sequenceserver 1.1.0.beta11 → 1.1.0.beta12

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: e7472a7e6ca36b52491902e61f4245a893183620
+  metadata.gz: cc2b025ab26f09234131859b1d60c39327111610
+  data.tar.gz: 149e0c2d93046a81ef5043795fd772ec23bcd706
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+  data.tar.gz: 976438929256906862c004244a9f1554496c0dd99aa15f8cf8bc2f84fd905cd1c0df258ed2ff90e057ed57edd5501b67c60080883524b7d701e94406e8c2c27c

data/.rubocop.yml

@@ -1,4 +1,5 @@
 AllCops:
+  TargetRubyVersion: 2.3
   Exclude:
     # Because these are vendor files.
     - 'node_modules/**/*'
@@ -21,15 +22,14 @@ Metrics/ModuleLength:
     - 'lib/sequenceserver.rb'
     - 'spec/blast_spec.rb'
 Metrics/ClassLength:
-  Exclude:
-    # TODO:
-    #   Evaluate whether to make class smaller or to increase 'Max'.
-    - 'lib/sequenceserver/database.rb'
+  Max: 150
 Metrics/BlockNesting:
   Exclude:
-    # TODO:
-    #   Fix in bin/sequenceserver and re-enable.
     - 'bin/sequenceserver'
+Metrics/BlockLength:
+  Exclude:
+    - 'bin/sequenceserver'
+    - 'sequenceserver.gemspec'
 
 Style/UnlessElse:
   # TODO:
@@ -48,9 +48,14 @@ Style/EachWithObject:
   Exclude:
     # Because we support 1.8.7.
     - '**/*.rb'
-Style/HashSyntax:
-  # Because we support 1.8.7.
-  EnforcedStyle: hash_rockets
 Style/AsciiComments:
   # Nothing wrong with non-ascii chars, like © in comments.
   Enabled: false
+Style/SignalException:
+  # Roughly, use fail to fail and raise to signal.
+  EnforcedStyle: semantic
+Style/FrozenStringLiteralComment:
+  # Immutability is good. Switching to immutable strings is like a paradigm
+  # shift and should be approached more carefully. Thus, disabling this cop
+  # for now.
+  Enabled: false

data/Rakefile

@@ -5,4 +5,4 @@ task :build do
   sh 'gem build sequenceserver.gemspec'
 end
 
-task :default => [:build]
+task default: [:build]

data/bin/sequenceserver

@@ -21,83 +21,83 @@ def download_from_url(url)
 end
 
 begin
-  Slop.parse!(:strict => true, :help => true) do
-    banner <<BANNER
-SUMMARY
+  Slop.parse!(strict: true, help: true) do
+    banner <<~BANNER
+      SUMMARY
 
-custom, local, BLAST server
+      custom, local, BLAST server
 
-USAGE
+      USAGE
 
-sequenceserver [options]
+      sequenceserver [options]
 
-EXAMPLE
+      EXAMPLE
 
-  # Launch SequenceServer. This will read configuration from
-  # ~/.sequenceserver.conf, if present.
-  $ sequenceserver
+        # Launch SequenceServer. This will read configuration from
+        # ~/.sequenceserver.conf, if present.
+        $ sequenceserver
 
-  # Use a different config file.
-  $ sequenceserver -c ~/.sequenceserver.ants.conf
+        # Use a different config file.
+        $ sequenceserver -c ~/.sequenceserver.ants.conf
 
-  # Set number of threads to use. This will save the number
-  # of threads to use in config file.
-  $ sequenceserver -s -n 16
+        # Set number of threads to use. This will save the number
+        # of threads to use in config file.
+        $ sequenceserver -s -n 16
 
-  # See if you have FASTA files in database dir that haven't
-  # been converted into BLAST database.
-  $ sequenceserver -u
+        # See if you have FASTA files in database dir that haven't
+        # been converted into BLAST database.
+        $ sequenceserver -u
 
-  # Search for FASTA files in database dir that haven't been
-  # converted into BLAST database yet, and convert them.
-  $ sequenceserver -m
+        # Search for FASTA files in database dir that haven't been
+        # converted into BLAST database yet, and convert them.
+        $ sequenceserver -m
 
-DESCRIPTION
+      DESCRIPTION
 
-SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
-interface for use locally or over the web. If BLAST+ is not installed on your
-system, SequenceServer will offer to install BLAST+ for you.  You should only
-ever have to point it to a directory of FASTA files / BLAST+ databases.
+      SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
+      interface for use locally or over the web. If BLAST+ is not installed on your
+      system, SequenceServer will offer to install BLAST+ for you.  You should only
+      ever have to point it to a directory of FASTA files / BLAST+ databases.
 
-In a given directory, SequenceServer is able to tell FASTA files that are yet
-to be formatted for use with BLAST+ and format them, and FASTA files that are
-already formatted for use with BLAST+, heuristically skipping all other files
-in the directory. Directories are scanned recursively. Type of sequences in a
-FASTA file is detected automagically. `parse_seqids` and `hash_index` options
-of `makeblastdb` are used to create BLAST+ databases.
-BANNER
+      In a given directory, SequenceServer is able to tell FASTA files that are yet
+      to be formatted for use with BLAST+ and format them, and FASTA files that are
+      already formatted for use with BLAST+, heuristically skipping all other files
+      in the directory. Directories are scanned recursively. Type of sequences in a
+      FASTA file is detected automagically. `parse_seqids` and `hash_index` options
+      of `makeblastdb` are used to create BLAST+ databases.
+    BANNER
 
     on 'c', 'config_file=',
        'Use the given configuration file',
-       :argument => true
+       argument: true
 
     on 'config=',
        'Same as --config_file (deprecated)',
-       :argument => true
+       argument: true
 
     on 'b', 'bin=',
        'Load BLAST+ binaries from this directory',
-       :argument => true
+       argument: true
 
     on 'd', 'database_dir=',
        'Read FASTA and BLAST database from this directory',
-       :argument => true
+       argument: true
 
     on 'n', 'num_threads=',
        'Number of threads to use to run a BLAST search',
-       :argument => true
+       argument: true
 
     on 'r', 'require=',
        'Load extension from this file',
-       :argument => true
+       argument: true
 
     on 'H', 'host=',
        'Host to run SequenceServer on',
-       :argument => true
+       argument: true
 
     on 'p', 'port=',
        'Port to run SequenceServer on',
-       :argument => true
+       argument: true
 
     on 's', 'set',
        'Set configuration value in default or given config file'
@@ -117,8 +117,8 @@ BANNER
     on 'i', 'interactive',
        'Run SequenceServer in interactive mode'
 
-    #on 'doctor',
-       #'Run SequenceServer doctor'
+    # on 'doctor',
+       # 'Run SequenceServer doctor'
 
     on 'D', 'devel',
        'Start SequenceServer in development mode'
@@ -162,21 +162,17 @@ BANNER
       # working SequenceServer installation. We expect to land following
       # error scenarios either when creating a new SequenceServer (first
       # time or later), or updating config values using -s CLI option.
-
       rescue SequenceServer::CONFIG_FILE_ERROR,
              SequenceServer::BLAST_DATABASE_ERROR => e
 
         puts e
         exit!
-
       rescue SequenceServer::ENOENT => e
         puts e
 
-        puts "Please consult sequenceserver --help for instructions on how to set the correct values."
+        puts 'Please consult sequenceserver --help for instructions on how to set the correct values.'
         exit!
-
       rescue SequenceServer::NUM_THREADS_INCORRECT => e
-
         puts e
 
         unless num_threads?
@@ -187,9 +183,7 @@ BANNER
         end
 
         exit!
-
       rescue SequenceServer::BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE,
-             SequenceServer::BLAST_NOT_INSTALLED,
              SequenceServer::BLAST_NOT_COMPATIBLE => e
 
         # Show original error message first.
@@ -203,15 +197,15 @@ BANNER
         # Ask user if she already has BLAST+ downloaded or offer to download
         # BLAST+ for her.
         puts
-        puts <<MSG
-SequenceServer can use NCBI BLAST+ that you may have on your system already, or
-download the correct package for itself. A recent system update may have broken
-your NCBI BLAST+ installation.
+        puts <<~MSG
+          SequenceServer can use NCBI BLAST+ that you may have on your system already, or
+          download the correct package for itself. A recent system update may have broken
+          your NCBI BLAST+ installation.
 
-Please enter the path to NCBI BLAST+ or press Enter to download.
+          Please enter the path to NCBI BLAST+ or press Enter to download.
 
-Press Ctrl+C to quit.
-MSG
+          Press Ctrl+C to quit.
+        MSG
         puts
         response = Readline.readline('>> ').to_s.strip
         if response.empty?
@@ -231,18 +225,18 @@ MSG
                   "#{version.chop}/" \
                   "ncbi-blast-#{version}-x64-macosx.tar.gz"
                 else
-                  puts <<ERR
-------------------------------------------------------------------------
-FAILED!! to install NCBI BLAST+.
+                  puts <<~ERR
+                    ------------------------------------------------------------------------
+                    FAILED!! to install NCBI BLAST+.
 
-We currently support Linux and Mac only (64 bit). If you
-believe you are running a supported platform, please open a support
-ticket titled "#{RUBY_PLATFORM}" at:
+                    We currently support Linux and Mac only (64 bit). If you
+                    believe you are running a supported platform, please open a support
+                    ticket titled "#{RUBY_PLATFORM}" at:
 
-https://github.com/yannickwurm/sequenceserver/issues
-------------------------------------------------------------------------
+                    https://github.com/yannickwurm/sequenceserver/issues
+                    ------------------------------------------------------------------------
 
-ERR
+                  ERR
                 end
           download_from_url(url)
           unless $CHILD_STATUS.success?
@@ -254,17 +248,15 @@ ERR
           end
           fetch_option(:bin).value =
             "~/.sequenceserver/ncbi-blast-#{version}/bin/"
-          redo
         else
           unless File.basename(response) == 'bin'
             response = File.join(response, 'bin')
           end
           fetch_option(:bin).value = File.join(response)
           puts
-          redo
         end
+        redo
       rescue SequenceServer::DATABASE_DIR_NOT_SET => e
-
         # Show original error message.
         puts
         puts e
@@ -276,18 +268,17 @@ ERR
         # Ask user for the directory containing sequences or BLAST+
         # databases.
         puts
-        puts <<MSG
-SequenceServer needs to know where your FASTA files or BLAST+ databases are.
-Please enter the path to the relevant directory (default: current directory).
+        puts <<~MSG
+          SequenceServer needs to know where your FASTA files or BLAST+ databases are.
+          Please enter the path to the relevant directory (default: current directory).
 
-Press Ctrl+C to quit.
-MSG
+          Press Ctrl+C to quit.
+        MSG
 
         puts
         response = Readline.readline('>> ').to_s.strip
         fetch_option(:database_dir).value = response
         redo
-
       rescue SequenceServer::NO_BLAST_DATABASE_FOUND => e
         unless list_databases? || list_unformatted_fastas? ||
                make_blast_databases?
@@ -299,14 +290,14 @@ MSG
           # Offer user to format the FASTA files.
           database_dir = SequenceServer.config[:database_dir]
           puts
-          puts <<MSG
-Search for FASTA files (.fa, .fasta, .fna) in '#{database_dir}' and try
-creating BLAST+ databases? [y/n] (Default: y).
-MSG
+          puts <<~MSG
+            Search for FASTA files (.fa, .fasta, .fna) in '#{database_dir}' and try
+            creating BLAST+ databases? [y/n] (Default: y).
+          MSG
           puts
           print '>> '
           response = STDIN.gets.to_s.strip
-          unless response.match(/^[n]$/i)
+          unless response =~ /^[n]$/i
             puts
             puts 'Searching ...'
             if SequenceServer::Database.unformatted_fastas.empty?
@@ -321,23 +312,22 @@ MSG
             exit! unless set?
           end
         end
-
       rescue => e
         # This will catch any unhandled error and some very special errors.
         # Ideally we will never hit this block. If we do, there's a bug in
         # SequenceServer or something really weird going on. If we hit this
         # error block we show the stacktrace to the user requesting them to
         # post the same to our Google Group.
-        puts <<MSG
-Something went wonky
+        puts <<~MSG
+          Something went wonky
 
-Looks like you have encountered a bug in SequenceServer. Please could you
-report this incident to our Google Group -
-https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
+          Looks like you have encountered a bug in SequenceServer. Please could you
+          report this incident to our Google Group -
+          https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
 
-Error:
-#{e.backtrace.unshift(e.message).join("\n")}
-MSG
+          Error:
+            #{e.backtrace.unshift(e.message).join("\n")}
+        MSG
         exit
       end
 

data/lib/sequenceserver.rb

@@ -16,13 +16,13 @@ require 'sequenceserver/doctor'
 # Top level module / namespace.
 module SequenceServer
   # Use a fixed minimum version of BLAST+
-  BLAST_VERSION = '2.6.0+'
+  BLAST_VERSION = '2.6.0+'.freeze
 
   # Default location of configuration file.
-  DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'
+  DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
 
   # Constant for denoting the path ~/.sequenceserver
-  DOTDIR = File.expand_path('~/.sequenceserver')
+  DOTDIR = File.expand_path('~/.sequenceserver').freeze
 
   class << self
     def environment
@@ -84,15 +84,13 @@ module SequenceServer
     #
     # Usage:
     #
-    # stdout, stderr = sys(command, :dir => '/path/to/directory',
-    # :path => '/path/to/directory')
+    # sys(command, dir: '/path/to/directory', path: '/path/to/directory',
+    #     stdout: '/path/to/stdout_file', stderr: '/path/to/stderr_file')
     #
-    # sys(command, :dir => '/path/to/directory',
-    # :path => '/path/to/directory', :stdout => '/path/to/stdout_file',
-    # :stderr => '/path/to/stderr_file')
+    # rubocop:disable Metrics/CyclomaticComplexity
     def sys(command, options = {})
       # Available output channels
-      channels = [:stdout, :stderr]
+      channels = %i[stdout stderr]
 
       # Make temporary files to store output from stdout and stderr.
       temp_files = {
@@ -150,6 +148,7 @@ module SequenceServer
       return temp_files.values if status.success?
       raise CommandFailed.new(status.exitstatus, **temp_files)
     end
+    # rubocop:enable Metrics/CyclomaticComplexity
 
     # Run SequenceServer as a self-hosted server using Thin webserver.
     def run
@@ -210,7 +209,7 @@ module SequenceServer
       if config[:bin]
         config[:bin] = File.expand_path config[:bin]
         unless File.exist?(config[:bin]) && File.directory?(config[:bin])
-          fail ENOENT.new("bin dir", config[:bin])
+          fail ENOENT.new('bin dir', config[:bin])
         end
         logger.debug("Will use NCBI BLAST+ at: #{config[:bin]}")
       else
@@ -227,7 +226,7 @@ module SequenceServer
       config[:database_dir] = File.expand_path(config[:database_dir])
       unless File.exist?(config[:database_dir]) &&
              File.directory?(config[:database_dir])
-        fail ENOENT.new("database dir", config[:database_dir])
+        fail ENOENT.new('database dir', config[:database_dir])
       end
 
       logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
@@ -240,13 +239,12 @@ module SequenceServer
 
     def check_num_threads
       num_threads = Integer(config[:num_threads])
-      fail NUM_THREADS_INCORRECT unless num_threads > 0
-
+      fail NUM_THREADS_INCORRECT unless num_threads.positive?
       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 ArgumentError
       raise NUM_THREADS_INCORRECT
     end
 
@@ -265,7 +263,7 @@ module SequenceServer
 
       config[:require] = File.expand_path config[:require]
       unless File.exist?(config[:require]) && File.file?(config[:require])
-        fail ENOENT.new("extension file", config[:require])
+        fail ENOENT.new('extension file', config[:require])
       end
 
       logger.debug("Loading extension: #{config[:require]}")
@@ -274,8 +272,8 @@ module SequenceServer
 
     def assert_blast_installed_and_compatible
       begin
-      out, _ = sys("blastdbcmd -version", path: config[:bin])
-      rescue
+        out, = sys('blastdbcmd -version', path: config[:bin])
+      rescue CommandFailed
         fail BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
       end
       version = out.split[1]
@@ -285,13 +283,16 @@ module SequenceServer
 
     def server_url
       host = config[:host]
-      host = 'localhost' if host == '127.0.0.1' || host == '0.0.0.0'
+      host = 'localhost' if ['127.0.0.1', '0.0.0.0'].include?(host)
       "http://#{host}:#{config[:port]}"
     end
 
     # Uses `open` on Mac or `xdg-open` on Linux to opens the search form in
     # user's default browser. This function is called when SequenceServer
     # is launched from the terminal. Errors, if any, are silenced.
+    #
+    # rubocop:disable Metrics/CyclomaticComplexity, Style/RescueStandardError,
+    # Lint/HandleExceptions
     def open_in_browser(server_url)
       return if using_ssh? || verbose?
       if RUBY_PLATFORM =~ /linux/ && xdg?
@@ -302,6 +303,8 @@ module SequenceServer
     rescue
       # fail silently
     end
+    # rubocop:enable Metrics/CyclomaticComplexity, Style/RescueStandardError,
+    # Lint/HandleExceptions
 
     def using_ssh?
       true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']