sequenceserver 1.1.0.beta11 → 1.1.0.beta12

data/lib/sequenceserver/exceptions.rb

@@ -22,10 +22,10 @@ module SequenceServer
     attr_reader :ent, :err
 
     def to_s
-      <<MSG
-Error reading config file: #{ent}.
-#{err}
-MSG
+      <<~MSG
+        Error reading config file: #{ent}.
+          #{err}
+      MSG
     end
   end
 
@@ -67,13 +67,7 @@ MSG
   # user's system.
   class BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE < StandardError
     def to_s
-      "BLAST not installed, or is not executable."
-    end
-  end
-
-  class BLAST_NOT_INSTALLED < StandardError
-    def to_s
-      'Could not locate BLAST+ binaries.'
+      'BLAST not installed, or is not executable.'
     end
   end
 
@@ -95,10 +89,10 @@ MSG
     attr_reader :version
 
     def to_s
-      <<MSG
-Your BLAST+ version #{version} is incompatible.
-SequenceServer needs NCBI BLAST+ version #{BLAST_VERSION}.
-MSG
+      <<~MSG
+        Your BLAST+ version #{version} is incompatible.
+        SequenceServer needs NCBI BLAST+ version #{BLAST_VERSION}.
+      MSG
     end
   end
 
@@ -134,20 +128,19 @@ MSG
     attr_reader :cmd, :out
 
     def to_s
-      <<MSG
-Error obtaining BLAST databases.
-Tried: #{cmd}
-Error:
-#{out.strip}
-
-Please could you report this to 'https://groups.google.com/forum/#!forum/sequenceserver'?
-MSG
+      <<~MSG
+        Error obtaining BLAST databases.
+        Tried: #{cmd}
+        Error:
+          #{out.strip}
+
+        Please could you report this to 'https://groups.google.com/forum/#!forum/sequenceserver'?
+      MSG
     end
   end
 
   # Raised if the 'sys' method could not successfully execute a shell command.
   class CommandFailed < StandardError
-
     def initialize(exitstatus, stdout: nil, stderr: nil)
       @exitstatus = exitstatus
       @stdout = stdout

data/lib/sequenceserver/job.rb

@@ -24,7 +24,7 @@ module SequenceServer
     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 @@ module SequenceServer
 
       # 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 @@ module SequenceServer
     # 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 @@ module SequenceServer
     # 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 @@ module SequenceServer
     # NOTE: Not used.
     def fetch(key)
       filename = File.join(dir, key)
-      raise if !File.exist? filename
+      fail unless File.exist? filename
       filename
     end
 

data/lib/sequenceserver/links.rb

@@ -1,12 +1,11 @@
+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+)\|/
     UNIPROT_ID_PATTERN = /sp\|(\w+)\|/
@@ -66,10 +65,10 @@ module SequenceServer
       ncbi_id = encode ncbi_id
       url = "http://www.ncbi.nlm.nih.gov/#{querydb.first.type}/#{ncbi_id}"
       {
-        :order => 2,
-        :title => 'NCBI',
-        :url   => url,
-        :icon  => 'fa-external-link'
+        order: 2,
+        title: 'NCBI',
+        url:   url,
+        icon:  'fa-external-link'
       }
     end
 
@@ -79,10 +78,10 @@ module SequenceServer
       uniprot_id = encode uniprot_id
       url = "http://www.uniprot.org/uniprot/#{uniprot_id}"
       {
-        :order => 2,
-        :title => 'Uniprot',
-        :url   => url,
-        :icon  => 'fa-external-link'
+        order: 2,
+        title: 'Uniprot',
+        url:   url,
+        icon:  'fa-external-link'
       }
     end
   end

data/lib/sequenceserver/logger.rb

@@ -11,7 +11,7 @@ module SequenceServer
 
     # 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'

data/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)

data/lib/sequenceserver/report.rb

@@ -6,7 +6,6 @@ module SequenceServer
   # Report is a generic superclass. Programs, like BLAST, must implement their
   # own report subclass.
   class Report
-
     class << self
       # Generates report for the given job. Returns generated report object.
       #

data/lib/sequenceserver/routes.rb

@@ -42,7 +42,7 @@ module SequenceServer
       # '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 @@ module SequenceServer
 
     # 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
 
@@ -104,26 +104,26 @@ module SequenceServer
     # 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(",")
-      database_ids = params[:database_ids].split(",")
+      sequence_ids = params[:sequence_ids].split(',')
+      database_ids = params[:database_ids].split(',')
       sequences = Sequence::Retriever.new(sequence_ids, database_ids)
       sequences.to_json
     end
 
     post '/get_sequence' do
-      sequence_ids = params["sequence_ids"].split(",")
-      database_ids = params["database_ids"].split(",")
+      sequence_ids = params['sequence_ids'].split(',')
+      database_ids = params['database_ids'].split(',')
       sequences = Sequence::Retriever.new(sequence_ids, database_ids, true)
       send_file(sequences.file.path,
-                :type     => sequences.mime,
-                :filename => sequences.filename)
+                type:     sequences.mime,
+                filename: sequences.filename)
     end
 
     # Download BLAST report in various formats.
     get '/download/:jid.:type' do |jid, type|
       job = Job.fetch(jid)
       out = BLAST::Formatter.new(job, type)
-      send_file out.file, :filename => out.filename, :type => out.mime
+      send_file out.file, filename: out.filename, type: out.mime
     end
 
     # Catches any exception raised within the app and returns JSON
@@ -155,13 +155,13 @@ module SequenceServer
       # 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

data/lib/sequenceserver/sequence.rb

@@ -67,7 +67,7 @@ module SequenceServer
     end
 
     def info
-      { :value => value, :id => id, :title => title }
+      { value: value, id: id, title: title }
     end
 
     # Returns FASTA formatted sequence.
@@ -97,7 +97,7 @@ module SequenceServer
         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
@@ -188,8 +188,8 @@ module SequenceServer
 
       def to_json
         {
-          :error_msgs => error_msgs,
-          :sequences  => sequences.map(&:info)
+          error_msgs: error_msgs,
+          sequences:  sequences.map(&:info)
         }.to_json
       end
 
@@ -200,7 +200,7 @@ module SequenceServer
                   " -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
@@ -233,21 +233,25 @@ module SequenceServer
         return [] if sequences.length == sequence_ids.length
         [
           ['ERROR: incorrect number of sequences found.',
-           <<MSG
-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 (or
-https://groups.google.com/forum/?fromgroups#!forum/sequenceserver
-if you are the admin) so that the issue can be resolved.
-
-If any sequences were retrieved, you can find them below
-(but some may be incorrect, so be careful!)
-MSG
+           <<~MSG
+             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.
+             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
           ]
         ]
       end

data/lib/sequenceserver/server.rb

@@ -35,13 +35,13 @@ module SequenceServer
     # 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
@@ -49,7 +49,7 @@ module SequenceServer
     private
 
     def setup_signal_handlers
-      [:INT, :TERM].each do |sig|
+      %i[INT TERM].each do |sig|
         trap sig do
           stop
         end

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta11'
+  VERSION = '1.1.0.beta12'.freeze
 end

data/public/js/search.js

@@ -197,23 +197,13 @@ var DnD = React.createClass({
 var Form = React.createClass({
 
     getInitialState: function () {
-        return {
-            databases: {},
-            preDefinedOpts: {
-                'blastn':  ['-task blastn', '-evalue 1e-5'],
-                'blastp':  ['-evalue 1e-5'],
-                'blastx':  ['-evalue 1e-5'],
-                'tblastx': ['-evalue 1e-5'],
-                'tblastn': ['-evalue 1e-5']
-            }
-        };
+        return { databases: {}, preDefinedOpts: {} };
     },
 
     componentDidMount: function () {
         $.getJSON("searchdata.json", _.bind(function(data) {
             this.setState({
-                databases: data["database"], preDefinedOpts: $.extend({},
-                this.state.preDefinedOpts, data["options"])
+                databases: data["database"], preDefinedOpts: data["options"]
             });
         }, this));
 

data/public/sequenceserver-search.min.js

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advanced parameters.",placeholder:"eg: -evalue 1.0e-5 -num_alignments 100",value:this.state.preOpts,onChange:this.updateBox}),d.createElement("div",{className:"input-group-addon cursor-pointer","data-toggle":"modal","data-target":"#help"},d.createElement("i",{className:"fa fa-question"}))))))}}),n=d.createClass({displayName:"SearchButton",inputGroup:function(){return $(d.findDOMNode(this.refs.inputGroup))},submitButton:function(){return $(d.findDOMNode(this.refs.submitButton))},initTooltip:function(){this.inputGroup().tooltip({trigger:"manual",title:c.bind(function(){return this.state.hasQuery||this.state.hasDatabases?this.state.hasQuery&&!this.state.hasDatabases?"You must select one or more databases above before you can run a search!":!this.state.hasQuery&&this.state.hasDatabases?"You must enter a query sequence above before you can run a search!":void 0:"You must enter a query sequence and select one or more databases above before you can run a search!"},this)}),this.submitButton().tooltip({title:c.bind(function(){var a="Click to BLAST or press Ctrl+Enter.";return this.state.methods.length>1&&(a+=" Click dropdown button on the right for other BLAST algorithms that can be used."),a},this)})},showTooltip:function(){this.inputGroup()._tooltip("show")},hideTooltip:function(){this.inputGroup()._tooltip("hide")},changeAlgorithm:function(a){var b=this.state.methods.slice();b.splice(b.indexOf(a),1),b.unshift(a),this.setState({methods:b})},decorate:function(a){return a.match(/(.?)(blast)(.?)/).slice(1).map(function(a,b){if(a)return"blast"!==a?d.createElement("strong",{key:a},a):a})},getInitialState:function(){return{methods:[],hasQuery:!1,hasDatabases:!1}},render:function(){var a=this.state.methods,b=a[0],e=a.length>1;return d.createElement("div",{className:"col-md-4"},d.createElement("div",{className:"form-group"},d.createElement("div",{className:"col-md-12"},d.createElement("div",{className:e&&"input-group",id:"methods",ref:"inputGroup",onMouseOver:this.showTooltip,onMouseOut:this.hideTooltip},d.createElement("button",{type:"submit",className:"btn btn-primary form-control text-uppercase",id:"method",ref:"submitButton",name:"method",value:b,disabled:!b},this.decorate(b||"blast")),e&&d.createElement("div",{className:"input-group-btn"},d.createElement("button",{className:"btn btn-primary dropdown-toggle","data-toggle":"dropdown"},d.createElement("span",{className:"caret"})),d.createElement("ul",{className:"dropdown-menu dropdown-menu-right"},c.map(a.slice(1),c.bind(function(a){return d.createElement("li",{key:a,className:"text-uppercase",onClick:c.bind(function(){this.changeAlgorithm(a)},this)},a)},this))))))))},componentDidMount:function(){this.initTooltip()},shouldComponentUpdate:function(a,b){return!c.isEqual(b.methods,this.state.methods)},componentDidUpdate:function(){this.state.methods.length>0?(this.inputGroup().wiggle(),this.props.onAlgoChanged(this.state.methods[0])):this.props.onAlgoChanged("")}}),d.render(d.createElement(e,null),document.getElementById("view"))}}})})(function(a){a()});

data/sequenceserver.gemspec

@@ -11,26 +11,27 @@ 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']
@@ -38,18 +39,18 @@ DESC
   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