sequenceserver 1.0.0.pre.2 → 1.0.0.pre.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3f26e8eac4c55a9a2a0997d2ab6e922c88ded0d8
-  data.tar.gz: 60684bb5f9291fcbbfefd410517ea3892df9ff5c
+  metadata.gz: ddd56505296b6813bedb5e400c5d2fd44bb9fcf3
+  data.tar.gz: 126f3e127d5d3a1eadfac6bf7940d0ec08875997
 SHA512:
-  metadata.gz: a51d9aff1dc67c12898295dbbc36452216820c22695a0e2b1507fa977d49fe8cf235f2da44762b0a5229bce2e59266b00358f40b51a072fbb9de007b9b60bef0
-  data.tar.gz: 8042ec1559d3719d2f910681c8cb4988d6cf0fe81d4205d5b596929be31045b0309ec44ad3bd335a457fae2c3ad0c1d80dc0be4c3322fc5d07501af494210695
+  metadata.gz: 9207f4705a670d0b4a652d4b0a95c17910ebe9e296209d033914e56bd3c2119fad1406ca84c4f3d7515a49c3a2ebead11b9482fd4a0c2743632ea7d196d08f91
+  data.tar.gz: 372f45058b21fdff4d7b922efc1c8e51eb358eef9cd2d9cb10e8ecbed943966d1c82d366e0acc9d55e795b2129bc602a2686900269c337373b195224f0c7b960

data/Gemfile

@@ -1,3 +1,3 @@
-source "http://rubygems.org"
+source 'http://rubygems.org'
 
 gemspec

data/README.md

@@ -1,7 +1,21 @@
-Thanks for downloading SequenceServer!
+[![build status](https://secure.travis-ci.org/yannickwurm/sequenceserver.png?branch=master)](https://travis-ci.org/yannickwurm/sequenceserver)
+[![Code Climate](https://codeclimate.com/github/yannickwurm/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/yannickwurm/sequenceserver)
+[![Test Coverage](https://codeclimate.com/github/yannickwurm/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/yannickwurm/sequenceserver)
+[![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/yannickwurm/sequenceserver)
 
-Documentation available at http://www.sequenceserver.com
+# SequenceServer - BLAST searching made easy!
 
-[![build status](https://secure.travis-ci.org/yannickwurm/sequenceserver.png?branch=master)](https://travis-ci.org/yannickwurm/sequenceserver)
+SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
+interface for use locally or over the web.
+
+## Installation
+
+Please see http://www.sequenceserver.com
+
+## Contributors
 
--- Yannick Wurm, Ben Woodcroft, Anurag Priyam
+* Anurag Priyam - [email](mailto:anurag08priyam@gmail.com) | [@yeban](//twitter.com/yeban)
+* [Vivek Rai](http://vivekiitkgp.github.io/)
+* Ben Woodcroft
+* Yannick Wurm  - [http://wurmlab.github.io](http://wurmlab.github.io) |
+  [@yannick__](//twitter.com/yannick__)

data/bin/sequenceserver

@@ -1,5 +1,6 @@
 #!/usr/bin/env ruby
 require 'readline'
+require 'English'
 require 'slop'
 
 ENV['RACK_ENV'] ||= 'production'
@@ -46,133 +47,195 @@ used to create BLAST+ databases.
 BANNER
 
     on 'c', 'config_file=',
-      'Use the given configuration file',
-      :argument => true
+       'Use the given configuration file',
+       :argument => true
+    on 'config=',
+       'Same as --config_file (deprecated)',
+       :argument => true
 
     on 'b', 'bin=',
-      'Load BLAST+ binaries from this directory',
-      :argument => true
+       'Load BLAST+ binaries from this directory',
+       :argument => true
 
     on 'd', 'database_dir=',
-      'Read FASTA and BLAST database from this directory',
-      :argument => true
+       'Read FASTA and BLAST database from this directory',
+       :argument => true
 
     on 'n', 'num_threads=',
-      'Number of threads to use to run a BLAST search',
-      :argument => true
-      #:as       => Integer
+       'Number of threads to use to run a BLAST search',
+       :argument => true
 
     on 'r', 'require=',
-      'Load extension from this file',
-      :argument => true
+       'Load extension from this file',
+       :argument => true
 
     on 'h', 'host=',
-      'Host to run SequenceServer on',
-      :argument => true
+       'Host to run SequenceServer on',
+       :argument => true
 
     on 'p', 'port=',
-      'Port to run SequenceServer on',
-      :argument => true
+       'Port to run SequenceServer on',
+       :argument => true
 
     on 's', 'set',
-      'Set configuration value in default or given config file'
+       'Set configuration value in default or given config file'
 
     on 'm', 'make-blast-databases',
-      'Create BLAST databases'
+       'Create BLAST databases'
 
     on 'l', 'list_databases',
-      'List BLAST databases'
+       'List BLAST databases'
 
     on 'u', 'list-unformatted-fastas',
-      'List unformatted FASTA files'
+       'List unformatted FASTA files'
 
     on 'i', 'interactive',
-      'Run SequenceServer in interactive mode'
+       'Run SequenceServer in interactive mode'
 
     on 'D', 'devel',
-      'Start SequenceServer in development mode'
+       'Start SequenceServer in development mode'
 
     on '-v', '--version',
-      'Print version number of SequenceServer that will be loaded'
+       'Print version number of SequenceServer that will be loaded'
 
     on '-h', '--help',
-      'Display this help message'
+       'Display this help message'
+
+    clean_opts = lambda do |hash|
+      hash.delete_if { |k, v| k == :set || v.nil? }
+      hash[:config_file] ||= hash.delete(:config)
+      hash
+    end
 
     run do
       if version?
-        gemspec_file = File.join(File.dirname(__FILE__), '..', 'sequenceserver.gemspec')
+        gemspec_file = File.join(File.dirname(__FILE__), '..',
+                                 'sequenceserver.gemspec')
         gemspec = eval File.read gemspec_file
         puts gemspec.version
         exit
       end
 
       ENV['RACK_ENV'] = 'development' if devel?
-      # Save the state of user terminal
-      stty_save = `stty -g`.chomp
-      # Exit gracefully on SIGINT
+
+      # Exit gracefully on SIGINT.
+      stty = `stty -g`.chomp
       trap('INT') do
         puts ''
         puts 'Aborted.'
-        system('stty', stty_save)
+        system('stty', stty)
         exit
       end
 
       require 'sequenceserver'
+
       begin
-        opts = to_h.delete_if{|k, v| v.nil?}
-        opts.delete :set
-        SequenceServer.init opts
-      rescue SystemExit => e
-        # The aim of following error recovery scenarios is to guide user to a
-        # 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.
-
-        # Try error recovery now.
-        case e.status
-        when SequenceServer::EXIT_CONFIG_FILE_NOT_FOUND
-          # Create an empty configuration file to make SequenceServer happy.
-          File.open(SequenceServer.config_file, 'w') {}
-          puts "    Created."
-          redo
-        when SequenceServer::EXIT_BLAST_NOT_INSTALLED,
-          SequenceServer::EXIT_BLAST_NOT_COMPATIBLE
+        SequenceServer.init clean_opts[to_h]
+
+      # The aim of following error recovery scenarios is to guide user to a
+      # 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 => e
+
+        puts e
+        exit!
+
+      rescue SequenceServer::BIN_DIR_NOT_FOUND => e
 
-          # Set a flag so that if we recovered from error resulting config can be
-          # saved. Config will be saved unless invoked with -b option.
-          fetch_option(:set).value = !bin?
+        puts e
 
-          # Ask user if she already has BLAST+ downloaded or offer to download
-          # BLAST+ for her.
+        unless bin?
+          puts 'You can set the correct value by running:'
           puts
-          print 'Do you have BLAST+ downloaded already? [y/n] (Default: n): '
-          response = STDIN.gets.to_s.strip
-          if response.match(/^[y]$/i)
-            response = Readline.readline('Where? ').to_s.strip
-            unless File.basename(response) == 'bin'
-              fetch_option(:bin).value = File.join(response, 'bin')
-            end
-            redo
-          end
+          puts '  sequenceserver -s -b <value>'
+          puts
+        end
+
+        exit!
+
+      rescue SequenceServer::DATABASE_DIR_NOT_FOUND => e
+
+        puts e
 
+        unless database_dir?
+          puts 'You can set the correct value by running:'
           puts
-          print "Install BLAST+? [y/n] (Default: y): "
-          response = STDIN.gets.to_s.strip
-          unless response.match(/^[n]$/i)
-            puts
-            puts "*** Installing BLAST+."
-            puts "RUBY_PLATFORM #{RUBY_PLATFORM}"
-
-            version = SequenceServer::MINIMUM_BLAST_VERSION
-            url = case RUBY_PLATFORM
-                  when /i686-linux/   # 32 bit Linux
-                    "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{version.chop}/ncbi-blast-#{version}-ia32-linux.tar.gz"
-                  when /x86_64-linux/ # 64 bit Linux
-                    "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{version.chop}/ncbi-blast-#{version}-x64-linux.tar.gz"
-                  when /darwin/       # Mac
-                    "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{version.chop}/ncbi-blast-#{version}-universal-macosx.tar.gz"
-                  else
-                    puts <<ERR
+          puts '  sequenceserver -s -d <value>'
+          puts
+        end
+
+        exit!
+
+      rescue SequenceServer::NUM_THREADS_INCORRECT => e
+
+        puts e
+
+        unless num_threads?
+          puts 'You can set the correct value by running:'
+          puts
+          puts '  sequenceserver -s -n <value>'
+          puts
+        end
+
+        exit!
+
+      rescue SequenceServer::EXTENSION_FILE_NOT_FOUND => e
+
+        puts e
+
+        unless require?
+          puts 'You can set the correct value by running:'
+          puts
+          puts '  sequenceserver -s -r <value>'
+          puts
+        end
+
+        exit!
+
+      rescue SequenceServer::BLAST_NOT_INSTALLED,
+             SequenceServer::BLAST_NOT_COMPATIBLE => e
+
+        # Show original error message first.
+        puts
+        puts e
+
+        # Set a flag so that if we recovered from error resulting config can be
+        # saved. Config will be saved unless invoked with -b option.
+        fetch_option(:set).value = !bin?
+
+        # 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. Please enter the path to NCBI BLAST+
+or press Enter to download.
+
+Press Ctrl+C to quit.
+MSG
+        puts
+        response = Readline.readline('>> ').to_s.strip
+        if response.empty?
+          puts
+          puts 'Installing NCBI BLAST+.'
+          puts "RUBY_PLATFORM #{RUBY_PLATFORM}"
+
+          version = SequenceServer::MINIMUM_BLAST_VERSION
+          url = case RUBY_PLATFORM
+                when /i686-linux/   # 32 bit Linux
+                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
+                  "#{version.chop}/ncbi-blast-#{version}-ia32-linux.tar.gz"
+                when /x86_64-linux/ # 64 bit Linux
+                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
+                  "#{version.chop}/ncbi-blast-#{version}-x64-linux.tar.gz"
+                when /darwin/       # Mac
+                  'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/' \
+                  "#{version.chop}/" \
+                  "ncbi-blast-#{version}-universal-macosx.tar.gz"
+                else
+                  puts <<ERR
 ------------------------------------------------------------------------
 FAILED!! to install NCBI BLAST+.
 
@@ -184,54 +247,87 @@ https://github.com/yannickwurm/sequenceserver/issues
 ------------------------------------------------------------------------
 
 ERR
-                  end
-
-            archive = File.join('/tmp', File.basename(url))
-            system "wget -c #{url} -O #{archive} && mkdir -p ~/.sequenceserver && tar xvf #{archive} -C ~/.sequenceserver"
-            unless $?.success?
-              puts "*** Failed to install BLAST+."
-              puts "    You may need to download BLAST+ from - "
-              puts "     http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download"
-              puts "    Please ensure that you download BLAST+ version
-              #{SequenceServer::MINIMUM_BLAST_VERSION} or higher."
-              exit SequenceServer::EXIT_BLAST_INSTALLATION_FAILED
-            end
-            fetch_option(:bin).value = "~/.sequenceserver/ncbi-blast-#{version}/bin/"
-            redo
-          else
-            exit e.status unless set?
+                end
+
+          archive = File.join('/tmp', File.basename(url))
+          system "wget -c #{url} -O #{archive} && mkdir -p ~/.sequenceserver" \
+            "&& tar xvf #{archive} -C ~/.sequenceserver"
+          unless $CHILD_STATUS.success?
+            puts 'Failed to install BLAST+.'
+            puts '  You may need to download BLAST+ from - '
+            puts '   http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download'
+            puts "  Please ensure that you download BLAST+ version
+            #{SequenceServer::MINIMUM_BLAST_VERSION} or higher."
+            exit!
           end
-        when SequenceServer::EXIT_NO_SEQUENCE_DIR
-          # Ask user for the directory containing sequences or BLAST+
-          # databases.
+          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
+      rescue SequenceServer::DATABASE_DIR_NOT_SET => e
+
+        # Show original error message.
+        puts
+        puts e
+
+        # Set a flag so that if we recovered from error resulting config can be
+        # saved. Config will be saved unless invoked with -d option.
+        fetch_option(:set).value = !database_dir?
 
-          # Set a flag so that if we recovered from error resulting config can be
-          # saved. Config will be saved unless invoked with -d option.
-          fetch_option(:set).value = !database_dir?
+        # 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).
 
+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?
+
+          # Print error raised.
           puts
-          prompt = 'Where are the sequences you would like to search?' \
-                   ' (Default: current dir) '
-          response = Readline.readline(prompt).to_s.strip
-          fetch_option(:database_dir).value = response
-          redo
-        when SequenceServer::EXIT_NO_BLAST_DATABASE
-          unless list_databases? or list_unformatted_fastas? or make_blast_databases?
-            # Offer user to format the FASTA files.
+          puts e
+
+          # Offer user to format the FASTA files.
+          database_dir = SequenceServer[: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
+          print '>> '
+          response = STDIN.gets.to_s.strip
+          unless response.match(/^[n]$/i)
             puts
-            print 'Create databases? [y/n] (Default: y): '
-            response = STDIN.gets.to_s.strip
-            unless response.match(/^[n]$/i)
-              puts
-              puts "*** Creating databases."
-              SequenceServer::Database.make_blast_databases
-              redo
+            puts 'Searching ...'
+            if SequenceServer::Database.unformatted_fastas.empty?
+              puts "Couldn't find any FASTA files."
+              exit!
             else
-              exit e.status unless set?
+              formatted = SequenceServer::Database.make_blast_databases
+              exit! if formatted.empty? && !set?
+              redo unless set?
             end
+          else
+            exit! unless set?
           end
-        else
-          exit e.status
         end
       end
 
@@ -245,10 +341,11 @@ ERR
         exit
       end
 
-      if list_unformatted_fastas? or make_blast_databases?
+      if list_unformatted_fastas? || make_blast_databases?
         unformatted_fastas = SequenceServer::Database.unformatted_fastas
         if unformatted_fastas.empty?
-          puts "All FASTA files in #{SequenceServer[:database_dir]} are formatted."
+          puts "All FASTA files in #{SequenceServer[:database_dir]} are "\
+               'formatted.'
           exit
         end
       end
@@ -264,19 +361,17 @@ ERR
       end
 
       if set?
-        SequenceServer.send :write_config_file
+        SequenceServer.config.write_config_file
         exit
       end
 
-      if fetch_option(:set).value
-        SequenceServer.send :write_config_file
-      end
+      SequenceServer.config.write_config_file if fetch_option(:set).value
 
       SequenceServer.run
     end
   end
 rescue Slop::Error => e
   puts e
-  puts "Run '#{$0} -h' for help with command line options."
+  puts "Run '#{$PROGRAM_NAME} -h' for help with command line options."
   exit
 end