Merge branch '12737-update-rails-wb'

Refs #12737

Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima@veritasgenetics.com>

diff --git a/apps/workbench/Gemfile b/apps/workbench/Gemfile
index 788dcf65764b75d345e4be5a7a408259307edd19..1e9a5cc70d8ece81b21d6c15233499dd31a35002 100644 (file)
--- a/apps/workbench/Gemfile
+++ b/apps/workbench/Gemfile
@@ -4,13 +4,16 @@
 
 source 'https://rubygems.org'
 
-gem 'rails', '~> 4.1'
+# Having a dependency '~> 4.1' make rails 4.2.10 to be installed when it's
+# supposed to avoid that.
+gem 'rails', '< 4.2'
 gem 'arvados', '>= 0.1.20150511150219'
 
 gem 'activerecord-nulldb-adapter'
 gem 'multi_json'
 gem 'oj'
 gem 'sass'
+gem 'mime-types'
 
 # Note: keeping this out of the "group :assets" section "may" allow us
 # to use Coffescript for UJS responses. It also prevents a
@@ -37,11 +40,13 @@ group :development do
 end
 
 group :test, :diagnostics, :performance do
-  gem 'minitest', '~> 5.0'
-  gem 'selenium-webdriver'
-  gem 'capybara'
-  gem 'poltergeist'
-  gem 'headless'
+  gem 'minitest', '~> 5.10.3'
+  # Selenium-webdriver 3.x is producing problems like the one described here:
+  # https://stackoverflow.com/questions/41310586/ruby-selenium-webdriver-unable-to-find-mozilla-geckodriver
+  gem 'selenium-webdriver', '~> 2.53.1'
+  gem 'capybara', '~> 2.5.0'
+  gem 'poltergeist', '~> 1.5.1'
+  gem 'headless', '~> 1.0.2'
 end
 
 group :test, :performance do
@@ -61,7 +66,7 @@ gem 'bootstrap-sass', '~> 3.1.0'
 gem 'bootstrap-x-editable-rails'
 gem 'bootstrap-tab-history-rails'
 
-gem 'angularjs-rails'
+gem 'angularjs-rails', '~> 1.3.8'
 
 gem 'less'
 gem 'less-rails'

diff --git a/apps/workbench/Gemfile.lock b/apps/workbench/Gemfile.lock
index 8ffc1d33b50c8175fe3804f281390dc09f67d2f8..93a92ce11cb85f57d43237c49d4fec7f07f9842f 100644 (file)
--- a/apps/workbench/Gemfile.lock
+++ b/apps/workbench/Gemfile.lock
@@ -8,45 +8,46 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    RedCloth (4.2.9)
-    actionmailer (4.1.12)
-      actionpack (= 4.1.12)
-      actionview (= 4.1.12)
+    RedCloth (4.3.2)
+    actionmailer (4.1.16)
+      actionpack (= 4.1.16)
+      actionview (= 4.1.16)
       mail (~> 2.5, >= 2.5.4)
-    actionpack (4.1.12)
-      actionview (= 4.1.12)
-      activesupport (= 4.1.12)
+    actionpack (4.1.16)
+      actionview (= 4.1.16)
+      activesupport (= 4.1.16)
       rack (~> 1.5.2)
       rack-test (~> 0.6.2)
-    actionview (4.1.12)
-      activesupport (= 4.1.12)
+    actionview (4.1.16)
+      activesupport (= 4.1.16)
       builder (~> 3.1)
       erubis (~> 2.7.0)
-    activemodel (4.1.12)
-      activesupport (= 4.1.12)
+    activemodel (4.1.16)
+      activesupport (= 4.1.16)
       builder (~> 3.1)
-    activerecord (4.1.12)
-      activemodel (= 4.1.12)
-      activesupport (= 4.1.12)
+    activerecord (4.1.16)
+      activemodel (= 4.1.16)
+      activesupport (= 4.1.16)
       arel (~> 5.0.0)
-    activerecord-nulldb-adapter (0.3.1)
+    activerecord-nulldb-adapter (0.3.8)
       activerecord (>= 2.0.0)
-    activesupport (4.1.12)
+    activesupport (4.1.16)
       i18n (~> 0.6, >= 0.6.9)
       json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
       thread_safe (~> 0.1)
       tzinfo (~> 1.1)
-    addressable (2.4.0)
+    addressable (2.5.2)
+      public_suffix (>= 2.0.2, < 4.0)
     andand (1.3.3)
-    angularjs-rails (1.3.8)
+    angularjs-rails (1.3.15)
     arel (5.0.1.20140414130214)
-    arvados (0.1.20160420143004)
-      activesupport (>= 3, < 4.2.6)
+    arvados (0.1.20180302192246)
+      activesupport (>= 3)
       andand (~> 1.3, >= 1.3.3)
-      google-api-client (>= 0.7, < 0.9)
+      google-api-client (>= 0.7, < 0.8.9)
       i18n (~> 0)
-      json (~> 1.7, >= 1.7.7)
+      json (>= 1.7.7, < 3)
       jwt (>= 0.1.5, < 2)
     autoparse (0.3.3)
       addressable (>= 2.3.1)
@@ -59,11 +60,8 @@ GEM
     bootstrap-x-editable-rails (1.5.1.1)
       railties (>= 3.0)
     builder (3.2.3)
-    byebug (3.5.1)
-      columnize (~> 0.8)
-      debugger-linecache (~> 1.2)
-      slop (~> 3.6)
-    capistrano (2.15.5)
+    byebug (10.0.0)
+    capistrano (2.15.9)
       highline
       net-scp (>= 1.0.0)
       net-sftp (>= 2.0.0)
@@ -75,36 +73,29 @@ GEM
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       xpath (~> 2.0)
-    childprocess (0.5.6)
+    childprocess (0.8.0)
       ffi (~> 1.0, >= 1.0.11)
     cliver (0.3.2)
-    coffee-rails (4.1.0)
+    coffee-rails (4.2.2)
       coffee-script (>= 2.2.0)
-      railties (>= 4.0.0, < 5.0)
-    coffee-script (2.3.0)
+      railties (>= 4.0.0)
+    coffee-script (2.4.1)
       coffee-script-source
       execjs
-    coffee-script-source (1.8.0)
-    columnize (0.9.0)
+    coffee-script-source (1.12.2)
     commonjs (0.2.7)
     concurrent-ruby (1.0.5)
-    daemon_controller (1.2.0)
-    debugger-linecache (1.2.0)
-    deep_merge (1.0.1)
+    deep_merge (1.2.1)
     docile (1.1.5)
     erubis (2.7.0)
     execjs (2.7.0)
     extlib (0.9.16)
-    faraday (0.9.2)
+    faraday (0.14.0)
       multipart-post (>= 1.2, < 3)
-    fast_stack (0.1.0)
-      rake
-      rake-compiler
-    ffi (1.9.10)
-    flamegraph (0.1.0)
-      fast_stack
-    google-api-client (0.8.6)
-      activesupport (>= 3.2)
+    ffi (1.9.23)
+    flamegraph (0.9.5)
+    google-api-client (0.8.7)
+      activesupport (>= 3.2, < 5.0)
       addressable (~> 2.3)
       autoparse (~> 0.3)
       extlib (~> 0.9)
@@ -114,70 +105,76 @@ GEM
       multi_json (~> 1.10)
       retriable (~> 1.4)
       signet (~> 0.6)
-    googleauth (0.5.1)
-      faraday (~> 0.9)
-      jwt (~> 1.4)
+    googleauth (0.6.2)
+      faraday (~> 0.12)
+      jwt (>= 1.4, < 3.0)
       logging (~> 2.0)
       memoist (~> 0.12)
       multi_json (~> 1.11)
       os (~> 0.9)
       signet (~> 0.7)
+    grease (0.3.1)
     headless (1.0.2)
-    highline (1.6.21)
-    httpclient (2.8.2.4)
-    i18n (0.9.0)
+    highline (1.7.10)
+    httpclient (2.8.3)
+    i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jquery-rails (3.1.2)
+    jquery-rails (3.1.4)
       railties (>= 3.0, < 5.0)
       thor (>= 0.14, < 2.0)
     json (1.8.6)
-    jwt (1.5.4)
+    jwt (1.5.6)
     launchy (2.4.3)
       addressable (~> 2.3)
     less (2.6.0)
       commonjs (~> 0.2.7)
-    less-rails (2.6.0)
-      actionpack (>= 3.1)
+    less-rails (3.0.0)
+      actionpack (>= 4.0)
+      grease
       less (~> 2.6.0)
-    libv8 (3.16.14.7)
+      sprockets (> 2, < 4)
+      tilt
+    libv8 (3.16.14.19)
     little-plugger (1.1.4)
-    logging (2.1.0)
+    logging (2.2.2)
       little-plugger (~> 1.1)
       multi_json (~> 1.10)
-    lograge (0.7.1)
-      actionpack (>= 4, < 5.2)
-      activesupport (>= 4, < 5.2)
-      railties (>= 4, < 5.2)
+    lograge (0.9.0)
+      actionpack (>= 4)
+      activesupport (>= 4)
+      railties (>= 4)
       request_store (~> 1.0)
     logstash-event (1.2.02)
-    mail (2.6.3)
-      mime-types (>= 1.16, < 3)
-    memoist (0.14.0)
+    mail (2.7.0)
+      mini_mime (>= 0.1.1)
+    memoist (0.16.0)
     metaclass (0.0.4)
-    mime-types (2.99)
-    mini_portile (0.6.2)
+    mime-types (3.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2016.0521)
+    mini_mime (1.0.0)
+    mini_portile2 (2.3.0)
     minitest (5.10.3)
-    mocha (1.1.0)
+    mocha (1.3.0)
       metaclass (~> 0.0.1)
-    morrisjs-rails (0.5.1)
-      railties (> 3.1, < 5)
-    multi_json (1.12.1)
+    morrisjs-rails (0.5.1.2)
+      railties (> 3.1, < 6)
+    multi_json (1.13.1)
     multipart-post (2.0.0)
     net-scp (1.2.1)
       net-ssh (>= 2.6.5)
     net-sftp (2.1.2)
       net-ssh (>= 2.6.5)
-    net-ssh (2.9.2)
-    net-ssh-gateway (1.2.0)
-      net-ssh (>= 2.6.5)
-    nokogiri (1.6.6.4)
-      mini_portile (~> 0.6.0)
+    net-ssh (4.2.0)
+    net-ssh-gateway (2.0.0)
+      net-ssh (>= 4.0.0)
+    nokogiri (1.8.2)
+      mini_portile2 (~> 2.3.0)
     npm-rails (0.2.1)
       rails (>= 3.2)
-    oj (2.11.2)
+    oj (3.5.0)
     os (0.9.6)
-    passenger (4.0.57)
-      daemon_controller (>= 1.2.0)
+    passenger (5.2.1)
       rack
       rake (>= 0.8.1)
     piwik_analytics (1.0.2)
@@ -189,89 +186,95 @@ GEM
       cliver (~> 0.3.1)
       multi_json (~> 1.0)
       websocket-driver (>= 0.2.0)
+    public_suffix (3.0.2)
     rack (1.5.5)
-    rack-mini-profiler (0.9.2)
-      rack (>= 1.1.3)
+    rack-mini-profiler (0.10.7)
+      rack (>= 1.2.0)
     rack-test (0.6.3)
       rack (>= 1.0)
-    rails (4.1.12)
-      actionmailer (= 4.1.12)
-      actionpack (= 4.1.12)
-      actionview (= 4.1.12)
-      activemodel (= 4.1.12)
-      activerecord (= 4.1.12)
-      activesupport (= 4.1.12)
+    rails (4.1.16)
+      actionmailer (= 4.1.16)
+      actionpack (= 4.1.16)
+      actionview (= 4.1.16)
+      activemodel (= 4.1.16)
+      activerecord (= 4.1.16)
+      activesupport (= 4.1.16)
       bundler (>= 1.3.0, < 2.0)
-      railties (= 4.1.12)
+      railties (= 4.1.16)
       sprockets-rails (~> 2.0)
-    rails-perftest (0.0.5)
-    railties (4.1.12)
-      actionpack (= 4.1.12)
-      activesupport (= 4.1.12)
+    rails-perftest (0.0.7)
+    railties (4.1.16)
+      actionpack (= 4.1.16)
+      activesupport (= 4.1.16)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    rake (12.2.1)
-    rake-compiler (0.9.5)
-      rake
+    rake (12.3.0)
     raphael-rails (2.1.2)
-    ref (1.0.5)
-    request_store (1.3.2)
+    rb-fsevent (0.10.3)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
+    ref (2.0.0)
+    request_store (1.4.0)
+      rack (>= 1.4)
     retriable (1.4.1)
     ruby-debug-passenger (0.2.0)
-    ruby-prof (0.15.2)
-    rubyzip (1.1.7)
-    rvm-capistrano (1.5.5)
+    ruby-prof (0.17.0)
+    rubyzip (1.2.1)
+    rvm-capistrano (1.5.6)
       capistrano (~> 2.15.4)
     safe_yaml (1.0.4)
-    sass (3.4.9)
-    sass-rails (5.0.1)
-      railties (>= 4.0.0, < 5.0)
+    sass (3.5.5)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sass-rails (5.0.7)
+      railties (>= 4.0.0, < 6)
       sass (~> 3.1)
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
-      tilt (~> 1.1)
-    selenium-webdriver (2.53.1)
+      tilt (>= 1.1, < 3)
+    selenium-webdriver (2.53.4)
       childprocess (~> 0.5)
-      multi_json (~> 1.0)
       rubyzip (~> 1.0)
       websocket (~> 1.0)
-    signet (0.7.2)
+    signet (0.8.1)
       addressable (~> 2.3)
       faraday (~> 0.9)
-      jwt (~> 1.5)
+      jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.9.1)
+    simplecov (0.15.1)
       docile (~> 1.1.0)
-      multi_json (~> 1.0)
-      simplecov-html (~> 0.8.0)
-    simplecov-html (0.8.0)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.2)
     simplecov-rcov (0.2.3)
       simplecov (>= 0.4.1)
-    slop (3.6.0)
-    sprockets (3.2.0)
-      rack (~> 1.0)
-    sprockets-rails (2.3.2)
+    sprockets (3.7.1)
+      concurrent-ruby (~> 1.0)
+      rack (> 1, < 3)
+    sprockets-rails (2.3.3)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       sprockets (>= 2.8, < 4.0)
-    sshkey (1.6.1)
-    therubyracer (0.12.1)
-      libv8 (~> 3.16.14.0)
+    sshkey (1.9.0)
+    therubyracer (0.12.3)
+      libv8 (~> 3.16.14.15)
       ref
     thor (0.20.0)
     thread_safe (0.3.6)
-    tilt (1.4.1)
-    tzinfo (1.2.4)
+    tilt (2.0.8)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
     uglifier (2.7.2)
       execjs (>= 0.3.0)
       json (>= 1.8.0)
-    websocket (1.2.2)
-    websocket-driver (0.5.1)
+    websocket (1.2.5)
+    websocket-driver (0.7.0)
       websocket-extensions (>= 0.1.0)
-    websocket-extensions (0.1.1)
+    websocket-extensions (0.1.3)
     wiselinks (1.2.1)
-    xpath (2.0.0)
+    xpath (2.1.0)
       nokogiri (~> 1.3)
 
 PLATFORMS
@@ -281,24 +284,25 @@ DEPENDENCIES
   RedCloth
   activerecord-nulldb-adapter
   andand
-  angularjs-rails
+  angularjs-rails (~> 1.3.8)
   arvados (>= 0.1.20150511150219)
   bootstrap-sass (~> 3.1.0)
   bootstrap-tab-history-rails
   bootstrap-x-editable-rails
   byebug
-  capybara
+  capybara (~> 2.5.0)
   coffee-rails
   deep_merge
   flamegraph
-  headless
+  headless (~> 1.0.2)
   httpclient (~> 2.5)
   jquery-rails
   less
   less-rails
   lograge
   logstash-event
-  minitest (~> 5.0)
+  mime-types
+  minitest (~> 5.10.3)
   mocha
   morrisjs-rails
   multi_json
@@ -306,9 +310,9 @@ DEPENDENCIES
   oj
   passenger
   piwik_analytics
-  poltergeist
+  poltergeist (~> 1.5.1)
   rack-mini-profiler
-  rails (~> 4.1)
+  rails (< 4.2)
   rails-perftest
   raphael-rails
   ruby-debug-passenger
@@ -317,7 +321,7 @@ DEPENDENCIES
   safe_yaml
   sass
   sass-rails
-  selenium-webdriver
+  selenium-webdriver (~> 2.53.1)
   simplecov (~> 0.7)
   simplecov-rcov
   sshkey
@@ -327,4 +331,4 @@ DEPENDENCIES
   wiselinks
 
 BUNDLED WITH
-   1.16.0
+   1.16.1

diff --git a/apps/workbench/config/application.default.yml b/apps/workbench/config/application.default.yml
index 76f7a3081751df228bb32b810b50208902aac8bc..137bba09e8365188a9d2cb8ac5ed49bb59f1b48c 100644 (file)
--- a/apps/workbench/config/application.default.yml
+++ b/apps/workbench/config/application.default.yml
@@ -212,7 +212,7 @@ common:
   # would be enabled in a collection's show page.
   # It is sufficient to list only applications here.
   # No need to list text and image types.
-  application_mimetypes_with_view_icon: [cwl, fasta, go, javascript, json, pdf, python, r, rtf, sam, sh, vnd.realvnc.bed, xml, xsl]
+  application_mimetypes_with_view_icon: [cwl, fasta, go, javascript, json, pdf, python, r, rtf, sam, x-sh, vnd.realvnc.bed, xml, xsl]
 
   # the maximum number of bytes to load in the log viewer
   log_viewer_max_bytes: 1000000

diff --git a/apps/workbench/config/initializers/mime_types.rb b/apps/workbench/config/initializers/mime_types.rb
index 0e7b1c798106854c7786ee3832f33ddb06df0847..69781a1bee0b1c376e3857684fb94b6b49bda25b 100644 (file)
--- a/apps/workbench/config/initializers/mime_types.rb
+++ b/apps/workbench/config/initializers/mime_types.rb
@@ -17,6 +17,7 @@ include MIME
   %w(go),
   %w(r),
   %w(sam),
+  %w(python py),
 ].each do |suffixes|
   if (MIME::Types.type_for(suffixes[0]).first.nil?)
     MIME::Types.add(MIME::Type.new(["application/#{suffixes[0]}", suffixes]))