sequenceserver 1.0.3 → 1.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 910445c0b05d5d6a4fa903c392c9db1bf591849e
-  data.tar.gz: 73971a25168f906c4dea26876f3a56b9033baaba
+  metadata.gz: 9040c6020c1e07fdb573d72393de66c9db7fc48c
+  data.tar.gz: 6d42a977fd1d4a26528f60738b35c3155eb65c12
 SHA512:
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+  data.tar.gz: d0d705074535ea97e6935e4e098aade727dad62b3aa641b3028da10309c959eb0b3a7726dfa02ec4f427b1317f42a23bb30eefbf24f24aad86523c92abe52b3e

data/.rubocop.yml

@@ -14,6 +14,12 @@ Metrics/MethodLength:
   Exclude:
     # TODO:
     - 'lib/sequenceserver.rb'
+Metrics/ModuleLength:
+  Exclude:
+    # TODO:
+    #   Revisit later.
+    - 'lib/sequenceserver.rb'
+    - 'spec/blast_spec.rb'
 Metrics/ClassLength:
   Exclude:
     # TODO:

data/bin/sequenceserver

@@ -8,6 +8,18 @@ ENV['RACK_ENV'] ||= 'production'
 # display name for tools like `ps`
 $PROGRAM_NAME = 'sequenceserver'
 
+# Given a url downloads the archive into a temporary file
+# and and extratcs it into ~/.sequenceserver
+def download_from_url(url)
+  archive = File.join('/tmp', File.basename(url))
+  # -ip4 is required  to avoid this curl bug http://sourceforge.net/p/curl/bugs/1424/?limit=25
+  # see also https://github.com/yannickwurm/sequenceserver/issues/139
+  cmd = "curl -ip4 -C - #{url} -o #{archive} && " \
+        'mkdir -p ~/.sequenceserver && '          \
+        "tar xvf #{archive} -C ~/.sequenceserver"
+  system cmd
+end
+
 begin
   Slop.parse!(:strict => true, :help => true) do
     banner <<BANNER
@@ -19,31 +31,40 @@ USAGE
 
 sequenceserver [options]
 
-Example:
+EXAMPLE
 
-  # launch SequenceServer with the given config file
+  # Launch SequenceServer. This will read configuration from
+  # ~/.sequenceserver.conf, if present.
+  $ sequenceserver
+
+  # Use a different config file.
   $ sequenceserver -c ~/.sequenceserver.ants.conf
 
-  # use the bundled database formatter utility to prepare databases for use
-  # with SequenceServer
+  # 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
+
+  # Search for FASTA files in database dir that haven't been
+  # converted into BLAST database yet, and convert them.
   $ sequenceserver -m
 
 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.
+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` option of `makeblastdb` is
-used to create BLAST+ databases.
+FASTA file is detected automagically. `parse_seqids` and `hash_index` options
+of `makeblastdb` are used to create BLAST+ databases.
 BANNER
 
     on 'c', 'config_file=',
@@ -83,6 +104,9 @@ BANNER
     on 'm', 'make-blast-databases',
        'Create BLAST databases'
 
+    on 'download-taxdb',
+       'Download the taxdb files'
+
     on 'l', 'list_databases',
        'List BLAST databases'
 
@@ -248,13 +272,7 @@ https://github.com/yannickwurm/sequenceserver/issues
 
 ERR
                 end
-
-          archive = File.join('/tmp', File.basename(url))
-          # -ip4 is required  to avoid this curl bug http://sourceforge.net/p/curl/bugs/1424/?limit=25
-          # see also https://github.com/yannickwurm/sequenceserver/issues/139
-          system "curl -ip4 -C - #{url} -o #{archive} && "    \
-                 'mkdir -p ~/.sequenceserver && '             \
-                 "tar xvf #{archive} -C ~/.sequenceserver"
+          download_from_url(url)
           unless $CHILD_STATUS.success?
             puts 'Failed to install BLAST+.'
             puts '  You may need to download BLAST+ from - '
@@ -381,6 +399,14 @@ MSG
         exit
       end
 
+      if download_taxdb?
+        download_from_url('ftp://ftp.ncbi.nlm.nih.gov/blast/db/'\
+                          'taxdb.tar.gz')
+        puts
+        puts 'taxdb downloaded!'
+        exit
+      end
+
       if set?
         SequenceServer.config.write_config_file
         exit

data/lib/sequenceserver/blast/constants.rb

@@ -1,4 +1,7 @@
+# Define constants used by SequenceServer module
 module SequenceServer
+  # Constant for denoting the path ~/.sequenceserver
+  DOTDIR = File.expand_path('~/.sequenceserver')
   # Define constanst used by BLAST module.
   module BLAST
     ERROR_LINE = /\(CArgException.*\)\s(.*)/

data/lib/sequenceserver/blast/exceptions.rb

@@ -11,7 +11,7 @@ module SequenceServer
     # RuntimeError is raised when BLAST+'s exits status is one of 2, 3, 4, or
     # 255; see [1].  These are rare, infrastructure errors, used internally,
     # and of concern only to the admins/developers.
-    class RuntimeError  < RuntimeError
+    class RuntimeError < RuntimeError
       def initialize(status, message)
         @status  = status
         @message = message

data/lib/sequenceserver/blast/formatter.rb

@@ -41,7 +41,7 @@ module SequenceServer
           " -outfmt '#{format} #{specifiers}'" \
           " -out '#{file.path}' 2> /dev/null"
         logger.debug("Executing: #{command}")
-        system command
+        system(command, :chdir => (File.exist?(DOTDIR) && DOTDIR || Dir.pwd))
       end
 
       def validate

data/lib/sequenceserver/blast/hit.rb

@@ -26,7 +26,7 @@ module SequenceServer
       def links
         links = Links.instance_methods.map { |m| send m }
         links.compact!
-        links.sort_by { |link| link[:order] }
+        links.sort_by { |link| [link[:order], link[:title]] }
       end
 
       # Returns an array of database objects which contain the queried sequence

data/lib/sequenceserver/blast/hsp.rb

@@ -27,6 +27,7 @@ module SequenceServer
       # Returns a Hash of stats common to all BLAST algorithms. Subclasses must
       # update the returned Hash to add relevant stats of their own.
       #
+      # rubocop:disable Metrics/AbcSize
       def stats
         {
           'Score'      => [in_twodecimal(bit_score), score],
@@ -37,6 +38,7 @@ module SequenceServer
                            in_percentage(gaps, length)]
         }
       end
+      # rubocop:enable Metrics/AbcSize
 
       # Returns pretty formatted alignment String.
       #

data/lib/sequenceserver/blast/query.rb

@@ -17,7 +17,8 @@ module SequenceServer
       end
 
       def sort_hits_by_evalue!
-        @hits = hits.sort_by(&:evalue)
+        # change made here
+        @hits = hits.sort_by { |h| [h.evalue, h.score] }
       end
 
       attr_reader :id, :title

data/lib/sequenceserver/database.rb

@@ -96,6 +96,8 @@ module SequenceServer
       end
 
       # Recurisvely scan `database_dir` for blast databases.
+      #
+      # rubocop:disable Metrics/AbcSize, Metrics/MethodLength
       def scan_databases_dir
         cmd = "blastdbcmd -recursive -list #{config[:database_dir]}" \
               ' -list_outfmt "%f	%t	%p	%n	%l	%d"'
@@ -115,6 +117,7 @@ module SequenceServer
           throw_scan_error(cmd, out, err, $CHILD_STATUS)
         end
       end
+      # rubocop:enable Metrics/AbcSize, Metrics/MethodLength
 
       def throw_scan_error(cmd, out, err, child_status)
         errpat = /BLAST Database error/
@@ -156,12 +159,14 @@ module SequenceServer
       def make_blast_database(file, type)
         return unless make_blast_database? file, type
         title = get_database_title(file)
-        _make_blast_database(file, type, title)
+        taxid = fetch_tax_id
+        _make_blast_database(file, type, title, taxid)
       end
 
-      def _make_blast_database(file, type, title, quiet = false)
+      def _make_blast_database(file, type, title, taxid, quiet = false)
         cmd = 'makeblastdb -parse_seqids -hash_index ' \
-              "-in #{file} -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'"
+              "-in #{file} -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
+              " -taxid #{taxid}"
         cmd << ' &> /dev/null' if quiet
         system cmd
       end
@@ -176,7 +181,6 @@ module SequenceServer
         puts "FASTA file: #{file}"
         puts "FASTA type: #{type}"
         print 'Proceed? [y/n] (Default: y): '
-
         response = STDIN.gets.to_s.strip
         !response.match(/n/i)
       end
@@ -188,8 +192,19 @@ module SequenceServer
       def get_database_title(path)
         default = make_db_title(File.basename(path))
         print "Enter a database title or will use '#{default}': "
-        from_user = STDIN.gets.to_s
-        from_user.strip.empty? && default || from_user
+        from_user = STDIN.gets.to_s.strip
+        from_user.empty? && default || from_user
+      end
+
+      # Get taxid from the user. Returns user input or 0.
+      #
+      # Using 0 as taxid is equivalent to not setting taxid for the database
+      # that will be created.
+      def fetch_tax_id
+        default = 0
+        print 'Enter taxid (optional): '
+        response_user = STDIN.gets.to_s.strip
+        response_user.empty? && default || response_user
       end
 
       # Returns true if the database name appears to be a multi-part database
@@ -200,7 +215,7 @@ module SequenceServer
       # /home/ben/pd.ben/sequenceserver/db/nr => no
       # /home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01 => yes
       def multipart_database_name?(db_name)
-        !(db_name.match(/.+\/\S+\d{2}$/).nil?)
+        !(db_name.match(%r{.+/\S+\d{2}$}).nil?)
       end
 
       # Returns true if first character of the file is '>'.

data/lib/sequenceserver/links.rb

@@ -8,7 +8,8 @@ module SequenceServer
     #
     alias_method :encode, :url_encode
 
-    NCBI_ID_PATTERN = /gi\|(\d+)\|/
+    NCBI_ID_PATTERN    = /gi\|(\d+)\|/
+    UNIPROT_ID_PATTERN = /sp\|(\w+)\|/
 
     # Link generators return a Hash like below.
     #
@@ -101,6 +102,19 @@ module SequenceServer
         :icon  => 'fa-external-link'
       }
     end
+
+    def uniprot
+      return nil unless id.match(UNIPROT_ID_PATTERN)
+      uniprot_id = Regexp.last_match[1]
+      uniprot_id = encode uniprot_id
+      url = "http://www.uniprot.org/uniprot/#{uniprot_id}"
+      {
+        :order => 2,
+        :title => 'Uniprot',
+        :url   => url,
+        :icon  => 'fa-external-link'
+      }
+    end
   end
 end
 

data/lib/sequenceserver/routes.rb

@@ -46,7 +46,7 @@ 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 }
       }
     end
 

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.0.3'
+  VERSION = '1.0.4'
 end

data/public/dist/js/sequenceserver.min.js

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window?window:{})},{}],"biojs-io-fasta":[function(a,b){b.exports.parse=a("./parser"),b.exports.writer=a("./writer")},{"./parser":6,"./writer":9}],"biojs-vis-sequence":[function(a,b){b.exports=a("./lib/index")},{"./lib/index":1}]},{},["biojs-vis-sequence"]),$.webshims.polyfill("forms"),function(a){a.fn.disable=function(){return this.prop("disabled",!0).addClass("disabled")},a.fn.enable=function(){return this.prop("disabled",!1).removeClass("disabled")},a.fn.check=function(){return this.prop("checked",!0)},a.fn.uncheck=function(){return this.prop("checked",!1)},a.fn._tooltip=a.fn.tooltip,a.fn.tooltip=function(b){return this._tooltip("destroy")._tooltip(a.extend({container:"body",placement:"left"},b))},a.modalActive=function(){var b=!1;return a(".modal").each(function(){var c=a(this).data("bs.modal");return c?(b=c.isShown,!b):void 0}),b},a.fn.wiggle=function(){this.finish().effect("bounce",{direction:"left",distance:24,times:4},250)},a.fn.poll=function(){var a,b=this,c=null;return function d(){a=b.val(),a!=c&&(c=a,b.change()),setTimeout(d,100)}(),this}}(jQuery);var SS;SS||(SS={}),function(){SS.FASTA_FORMAT=/^>/,SS.decorate=function(a){return a.match(/(.?)(blast)(.?)/).slice(1).map(function(a){return a?"blast"!==a?"<strong>"+a+"</strong>":a:void 0}).join("")},SS.onedb=function(){var a=$(".databases input:checkbox");1===a.length&&a.check()},SS.generateGraphicalOverview=function(){$("[data-graphit='overview']").each(function(){var a=$(this),b=$("<div/>").addClass("graphical-overview");a.children().eq(1).children().eq(0).before(b),$.graphIt(a,b,0,20)})},SS.updateDownloadFastaOfAllLink=function(){var a=$(".hitn").length,b=$(".download-fasta-of-all");if(a>=1&&30>=a){var c=$(".hitn :checkbox").map(function(){return this.value}).get();return void b.enable().attr("href",SS.generateURI(c,b.data().databases)).tooltip({title:a+" hit(s)."})}0===a&&b.tooltip({title:"No hit to download."}),a>30&&b.tooltip({title:"Can't download more than 30 hits."}),b.disable().removeAttr("href")},SS.updateDownloadFastaOfSelectedLink=function(){var a=$(".hitn :checkbox:checked").length,b=$(".download-fasta-of-selected"),c=b.find("span");if(a>=1&&30>=a){var d=$(".hitn :checkbox:checked").map(function(){return this.value}).get();return void b.enable().attr("href",SS.generateURI(d,b.data().databases)).tooltip({title:a+" hit(s) selected."}).find("span").html(a)}0===a&&(c.empty(),b.tooltip({title:"No hit selected."})),a>30&&b.tooltip({title:"Can't download more than 30 hits."}),b.disable().removeAttr("href")},SS.updateSequenceViewerLinks=function(){var a=1e4;$(".view-sequence").each(function(){var b=$(this),c=b.closest(".hitn");c.data().hitLen>a&&b.disable().removeAttr("href").tooltip({title:"Sequence too long to show. Please view it locally after download."})})},SS.setupTooltips=function(){$(".pos-label").each(function(){$(this).tooltip({placement:"right"})}),$(".downloads a").each(function(){$(this).tooltip()})},SS.setupDownloadLinks=function(){$(".download").on("click",function(a){if(a.preventDefault(),a.stopPropagation(),!a.target.disabled){var b=this.href;$.get(b).done(function(){window.location.href=b}).fail(function(a){SS.showErrorModal(a,function(){})})}})},SS.generateURI=function(a,b){a=encodeURIComponent(a.join(" ")),b=encodeURIComponent(b);var c="get_sequence/?sequence_ids="+a+"&database_ids="+b+"&download=fasta";return c},SS.showErrorModal=function(a,b){setTimeout(function(){b(),a.responseText?$("#error").html(a.responseText).modal():$("#error-no-response").modal()},500)},SS.init=function(){this.$sequence=$("#sequence"),this.$sequenceFile=$("#sequence-file"),this.$sequenceControls=$(".sequence-controls"),SS.blast.init()}}(),SS.selectHit=function(a){if(a&&a.value){var b=$($(a).data("target"));a.checked?b.addClass("glow").find(":checkbox").not(a).check():b.removeClass("glow").find(":checkbox").not(a).uncheck(),this.updateDownloadFastaOfSelectedLink()}},SS.showSequenceViewer=function(){var a=$("#sequence-viewer"),b=$(".spinner",a),c=$(".modal-body",a),d=$(".modal-footer",a),e="biojs-vis-sequence",f=function(e){c.empty(),d.empty(),g(e),b.show(),a.modal("show")},g=function(a){var b=a.parent().clone(),c=b.find(".view-sequence"),e=$(c[0].nextSibling);c.remove(),e.remove(),d.empty().append(b)},h=function(a,b){a.forEach(j),b.forEach(i)},i=function(a){var b=a.id+"<small>&nbsp;"+a.title+"</small>",d=e+(new Date).getUTCMilliseconds();c.append($("<div/>").addClass("fastan").append($("<div/>").addClass("page-header").append($("<h4/>").html(b)),$("<div/>").attr("id",d).addClass(e).addClass("page-content")));var f=new Sequence({sequence:a.value,target:d,format:"PRIDE",columns:{size:40,spacedEach:5},formatOptions:{title:!1,footer:!1}});f.hideFormatSelector()},j=function(a){c.append($("<div/>").addClass("page-header").append($("<h4/>").html(a[0])),$("<div/>").addClass("page-content").append($("<pre/>").addClass("pre-reset").html(a[1])),$("<br>"))};return function(c){var d=$(c);f(d);var e=d.attr("href");$.getJSON(e).done(function(a){h(a.error_msgs,a.sequences),b.hide()}).fail(function(b){SS.showErrorModal(b,function(){a.modal("hide")})})}}(),$(document).ready(function(){SS.init();var a,b=$(".dnd-overlay"),c=$("#sequence"),d=function(a){$(".dnd-error").hide(),$("#"+a+"-notification").show(),b.effect("fade",2500)};$(document).on("dragenter",function(a){if(!$.modalActive()){var d=a.originalEvent.dataTransfer,e=d.types&&(d.types.indexOf&&-1!=d.types.indexOf("Files")||d.types.contains&&d.types.contains("application/x-moz-file"));e&&($(".dnd-error").hide(),b.stop(!0,!0),b.show(),d.effectAllowed="copy",""===c.val()?($(".dnd-overlay-overwrite").hide(),$(".dnd-overlay-drop").show("drop",{direction:"down"},"fast")):($(".dnd-overlay-drop").hide(),$(".dnd-overlay-overwrite").show("drop",{direction:"down"},"fast")))}}).on("dragleave",".dnd-overlay",function(){b.hide(),$(".dnd-overlay-drop").hide(),$(".dnd-overlay-overwrite").hide()}).on("dragover",".dnd-overlay",function(a){a.originalEvent.dataTransfer.dropEffect="copy",a.preventDefault()}).on("drop",".dnd-overlay",function(a){a.preventDefault(),a.stopPropagation();var c=$("#sequence"),e=$("#sequence-file");c.focus();var f=a.originalEvent.dataTransfer.files;if(f.length>1)return void d("dnd-multi");var g=f[0];if(g.size>10485760)return void d("dnd-large-file");var h=new FileReader;h.onload=function(a){var f=a.target.result;SS.FASTA_FORMAT.test(f)?(c.val(f),e.text(g.name),b.hide()):d("dnd-format")},h.onerror=function(){d("dnd-format")},h.readAsText(g)}),SS.$sequence.change(function(){if(SS.$sequence.val()){var a=SS.$sequence[0].offsetWidth-SS.$sequence[0].clientWidth;SS.$sequenceControls.css("right",a+17),SS.$sequenceControls.removeClass("hidden")}else SS.$sequenceFile.empty(),SS.$sequenceControls.addClass("hidden"),SS.$sequence.parent().removeClass("has-error")}),$("#btn-sequence-clear").click(function(){$("#sequence").val("").focus()}),SS.onedb(),$("#methods").tooltip({title:function(){var a=$(".databases input:checkbox:checked");return 0===a.length?"You must select one or more databases above before you can run a search!":void 0}}),$("#method").tooltip({title:function(){var a="Click to BLAST or press Ctrl+Enter.";return 0!==$(this).siblings().length&&(a+=" Click dropdown button on the right for other BLAST algorithms that can be used."),a},delay:{show:1e3,hide:0}}),$(document).bind("keydown",function(a){a.ctrlKey&&13===a.keyCode&&!$("#method").is(":disabled")&&$("#method").trigger("submit")}),$("#sequence").on("sequence_type_changed",function(b,c){clearTimeout(a),$(this).parent().removeClass("has-error"),$(".notifications .active").hide().removeClass("active"),c&&($("#"+c+"-sequence-notification").show("drop",{direction:"up"}).addClass("active"),a=setTimeout(function(){$(".notifications .active").hide("drop",{direction:"up"}).removeClass("active")},5e3),"mixed"===c&&$(this).parent().addClass("has-error"))}),$("body").click(function(){$(".notifications .active").hide("drop",{direction:"up"}).removeClass("active")}),$(".databases").on("database_type_changed",function(a,b){switch(b){case"protein":$(".databases.nucleotide input:checkbox").disable(),$(".databases.nucleotide .checkbox").addClass("disabled");break;case"nucleotide":$(".databases.protein input:checkbox").disable(),$(".databases.protein .checkbox").addClass("disabled");break;default:$(".databases input:checkbox").enable(),$(".databases .checkbox").removeClass("disabled")}}),$("form").on("blast_method_changed",function(a,b){if($("#method").disable().val("").html("blast"),$("#methods").removeClass("input-group").children().not("#method").remove(),b.length>0){var c=b.shift();$("#method").enable().val(c).html(SS.decorate(c)),b.length>=1&&$("#methods").addClass("input-group").append($("<div/>").addClass("input-group-btn").append($("<button/>").attr("type","button").addClass("btn btn-primary dropdown-toggle").attr("data-toggle","dropdown").append($("<span/>").addClass("caret")),$("<ul/>").addClass("dropdown-menu dropdown-menu-right").append($.map(b,function(a){return $("<li/>").html(SS.decorate(a))})))),$("#methods").wiggle()}}),$(document).on("click","#methods .dropdown-menu li",function(){var a=$(this),b=$("#method"),c=b.text(),d=a.text();a.html(SS.decorate(c)),b.val(d).html(SS.decorate(d)),$("#methods").wiggle()}),$(".result").on("mousedown",".hitn > .page-header > h4",function(){var a=$(this);a.on("mouseup mousemove",function b(c){"mouseup"===c.type?(a.attr("data-toggle","collapse"),a.find(".fa-chevron-down").toggleClass("fa-rotate-270")):a.attr("data-toggle",""),a.off("mouseup mousemove",b)})}),$(".result").on("click",".view-sequence",function(a){a.preventDefault(),a.stopPropagation(),a.target.disabled||SS.showSequenceViewer(a.target)}),$(document).on("change",".hitn :checkbox",function(a){a.stopPropagation(),SS.selectHit(this)}),$("#blast").submit(function(){var a=$(this).attr("action"),b=a.indexOf("#"),c=a.slice(0,b),d=a.slice(b,a.length);location.hash="",$("#spinner").modal();var e=$(this).serialize()+"&method="+$("#method").val();return $.post(c,e).done(function(a){$(".result").html(a).show();var b=$(".sidebar");0!==b.length&&b.affix({offset:{top:b.offset().top}}).width(b.width()),location.hash=d,SS.generateGraphicalOverview(),SS.updateDownloadFastaOfAllLink(),SS.updateDownloadFastaOfSelectedLink(),SS.updateSequenceViewerLinks(),SS.setupTooltips(),SS.setupDownloadLinks(),$("body").scrollspy({target:".sidebar"}),$("#spinner").modal("hide")}).fail(function(a){SS.showErrorModal(a,function(){$("#spinner").modal("hide")})}),!1}),SS.$sequence.poll()}),function(a){var b=function(){a('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true","white-space":"nowrap"})},c=function(b){a("a",b).click(function(b){b.preventDefault(),b.stopPropagation(),window.location.hash=a(this).attr("href")})},d=function(b,c,d,e){var f=a(window).width(),g=_.debounce(function(){if(f!==a(window).width()){var g=b.find(".ghit > g").length;a.graphIt(b,c,g,d,e),f=a(window).width()}},125);a(window).resize(g)},e=function(c,d,e){var f,g,h,i,j=20,k=function(){f=c.data().hitCount,g=c.find(".ghit > g").length},l=function(b,c){c.append(a("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",b.attr("id")).html("View More&nbsp;").append(a("<i/>").addClass("fa fa-angle-double-down")),a("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",b.attr("id")).html("View Less&nbsp;").append(a("<i/>").addClass("fa fa-angle-double-up"))),h=a(".less",c),i=a(".more",c)},m=function(){k(),f===j||j>g?(h.hide(),i.hide()):g===f?(i.hide(),h.show()):g===j?(h.hide(),i.show()):(h.show(),i.show())};e===!0&&(l(c,d),m()),i.on("click",function(e){k(),a.graphIt(c,d,g,j),m(),b(),e.stopPropagation()}),h.on("click",function(e){k();var f=g-j;f>=j?(a.graphIt(c,d,g,-j),m()):0!==f&&(a.graphIt(c,d,g,j-g),m()),b(),e.stopPropagation()})},f=function(b,c,d){var e,f=[];return e=b.find(".hitn").slice(0,c+d),e.map(function(){var b=a(this),c=[];b.find(".hsp").each(function(){var b=[];b=a(this).data(),b.hspId=this.id,c.push(b)}),c.hitId=b.attr("id"),c.hitDef=b.data().hitDef,c.hitEvalue=b.data().hitEvalue,f.push(c)}),f},g=function(a,b,c,d){var e=a.append("g").attr("transform","translate(0,"+(d-b.margin-1.25*b.legend)+")");e.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})};a.extend({graphIt:function(h,i,j,k,l){var m={barHeight:4,barPadding:5,legend:10,margin:20},n=a.extend(m,l),o=f(h,j,k);if(o.length<1)return!1;0!==j&&i.find("svg").remove();var p=h.data().queryLen,q=h.attr("id"),r=i.width(),s=o.length*(n.barHeight+n.barPadding)+5*n.margin+3*n.legend,t=d3.select(i[0]).selectAll("svg").data([o]).enter().insert("svg",":first-child").attr("width",r).attr("height",s).append("g").attr("transform","translate("+n.margin/4+", "+n.margin/4+")"),u=d3.scale.linear().range([0,r-n.margin]);u.domain([1,p]);var v=u.ticks(11);v.pop();var w=d3.svg.axis().scale(u).orient("top").tickValues(v.concat([1,p]));t.append("g").attr("transform","translate(0, "+n.margin+")").append("g").attr("class","x axis").call(w);var x=d3.scale.ordinal().rangeBands([0,s-3*n.margin-2*n.legend],.3);x.domain(o.map(function(a){return a.hitId}));var y=d3.scale.log().domain([d3.min([1e-5,d3.min(o.map(function(a){return 0===parseFloat(a.hitEvalue)?void 0:a.hitEvalue}))]),d3.max(o.map(function(a){return a.hitEvalue}))]).range([40,150]);t.append("g").attr("class","ghit").attr("transform","translate(0, "+(2*n.margin-n.legend)+")").selectAll(".hits").data(o).enter().append("g").attr("data-toggle","tooltip").attr("title",function(a){var b=/(\d*\.\d*)e?([+-]\d*)?/,c=b.exec(a.hitEvalue),d=parseFloat(c[1]).toFixed(3),e=a.hitDef+"<br><strong>E value:</strong> "+d;return void 0!==c[2]&&(e+=" &times; 10<sup>"+c[2]+"</sup>"),e}).each(function(a,b){var c=b+1,d=a,e=a.hitId,f=a.length;d3.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(a,b){var g=x(e)+n.barHeight/2,h=d3.rgb(y(d.hitEvalue),y(d.hitEvalue),y(d.hitEvalue));f>b+1&&(d[b].hspEnd<=d[b+1].hspStart?d3.select(this.parentNode).append("line").attr("x1",u(d[b].hspEnd)).attr("y1",g).attr("x2",u(d[b+1].hspStart)).attr("y2",g).attr("stroke",h):d[b].hspStart>d[b+1].hspEnd&&d3.select(this.parentNode).append("line").attr("x1",u(d[b+1].hspEnd)).attr("y1",g).attr("x2",u(d[b].hspStart)).attr("y2",g).attr("stroke",h)),d3.select(this).attr("xlink:href","#"+q+"_hit_"+c).append("rect").attr("x",function(a){return u(a.hspStart)}).attr("y",x(e)).attr("width",function(a){return u(a.hspEnd-a.hspStart+1)}).attr("height",n.barHeight).attr("fill",d3.rgb(h))})}),o.length>1&&g(t,n,r,s),0===j&&(e(h,i,!0),d(h,i,j,l)),b(),c(i)}})}(jQuery),SS.blast=function(){var a=function(a){if(a=a.replace(/[^A-Z]/gi,""),a=a.replace(/[NX]/gi,""),a.length<10)return void 0;var b,c,d;for(b=0,c=.9*a.length,d=0;d<a.length;d++)a[d].match(/[ACGTU]/i)&&(b+=1);return b>c?"nucleotide":"protein"},b=function(){var b,c,d,e=$("#sequence").val().split(/>.*/);for(d=0;d<e.length;d++)if(c=a(e[d]))if(b){if(c!==b)return"mixed"}else b=c;return b},c=function(){return $(".databases input:checked").data("type")},d=function(){return $("#sequence").val()&&$(".databases input:checked").val()?!0:!1},e=function(){var a,c;$("#sequence").change(function(){c=b(),c&&c===a||(a=c,$(this).trigger("sequence_type_changed",a))})},f=function(){var a,b=c();$(".databases input").change(function(){a=c(),a!=b&&(b=a,$(this).trigger("database_type_changed",b))})},g=function(){var a,b;$("#blast").on("sequence_type_changed database_type_changed",function(){b=h(),_.isEqual(b,a)||(a=b,$(this).trigger("blast_method_changed",[a.slice()]))})},h=function(){if(!d())return[];var a=c(),e=b();switch(a){case"protein":switch(e){case void 0:return["blastp","blastx"];case"protein":return["blastp"];case"nucleotide":return["blastx"]}break;case"nucleotide":switch(e){case void 0:return["tblastn","blastn","tblastx"];case"protein":return["tblastn"];case"nucleotide":return["blastn","tblastx"]}}return[]},i=function(){return void 0};return i.init=function(){e(),f(),g()},i}();

data/public/js/sequenceserver.js

@@ -479,7 +479,7 @@ $(document).ready(function(){
     $(document)
     .on('dragenter', function (evt) {
         // Do not activate DnD if a modal is active.
-        if ($.modalActive) return;
+        if ($.modalActive()) return;
 
         // Based on http://stackoverflow.com/a/8494918/1205465.
         // Contrary to what the above link says, the snippet below can't

data/sequenceserver.gemspec

@@ -25,7 +25,7 @@ DESC
   s.add_development_dependency('rack-test',       '~> 0.6',  '>= 0.6.2')
   s.add_development_dependency('rspec',           '~> 2.8',  '>= 2.8.0')
   s.add_development_dependency('rake',            '~> 10.3', '>= 10.3.2')
-  s.add_development_dependency('rubocop',         '~> 0.28', '>= 0.28.0')
+  s.add_development_dependency('rubocop',         '~> 0.31', '>= 0.31.0')
   s.add_development_dependency('capybara',        '~> 2.4',  '>= 2.4.4')
   s.add_development_dependency('capybara-webkit', '~> 1.3',  '>= 1.3.0')
   s.add_development_dependency('codeclimate-test-reporter',

data/views/result.erb

@@ -42,6 +42,7 @@
                 <th>Sequences producing significant alignments</th>
                 <th class="text-right"> Total score </th>
                 <th class="text-right"> E value </th>
+                <th class="text-right"> Length </th>
               </thead>
               <tbody>
               <% query.hits.each_with_index do |hit, h| %>
@@ -50,6 +51,7 @@
                   <td> <a href="<%="#Query_#{query.number}_hit_#{hit.number}"%>"><%= "#{hit.id}" %></a> </td>
                   <td class="text-right"><%= prettify hit.score  %></td>
                   <td class="text-right"><%= prettify hit.evalue %></td>
+                  <td class="text-right"><%= prettify hit.length %></td>
                 </tr>
               <% end %>
               </tbody>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.0.4
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-12 00:00:00.000000000 Z
+date: 2015-05-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra
@@ -159,20 +159,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.28'
+        version: '0.31'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.28.0
+        version: 0.31.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.28'
+        version: '0.31'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.28.0
+        version: 0.31.0
 - !ruby/object:Gem::Dependency
   name: capybara
   requirement: !ruby/object:Gem::Requirement
@@ -689,3 +689,4 @@ signing_key:
 specification_version: 4
 summary: BLAST search made easy!
 test_files: []
+has_rdoc: