sequenceserver 1.0.0.pre.3 → 1.0.0.pre.4

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@@ -1,7 +1,7 @@
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data/README.md

@@ -1,7 +1,10 @@
 [![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)
+[![code climate](https://codeclimate.com/github/yannickwurm/sequenceserver/badges/gpa.svg)](https://codeclimate.com/github/yannickwurm/sequenceserver)
+[![coverage](https://codeclimate.com/github/yannickwurm/sequenceserver/badges/coverage.svg)](https://codeclimate.com/github/yannickwurm/sequenceserver)
+[![gem version](https://badge.fury.io/rb/sequenceserver.svg)](http://rubygems.org/gems/sequenceserver)
+[![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/sequenceserver?type=total&color=brightgreen)](http://rubygems.org/gems/sequenceserver)
+
+[![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/yannickwurm/sequenceserver)
 
 # SequenceServer - BLAST searching made easy!
 
@@ -10,7 +13,47 @@ interface for use locally or over the web.
 
 ## Installation
 
-Please see http://www.sequenceserver.com
+Please see http://www.sequenceserver.com.
+
+## Contribute
+
+You will need Ruby and NodeJS and respective package managers (RubyGems and
+npm) for development.
+
+##### Get source code.
+```
+git clone https://github.com/yannickwurm/sequenceserver
+cd sequenceserver
+```
+
+##### Install dependencies.
+###### Ruby
+```
+gem install bundler && bundle
+```
+
+###### Node
+```
+npm install
+```
+
+#### Run, test, lint
+```
+# Launch SequenceServer in development mode.
+bundle exec bin/sequenceserver -D
+
+# Run RSpec, Capybara, and RuboCop.
+rake
+
+# Run bootlint, csslint, jshint
+npm run-script cop
+
+# Minify JS and CSS
+npm run-script build
+```
+
+SequenceServer runs in production mode by default. Minified JS and CSS are
+picked in production mode only.
 
 ## Contributors
 

data/lib/sequenceserver.rb

@@ -1,16 +1,14 @@
-require 'yaml'
 require 'English'
-require 'fileutils'
-require 'sinatra/base'
 require 'thin'
-require 'json'
 
 require 'sequenceserver/exceptions'
 require 'sequenceserver/config'
 require 'sequenceserver/logger'
+require 'sequenceserver/search'
 require 'sequenceserver/sequence'
 require 'sequenceserver/database'
 require 'sequenceserver/blast'
+require 'sequenceserver/routes'
 
 # Top level module / namespace.
 module SequenceServer
@@ -90,7 +88,7 @@ module SequenceServer
     # controller.
     def call(env)
       env['rack.logger'] = logger
-      App.call(env)
+      Routes.call(env)
     end
 
     # Run SequenceServer interactively.
@@ -201,176 +199,4 @@ module SequenceServer
       system("which #{command} > /dev/null 2>&1")
     end
   end
-
-  # Controller.
-  class App < Sinatra::Base
-    # See
-    # http://www.sinatrarb.com/configuration.html
-    configure do
-      # We don't need Rack::MethodOverride. Let's avoid the overhead.
-      disable :method_override
-
-      # Ensure exceptions never leak out of the app. Exceptions raised within
-      # the app must be handled by the app. We do this by attaching error
-      # blocks to exceptions we know how to handle and attaching to Exception
-      # as fallback.
-      disable :show_exceptions, :raise_errors
-
-      # Make it a policy to dump to 'rack.errors' any exception raised by the
-      # app so that error handlers don't have to do it themselves. But for it
-      # to always work, Exceptions defined by us should not respond to `code`
-      # or http_status` methods. Error blocks errors must explicitly set http
-      # status, if needed, by calling `status` method.
-      # method.
-      enable :dump_errors
-
-      # We don't want Sinatra do setup any loggers for us. We will use our own.
-      set :logging, nil
-
-      # Public, and views directory will be found here.
-      set :root,    lambda { SequenceServer.root }
-    end
-
-    # See
-    # http://www.sinatrarb.com/intro.html#Mime%20Types
-    configure do
-      mime_type :fasta, 'text/fasta'
-      mime_type :xml,   'text/xml'
-      mime_type :tsv,   'text/tsv'
-    end
-
-    configure :production do
-      set :public_folder,
-          lambda { File.join SequenceServer.root, 'public', 'dist' }
-    end
-
-    helpers do
-      # Render an anchor element from the given Hash.
-      #
-      # See links.rb for example of a Hash object that will be rendered.
-      def a(link)
-        return unless link[:title] && link[:url]
-        a = ['<a']
-        a <<   "href=#{link[:url]}"
-        a <<   "class=\"#{link[:class]}\"" if link[:class]
-        a <<   "target=\"_blank\""         if absolute? link[:url]
-        a << '>'
-        a <<   "<i class=\"fa #{link[:icon]}\"></i>" if link[:icon]
-        a <<   link[:title]
-        a << '</a>'
-        a.join("\n")
-      end
-
-      # Is the given URI absolute? (or relative?)
-      def absolute?(uri)
-        URI.parse(uri).absolute?
-      end
-
-      # Prettify given data.
-      def prettify(data)
-        return prettify_tuple(data) if tuple? data
-        return prettify_float(data) if data.is_a? Float
-        data
-      end
-
-      # Formats float as "a.bcd" or "a x b^c". The latter if float is
-      # scientific notation. Former otherwise.
-      def prettify_float(float)
-        float.to_s.sub(/(\d*\.\d*)e?([+-]\d*)?/) do
-          base  = Regexp.last_match[1]
-          power = Regexp.last_match[2]
-          s = format '%.2f', base
-          s << " &times; 10<sup>#{power}</sup>" if power
-          s
-        end
-      end
-
-      # Formats an array of two elements as "first (last)".
-      def prettify_tuple(tuple)
-        "#{tuple.first} (#{tuple.last})"
-      end
-
-      # Is the given value a tuple? (array of length two).
-      def tuple?(data)
-        return true if data.is_a?(Array) && data.length == 2
-      end
-    end
-
-    # For any request that hits the app in development mode, log incoming
-    # params.
-    before do
-      logger.debug params
-    end
-
-    # Render the search form.
-    get '/' do
-      erb :search, :locals => { :databases => Database.group_by(&:type) }
-    end
-
-    # BLAST search!
-    post '/' do
-      erb :result, :locals => { :report => BLAST.run(params) }
-    end
-
-    # @params sequence_ids: whitespace separated list of sequence ids to
-    # retrieve
-    # @params database_ids: whitespace separated list of database ids to
-    # retrieve the sequence from.
-    # @params download: whether to return raw response or initiate file
-    # download
-    #
-    # Use whitespace to separate entries in sequence_ids (all other chars exist
-    # in identifiers) and retreival_databases (we don't allow whitespace in a
-    # database's name, so it's safe).
-    get '/get_sequence/' do
-      sequence_ids = params[:sequence_ids].split(/\s/)
-      database_ids = params[:database_ids].split(/\s/)
-
-      sequences = Sequence.from_blastdb(sequence_ids, database_ids)
-
-      if params[:download]
-        file_name = "sequenceserver_#{sequence_ids.first}.fasta"
-        file = Tempfile.new file_name
-        sequences.each do |sequence|
-          file.puts sequence.fasta
-        end
-        file.close
-        send_file file.path, :type => :fasta, :filename => file_name
-      else
-        {
-          :sequence_ids => sequence_ids,
-          :databases    => Database[database_ids].map(&:title),
-          :sequences    => sequences.map(&:info)
-        }.to_json
-      end
-    end
-
-    get '/get_report/' do
-      ofile = BLAST.format(params)
-
-      send_file ofile[:filepath],
-                :filename => ofile[:filename],
-                :type => ofile[:type].to_sym
-    end
-
-    # This error block will only ever be hit if the user gives us a funny
-    # sequence or incorrect advanced parameter. Well, we could hit this block
-    # if someone is playing around with our HTTP API too.
-    error BLAST::ArgumentError do
-      status 400
-      error = env['sinatra.error']
-      erb :'400', :locals => { :error => error }
-    end
-
-    # 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.
-    error Exception, BLAST::RuntimeError do
-      status 500
-      error = env['sinatra.error']
-      erb :'500', :locals => { :error => error }
-    end
-  end
 end

data/lib/sequenceserver/blast.rb

@@ -5,6 +5,8 @@ require 'ox'
 
 require 'sequenceserver/links'
 require 'sequenceserver/blast/exceptions'
+require 'sequenceserver/blast/constants'
+require 'sequenceserver/blast/formatter'
 require 'sequenceserver/blast/report'
 require 'sequenceserver/blast/query'
 require 'sequenceserver/blast/hit'
@@ -16,25 +18,6 @@ module SequenceServer
   # `BLAST::ArgumentError` and `BLAST::RuntimeError` signal errors encountered
   # when attempting a BLAST search.
   module BLAST
-    ERROR_LINE = /\(CArgException.*\)\s(.*)/
-
-    ALGORITHMS = %w(blastn blastp blastx tblastn tblastx)
-
-    OUTFMT = {
-      'pairwise'        => [0, 'txt'],
-      'qa_identity'     => [1, 'txt'],
-      'qa_no_identity'  => [2, 'txt'],
-      'fqa_identity'    => [3, 'txt'],
-      'fqa_no_identity' => [4, 'txt'],
-      'xml'             => [5, 'xml'],
-      'tsv'             => [6, 'tsv'],
-      'tsv_commented'   => [7, 'tsv'],
-      'asn_text'        => [8, 'asn'],
-      'asn_binary'      => [9, 'asn'],
-      'csv'             => [10, 'csv'],
-      'archive'         => [11, 'txt']
-    } # See [1]
-
     class << self
       extend Forwardable
 
@@ -109,30 +92,8 @@ module SequenceServer
           fail RuntimeError.new(status, error)
         end
 
-        Report.new(File.basename(rfile), databases)
-      end
-
-      def format(params)
-        validate_format_params params
-
-        rfile = create_file_path params['report']
-        ofmt  = OUTFMT[params['format']]
-        type  = params['type']
-
-        oname = "seqserv_#{type}_#{Time.now.strftime('%H%M')}.#{ofmt[1]}"
-        ofile = Tempfile.new oname
-
-        command =  "blast_formatter -archive '#{rfile}' -out #{ofile.path}" \
-                   " -outfmt '#{ofmt[0]} #{params['specifiers']}' 2> /dev/null"
-
-        logger.debug("Executing: #{command}")
-        system command
-
-        {
-          :filepath => ofile.path,
-          :filename => oname,
-          :type     => ofmt[1]
-        }
+        Search << rfile
+        Report.new(File.basename(rfile.path), databases)
       end
       # rubocop:enable Metrics/AbcSize, Metrics/CyclomaticComplexity
       # rubocop:enable Metrics/MethodLength
@@ -141,16 +102,6 @@ module SequenceServer
         params[:sequence].strip! unless params[:sequence].nil?
       end
 
-      def validate_format_params(params)
-        return true if params.include?('report') &&
-                       params.include?('format') &&
-                       File.exist?(create_file_path params['report'])
-        fail ArgumentError, <<MSG
-Incorrect request parameters. Please ensure that requested file name is
-correct and the file type is either xml or tsv.
-MSG
-      end
-
       def validate_blast_params(params)
         validate_blast_method params[:method]
         validate_blast_sequences params[:sequence]
@@ -201,12 +152,6 @@ MSG
         true
       end
 
-      # Returns filename if path exists otherwise returns a path to tmp dir.
-      def create_file_path(filename)
-        return File.join(Dir.tmpdir, filename) unless File.exist? filename
-        filename
-      end
-
       def allowed_chars
         /\A[a-z0-9\-_\. ']*\Z/i
       end

data/lib/sequenceserver/blast/constants.rb

@@ -0,0 +1,34 @@
+module SequenceServer
+  # Define constanst used by BLAST module.
+  module BLAST
+    ERROR_LINE = /\(CArgException.*\)\s(.*)/
+
+    ALGORITHMS = %w(blastn blastp blastx tblastn tblastx)
+
+    OUTFMT_SPECIFIERS = %w(qseqid qgi qacc sseqid sallseqid sgi sallgi sacc
+                           sallacc qstart qend sstart send qseq sseq evalue
+                           bitscore score length length pident nident
+                           mismatch positive gapopen gaps ppos frames
+                           qframe hframe btop staxids sscinames scomnames
+                           sblastnames sskingdoms stitle salltitles sstrand
+                           qcovs qcovhsp)
+    OUTFMT = {
+      'pairwise'        => [0, :txt],
+      'qa'              => [1, :txt],
+      'qa_no_identity'  => [2, :txt],
+      'fqa'             => [3, :txt],
+      'fqa_no_identity' => [4, :txt],
+      'xml'             => [5, :xml],
+      'std_tsv'         => [7, :tsv],
+      'full_tsv'        => [7, :tsv, OUTFMT_SPECIFIERS],
+      'asn_text'        => [8, :asn],
+      'asn_binary'      => [9, :asn],
+      'csv'             => [10, :csv],
+      'archive'         => [11, :txt]
+    }
+  end
+end
+
+# References
+# ----------
+# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/

data/lib/sequenceserver/blast/formatter.rb

@@ -0,0 +1,69 @@
+require 'forwardable'
+
+module SequenceServer
+  module BLAST
+    # Formats BLAST+ archive file format into other file formats.
+    class Formatter
+      class << self
+        alias_method :run, :new
+      end
+
+      extend Forwardable
+
+      def_delegators SequenceServer, :logger
+
+      def initialize(search_id, type)
+        @archive_file = get_archive_file search_id
+        @format, @mime, @specifiers = OUTFMT[type]
+        @type = type
+
+        validate && run
+      end
+
+      attr_reader :archive_file, :type
+
+      attr_reader :format, :mime, :specifiers
+
+      def file
+        @file ||= Tempfile.new filename
+      end
+
+      def filename
+        @filename ||=
+          "sequenceserver-#{type}_report.#{mime}"
+      end
+
+      private
+
+      def run
+        command =
+          "blast_formatter -archive '#{archive_file}'" \
+          " -outfmt '#{format} #{specifiers}'" \
+          " -out '#{file.path}' 2> /dev/null"
+        logger.debug("Executing: #{command}")
+        system command
+      end
+
+      def validate
+        return true if archive_file && format &&
+                       File.exist?(archive_file)
+        fail ArgumentError, <<MSG
+Incorrect request parameters. Please ensure that requested file name is
+correct and the file type is either xml or tsv.
+MSG
+      end
+
+      # Returns filename if path exists otherwise returns a path to tmp dir.
+      def get_archive_file(file)
+        return unless file
+        return file.path if file.respond_to? :path
+        return file if File.exist? file
+        File.join Dir.tmpdir, file
+      end
+    end
+  end
+end
+
+# References
+# ----------
+# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/