sequenceserver-beta 0.8.7.beta1

data/lib/sequenceserver/sequencehelpers.rb

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+module SequenceServer
+  # Module to collect some sequence-related helper functions
+  module SequenceHelpers
+
+    # copied from bioruby's Bio::Sequence
+    # returns a Hash. Eg: composition("asdfasdfffffasdf")
+    #                      => {"a"=>3, "d"=>3, "f"=>7, "s"=>3}
+    def composition(sequence_string)
+      count = Hash.new(0)
+      sequence_string.scan(/./) do |x|
+        count[x] += 1
+      end
+      return count
+    end
+
+    # Strips all non-letter characters. guestimates sequence based on that.
+    # If less than 10 useable characters... returns nil
+    # If more than 90% ACGTU returns :nucleotide. else returns :protein
+    def guess_sequence_type(sequence_string)
+      cleaned_sequence = sequence_string.gsub(/[^A-Z]/i, '')  # removing non-letter characters
+      cleaned_sequence.gsub!(/[NX]/i, '')                     # removing ambiguous  characters
+
+      return nil if cleaned_sequence.length < 10 # conservative
+
+      composition = composition(cleaned_sequence)       
+      composition_NAs    = composition.select { |character, count|character.match(/[ACGTU]/i) } # only putative NAs
+      putative_NA_counts = composition_NAs.collect { |key_value_array| key_value_array[1] }     # only count, not char
+      putative_NA_sum    = putative_NA_counts.inject { |sum, n| sum + n }                       # count of all putative NA
+      putative_NA_sum    = 0 if putative_NA_sum.nil?
+
+      if putative_NA_sum > (0.9 * cleaned_sequence.length)
+        return :nucleotide
+      else
+        return :protein
+      end
+    end
+
+    # splits input at putative fasta definition lines (like ">adsfadsf"), guesses sequence type for each sequence. 
+    # if not enough sequence to determine, returns nil.
+    # if 2 kinds of sequence mixed together, raises ArgumentError
+    # otherwise, returns :nucleotide or :protein
+    def type_of_sequences(fasta_format_string)
+      # the first sequence does not need to have a fasta definition line
+      sequences = fasta_format_string.split(/^>.*$/).delete_if { |seq| seq.empty? }
+
+      # get all sequence types
+      sequence_types = sequences.collect { |seq|  guess_sequence_type(seq) }.uniq.compact
+
+      return nil if sequence_types.empty?
+
+      if sequence_types.length == 1
+        return sequence_types.first # there is only one (but yes its an array)
+      else 
+        raise ArgumentError, "Insufficient info to determine sequence type. Cleaned queries are: #{ sequences.to_s }"
+      end
+    end
+
+    def sequence_from_blastdb(ids, db)  # helpful when displaying parsed blast results
+      # we know how to handle an Array of ids
+      ids = ids.join(',') if ids.is_a? Array
+
+      # we don't know what to do if the arguments ain't String
+      raise TypeError unless ids.is_a? String and db.is_a? String
+
+      # query now!
+      #
+      # If `blastdbcmd` throws error, we assume sequence not found.
+      blastdbcmd = settings.binaries['blastdbcmd']
+      %x|#{blastdbcmd} -db #{db} -entry '#{ids}' 2> /dev/null|
+    end
+
+    # Given a sequence_id and databases, apply the default (standard)
+    # way to convert a sequence_id into a hyperlink, so that the
+    # blast results include hyperlinks.
+    def construct_standard_sequence_hyperlink(options)
+      if options[:sequence_id].match(/^[^ ]/) #if there is a space right after the '>', makeblastdb was run without -parse_seqids
+        # By default, add a link to a fasta file of the sequence (if makeblastdb was called with -parse_seqids)
+
+        sid = options[:sequence_id].gsub(/<\/?[^>]*>/, '') # strip html
+        cid = sid[/^(\S+)\s*.*/, 1]                        # get id part
+        id  = cid.include?('|') ? cid.split('|')[1] : cid.split('|')[0]
+        @all_retrievable_ids ||= []
+        @all_retrievable_ids.push(id)
+
+        link = "/get_sequence/?id=#{id}&db=#{options[:databases].join(' ')}" # several dbs... separate by ' '
+        return link
+      else
+        # do nothing - link == nil means no link will be incorporated
+        return nil
+      end
+    end
+  end
+end

data/lib/sequenceserver/sinatralikeloggerformatter.rb

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+module SequenceServer
+  # We change Logging format so that it is consistent with Sinatra's
+  class SinatraLikeLogFormatter < Logger::Formatter 
+    MyFormat = "[%s] %s  %s\n"
+    def initialize
+      self.datetime_format = "%Y-%m-%d %H:%M:%S" 
+    end
+    def call(severity, time, progname, msg)
+      MyFormat % [format_datetime(time), severity, msg2str(msg)]
+    end
+  end
+end

data/lib/sequenceserver/version.rb

@@ -0,0 +1,9 @@
+module SequenceServer
+
+  # Return version number of SequenceServer from the gemspec.  Version number
+  # is read from gemspec, which might fail on older versions of Bundler or
+  # RubyGems.  Return `nil` if version number couldn't be determined.
+  def self.version
+    Bundler.rubygems.loaded_specs('sequenceserver').version rescue nil
+  end
+end

data/public/css/beige.css.css

@@ -0,0 +1,254 @@
+body {
+	background-color: #2B3E42;
+	/*background: #3f4555;*/
+	font-family: Tahoma, Arial, sans-serif;
+}
+
+.container {
+	width: 800px;  
+	margin: 50px auto;
+	background-color: white;
+	border: 2px solid white;
+	border-radius: 10px;
+	-moz-border-radius: 10px;
+}
+
+h1 {
+    margin: 0px;
+	padding: 0px;
+}
+
+.banner {
+	font-weight: bold;
+	background: #ebcd7b;
+	font-size: 300%;
+	font-family: Tahoma, Arial, sans-serif;
+	color: black;
+	padding: 2%;
+	margin-bottom: 2%;
+
+	border-bottom-left-radius: 0px;
+	border-bottom-right-radius: 0px;
+	border-top-left-radius: 10px;
+	border-top-right-radius: 10px;
+
+	-moz-border-radius-bottomleft: 0px;
+	-moz-border-radius-bottomright: 0px;
+	-moz-border-radius-topleft: 10px;
+	-moz-border-radius-topright: 10px;
+
+}
+
+.underbar { 
+	background-color: #ebcd7b; 
+	font-family:arial;
+	font-size: 12px;
+	text-align: center;
+	color: #333333;
+	padding: 1px 1px 1px 1px;
+	margin: 2% 0 0 0;
+	border-bottom-left-radius: 10px;
+	border-bottom-right-radius: 10px;
+}
+
+
+.entryfield {
+	padding:0;
+	margin:0;
+}
+
+.entryfield textarea {
+	padding:0;
+	margin:0;
+	width:100%;
+	height: 168px;
+	border-color:black;
+}
+
+.blastmethods {
+	float					: right;
+	background				: #222222;
+	border					: none;
+	height                  :  150px;
+
+	border-top-right-radius	: 10px;
+	border-top-left-radius	: 0px;
+	border-bottom-right-radius: 10px;
+	border-bottom-left-radius	:  0px;
+
+	-moz-border-radius-topright: 10px;
+	-moz-border-radius-topleft: 0px;
+	-moz-border-radius-bottomright: 10px;
+	-moz-border-radius-bottomleft:  0px;
+
+
+	font-size					: 1.5em; 
+	font-family: Tahoma, Arial, sans-serif; 
+	color: black;
+	margin:0;
+	padding:0;
+}
+
+fieldset {
+	margin:0;
+	padding:0;
+}
+
+.horizontal {
+	margin: 2%;
+	padding-bottom:15px;
+	padding-top:15px;
+	width: 96%;
+	clear:both;
+}
+
+.rounded {
+	border-radius  :10px;
+	-moz-border-radius:10px;
+}
+
+.box {
+	background  : #D5E1DD;
+	/* background: -webkit-gradient(linear, left top, left bottom, from(#ccc), to(#000));   */
+
+	border      : none;
+
+	padding     : 10px;
+	margin: 0;
+	font-family : Tahoma, Arial, sans-serif;
+	color       : black;
+}
+
+.databases {
+	width       :46.5%;
+}
+.nucleotide {
+	float    :left;
+}
+.protein {
+	float    : right;
+}
+
+.radiobutton{
+	margin: 9px 5px 0px 0px;
+	padding: 0;
+	vertical-align: top;
+}
+.dbcheckbox {   /* within each "database box" */
+float:left;
+clear:both;
+margin: 5px 10px 0 0;
+padding: 0;
+}
+.dbdescription {
+	float:left;
+}
+
+.advanced {
+	float:left;
+	width: 78%;
+}
+
+.greytext {
+  color: #A9A9A9;
+}
+
+.pointer {
+	cursor:pointer;
+}
+
+.advanced pre {
+	display: none;
+}
+.advanced input {
+	float:right;
+	width: 60%;
+}
+
+.submit_button {
+	float:right;
+	width: 17.5%;
+}
+.submit_button input {
+	width: 100%;
+	background-color	: #323292;
+	background: -webkit-gradient(linear, left top, right bottom, from(#0066CC), to(#192D53));
+	background: -moz-linear-gradient(45deg,#0066CC,#192D53);
+
+	border			: 2px solid #192D53;
+	border-radius		: 10px;
+	-moz-border-radius: 10px;
+	color				: white;
+	padding			: 2.5px 10px 2.5px 10px;
+	cursor			: pointer;
+	font-size			: 1.8em;
+	font-family		: Tahoma, Arial, sans-serif;
+	margin: 0 0 0 0;
+
+}
+.submit_button input:active {
+	color: #1f2126;
+
+}
+.submit_button input:hover {
+	background: -webkit-gradient(linear, left top, right bottom, from(#009cff), to(#0261c2));
+	background: -moz-linear-gradient(45deg,#009cff,#0261c2);
+
+}
+
+h2, .bigtext{
+	font-family: Tahoma, Arial, serif;
+	font-weight: bold;
+	font-size: 20px;
+	color: black;
+	margin:0;
+	padding: 0px;
+	/*	margin: 8px 0 10px 0;*/
+}
+
+h3{
+	font-family: Tahoma, Arial, serif;
+	font-weight: bold;
+	font-size: 16px;
+	color: black;
+	margin:0;
+	padding: 0px;
+	/*	margin: 8px 0 10px 0;*/
+}
+
+.smalltext{
+	font-size:10px;
+}
+
+
+#result{
+	clear:both;
+	background-color: white;
+}
+.result_even_true{
+	background-color: #ffe0f9;
+   margin: 0 18px 0 18px;
+	border-radius  :10px;
+	-moz-border-radius:10px;
+	padding-left: 3%;
+	padding-top: 3%;
+}
+.result_even_false{
+	background-color: #dfefe6;
+	margin: 0 18px 0 18px;
+	border-radius  :10px;
+	-moz-border-radius:10px;
+	padding-left: 3%;
+	padding-top: 3%;
+}
+.blast_result{
+	font-family: "Lucida Console", Lucida, monospace;
+	background-color: #A9A9A9;
+	border-radius  :10px;
+	-moz-border-radius:10px;
+	padding-left: 2%;
+}
+
+a {
+    color: #b22222;
+}

data/public/css/bootstrap.dropdown.css

@@ -0,0 +1,29 @@
+/*!
+ * Bootstrap v2.0.2
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}
+.clearfix:after{clear:both;}
+.hide-text{overflow:hidden;text-indent:100%;white-space:nowrap;}
+.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;}
+.dropdown{position:relative;}
+.dropdown-toggle{*margin-bottom:-3px;}
+.dropdown-toggle:active,.open .dropdown-toggle{outline:0;}
+.caret{display:inline-block;width:0;height:0;vertical-align:top;border-left:4px solid transparent;border-right:4px solid transparent;border-top:4px solid #000000;opacity:0.3;filter:alpha(opacity=30);content:"";}
+.dropdown .caret{margin-top:8px;margin-left:2px;}
+.dropdown:hover .caret,.open.dropdown .caret{opacity:1;filter:alpha(opacity=100);}
+.dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;float:left;display:none;min-width:160px;padding:4px 0;margin:0;list-style:none;background-color:#ffffff;border-color:#ccc;border-color:rgba(0, 0, 0, 0.2);border-style:solid;border-width:1px;-webkit-border-radius:0 0 5px 5px;-moz-border-radius:0 0 5px 5px;border-radius:0 0 5px 5px;-webkit-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-moz-box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);box-shadow:0 5px 10px rgba(0, 0, 0, 0.2);-webkit-background-clip:padding-box;-moz-background-clip:padding;background-clip:padding-box;*border-right-width:2px;*border-bottom-width:2px;}.dropdown-menu.pull-right{right:0;left:auto;}
+.dropdown-menu .divider{height:1px;margin:8px 1px;overflow:hidden;background-color:#e5e5e5;border-bottom:1px solid #ffffff;*width:100%;*margin:-5px 0 5px;}
+.dropdown-menu a{display:block;padding:3px 15px;clear:both;font-weight:normal;line-height:18px;color:#333333;white-space:nowrap;}
+.dropdown-menu li>a:hover,.dropdown-menu .active>a,.dropdown-menu .active>a:hover{color:#ffffff;text-decoration:none;background-color:#0088cc;}
+.dropdown.open{*z-index:1000;}.dropdown.open .dropdown-toggle{color:#ffffff;background:#ccc;background:rgba(0, 0, 0, 0.3);}
+.dropdown.open .dropdown-menu{display:block;}
+.pull-right .dropdown-menu{left:auto;right:0;}
+.dropup .caret,.navbar-fixed-bottom .dropdown .caret{border-top:0;border-bottom:4px solid #000000;content:"\2191";}
+.dropup .dropdown-menu,.navbar-fixed-bottom .dropdown .dropdown-menu{top:auto;bottom:100%;margin-bottom:1px;}
+.typeahead{margin-top:2px;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;}

data/public/css/bootstrap.icons.css

@@ -0,0 +1,155 @@
+/*!
+ * Bootstrap v2.0.3
+ *
+ * Copyright 2012 Twitter, Inc
+ * Licensed under the Apache License v2.0
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Designed and built with all the love in the world @twitter by @mdo and @fat.
+ */
+.clearfix{*zoom:1;}.clearfix:before,.clearfix:after{display:table;content:"";}
+.clearfix:after{clear:both;}
+.hide-text{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0;}
+.input-block-level{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;}
+[class^="icon-"],[class*=" icon-"]{display:inline-block;width:14px;height:14px;*margin-right:.3em;line-height:14px;vertical-align:text-top;background-image:url("../img/glyphicons-halflings.png");background-position:14px 14px;background-repeat:no-repeat;}[class^="icon-"]:last-child,[class*=" icon-"]:last-child{*margin-left:0;}
+.icon-white{background-image:url("../img/glyphicons-halflings-white.png");}
+.icon-glass{background-position:0 0;}
+.icon-music{background-position:-24px 0;}
+.icon-search{background-position:-48px 0;}
+.icon-envelope{background-position:-72px 0;}
+.icon-heart{background-position:-96px 0;}
+.icon-star{background-position:-120px 0;}
+.icon-star-empty{background-position:-144px 0;}
+.icon-user{background-position:-168px 0;}
+.icon-film{background-position:-192px 0;}
+.icon-th-large{background-position:-216px 0;}
+.icon-th{background-position:-240px 0;}
+.icon-th-list{background-position:-264px 0;}
+.icon-ok{background-position:-288px 0;}
+.icon-remove{background-position:-312px 0;}
+.icon-zoom-in{background-position:-336px 0;}
+.icon-zoom-out{background-position:-360px 0;}
+.icon-off{background-position:-384px 0;}
+.icon-signal{background-position:-408px 0;}
+.icon-cog{background-position:-432px 0;}
+.icon-trash{background-position:-456px 0;}
+.icon-home{background-position:0 -24px;}
+.icon-file{background-position:-24px -24px;}
+.icon-time{background-position:-48px -24px;}
+.icon-road{background-position:-72px -24px;}
+.icon-download-alt{background-position:-96px -24px;}
+.icon-download{background-position:-120px -24px;}
+.icon-upload{background-position:-144px -24px;}
+.icon-inbox{background-position:-168px -24px;}
+.icon-play-circle{background-position:-192px -24px;}
+.icon-repeat{background-position:-216px -24px;}
+.icon-refresh{background-position:-240px -24px;}
+.icon-list-alt{background-position:-264px -24px;}
+.icon-lock{background-position:-287px -24px;}
+.icon-flag{background-position:-312px -24px;}
+.icon-headphones{background-position:-336px -24px;}
+.icon-volume-off{background-position:-360px -24px;}
+.icon-volume-down{background-position:-384px -24px;}
+.icon-volume-up{background-position:-408px -24px;}
+.icon-qrcode{background-position:-432px -24px;}
+.icon-barcode{background-position:-456px -24px;}
+.icon-tag{background-position:0 -48px;}
+.icon-tags{background-position:-25px -48px;}
+.icon-book{background-position:-48px -48px;}
+.icon-bookmark{background-position:-72px -48px;}
+.icon-print{background-position:-96px -48px;}
+.icon-camera{background-position:-120px -48px;}
+.icon-font{background-position:-144px -48px;}
+.icon-bold{background-position:-167px -48px;}
+.icon-italic{background-position:-192px -48px;}
+.icon-text-height{background-position:-216px -48px;}
+.icon-text-width{background-position:-240px -48px;}
+.icon-align-left{background-position:-264px -48px;}
+.icon-align-center{background-position:-288px -48px;}
+.icon-align-right{background-position:-312px -48px;}
+.icon-align-justify{background-position:-336px -48px;}
+.icon-list{background-position:-360px -48px;}
+.icon-indent-left{background-position:-384px -48px;}
+.icon-indent-right{background-position:-408px -48px;}
+.icon-facetime-video{background-position:-432px -48px;}
+.icon-picture{background-position:-456px -48px;}
+.icon-pencil{background-position:0 -72px;}
+.icon-map-marker{background-position:-24px -72px;}
+.icon-adjust{background-position:-48px -72px;}
+.icon-tint{background-position:-72px -72px;}
+.icon-edit{background-position:-96px -72px;}
+.icon-share{background-position:-120px -72px;}
+.icon-check{background-position:-144px -72px;}
+.icon-move{background-position:-168px -72px;}
+.icon-step-backward{background-position:-192px -72px;}
+.icon-fast-backward{background-position:-216px -72px;}
+.icon-backward{background-position:-240px -72px;}
+.icon-play{background-position:-264px -72px;}
+.icon-pause{background-position:-288px -72px;}
+.icon-stop{background-position:-312px -72px;}
+.icon-forward{background-position:-336px -72px;}
+.icon-fast-forward{background-position:-360px -72px;}
+.icon-step-forward{background-position:-384px -72px;}
+.icon-eject{background-position:-408px -72px;}
+.icon-chevron-left{background-position:-432px -72px;}
+.icon-chevron-right{background-position:-456px -72px;}
+.icon-plus-sign{background-position:0 -96px;}
+.icon-minus-sign{background-position:-24px -96px;}
+.icon-remove-sign{background-position:-48px -96px;}
+.icon-ok-sign{background-position:-72px -96px;}
+.icon-question-sign{background-position:-96px -96px;}
+.icon-info-sign{background-position:-120px -96px;}
+.icon-screenshot{background-position:-144px -96px;}
+.icon-remove-circle{background-position:-168px -96px;}
+.icon-ok-circle{background-position:-192px -96px;}
+.icon-ban-circle{background-position:-216px -96px;}
+.icon-arrow-left{background-position:-240px -96px;}
+.icon-arrow-right{background-position:-264px -96px;}
+.icon-arrow-up{background-position:-289px -96px;}
+.icon-arrow-down{background-position:-312px -96px;}
+.icon-share-alt{background-position:-336px -96px;}
+.icon-resize-full{background-position:-360px -96px;}
+.icon-resize-small{background-position:-384px -96px;}
+.icon-plus{background-position:-408px -96px;}
+.icon-minus{background-position:-433px -96px;}
+.icon-asterisk{background-position:-456px -96px;}
+.icon-exclamation-sign{background-position:0 -120px;}
+.icon-gift{background-position:-24px -120px;}
+.icon-leaf{background-position:-48px -120px;}
+.icon-fire{background-position:-72px -120px;}
+.icon-eye-open{background-position:-96px -120px;}
+.icon-eye-close{background-position:-120px -120px;}
+.icon-warning-sign{background-position:-144px -120px;}
+.icon-plane{background-position:-168px -120px;}
+.icon-calendar{background-position:-192px -120px;}
+.icon-random{background-position:-216px -120px;}
+.icon-comment{background-position:-240px -120px;}
+.icon-magnet{background-position:-264px -120px;}
+.icon-chevron-up{background-position:-288px -120px;}
+.icon-chevron-down{background-position:-313px -119px;}
+.icon-retweet{background-position:-336px -120px;}
+.icon-shopping-cart{background-position:-360px -120px;}
+.icon-folder-close{background-position:-384px -120px;}
+.icon-folder-open{background-position:-408px -120px;}
+.icon-resize-vertical{background-position:-432px -119px;}
+.icon-resize-horizontal{background-position:-456px -118px;}
+.icon-hdd{background-position:0 -144px;}
+.icon-bullhorn{background-position:-24px -144px;}
+.icon-bell{background-position:-48px -144px;}
+.icon-certificate{background-position:-72px -144px;}
+.icon-thumbs-up{background-position:-96px -144px;}
+.icon-thumbs-down{background-position:-120px -144px;}
+.icon-hand-right{background-position:-144px -144px;}
+.icon-hand-left{background-position:-168px -144px;}
+.icon-hand-up{background-position:-192px -144px;}
+.icon-hand-down{background-position:-216px -144px;}
+.icon-circle-arrow-right{background-position:-240px -144px;}
+.icon-circle-arrow-left{background-position:-264px -144px;}
+.icon-circle-arrow-up{background-position:-288px -144px;}
+.icon-circle-arrow-down{background-position:-312px -144px;}
+.icon-globe{background-position:-336px -144px;}
+.icon-wrench{background-position:-360px -144px;}
+.icon-tasks{background-position:-384px -144px;}
+.icon-filter{background-position:-408px -144px;}
+.icon-briefcase{background-position:-432px -144px;}
+.icon-fullscreen{background-position:-456px -144px;}