genevalidatorapp 2.1.1 → 2.1.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 5fef79353732230b2ca0f21f183b6232a27761422b7126577a553f11278518c7
+  data.tar.gz: 25795b4b7865762e8dc408b030748cd9584205d9ad00958e8d51d4908e50acfb
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data/Rakefile

@@ -1,5 +1,5 @@
 require 'rake/testtask'
-GEMSPEC = Gem::Specification::load('genevalidatorapp.gemspec')
+GEMSPEC = Gem::Specification.load('genevalidatorapp.gemspec')
 
 task default: [:build]
 

data/genevalidatorapp.gemspec

@@ -1,5 +1,4 @@
-# coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
+lib = File.expand_path('lib', __dir__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require 'genevalidatorapp/version'
 

data/lib/genevalidatorapp/config.rb

@@ -61,7 +61,7 @@ module GeneValidatorApp
 
       logger.debug "Reading configuration file: #{config_file}."
       symbolise YAML.load_file(config_file)
-    rescue => error
+    rescue StandardError => error
       raise CONFIG_FILE_ERROR.new(config_file, error)
     end
 
@@ -72,12 +72,13 @@ module GeneValidatorApp
     # Default configuration data.
     def defaults
       {
-        :num_threads    => 1,
-        :mafft_threads  => 1,
-        :port           => 5678,
-        :host           => '0.0.0.0',
-        :gv_public_dir  => File.join(Dir.home, '.genevalidatorapp/'),
-        :max_characters => 'undefined'
+        num_threads: 1,
+        mafft_threads: 1,
+        port: 5678,
+        ssl: false,
+        host: '0.0.0.0',
+        gv_public_dir: File.join(Dir.home, '.genevalidatorapp/'),
+        max_characters: 'undefined'
       }
     end
 

data/lib/genevalidatorapp/exceptions.rb

@@ -103,7 +103,7 @@ MSG
   # system but not meeting SequenceServer's minimum version requirement.
   class BLAST_NOT_COMPATIBLE < StandardError
     def initialize(version)
-      @version  = version
+      @version = version
     end
 
     attr_reader :version

data/lib/genevalidatorapp/genevalidator.rb

@@ -211,7 +211,7 @@ module GeneValidatorApp
 
       def parse_output_json
         json_contents = File.read(output_json_file_path)
-        JSON.parse(json_contents,symbolize_names: true)
+        JSON.parse(json_contents, symbolize_names: true)
       end
 
       def output_json_file_path

data/lib/genevalidatorapp/logger.rb

@@ -10,14 +10,14 @@ module GeneValidatorApp
 
     # We change Logging format so that it is consistent with Sinatra's
     class Formatter < Formatter
-      Format = "[%s] %s  %s\n"
+      Format = "[%s] %s  %s\n".freeze
 
       def initialize
         self.datetime_format = '%Y-%m-%d %H:%M:%S'
       end
 
       def call(severity, time, _progname, msg)
-        Format % [format_datetime(time), severity, msg2str(msg)]
+        format(Format, format_datetime(time), severity, msg2str(msg))
       end
     end
   end

data/lib/genevalidatorapp/routes.rb

@@ -36,6 +36,48 @@ module GeneValidatorApp
       set :public_folder, -> { GeneValidatorApp.public_dir }
     end
 
+    helpers do
+      # Overide default URI helper method - to hardcode a https://
+      # In our setup, we are running passenger on http:// (not secure) and then
+      # reverse proxying that onto a 443 port (i.e. https://)
+      # Generates the absolute URI for a given path in the app.
+      # Takes Rack routers and reverse proxies into account.
+      def uri(addr = nil, absolute = true, add_script_name = true)
+        return addr if addr =~ /\A[a-z][a-z0-9\+\.\-]*:/i
+        uri = [host = '']
+        if absolute
+          host << (GeneValidatorApp.ssl? ? 'https://' : 'http://')
+          host << if request.forwarded? || request.port != (request.secure? ? 443 : 80)
+                    request.host_with_port
+                  else
+                    request.host
+                  end
+        end
+        uri << request.script_name.to_s if add_script_name
+        uri << (addr || request.path_info).to_s
+        File.join uri
+      end
+
+      def host_with_port
+        forwarded = request.env['HTTP_X_FORWARDED_HOST']
+        if forwarded
+          forwarded.split(/,\s?/).last
+        else
+          request.env['HTTP_HOST'] || "#{request.env['SERVER_NAME'] ||
+            request.env['SERVER_ADDR']}:#{request.env['SERVER_PORT']}"
+        end
+      end
+
+      # Remove port number.
+      def host
+        host_with_port.to_s.sub(/:\d+\z/, '')
+      end
+
+      def base_url
+        @base_url ||= "#{GeneValidatorApp.ssl? ? 'https' : 'http'}://#{host}"
+      end
+    end
+
     # Set up global variables for the templates...
     before '/' do
       @default_db         = Database.default_db

data/lib/genevalidatorapp/server.rb

@@ -35,13 +35,13 @@ module GeneValidatorApp
     # rubocop:disable Metrics/AbcSize
     def options
       @options ||= {
-        :BindAddress      => app.config[:host],
-        :Port             => app.config[:port],
-        :StartCallback    => proc { app.on_start },
-        :StopCallback     => proc { app.on_stop  },
-        :OutputBufferSize => 5,
-        :AccessLog        => [[logdev, WEBrick::AccessLog::COMMON_LOG_FORMAT]],
-        :Logger           => WEBrick::Log.new(logdev)
+        BindAddress: app.config[:host],
+        Port: app.config[:port],
+        StartCallback: proc { app.on_start },
+        StopCallback: proc { app.on_stop },
+        OutputBufferSize: 5,
+        AccessLog: [[logdev, WEBrick::AccessLog::COMMON_LOG_FORMAT]],
+        Logger: WEBrick::Log.new(logdev)
       }
     end
     # rubocop:enable Metrics/AbcSize

data/lib/genevalidatorapp/version.rb

@@ -1,3 +1,3 @@
 module GeneValidatorApp
-  VERSION = '2.1.1'
+  VERSION = '2.1.2'.freeze
 end

data/lib/genevalidatorapp.rb

@@ -12,7 +12,7 @@ require 'genevalidatorapp/version'
 
 module GeneValidatorApp
   # Use a fixed minimum version of BLAST+
-  MINIMUM_BLAST_VERSION = '2.2.30+'
+  MINIMUM_BLAST_VERSION = '2.2.30+'.freeze
 
   class << self
     def environment
@@ -27,6 +27,10 @@ module GeneValidatorApp
       File.dirname(File.dirname(__FILE__))
     end
 
+    def ssl?
+      @config[:ssl]
+    end
+
     def logger
       @logger ||= Logger.new(STDERR, verbose?)
     end
@@ -92,7 +96,7 @@ module GeneValidatorApp
 
     def init_dirs
       config[:gv_public_dir] = File.expand_path(config[:gv_public_dir])
-      unique_start_id        = 'GV_' + "#{Time.now.strftime('%Y%m%d-%H-%M-%S')}"
+      unique_start_id        = 'GV_' + Time.now.strftime('%Y%m%d-%H-%M-%S').to_s
       @public_dir = File.join(config[:gv_public_dir], unique_start_id)
       init_public_dir
     end
@@ -114,12 +118,12 @@ module GeneValidatorApp
     end
 
     def init_database
-      fail DATABASE_DIR_NOT_SET unless config[:database_dir]
+      raise DATABASE_DIR_NOT_SET unless config[:database_dir]
 
       config[:database_dir] = File.expand_path(config[:database_dir])
       unless File.exist?(config[:database_dir]) &&
              File.directory?(config[:database_dir])
-        fail DATABASE_DIR_NOT_FOUND, config[:database_dir]
+        raise DATABASE_DIR_NOT_FOUND, config[:database_dir]
       end
 
       assert_blast_databases_present_in_database_dir
@@ -136,7 +140,7 @@ module GeneValidatorApp
       return unless config[:require]
       config[:require] = File.expand_path config[:require]
       unless File.exist?(config[:require]) && File.file?(config[:require])
-        fail EXTENSION_FILE_NOT_FOUND, config[:require]
+        raise EXTENSION_FILE_NOT_FOUND, config[:require]
       end
 
       logger.debug("Loading extension: #{config[:require]}")
@@ -147,24 +151,24 @@ module GeneValidatorApp
       cmd = "blastdbcmd -recursive -list '#{config[:database_dir]}'"
       out = `#{cmd}`
       errpat = /BLAST Database error/
-      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
-      fail BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) ||
-                                             !$CHILD_STATUS.success?
+      raise NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
+      raise BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) ||
+                                              !$CHILD_STATUS.success?
       type = []
       out.lines.each { |l| type << l.split[1] }
       return if type.include? 'Protein'
-      fail NO_PROTEIN_BLAST_DATABASE_FOUND, config[:database_dir]
+      raise NO_PROTEIN_BLAST_DATABASE_FOUND, config[:database_dir]
     end
 
     def check_num_threads
       num_threads = Integer(config[:num_threads])
-      fail NUM_THREADS_INCORRECT unless num_threads > 0
+      raise NUM_THREADS_INCORRECT unless num_threads > 0
 
       logger.debug "Will use #{num_threads} threads to run BLAST."
       if num_threads > 256
         logger.warn "Number of threads set at #{num_threads} is unusually high."
       end
-    rescue
+    rescue StandardError
       raise NUM_THREADS_INCORRECT
     end
 
@@ -172,7 +176,7 @@ module GeneValidatorApp
       if config[:max_characters] != 'undefined'
         config[:max_characters] = Integer(config[:max_characters])
       end
-    rescue
+    rescue StandardError
       raise MAX_CHARACTERS_INCORRECT
     end
 
@@ -181,7 +185,7 @@ module GeneValidatorApp
       Array(config[:bin]).each do |bin|
         bins << File.expand_path(bin)
         unless File.exist?(bin) && File.directory?(bin)
-          fail BIN_DIR_NOT_FOUND, config[:bin]
+          raise BIN_DIR_NOT_FOUND, config[:bin]
         end
         export_bin_dir(bin)
       end
@@ -196,13 +200,13 @@ module GeneValidatorApp
     end
 
     def assert_blast_installed_and_compatible
-      fail BLAST_NOT_INSTALLED unless command? 'blastdbcmd'
+      raise BLAST_NOT_INSTALLED unless command? 'blastdbcmd'
       version = `blastdbcmd -version`.split[1]
-      fail BLAST_NOT_COMPATIBLE, version unless version >= MINIMUM_BLAST_VERSION
+      raise BLAST_NOT_COMPATIBLE, version unless version >= MINIMUM_BLAST_VERSION
     end
 
     def assert_mafft_installed
-      fail MAFFT_NOT_INSTALLED unless command? 'mafft'
+      raise MAFFT_NOT_INSTALLED unless command? 'mafft'
     end
 
     # Check and warn user if host is 0.0.0.0 (default).

data/test/test_route_spec.rb

@@ -66,14 +66,14 @@ module GeneValidatorApp
 
     # W3C_Validator Gem is broken - https://github.com/alexdunae/w3c_validators/issues/16
     # it 'validate the html' do
-      # get '/'
-      # html = last_response.body
+    # get '/'
+    # html = last_response.body
 
-      # validator = MarkupValidator.new
-      # results = validator.validate_text(html.to_s)
-      # results.errors.each { |err| puts err.to_s } if results.errors.length > 0
-      # puts results.errors
-      # results.errors.length.should == 0
+    # validator = MarkupValidator.new
+    # results = validator.validate_text(html.to_s)
+    # results.errors.each { |err| puts err.to_s } if results.errors.length > 0
+    # puts results.errors
+    # results.errors.length.should == 0
     # end
   end
 end

data/views/layout.slim

@@ -54,7 +54,7 @@ html lang="en"
     footer#footer
       p.text-muted.text-center
         | Please cite: 
-        <a href="http://doi.org/10.1093/bioinformatics/btw015">Dragan M<sup>&Dagger;</sup>, Moghul MI<sup>&Dagger;</sup>, Priyam A, Bustos C &amp; Wurm Y. 2016. GeneValidator: identify problematic gene predictions. 
+        <a href="https://academic.oup.com/bioinformatics/article/32/10/1559/1742817">Dragan M<sup>&Dagger;</sup>, Moghul I<sup>&Dagger;</sup>, Priyam A, Bustos C &amp; Wurm Y. 2016. GeneValidator: identify problematic gene predictions. 
         <em>Bioinformatics</em>, doi: 10.1093/bioinformatics/btw015</a>.
         br
         |  Developed at 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidatorapp
 version: !ruby/object:Gem::Version
-  version: 2.1.1
+  version: 2.1.2
 platform: ruby
 authors:
 - Monica Dragan
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-14 00:00:00.000000000 Z
+date: 2018-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: capybara