sequenceserver 0.6.8 → 0.6.9

data/bin/database_formatter

@@ -2,10 +2,8 @@
 # copyright yannick . wurm at unil . ch
 # Finds files, reads first char. if its '>', read 500 lines. Guess sequence type, ask user for title to format as blast database.
 
-# ensure 'lib/' is in the load path
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-
 require 'rubygems'
+require 'bundler/setup'
 require 'ptools' # for File.binary?(file)
 require 'find'
 require 'logger'

data/bin/sequenceserver

@@ -1,10 +1,8 @@
 #!/usr/bin/env ruby
 
-# application root
-root = File.dirname(File.dirname(__FILE__))
-
 require 'rubygems'
-require File.join(root, 'lib', 'sequenceserver')
+require 'bundler/setup'
+require 'sequenceserver'
 
 # display name for tools like `ps`
 $PROGRAM_NAME = 'sequenceserver'

data/lib/sequenceserver.rb

@@ -1,9 +1,5 @@
 # sequenceserver.rb
 
-# ensure 'lib/' is in the load path
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-
-require 'rubygems'
 require 'sinatra/base'
 require 'yaml'
 require 'logger'
@@ -233,8 +229,10 @@ module SequenceServer
       # evaluate empty sequence as nil, otherwise as fasta
       sequence = sequence.empty? ? nil : to_fasta(sequence)
 
+      # TODO: detect sequence type in the browser itself (no AJAX)
       if request.xhr?
-        return (sequence && type_of_sequences(sequence)).to_s
+        # if the AJAX request didn't specify a blast method, it must be interested in sequence type only
+        return (sequence && type_of_sequences(sequence)).to_s unless method
       end
 
       # Raise ArgumentError if there is no database selected
@@ -293,6 +291,10 @@ module SequenceServer
 
       @blast = format_blast_results(blast.result, databases)
 
+      if request.xhr?
+        return @blast
+      end
+
       erb :search
     end
 

data/public/css/custom.css

@@ -66,6 +66,7 @@ body {
   border-radius: 6px;
   -moz-border-radius: 6px;
   padding: 3%;
+  border: 1px solid transparent;
 }
 
 .focussed {

data/public/js/jquery.activity.js

@@ -0,0 +1,224 @@
+/*!
+ * NETEYE Activity Indicator jQuery Plugin
+ *
+ * Copyright (c) 2010 NETEYE GmbH
+ * Licensed under the MIT license
+ *
+ * Author: Felix Gnass [fgnass at neteye dot de]
+ * Version: @{VERSION}
+ */
+ 
+/**
+ * Plugin that renders a customisable activity indicator (spinner) using SVG or VML.
+ */
+(function($) {
+
+	$.fn.activity = function(opts) {
+		this.each(function() {
+			var $this = $(this);
+			var el = $this.data('activity');
+			if (el) {
+				clearInterval(el.data('interval'));
+				el.remove();
+				$this.removeData('activity');
+			}
+			if (opts !== false) {
+				opts = $.extend({color: $this.css('color')}, $.fn.activity.defaults, opts);
+				
+				el = render($this, opts).css('position', 'absolute').prependTo(opts.outside ? 'body' : $this);
+				var h = $this.outerHeight() - el.height();
+				var w = $this.outerWidth() - el.width();
+				var margin = {
+					top: opts.valign == 'top' ? opts.padding : opts.valign == 'bottom' ? h - opts.padding : Math.floor(h / 2),
+					left: opts.align == 'left' ? opts.padding : opts.align == 'right' ? w - opts.padding : Math.floor(w / 2)
+				};
+				var offset = $this.offset();
+				if (opts.outside) {
+					el.css({top: offset.top + 'px', left: offset.left + 'px'});
+				}
+				else {
+					margin.top -= el.offset().top - offset.top;
+					margin.left -= el.offset().left - offset.left;
+				}
+				el.css({marginTop: margin.top + 'px', marginLeft: margin.left + 'px'});
+				animate(el, opts.segments, Math.round(10 / opts.speed) / 10);
+				$this.data('activity', el);
+			}
+		});
+		return this;
+	};
+	
+	$.fn.activity.defaults = {
+		segments: 12,
+		space: 3,
+		length: 7,
+		width: 4,
+		speed: 1.2,
+		align: 'center',
+		valign: 'center',
+		padding: 4
+	};
+	
+	$.fn.activity.getOpacity = function(opts, i) {
+		var steps = opts.steps || opts.segments-1;
+		var end = opts.opacity !== undefined ? opts.opacity : 1/steps;
+		return 1 - Math.min(i, steps) * (1 - end) / steps;
+	};
+	
+	/**
+	 * Default rendering strategy. If neither SVG nor VML is available, a div with class-name 'busy' 
+	 * is inserted, that can be styled with CSS to display an animated gif as fallback.
+	 */
+	var render = function() {
+		return $('<div>').addClass('busy');
+	};
+	
+	/**
+	 * The default animation strategy does nothing as we expect an animated gif as fallback.
+	 */
+	var animate = function() {
+	};
+	
+	/**
+	 * Utility function to create elements in the SVG namespace.
+	 */
+	function svg(tag, attr) {
+		var el = document.createElementNS("http://www.w3.org/2000/svg", tag || 'svg');
+		if (attr) {
+			$.each(attr, function(k, v) {
+				el.setAttributeNS(null, k, v);
+			});
+		}
+		return $(el);
+	}
+	
+	if (document.createElementNS && document.createElementNS( "http://www.w3.org/2000/svg", "svg").createSVGRect) {
+	
+		// =======================================================================================
+		// SVG Rendering
+		// =======================================================================================
+		
+		/**
+		 * Rendering strategy that creates a SVG tree.
+		 */
+		render = function(target, d) {
+			var innerRadius = d.width*2 + d.space;
+			var r = (innerRadius + d.length + Math.ceil(d.width / 2) + 1);
+			
+			var el = svg().width(r*2).height(r*2);
+			
+			var g = svg('g', {
+				'stroke-width': d.width, 
+				'stroke-linecap': 'round', 
+				stroke: d.color
+			}).appendTo(svg('g', {transform: 'translate('+ r +','+ r +')'}).appendTo(el));
+			
+			for (var i = 0; i < d.segments; i++) {
+				g.append(svg('line', {
+					x1: 0, 
+					y1: innerRadius, 
+					x2: 0, 
+					y2: innerRadius + d.length, 
+					transform: 'rotate(' + (360 / d.segments * i) + ', 0, 0)',
+					opacity: $.fn.activity.getOpacity(d, i)
+				}));
+			}
+			return $('<div>').append(el).width(2*r).height(2*r);
+		};
+				
+		// Check if Webkit CSS animations are available, as they work much better on the iPad
+		// than setTimeout() based animations.
+		
+		if (document.createElement('div').style.WebkitAnimationName !== undefined) {
+
+			var animations = {};
+		
+			/**
+			 * Animation strategy that uses dynamically created CSS animation rules.
+			 */
+			animate = function(el, steps, duration) {
+				if (!animations[steps]) {
+					var name = 'spin' + steps;
+					var rule = '@-webkit-keyframes '+ name +' {';
+					for (var i=0; i < steps; i++) {
+						var p1 = Math.round(100000 / steps * i) / 1000;
+						var p2 = Math.round(100000 / steps * (i+1) - 1) / 1000;
+						var value = '% { -webkit-transform:rotate(' + Math.round(360 / steps * i) + 'deg); }\n';
+						rule += p1 + value + p2 + value; 
+					}
+					rule += '100% { -webkit-transform:rotate(100deg); }\n}';
+					document.styleSheets[0].insertRule(rule);
+					animations[steps] = name;
+				}
+				el.css('-webkit-animation', animations[steps] + ' ' + duration +'s linear infinite');
+			};
+		}
+		else {
+		
+			/**
+			 * Animation strategy that transforms a SVG element using setInterval().
+			 */
+			animate = function(el, steps, duration) {
+				var rotation = 0;
+				var g = el.find('g g').get(0);
+				el.data('interval', setInterval(function() {
+					g.setAttributeNS(null, 'transform', 'rotate(' + (++rotation % steps * (360 / steps)) + ')');
+				},  duration * 1000 / steps));
+			};
+		}
+		
+	}
+	else {
+		
+		// =======================================================================================
+		// VML Rendering
+		// =======================================================================================
+		
+		var s = $('<shape>').css('behavior', 'url(#default#VML)');
+
+		$('body').append(s);
+
+		if (s.get(0).adj) {
+		
+			// VML support detected. Insert CSS rules for group, shape and stroke.
+			var sheet = document.createStyleSheet();
+			$.each(['group', 'shape', 'stroke'], function() {
+				sheet.addRule(this, "behavior:url(#default#VML);");
+			});
+			
+			/**
+			 * Rendering strategy that creates a VML tree. 
+			 */
+			render = function(target, d) {
+			
+				var innerRadius = d.width*2 + d.space;
+				var r = (innerRadius + d.length + Math.ceil(d.width / 2) + 1);
+				var s = r*2;
+				var o = -Math.ceil(s/2);
+				
+				var el = $('<group>', {coordsize: s + ' ' + s, coordorigin: o + ' ' + o}).css({top: o, left: o, width: s, height: s});
+				for (var i = 0; i < d.segments; i++) {
+					el.append($('<shape>', {path: 'm ' + innerRadius + ',0  l ' + (innerRadius + d.length) + ',0'}).css({
+						width: s,
+						height: s,
+						rotation: (360 / d.segments * i) + 'deg'
+					}).append($('<stroke>', {color: d.color, weight: d.width + 'px', endcap: 'round', opacity: $.fn.activity.getOpacity(d, i)})));
+				}
+				return $('<group>', {coordsize: s + ' ' + s}).css({width: s, height: s, overflow: 'hidden'}).append(el);
+			};
+		
+			/**
+		     * Animation strategy that modifies the VML rotation property using setInterval().
+		     */
+			animate = function(el, steps, duration) {
+				var rotation = 0;
+				var g = el.get(0);
+				el.data('interval', setInterval(function() {
+					g.style.rotation = ++rotation % steps * (360 / steps);
+				},  duration * 1000 / steps));
+			};
+		}
+		$(s).remove();
+	}
+
+})(jQuery);

data/public/js/search.js

@@ -129,6 +129,23 @@ $(document).ready(function(){
         $.onedb();
     });
 
+    $('input:submit').click(function(){
+        var button = $(this);
+
+        //prevent submitting another query while this one is being processed
+        button.disable();
+
+        //fetch results now
+        $.post('', $('form').serialize(), function(data){
+            $('#result').html(data);
+            location.hash = '#result';
+
+            //result of previous query loaded; allow submitting a new query now
+            button.enable();
+        });
+        return false;
+    });
+
     $(window).scroll(function() {
       var areaHeight = $(this).height();
 

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.6.8'
+  s.version     = '0.6.9'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'
@@ -13,6 +13,7 @@ SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user in
 DESC
 
   # dependencies
+  s.add_dependency('bundler')
   s.add_dependency('sinatra', '>= 1.2.0')
   s.add_dependency('ptools')
 

data/views/search.erb

@@ -1,11 +1,12 @@
 <!DOCTYPE html>
 <html lang="en">
 <head>
-  <title>SequenceServer</title>
+  <title>SequenceServer: Custom BLAST Server</title>
   <meta name="author" content="Anurag Priyam" />
   <meta name="author" content="Ben J. Woodcroft" />
   <meta name="author" content="Yannick Wurm" />
   <meta name="author" content="Cedric Wurm" />
+  <meta name="description" content="Custom BLAST server provided by SequenceServer (http://www.sequenceserver.com)"/>
   <meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/>
   <script type="text/javascript" src="<%= uri('/js/jquery.js') %>"></script>
   <script type="text/javascript" src="<%= uri('/js/jquery.enablePlaceholder.min.js') %>"></script>
@@ -213,7 +214,7 @@
       </div>
 
       <div id="underbar">
-        <p>&copy; <a href='http://www.sequenceserver.com'>sequenceserver.com</a></p>
+        <p>&copy; <a href='http://www.sequenceserver.com'>SequenceServer: BLAST search made easy!</a></p>
       </div>
     </div> <!-- /page -->
   </div> <!-- /container -->

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: sequenceserver
 version: !ruby/object:Gem::Version 
-  hash: 23
+  hash: 21
   prerelease: 
   segments: 
   - 0
   - 6
-  - 8
-  version: 0.6.8
+  - 9
+  version: 0.6.9
 platform: ruby
 authors: 
 - Anurag Priyam
@@ -17,12 +17,26 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-12-15 00:00:00 Z
+date: 2011-12-16 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: sinatra
+  name: bundler
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: sinatra
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -34,11 +48,11 @@ dependencies:
         - 0
         version: 1.2.0
   type: :runtime
-  version_requirements: *id001
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: ptools
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -48,7 +62,7 @@ dependencies:
         - 0
         version: "0"
   type: :runtime
-  version_requirements: *id002
+  version_requirements: *id003
 description: |
   SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
 
@@ -76,6 +90,7 @@ files:
 - public/js/jquery.js
 - public/js/jquery.enablePlaceholder.min.js
 - public/js/search.js
+- public/js/jquery.activity.js
 - tests/test_sequencehelpers.rb
 - tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
 - tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
@@ -140,3 +155,4 @@ specification_version: 3
 summary: iPod of BLAST searching
 test_files: []
 
+has_rdoc: