15699: Update apiserver and workbench bundles to latest arvados gem.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tclegg@veritasgenetics.com>

diff --git a/apps/workbench/Gemfile b/apps/workbench/Gemfile
index bc62407bc5173fa77b63daaa7f6f58882c29be33..559c2fdc224a613a3d2d2a1757b56c4762c7b7f8 100644 (file)
--- a/apps/workbench/Gemfile
+++ b/apps/workbench/Gemfile
@@ -5,7 +5,7 @@
 source 'https://rubygems.org'
 
 gem 'rails', '~> 5.0.0'
-gem 'arvados', '>= 0.1.20150511150219'
+gem 'arvados', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/ruby/arvados.gemspec'
 
 gem 'activerecord-nulldb-adapter', git: 'https://github.com/curoverse/nulldb'
 gem 'multi_json'

diff --git a/apps/workbench/Gemfile.lock b/apps/workbench/Gemfile.lock
index ce328dc8954393d24b295fddaccf1b1487715a5f..409ed6615b2413719bfb76ad05dd5602865d386a 100644 (file)
--- a/apps/workbench/Gemfile.lock
+++ b/apps/workbench/Gemfile.lock
@@ -1,3 +1,17 @@
+GIT
+  remote: https://github.com/curoverse/arvados.git
+  revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
+  glob: sdk/ruby/arvados.gemspec
+  specs:
+    arvados (1.4.1.20191019025325)
+      activesupport (>= 3)
+      andand (~> 1.3, >= 1.3.3)
+      arvados-google-api-client (>= 0.7, < 0.8.9)
+      faraday (< 0.16)
+      i18n (~> 0)
+      json (>= 1.7.7, < 3)
+      jwt (>= 0.1.5, < 2)
+
 GIT
   remote: https://github.com/curoverse/nulldb
   revision: d8e0073b665acdd2537c5eb15178a60f02f4b413
@@ -58,14 +72,7 @@ GEM
     andand (1.3.3)
     angularjs-rails (1.3.15)
     arel (7.1.4)
-    arvados (1.3.3.20190320201707)
-      activesupport (>= 3)
-      andand (~> 1.3, >= 1.3.3)
-      arvados-google-api-client (>= 0.7, < 0.8.9)
-      i18n (~> 0)
-      json (>= 1.7.7, < 3)
-      jwt (>= 0.1.5, < 2)
-    arvados-google-api-client (0.8.7.2)
+    arvados-google-api-client (0.8.7.3)
       activesupport (>= 3.2, < 5.1)
       addressable (~> 2.3)
       autoparse (~> 0.3)
@@ -127,13 +134,13 @@ GEM
     flamegraph (0.9.5)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
-    googleauth (0.9.0)
+    googleauth (0.10.0)
       faraday (~> 0.12)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.7)
+      signet (~> 0.12)
     headless (1.0.2)
     highline (2.0.2)
     httpclient (2.8.3)
@@ -153,7 +160,7 @@ GEM
       actionpack (>= 4)
       less (~> 2.6.0)
       sprockets (>= 2)
-    libv8 (3.16.14.19-x86_64-linux)
+    libv8 (3.16.14.19)
     lograge (0.10.0)
       actionpack (>= 4)
       activesupport (>= 4)
@@ -178,7 +185,7 @@ GEM
       metaclass (~> 0.0.1)
     morrisjs-rails (0.5.1.2)
       railties (> 3.1, < 6)
-    multi_json (1.13.1)
+    multi_json (1.14.1)
     multipart-post (2.1.1)
     net-scp (2.0.0)
       net-ssh (>= 2.6.5, < 6.0.0)
@@ -275,7 +282,7 @@ GEM
     selenium-webdriver (3.141.0)
       childprocess (~> 0.5)
       rubyzip (~> 1.2, >= 1.2.2)
-    signet (0.11.0)
+    signet (0.12.0)
       addressable (~> 2.3)
       faraday (~> 0.9)
       jwt (>= 1.5, < 3.0)
@@ -320,7 +327,7 @@ DEPENDENCIES
   activerecord-nulldb-adapter!
   andand
   angularjs-rails (~> 1.3.8)
-  arvados (>= 0.1.20150511150219)
+  arvados!
   bootstrap-sass (~> 3.4.1)
   bootstrap-tab-history-rails
   bootstrap-x-editable-rails

diff --git a/services/api/Gemfile b/services/api/Gemfile
index 804d2a479d3d4701489c8d1bed812c7a6873c252..b106ab199c6a3b2db2ca64788506c5fbdedc43b5 100644 (file)
--- a/services/api/Gemfile
+++ b/services/api/Gemfile
@@ -25,9 +25,6 @@ group :test, :development do
   gem 'byebug'
 end
 
-# We need this dependency because of crunchv1
-gem 'arvados-cli'
-
 gem 'pg', '~> 1.0'
 
 gem 'multi_json'
@@ -58,7 +55,12 @@ gem 'faye-websocket'
 
 gem 'themes_for_rails', git: 'https://github.com/curoverse/themes_for_rails'
 
-gem 'arvados', '>= 1.3.1.20190301212059'
+# We need arvados-cli because of crunchv1. Note: bundler can't handle
+# two gems with the same "git" url but different "glob" values, hence
+# the use of a wildcard here instead of literal paths
+# (sdk/cli/arvados-cli.gem and sdk/ruby/arvados.gem).
+gem 'arvados-cli', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/*/*.gemspec'
+gem 'arvados', git: 'https://github.com/curoverse/arvados.git', glob: 'sdk/*/*.gemspec'
 gem 'httpclient'
 
 gem 'sshkey'

diff --git a/services/api/Gemfile.lock b/services/api/Gemfile.lock
index b5ac62c9fb397dfe2d429ab365bce8ea7b5c1aba..e80f87e2a570f1fb351a2e20b1936543fd7c960e 100644 (file)
--- a/services/api/Gemfile.lock
+++ b/services/api/Gemfile.lock
@@ -1,3 +1,27 @@
+GIT
+  remote: https://github.com/curoverse/arvados.git
+  revision: dd9f2403f43bcb93da5908ddde57d8c0491bb4c2
+  glob: sdk/*/*.gemspec
+  specs:
+    arvados (1.4.1.20191019025325)
+      activesupport (>= 3)
+      andand (~> 1.3, >= 1.3.3)
+      arvados-google-api-client (>= 0.7, < 0.8.9)
+      faraday (< 0.16)
+      i18n (~> 0)
+      json (>= 1.7.7, < 3)
+      jwt (>= 0.1.5, < 2)
+    arvados-cli (1.4.1.20191017145711)
+      activesupport (>= 3.2.13, < 5.1)
+      andand (~> 1.3, >= 1.3.3)
+      arvados (>= 1.4.1.20190320201707)
+      arvados-google-api-client (~> 0.6, >= 0.6.3, < 0.8.9)
+      curb (~> 0.8)
+      faraday (< 0.16)
+      json (>= 1.7.7, < 3)
+      oj (~> 3.0)
+      optimist (~> 3.0)
+
 GIT
   remote: https://github.com/curoverse/themes_for_rails
   revision: ddf6e592b3b6493ea0c2de7b5d3faa120ed35be0
@@ -49,27 +73,11 @@ GEM
       activemodel (>= 3.0.0)
       activesupport (>= 3.0.0)
       rack (>= 1.1.0)
-    addressable (2.6.0)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     andand (1.3.3)
     arel (7.1.4)
-    arvados (1.3.1.20190320201707)
-      activesupport (>= 3)
-      andand (~> 1.3, >= 1.3.3)
-      arvados-google-api-client (>= 0.7, < 0.8.9)
-      i18n (~> 0)
-      json (>= 1.7.7, < 3)
-      jwt (>= 0.1.5, < 2)
-    arvados-cli (1.3.1.20190320201707)
-      activesupport (>= 3.2.13, < 5.1)
-      andand (~> 1.3, >= 1.3.3)
-      arvados (~> 1.3.0, >= 1.3.0)
-      arvados-google-api-client (~> 0.6, >= 0.6.3, < 0.8.9)
-      curb (~> 0.8)
-      json (>= 1.7.7, < 3)
-      oj (~> 3.0)
-      optimist (~> 3.0)
-    arvados-google-api-client (0.8.7.2)
+    arvados-google-api-client (0.8.7.3)
       activesupport (>= 3.2, < 5.1)
       addressable (~> 2.3)
       autoparse (~> 0.3)
@@ -94,7 +102,7 @@ GEM
       net-ssh-gateway (>= 1.1.0)
     concurrent-ruby (1.1.5)
     crass (1.0.4)
-    curb (0.9.9)
+    curb (0.9.10)
     database_cleaner (1.7.0)
     erubis (2.7.0)
     eventmachine (1.2.7)
@@ -113,13 +121,13 @@ GEM
     ffi (1.9.25)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
-    googleauth (0.8.0)
+    googleauth (0.10.0)
       faraday (~> 0.12)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.7)
+      signet (~> 0.12)
     hashie (3.6.0)
     highline (2.0.1)
     httpclient (2.8.3)
@@ -153,9 +161,9 @@ GEM
     minitest (5.10.3)
     mocha (1.8.0)
       metaclass (~> 0.0.1)
-    multi_json (1.13.1)
+    multi_json (1.14.1)
     multi_xml (0.6.0)
-    multipart-post (2.0.0)
+    multipart-post (2.1.1)
     net-scp (2.0.0)
       net-ssh (>= 2.6.5, < 6.0.0)
     net-sftp (2.1.2)
@@ -172,7 +180,7 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    oj (3.7.11)
+    oj (3.9.2)
     omniauth (1.4.3)
       hashie (>= 1.2, < 4)
       rack (>= 1.6.2, < 3)
@@ -180,13 +188,13 @@ GEM
       oauth2 (~> 1.1)
       omniauth (~> 1.2)
     optimist (3.0.0)
-    os (1.0.0)
+    os (1.0.1)
     passenger (6.0.2)
       rack
       rake (>= 0.8.1)
     pg (1.1.4)
     power_assert (1.1.4)
-    public_suffix (3.0.3)
+    public_suffix (4.0.1)
     rack (2.0.7)
     rack-test (0.6.3)
       rack (>= 1.0)
@@ -246,7 +254,7 @@ GEM
       sprockets (>= 2.8, < 4.0)
       sprockets-rails (>= 2.0, < 4.0)
       tilt (>= 1.1, < 3)
-    signet (0.11.0)
+    signet (0.12.0)
       addressable (~> 2.3)
       faraday (~> 0.9)
       jwt (>= 1.5, < 3.0)
@@ -288,8 +296,8 @@ PLATFORMS
 DEPENDENCIES
   acts_as_api
   andand
-  arvados (>= 1.3.1.20190301212059)
-  arvados-cli
+  arvados!
+  arvados-cli!
   byebug
   database_cleaner
   factory_bot_rails