diff --git a/Gemfile.lock b/Gemfile.lock index 41740b2f..7b1f8fbc 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -7,9 +7,12 @@ PATH genevalidatorapp (~> 2.1.8) matrix (~> 0.4.2) net-ftp (~> 0.1.3) + prime (~> 0.1.2) rack (~> 2.0) + rexml (~> 3.2, >= 3.2.6) slim (~> 3.0) statsample (= 2.1.0) + webrick (~> 1.8) GEM remote: http://rubygems.org/ @@ -31,6 +34,7 @@ GEM distribution (0.8.0) docile (1.4.0) extendmatrix (0.4) + forwardable (1.3.3) genevalidatorapp (2.1.8) bio (~> 1.4) sinatra (~> 2.0) @@ -61,6 +65,9 @@ GEM prawn-security (0.8.4) prawn-svg (0.9.1.11) prawn (>= 0.8.4) + prime (0.1.2) + forwardable + singleton racc (1.7.3) rack (2.2.8) rack-protection (2.2.4) @@ -71,6 +78,7 @@ GEM prawn (~> 0.8.4) prawn-svg (~> 0.9.1) text-table (~> 1.2) + rexml (3.2.6) rserve-client (0.3.5) ruby-ole (1.2.12.2) ruby2_keywords (0.0.5) @@ -87,6 +95,7 @@ GEM rack-protection (= 2.2.4) tilt (~> 2.0) sinatra-cross_origin (0.4.0) + singleton (0.1.1) slim (3.0.9) temple (>= 0.7.6, < 0.9) tilt (>= 1.3.3, < 2.1) @@ -110,6 +119,7 @@ GEM time (0.3.0) date timeout (0.4.1) + webrick (1.8.1) yard (0.9.34) PLATFORMS diff --git a/genevalidator.gemspec b/genevalidator.gemspec index 35f43486..1b616a42 100644 --- a/genevalidator.gemspec +++ b/genevalidator.gemspec @@ -26,9 +26,12 @@ Gem::Specification.new do |s| s.add_dependency 'genevalidatorapp', '~> 2.1.8' s.add_dependency 'matrix', '~> 0.4.2' # required by statsample s.add_dependency 'net-ftp', '~> 0.1.3' # required by ncbi-blast-dbs + s.add_dependency 'prime', '~> 0.1.2' # required by distribution (statsample) s.add_dependency 'rack', '~> 2.0' s.add_dependency 'slim', '~>3.0' s.add_dependency 'statsample', '2.1.0' + s.add_dependency 'rexml', '~> 3.2', '>= 3.2.6' # required by prawn (statsample) + s.add_dependency 'webrick', '~> 1.8' s.files = `git ls-files -z`.split("\x0") s.executables = s.files.grep(%r{^bin/}) { |f| File.basename(f) } diff --git a/lib/genevalidator/ext/file.rb b/lib/genevalidator/ext/file.rb new file mode 100644 index 00000000..e0d87c0f --- /dev/null +++ b/lib/genevalidator/ext/file.rb @@ -0,0 +1,6 @@ +# Needed for Prawn (from Statsample) +class File + class << self + alias_method :exists?, :exist? unless respond_to?(:exists?) + end +end diff --git a/lib/genevalidator/validation.rb b/lib/genevalidator/validation.rb index 12fec5eb..1f79a344 100644 --- a/lib/genevalidator/validation.rb +++ b/lib/genevalidator/validation.rb @@ -1,5 +1,7 @@ require 'forwardable' -# Statsample: must loaded before /ext/array as they modify a built-in class +# Statsample: must loaded after ext/file as they use a deprecated method - File.exists? +# And before /ext/array as they modify a built-in class +require 'genevalidator/ext/file' require 'statsample' require 'genevalidator/blast'