Merge branch 'master' into 14946-ruby-2.5

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

diff --git a/build/package-build-dockerfiles/centos7/Dockerfile b/build/package-build-dockerfiles/centos7/Dockerfile
index ad6f4e1e8f5051c8bb90e449eb89873ca13ea107..cc8265c3d4b3098aeff6ee46bfdeeb249cd823bc 100644 (file)
--- a/build/package-build-dockerfiles/centos7/Dockerfile
+++ b/build/package-build-dockerfiles/centos7/Dockerfile
@@ -14,9 +14,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
-    /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
     /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
 
 # Install golang binary

diff --git a/build/package-build-dockerfiles/debian8/Dockerfile b/build/package-build-dockerfiles/debian8/Dockerfile
index ec7ae07d826e440cf653dbc0ebcfb8b5bca255ca..a1a1ed6f798676be5e862551df47952d80eb0e1e 100644 (file)
--- a/build/package-build-dockerfiles/debian8/Dockerfile
+++ b/build/package-build-dockerfiles/debian8/Dockerfile
@@ -21,9 +21,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
-    /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
     /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
 
 # Install golang binary

diff --git a/build/package-build-dockerfiles/debian9/Dockerfile b/build/package-build-dockerfiles/debian9/Dockerfile
index 6f7f3faafe8c4e18f580be1f8e341a978cf38c84..770db51e7c5180bd0ba83d7e5c57d2899b269c61 100644 (file)
--- a/build/package-build-dockerfiles/debian9/Dockerfile
+++ b/build/package-build-dockerfiles/debian9/Dockerfile
@@ -20,9 +20,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
-    /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
     /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
 
 # Install golang binary

diff --git a/build/package-build-dockerfiles/ubuntu1604/Dockerfile b/build/package-build-dockerfiles/ubuntu1604/Dockerfile
index a83fc77132315651dfd432877c7fecb5b4090f4e..dac82097bd6c7b3ab4b9dd02a5e41dbb88f6fc61 100644 (file)
--- a/build/package-build-dockerfiles/ubuntu1604/Dockerfile
+++ b/build/package-build-dockerfiles/ubuntu1604/Dockerfile
@@ -19,9 +19,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
-    /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
     /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
 
 # Install golang binary

diff --git a/build/package-build-dockerfiles/ubuntu1804/Dockerfile b/build/package-build-dockerfiles/ubuntu1804/Dockerfile
index d0a099911ce91ac9c0e7892d75072310c91e710e..fdfbd04206f4a90e923034dcaee1474504b3e149 100644 (file)
--- a/build/package-build-dockerfiles/ubuntu1804/Dockerfile
+++ b/build/package-build-dockerfiles/ubuntu1804/Dockerfile
@@ -19,9 +19,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3 && \
-    /usr/local/rvm/bin/rvm-exec default gem install bundler && \
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5 && \
     /usr/local/rvm/bin/rvm-exec default gem install fpm --version 1.10.2
 
 # Install golang binary

diff --git a/build/package-test-dockerfiles/debian8/Dockerfile b/build/package-test-dockerfiles/debian8/Dockerfile
index 82d679abfba0e7321d9229280ad1e1d10995d5c1..1d3bb87f699079f20175884295bf194ceb53d864 100644 (file)
--- a/build/package-test-dockerfiles/debian8/Dockerfile
+++ b/build/package-test-dockerfiles/debian8/Dockerfile
@@ -19,8 +19,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5
 
 # udev daemon can't start in a container, so don't try.
 RUN mkdir -p /etc/udev/disabled

diff --git a/build/package-test-dockerfiles/debian9/Dockerfile b/build/package-test-dockerfiles/debian9/Dockerfile
index 9c46ef601313939d38549fbd44fa32bee44bfbfb..e759c9ce1dc1966e846f9bb6899f87b7ab52089c 100644 (file)
--- a/build/package-test-dockerfiles/debian9/Dockerfile
+++ b/build/package-test-dockerfiles/debian9/Dockerfile
@@ -17,8 +17,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5
 
 # udev daemon can't start in a container, so don't try.
 RUN mkdir -p /etc/udev/disabled

diff --git a/build/package-test-dockerfiles/ubuntu1604/Dockerfile b/build/package-test-dockerfiles/ubuntu1604/Dockerfile
index 615ab1c00e9a48ba598f88c323b0fbc69e084d46..422ee43e061eb80382368e7bb5c6ce9c850aac7f 100644 (file)
--- a/build/package-test-dockerfiles/ubuntu1604/Dockerfile
+++ b/build/package-test-dockerfiles/ubuntu1604/Dockerfile
@@ -17,8 +17,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5
 
 # udev daemon can't start in a container, so don't try.
 RUN mkdir -p /etc/udev/disabled

diff --git a/build/package-test-dockerfiles/ubuntu1804/Dockerfile b/build/package-test-dockerfiles/ubuntu1804/Dockerfile
index d530d22a292545873331b65e8d27201e1d5ab747..68babe3fd58c3fd8f308b639347ca7c0b2d12ff0 100644 (file)
--- a/build/package-test-dockerfiles/ubuntu1804/Dockerfile
+++ b/build/package-test-dockerfiles/ubuntu1804/Dockerfile
@@ -17,8 +17,8 @@ ADD generated/pkuczynski.asc /tmp/
 RUN gpg --import --no-tty /tmp/mpapis.asc && \
     gpg --import --no-tty /tmp/pkuczynski.asc && \
     curl -L https://get.rvm.io | bash -s stable && \
-    /usr/local/rvm/bin/rvm install 2.3 && \
-    /usr/local/rvm/bin/rvm alias create default ruby-2.3
+    /usr/local/rvm/bin/rvm install 2.5 && \
+    /usr/local/rvm/bin/rvm alias create default ruby-2.5
 
 # udev daemon can't start in a container, so don't try.
 RUN mkdir -p /etc/udev/disabled

diff --git a/build/run-tests.sh b/build/run-tests.sh
index 0daf80f76742eb0f58e1dfb320f9b62841ed19b1..937fb5fa0671380e39b16c0831dad464e07a0ffe 100755 (executable)
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -903,7 +903,7 @@ install_gem() {
         && cd "$WORKSPACE/$srcpath" \
         && bundle_install_trylocal \
         && gem build "$gemname.gemspec" \
-        && with_test_gemset gem install --no-ri --no-rdoc $(ls -t "$gemname"-*.gem|head -n1)
+        && with_test_gemset gem install --no-document $(ls -t "$gemname"-*.gem|head -n1)
 }
 
 install_sdk/ruby() {

diff --git a/doc/_includes/_install_ruby_and_bundler.liquid b/doc/_includes/_install_ruby_and_bundler.liquid
index d5a5a15362f40dfa4efae9def5ebea1a7deeb193..a8323f592d00643e90b5d6ed68e48fd4094e49d5 100644 (file)
--- a/doc/_includes/_install_ruby_and_bundler.liquid
+++ b/doc/_includes/_install_ruby_and_bundler.liquid
@@ -4,13 +4,13 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-Ruby 2.3 is recommended; Ruby 2.1 is also known to work.
+Ruby 2.5 is recommended; Ruby 2.3 is also known to work.
 
 h4(#rvm). *Option 1: Install with RVM*
 
 <notextile>
-<pre><code><span class="userinput">sudo gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
-\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.3
+<pre><code><span class="userinput">sudo gpg --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.5
 </span></code></pre></notextile>
 
 Either log out and log back in to activate RVM, or explicitly load it in all open shells like this:
@@ -59,8 +59,8 @@ Build and install Ruby:
 <notextile>
 <pre><code><span class="userinput">mkdir -p ~/src
 cd ~/src
-curl -f http://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.3.tar.gz | tar xz
-cd ruby-2.3.3
+curl -f http://cache.ruby-lang.org/pub/ruby/2.5/ruby-2.5.5.tar.gz | tar xz
+cd ruby-2.5.5
 ./configure --disable-install-rdoc
 make
 sudo make install

diff --git a/doc/_includes/_install_ruby_and_bundler_sso.liquid b/doc/_includes/_install_ruby_and_bundler_sso.liquid
new file mode 100644 (file)
index 0000000..a8d14ef
--- /dev/null
+++ b/doc/_includes/_install_ruby_and_bundler_sso.liquid
@@ -0,0 +1,69 @@
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
+
+Ruby 2.3 is recommended; Ruby 2.1 is also known to work.
+
+h4(#rvm). *Option 1: Install with RVM*
+
+<notextile>
+<pre><code><span class="userinput">sudo gpg --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
+\curl -sSL https://get.rvm.io | sudo bash -s stable --ruby=2.3
+</span></code></pre></notextile>
+
+Either log out and log back in to activate RVM, or explicitly load it in all open shells like this:
+
+<notextile>
+<pre><code><span class="userinput">source /usr/local/rvm/scripts/rvm
+</span></code></pre></notextile>
+
+Once RVM is activated in your shell, install Bundler:
+
+<notextile>
+<pre><code>~$ <span class="userinput">gem install bundler</span>
+</code></pre></notextile>
+
+h4(#fromsource). *Option 2: Install from source*
+
+Install prerequisites for Debian 8:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+    bison build-essential gettext libcurl3 libcurl3-gnutls \
+    libcurl4-openssl-dev libpcre3-dev libreadline-dev \
+    libssl-dev libxslt1.1 zlib1g-dev
+</span></code></pre></notextile>
+
+Install prerequisites for CentOS 7:
+
+<notextile>
+<pre><code><span class="userinput">sudo yum install \
+    libyaml-devel glibc-headers autoconf gcc-c++ glibc-devel \
+    patch readline-devel zlib-devel libffi-devel openssl-devel \
+    make automake libtool bison sqlite-devel tar
+</span></code></pre></notextile>
+
+Install prerequisites for Ubuntu 12.04 or 14.04:
+
+<notextile>
+<pre><code><span class="userinput">sudo apt-get install \
+    gawk g++ gcc make libc6-dev libreadline6-dev zlib1g-dev libssl-dev \
+    libyaml-dev libsqlite3-dev sqlite3 autoconf libgdbm-dev \
+    libncurses5-dev automake libtool bison pkg-config libffi-dev curl
+</span></code></pre></notextile>
+
+Build and install Ruby:
+
+<notextile>
+<pre><code><span class="userinput">mkdir -p ~/src
+cd ~/src
+curl -f http://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.3.tar.gz | tar xz
+cd ruby-2.3.3
+./configure --disable-install-rdoc
+make
+sudo make install
+
+sudo -i gem install bundler</span>
+</code></pre></notextile>

diff --git a/doc/install/install-sso.html.textile.liquid b/doc/install/install-sso.html.textile.liquid
index b2a4f671a3fa0e1e2484f2e2625e9631422a4144..fbed12495b6d5f541f2d01286d929ead4ff5113b 100644 (file)
--- a/doc/install/install-sso.html.textile.liquid
+++ b/doc/install/install-sso.html.textile.liquid
@@ -15,7 +15,7 @@ The Arvados package repository includes an SSO server package that can help auto
 
 h3(#install_ruby_and_bundler). Install Ruby and Bundler
 
-{% include 'install_ruby_and_bundler' %}
+{% include 'install_ruby_and_bundler_sso' %}
 
 h3(#install_web_server). Set up a Web server
 

diff --git a/services/api/Gemfile.lock b/services/api/Gemfile.lock
index 078b2b7f418d1e94ca2b4ab424be702cdad1197b..b5ac62c9fb397dfe2d429ab365bce8ea7b5c1aba 100644 (file)
--- a/services/api/Gemfile.lock
+++ b/services/api/Gemfile.lock
@@ -325,4 +325,4 @@ DEPENDENCIES
   uglifier (~> 2.0)
 
 BUNDLED WITH
-   1.16.6
+   1.17.3

diff --git a/services/api/app/models/commit.rb b/services/api/app/models/commit.rb
index a3cef64212ba04122b28148482a03c3b431470cb..2f7e9cd9345ff347c9f5bee05abe58a113dd267b 100644 (file)
--- a/services/api/app/models/commit.rb
+++ b/services/api/app/models/commit.rb
@@ -235,7 +235,7 @@ class Commit < ActiveRecord::Base
     begin
       must_git gitdir, "branch"
     rescue GitError => e
-      raise unless /Not a git repository/ =~ e.to_s
+      raise unless /Not a git repository/i =~ e.to_s
       # OK, this just means we need to create a blank cache repository
       # before fetching.
       FileUtils.mkdir_p gitdir

diff --git a/services/login-sync/.gitignore b/services/login-sync/.gitignore
index cec3cb55a9e83385313b49333523f08532e6e6d2..c111b331371ae211d3bc2e3a9e34ad2a7d6b3982 100644 (file)
--- a/services/login-sync/.gitignore
+++ b/services/login-sync/.gitignore
@@ -1,2 +1 @@
 *.gem
-Gemfile.lock

diff --git a/services/login-sync/Gemfile.lock b/services/login-sync/Gemfile.lock
new file mode 100644 (file)
index 0000000..e82c6b3
--- /dev/null
+++ b/services/login-sync/Gemfile.lock
@@ -0,0 +1,87 @@
+PATH
+  remote: .
+  specs:
+    arvados-login-sync (1.3.3.20190402172810)
+      arvados (~> 1.3.0, >= 1.3.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (5.0.7.2)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      i18n (>= 0.7, < 2)
+      minitest (~> 5.1)
+      tzinfo (~> 1.1)
+    addressable (2.6.0)
+      public_suffix (>= 2.0.2, < 4.0)
+    andand (1.3.3)
+    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)
+      activesupport (>= 3.2, < 5.1)
+      addressable (~> 2.3)
+      autoparse (~> 0.3)
+      extlib (~> 0.9)
+      faraday (~> 0.9)
+      googleauth (~> 0.3)
+      launchy (~> 2.4)
+      multi_json (~> 1.10)
+      retriable (~> 1.4)
+      signet (~> 0.6)
+    autoparse (0.3.3)
+      addressable (>= 2.3.1)
+      extlib (>= 0.9.15)
+      multi_json (>= 1.0.0)
+    concurrent-ruby (1.1.5)
+    extlib (0.9.16)
+    faraday (0.15.4)
+      multipart-post (>= 1.2, < 3)
+    googleauth (0.8.1)
+      faraday (~> 0.12)
+      jwt (>= 1.4, < 3.0)
+      memoist (~> 0.16)
+      multi_json (~> 1.11)
+      os (>= 0.9, < 2.0)
+      signet (~> 0.7)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    json (2.2.0)
+    jwt (1.5.6)
+    launchy (2.4.3)
+      addressable (~> 2.3)
+    memoist (0.16.0)
+    metaclass (0.0.4)
+    minitest (5.11.3)
+    mocha (1.8.0)
+      metaclass (~> 0.0.1)
+    multi_json (1.13.1)
+    multipart-post (2.1.1)
+    os (1.0.1)
+    public_suffix (3.0.3)
+    rake (12.3.2)
+    retriable (1.4.1)
+    signet (0.11.0)
+      addressable (~> 2.3)
+      faraday (~> 0.9)
+      jwt (>= 1.5, < 3.0)
+      multi_json (~> 1.10)
+    thread_safe (0.3.6)
+    tzinfo (1.2.5)
+      thread_safe (~> 0.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  arvados-login-sync!
+  minitest (>= 5.0.0)
+  mocha (>= 1.5.0)
+  rake
+
+BUNDLED WITH
+   1.17.3