1)
popper_js (1.14.3)
pry (0.11.3)
coderay (~> 1.1.0)
method_source (~> 0.9.0)
rack (1.6.9)
rack (1.6.10)
rack-mini-profiler (1.0.0)
rack (>= 1.2.0)
rack-test (0.6.3)
rack (>= 1.0)
rails (4.2.6)
actionmailer (= 4.2.6)
actionpack (= 4.2.6)
actionview (= 4.2.6)
activejob (= 4.2.6)
activemodel (= 4.2.6)
activerecord (= 4.2.6)
activesupport (= 4.2.6)
rails (4.2.10)
actionmailer (= 4.2.10)
actionpack (= 4.2.10)
actionview (= 4.2.10)
activejob (= 4.2.10)
activemodel (= 4.2.10)
activerecord (= 4.2.10)
activesupport (= 4.2.10)
bundler (>= 1.3.0, < 2.0)
railties (= 4.2.6)
railties (= 4.2.10)
sprockets-rails
rails-deprecated_sanitizer (1.0.3)
activesupport (>= 4.2.0.alpha)
Expand All @@ -188,24 +184,24 @@ GEM
loofah (~> 2.2, >= 2.2.2)
rails_autolink (1.1.6)
rails (> 3.1)
railties (4.2.6)
actionpack (= 4.2.6)
activesupport (= 4.2.6)
railties (4.2.10)
actionpack (= 4.2.10)
activesupport (= 4.2.10)
rake (>= 0.8.7)
thor (>= 0.18.1, < 2.0)
rake (12.3.1)
rb-fsevent (0.10.3)
rb-inotify (0.9.10)
ffi (>= 0.5.0, < 2)
rdoc (6.0.3)
rdoc (6.0.4)
recaptcha (0.4.0)
rest-client (1.8.0)
http-cookie (>= 1.0.2, < 2.0)
mime-types (>= 1.16, < 3.0)
netrc (~> 0.7)
ruby_parser (3.11.0)
sexp_processor (~> 4.9)
sass (3.5.6)
sass (3.5.7)
sass-listen (~> 4.0.0)
sass-listen (4.0.0)
rb-fsevent (~> 0.9, >= 0.9.4)
Expand All @@ -220,17 +216,17 @@ GEM
thor (~> 0.14)
sexp_processor (4.11.0)
spawnling (2.1.6)
sprockets (3.7.1)
sprockets (3.7.2)
concurrent-ruby (~> 1.0)
rack (> 1, < 3)
sprockets-rails (3.2.1)
actionpack (>= 4.0)
activesupport (>= 4.0)
sprockets (>= 3.0.0)
sshkit (1.16.0)
sshkit (1.17.0)
net-scp (>= 1.1.2)
net-ssh (>= 2.8.0)
stackprof (0.2.11)
stackprof (0.2.12)
thin (1.7.2)
daemons (~> 1.0, >= 1.0.9)
eventmachine (~> 1.0, >= 1.0.4)
Expand All @@ -240,7 +236,7 @@ GEM
tilt (2.0.8)
tzinfo (1.2.5)
thread_safe (~> 0.1)
uglifier (4.1.9)
uglifier (4.1.19)
execjs (>= 0.3.0, < 3)
unf (0.1.4)
unf_ext
Expand All @@ -250,9 +246,10 @@ GEM
PLATFORMS
ruby
x86_64-darwin-16
x86_64-darwin-17

DEPENDENCIES
bootstrap-sass (~> 3.3.7)
bootstrap (~> 4.1.0)
capistrano (~> 3.8.2)
capistrano-bundler
capistrano-locally
Expand All @@ -263,17 +260,15 @@ DEPENDENCIES
cube-ruby
dalli
flamegraph
font-awesome-sass (~> 4.7.0)
haml (~> 4.0.0)
html2haml
i18n (~> 0)
i18n-debug
iconv
jquery-rails
jquery-ui-rails
logstash-logger
multi_json
mysql (~> 2.9.1)
mysql2 (~> 0.4.0)
newrelic_rpm
nokogiri
oj
Expand All @@ -282,7 +277,7 @@ DEPENDENCIES
pry
rack-mini-profiler
rackstash!
rails (= 4.2.6)
rails (= 4.2.10)
rails_autolink
rdoc
recaptcha (= 0.4.0)
Expand All @@ -295,4 +290,4 @@ DEPENDENCIES
will_paginate (~> 3.0)

BUNDLED WITH
1.16.0
1.16.3
1 change: 1 addition & 0 deletions app/assets/javascripts/application.js
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Expand Up @@ -29,6 +29,7 @@
//= require bp_recommender
//= require bp_property_tree
//= require bp_ont_chart
//= require home
//= require projects
//= require submissions

2 changes: 1 addition & 1 deletion app/assets/javascripts/bioportal.js.erb
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Expand Up @@ -528,7 +528,7 @@ function bpPopWindow(e) {
newWindow.focus()
};
}
jQuery("div.footer-support, ul.dropdown-menu.support-menu").on("click", "a.pop_window", { w: "800", h: "600" }, bpPopWindow)
jQuery("div.footer-support, div.dropdown-menu.dropdown-menu-right").on("click", "a.pop_window", { w: "800", h: "600" }, bpPopWindow)

/**************************************************************
* Standardized BP modal popups
Expand Down
21 changes: 19 additions & 2 deletions app/assets/javascripts/bp_class_tree.js.erb
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Expand Up @@ -101,11 +101,10 @@ function nodeClicked(node_id) {
setConcept(node_id);

// Deal with permalink
jQuery("#purl_link_container").hide();
var concept_uri = (node_id.indexOf("http://") == 0 || node_id.indexOf(encodeURIComponent("http://")) == 0 );
var purl_anchor = concept_uri ? "?conceptid="+node_id : "/"+node_id;
var selectedTab = jQuery("#bd_content div.tabs li.selected a").attr("href").slice(1);
jQuery("#purl_input").val(jQuery(document).data().bp.ont_viewer.purl_prefix + purl_anchor);
jQuery("a.class-permalink").data("current-purl", jQuery(document).data().bp.ont_viewer.purl_prefix + purl_anchor);

if (getCache(node_id) != null) {
var tabData = getCache(node_id);
Expand Down Expand Up @@ -155,12 +154,30 @@ function nodeClicked(node_id) {
}

// Keep trying to put the tree view content in place (looks for #sd_content)
var classesPaneSplitter;
function placeTreeView(treeHTML) {
if (jQuery("#sd_content").length == 0) {
setTimeout(function(){placeTreeView(treeHTML)}, 500);
} else {
document.getElementById("sd_content").innerHTML = treeHTML;
initClassTree();

classesPaneSplitter = Split(['div#bd_content .sidebar', 'div#bd_content .cls-info-container'], {
elementStyle: function (dimension, size, gutterSize) {
return {
'flex-basis': 'calc(' + size + '% - ' + gutterSize + 'px)'
}
},
gutterStyle: function (dimension, gutterSize) {
return {
'flex-basis': gutterSize + 'px'
}
},
gutterSize: 10,
direction: "horizontal",
sizes: [30, 70],
cursor: "col-resize"
})
}
}

Expand Down
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