Code style improvements

[ci skip]

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

lib/sequenceserver/blast/job.rb

@@ -33,7 +33,7 @@ def command
       # and using contents of stderr to provide context about the error.
       def raise!
         # Return true exit status is 0 and stdout is not empty.
-        return true if exitstatus == 0 && !File.zero?(stdout)
+        return true if exitstatus.zero? && !File.zero?(stdout)
 
         # Handle error. See [1].
         case exitstatus
@@ -71,7 +71,7 @@ def raise!
 
       private
 
-      def parse_advanced param_line
+      def parse_advanced(param_line)
         param_list = (param_line || '').split(' ')
         res = {}
 

lib/sequenceserver/database.rb

@@ -38,7 +38,7 @@ def initialize(*args)
 
     def include?(accession)
       cmd = "blastdbcmd -entry '#{accession}' -db #{name}"
-      out, _ = sys(cmd, path: config[:bin])
+      out, = sys(cmd, path: config[:bin])
       !out.empty?
     end
 

lib/sequenceserver/doctor.rb

@@ -11,7 +11,7 @@ class Doctor
     ERROR_NUMERIC_IDS         = 2
     ERROR_PROBLEMATIC_IDS     = 3
 
-    AVOID_ID_REGEX            = /^(?!gi|bbs)\w+\|\w*\|?/.freeze
+    AVOID_ID_REGEX            = /^(?!gi|bbs)\w+\|\w*\|?/
 
     class << self
       extend Forwardable
@@ -92,7 +92,7 @@ def show_message(error, values)
           MSG
         end
       end
-      # rubocop:disable Metrics/MethodLength
+      # rubocop:enable Metrics/MethodLength
     end
 
     def initialize

lib/sequenceserver/job.rb

@@ -24,7 +24,7 @@ class Job
     class << self
       # Creates and queues a job. Returns created job object.
       def create(params)
-        job = BLAST::Job.new(params)# TODO: Dynamic dispatch.
+        job = BLAST::Job.new(params) # TODO: Dynamic dispatch.
         SequenceServer.pool.queue { job.run }
         job
       end
@@ -43,8 +43,8 @@ def delete(id)
 
       # Returns an Array of all jobs.
       def all
-        Dir["#{DOTDIR}/**/job.yaml"].
-          map { |f| fetch File.basename File.dirname f }
+        Dir["#{DOTDIR}/**/job.yaml"]
+          .map { |f| fetch File.basename File.dirname f }
       end
     end
 
@@ -58,14 +58,14 @@ def all
     # of job data will be held, yields (if block given) and saves the job.
     #
     # Subclasses should extend `initialize` as per requirement.
-    def initialize(*args)
+    def initialize(*)
       @id = SecureRandom.uuid
       @submitted_at = Time.now
       mkdir_p dir
       yield if block_given?
       save
     rescue Errno::ENOSPC
-      raise SystemError, "Not enough disk space to start a new job"
+      raise SystemError, 'Not enough disk space to start a new job'
     rescue Errno::EACCES
       raise SystemError, "Permission denied to write to #{DOTDIR}"
     rescue => e
@@ -78,7 +78,7 @@ def initialize(*args)
     # Returns shell command that will be executed. Subclass needs to provide a
     # concrete implementation.
     def command
-      raise 'Not implemented.'
+      fail 'Not implemented.'
     end
 
     # Shell out and execute the job.
@@ -145,7 +145,7 @@ def store(key, value)
     # NOTE: Not used.
     def fetch(key)
       filename = File.join(dir, key)
-      raise if !File.exist? filename
+      fail unless File.exist? filename
       filename
     end
 

lib/sequenceserver/links.rb

@@ -1,15 +1,14 @@
+require 'erb'
+
 module SequenceServer
   # Module to contain methods for generating sequence retrieval links.
   module Links
-    require 'erb'
-
     # Provide a method to URL encode _query parameters_. See [1].
     include ERB::Util
-    #
-    alias_method :encode, :url_encode
+    alias encode url_encode
 
-    NCBI_ID_PATTERN    = /gi\|(\d+)\|/.freeze
-    UNIPROT_ID_PATTERN = /sp\|(\w+)\|/.freeze
+    NCBI_ID_PATTERN    = /gi\|(\d+)\|/
+    UNIPROT_ID_PATTERN = /sp\|(\w+)\|/
 
     # Link generators return a Hash like below.
     #

lib/sequenceserver/pool.rb

@@ -18,8 +18,6 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-require 'thread'
-
 # Simple thread pool [1].
 class Pool
   def initialize(size)

lib/sequenceserver/routes.rb

@@ -42,7 +42,7 @@ class Routes < Sinatra::Base
       # 'ALLOW-FROM uri'.
       set :protection, lambda {
         frame_options = SequenceServer.config[:frame_options]
-        frame_options && { :frame_options => frame_options }
+        frame_options && { frame_options: frame_options }
       }
 
       # Serve compressed responses.
@@ -89,7 +89,7 @@ class Routes < Sinatra::Base
 
     # Returns base HTML. Rest happens client-side: polling for and rendering
     # the results.
-    get '/:jid' do |jid|
+    get '/:jid' do
       erb :report, layout: true
     end
 
@@ -155,13 +155,13 @@ class Routes < Sinatra::Base
       # All errors will have a message.
       error_data = { message: error.message }
 
-      # If error object has a title method, use that, or use error class for
-      # title.
-      if error.respond_to? :title
-        error_data[:title] = error.title
-      else
-        error_data[:title] = error.class.to_s
-      end
+      # If error object has a title method, use that, or use name of the
+      # error class as title.
+      error_data[:title] = if error.respond_to? :title
+                             error.title
+                           else
+                             error.class.name
+                           end
 
       # If error object has a more_info method, use that. If the error does
       # not have more_info and the error is not APIError, use backtrace as

lib/sequenceserver/sequence.rb

@@ -67,7 +67,7 @@ def to_s
     end
 
     def info
-      { :value => value, :id => id, :title => title }
+      { value: value, id: id, title: title }
     end
 
     # Returns FASTA formatted sequence.
@@ -97,7 +97,7 @@ def guess_type(sequence)
         na_count = 0
         composition = composition(cleaned_sequence)
         composition.each do |character, count|
-          na_count += count if character.match(/[ACGTU]/i)
+          na_count += count if character =~ /[ACGTU]/i
         end
 
         na_count > (0.9 * cleaned_sequence.length) ? :nucleotide : :protein
@@ -200,7 +200,7 @@ def run
                   " -db '#{database_names.join(' ')}'" \
                   " -entry '#{sequence_ids.join(',')}'"
 
-        out, _ = sys(command, path: config[:bin])
+        out, = sys(command, path: config[:bin])
 
         @sequences = out.each_line.map do |line|
           # Stop codons in amino acid sequence databases show up as invalid
@@ -234,20 +234,21 @@ def error_msgs
         [
           ['ERROR: incorrect number of sequences found.',
            <<~MSG
-           You requested #{sequence_ids.length} sequence(s) with the following identifiers:
-             #{sequence_ids.join(', ')}
+             You requested #{sequence_ids.length} sequence(s) with the following
+             identifiers:
+               #{sequence_ids.join(', ')}
              from the following databases:
                #{database_titles.join(', ')}
              but we found #{sequences.length} sequence(s).
 
              This is likley due to a problem with how databases are formatted.
-             Please share this text with the person managing this website. 
-             
-             If you are the admin and are confident that your databases are 
-             correctly formatted, you have likely encountered a weird bug. 
+             Please share this text with the person managing this website.
+
+             If you are the admin and are confident that your databases are
+             correctly formatted, you have likely encountered a weird bug.
              In this case, please raise an issue at:
              https://github.com/wurmlab/sequenceserver/issues
-             
+
              If any sequences were retrieved, you can find them below
              (but some may be incorrect, so be careful!)
            MSG

sequenceserver.gemspec

@@ -11,45 +11,46 @@ Gem::Specification.new do |s|
   s.license     = 'AGPL-3.0'
 
   s.summary     = 'BLAST search made easy!'
-  s.description = <<DESC
-SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
-interface for use locally or over the web.
-DESC
+  s.description = <<~DESC
+    SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
+    user interface for use locally or over the web.
+  DESC
 
   # dependencies
   s.required_ruby_version = '>= 2.3.0'
 
-  s.add_dependency('sinatra',   '~> 2.0',  '>= 2.0.0')
   s.add_dependency('json_pure', '~> 1.8',  '>= 1.8.2')
   s.add_dependency('ox',        '~> 2.1',  '>= 2.1.1')
+  s.add_dependency('sinatra',   '~> 2.0',  '>= 2.0.0')
   s.add_dependency('slop',      '~> 3.6',  '>= 3.6.0')
 
+  s.add_development_dependency('capybara', '~> 2.18', '>= 2.18.0')
+  s.add_development_dependency('codeclimate-test-reporter',
+                               '~> 1.0', '>= 1.0.8')
+  s.add_development_dependency('rack-test', '~> 1.0', '>= 1.0.0')
   s.add_development_dependency('rake', '~> 10.3', '>= 10.3.2')
-  s.add_development_dependency('rspec', '~> 3.7',  '>= 3.7.0')
-  s.add_development_dependency('capybara', '~> 2.18',  '>= 2.18.0')
-  s.add_development_dependency('rack-test', '~> 1.0',  '>= 1.0.0')
+  s.add_development_dependency('rspec', '~> 3.7', '>= 3.7.0')
   s.add_development_dependency('sauce_whisk', '~> 0.0', '>= 0.0.19')
   s.add_development_dependency('selenium-webdriver', '~> 3.11', '>= 3.11.0')
-  s.add_development_dependency('codeclimate-test-reporter', '~> 1.0', '>= 1.0.8')
 
   # gem
   s.files         = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']
   s.executables   = ['sequenceserver']
   s.require_paths = ['lib']
 
   # post install information
-  s.post_install_message = <<INFO
+  s.post_install_message = <<~INFO
 
-------------------------------------------------------------------------
-  Thank you for installing SequenceServer :)!
+    ------------------------------------------------------------------------
+      Thank you for installing SequenceServer :)
 
-  To launch SequenceServer execute 'sequenceserver' from command line.
+      To launch SequenceServer execute 'sequenceserver' from command line.
 
-    $ sequenceserver
+        $ sequenceserver
 
 
-  Visit http://sequenceserver.com for more.
-------------------------------------------------------------------------
+      Visit http://sequenceserver.com for more.
+    ------------------------------------------------------------------------
 
-INFO
+  INFO
 end