sequenceserver 0.7.4 → 0.7.5

data/LICENSE.Apache.txt

@@ -0,0 +1,176 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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+
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+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
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+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
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+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      whether in tort (including negligence), contract, or otherwise,
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data/LICENSE.txt

@@ -4,7 +4,12 @@ Copyright (c) 2010-2011  Yannick Wurm, Benjamin J. Woodcroft, Anurag Priyam.
 
 1.  Definitions 
 
-The software: the SequenceServer software and associated documentation.
+The software: the SequenceServer software and associated documentation. The
+term does not extend to unmodified open source software components used within
+SequenceServer which are governed by their own license agreements. However,
+modfications to such components shall be deemed a part of the SequenceServer
+software.
+
 The authors: Yannick Wurm, Anurag Priyam, Benjamin J. Woodcroft. 
 
 

data/lib/sequenceserver.rb

@@ -270,8 +270,11 @@ module SequenceServer
       advanced_opts = params['advanced']
       validate_advanced_parameters(advanced_opts) #check the advanced options are sensible
 
-      # blastn implies blastn, not megablast
-      advanced_opts << '-task blastn ' if method == 'blastn'
+      # blastn implies blastn, not megablast; but let's not interfere if a user
+      # specifies `task` herself
+      if method == 'blastn' and not advanced_opts =~ /task/
+        advanced_opts << ' -task blastn '
+      end
 
       method = settings.binaries[ method ]
       settings.log.debug('settings.databases:   ' + settings.databases.inspect)

data/lib/sequenceserver/helpers.rb

@@ -95,6 +95,13 @@ module SequenceServer
           type = type.downcase
           name = name.freeze
           title = title.join(' ').freeze
+
+          # skip past all but alias file of a NCBI multi-part BLAST database
+          if name.match(/\/\w*[.]\d{2,}[.\w]*/)
+            log.info(%|Found a multi-part database volume at #{name} - ignoring it.|)
+            next
+          end
+
           #LOG.info("Found #{type} database: #{title} at #{name}")
           (db[type] ||= []) << Database.new(name, title)
         end

data/public/js/liveclip.jquery.js

@@ -0,0 +1,246 @@
+/**
+ * jQuery Live Clipboard
+ *
+ * Copyright (c) 2009 Shinichi Tomita (shinichi.tomita@gmail.com)
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+(function($) {
+
+  var namespace = 'liveclip';
+  var relayEvents = 
+    'click,dblclick,mousedown,mouseup,mousemove,mouseover,mouseout,keypress,keyup'.split(',');
+
+  /**
+   * Adjust clipboard textarea size to cover parent clippable element.
+   */
+  function track() {
+    var target = $(this);
+    var clipboard = target.clipboard();
+    var w = target.outerWidth(), h = target.outerHeight(), offset = target.offset();
+    if (/^(auto|scroll)$/.test(target.css('overflow'))) w -= 20;
+    if (clipboard) clipboard.css({ width : w, height : h, top : offset.top, left : offset.left });
+  }
+
+  /**
+   * Finding and capture event target element, excluding clipboard textarea.
+   * This is "pseudo" capturing, assuming no layered elements covering over the target.
+   */
+  function capture(el, e) {
+    var captured = _capture(el);
+    var clipboard = captured.clipboard();
+    // if captured element has clipboard, return it. 
+    return captured !== el && clipboard ? clipboard : captured;
+
+    function _capture(el) {
+      var target = el;
+      el.children().each(function() {
+        var child = $(this);
+        var w = child.width(), h = child.innerHeight(), offset = child.offset();
+        if (e.pageX > offset.left && e.pageX < offset.left + w &&
+            e.pageY > offset.top  && e.pageY < offset.top  + h) {
+          target = _capture(child);
+        }
+      })
+      return target;
+    }
+  }
+
+  /**
+   * Context menu event handler 
+   */
+  function contextmenuHandler(e) {
+    var clipboard = $(this);
+    var target = clipboard.data(namespace + '-target');
+    var options = target.data(namespace + '-clipboard-options');
+
+    if (options.active && options.active.call(target) === false) {
+      clipboard.attr('readonly', 'readonly');
+      return;
+    }
+
+    if (options.paste || options.del) {
+      clipboard.removeAttr('readonly');
+    } else {
+      clipboard.attr('readonly', 'readonly');
+    }
+
+    var val = options.copy ? options.copy.call(target) : '';
+    clipboard.val(val);
+    clipboard.get(0).select(); 
+    if (options.paste || options.del) {
+      val = clipboard.val();
+      var watchPID = clipboard.data(namespace+'-watcher');
+      if (watchPID) {
+        clearInterval(watchPID);
+        clipboard.removeData(namespace+'-watcher');
+      }
+      watchPID = setInterval(function() {
+        var v = clipboard.val();
+        if (v !== val) {
+          try {
+            if (v === '') {
+              if (options.del) options.del.call(target)
+            } else {
+              if (options.paste) options.paste.call(target, v);
+              clipboard.val('');
+            }
+          } catch(e) {}
+          clearInterval(watchPID);
+          clipboard.removeData(namespace+'-watcher');
+        }
+      }, 100);
+      clipboard.data(namespace+'-watcher', watchPID);
+    }
+  }
+
+
+  /**
+   * Keyboard down event handler
+   */
+  function keydownHandler(e) {
+    var clipboard = $(this);
+    var target = clipboard.data(namespace + '-target');
+    var options = target.data(namespace + '-clipboard-options');
+
+    if (e.metaKey) {
+      switch (e.keyCode) {
+        case 67 : // Command + C
+          var val = options.copy ? options.copy.call(target) : '';
+          clipboard.val(val)
+          clipboard.get(0).select(); 
+          break;
+        case 86 : // Command + V
+          if (options.paste) {
+            clipboard.get(0).select(); 
+            setTimeout(function() {
+              var data = clipboard.val();
+              options.paste.call(target, data);
+              clipboard.val('')
+            }, 10);
+          }
+          break;
+        case 88 : // Command + X
+          var val = options.copy ? options.copy.call(target) : '';
+          clipboard.val(val)
+          clipboard.get(0).select(); 
+          if (options.del) {
+            setTimeout(function() {
+              options.del.call(target)
+            }, 10);
+          }
+          break;
+        default :
+          break;
+      }
+    } else if (e.keyCode==46) { // delete
+      if (options.del) options.del.call(target);
+    }
+
+  }
+
+
+  $.fn.extend({
+
+    /**
+     * Attach clipboard feature to block element
+     * Get current clipboard proxy textarea
+     */
+    clipboard : function(options) {
+      var elements = this;
+
+      if (options) { // setter
+
+        $(elements).each(function() {
+          var target = $(this);
+          var clipboard = target.data(namespace + '-clipboard');
+          if (!clipboard) { 
+            clipboard = $('<textarea></textarea>')
+              .addClass(namespace+'-clipboard')
+              .addClass(options.cls ? options.cls : '')
+              .css({ 
+                cursor : 'default',
+                position : 'absolute', 
+                fontSize : $.liveclip.debug ? '12px' : '1px',
+                opacity : $.liveclip.debug ? .5 : .01 
+              })
+              .appendTo(document.body)
+              .bind('contextmenu', contextmenuHandler)
+              .bind('keydown', keydownHandler);
+            $.each(relayEvents, function(i, eventName) {
+              clipboard.bind(eventName+'.'+namespace, function(e) { 
+                capture(target, e).trigger(e);
+              });
+            });
+            if ($.liveclip.autoTrack) { target.bind('mouseover.'+namespace, track) }
+            target.data(namespace+'-clipboard', clipboard);
+            clipboard.data(namespace+'-target', target);
+          }
+          target.data(namespace+'-clipboard-options', options);
+          track.call(target);
+        });
+        return this;
+
+      } else { // getter
+        return $(this).data(namespace + '-clipboard');
+      }
+
+    }
+    ,
+
+    /**
+     * remove attached clipboard feature
+     */
+    removeClipboard : function() {
+      $(this).each(function() {
+        $(this).clipboard().remove();
+        $(this).unbind('mouseover.'+namespace, track)
+               .removeData(namespace + '-clipboard')
+               .removeData(namespace + '-clipboard-options');
+      });
+      return this;
+    }
+
+  });
+
+  $.liveclip = {
+    debug : false,
+    autoTrack : false
+  }
+
+  /**
+   * Track all clipboard, aligning to target element position and size
+   * If no target element available in document, removing clipboard.
+   */
+  $.trackClipboards = function() {
+    $('body > textarea.'+namespace+'-clipboard').each(function() {
+      var clipboard = $(this);
+      var target = clipboard.data(namespace + '-target');
+      if (target && target.parent()) {
+        track.call(target);
+      } else {
+        clipboard.remove();
+      }
+    });
+  }
+
+  $(function() {
+    if ($.liveclip.autoTrack) {
+      $(document).mousemove($.trackClipboards);
+    }
+  })
+
+})(jQuery)

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.7.4'
+  s.version     = '0.7.5'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'
@@ -20,7 +20,7 @@ DESC
   # gem
   s.files         = Dir['lib/**/*'] + Dir['views/**/*'] + Dir['public/**/*'] + Dir['tests/**/*']
   s.files         = s.files + ['config.ru',   'example.config.yml']
-  s.files         = s.files + ['LICENSE.txt', 'README.txt']
+  s.files         = s.files + ['LICENSE.txt', 'LICENSE.Apache.txt', 'README.txt']
   s.files         = s.files + ['Gemfile',     'sequenceserver.gemspec']
   s.executables   = ['sequenceserver']
   s.require_paths = ['lib']

data/tests/ui.specs.todo

@@ -0,0 +1,10 @@
+it "should automatically focus sequence input box" do
+  # when the page loads, check that sequence input box is focussed
+  #
+  # NOTE: unless #75 is resolved, make sure to test this functionality only if
+  # HTML5 autofocus attribute is supported
+end
+
+it "should ensure spell checking is disabled for sequence input box" do
+  # NOTE: only if the browser supports it
+end

data/views/search.erb

@@ -31,7 +31,7 @@
           <div class="span12">
             <div class="offset-left sequence">
               <div class="clearfix">
-                <textarea name="sequence" id="sequence" rows="11" placeholder="Paste your sequence(s) here..." ></textarea>
+                <textarea name="sequence" id="sequence" rows="11" spellcheck="false" <%= 'autofocus="true"' unless @blast %> placeholder="Paste your sequence(s) here..." ></textarea>
               </div>
             </div>
           </div>

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: sequenceserver
 version: !ruby/object:Gem::Version 
-  hash: 11
+  hash: 9
   prerelease: 
   segments: 
   - 0
   - 7
-  - 4
-  version: 0.7.4
+  - 5
+  version: 0.7.5
 platform: ruby
 authors: 
 - Anurag Priyam
@@ -17,7 +17,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-12-23 00:00:00 Z
+date: 2012-02-09 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: bundler
@@ -89,6 +89,7 @@ files:
 - public/css/custom.css
 - public/js/jquery.js
 - public/js/jquery.enablePlaceholder.min.js
+- public/js/liveclip.jquery.js
 - public/js/sequenceserver.js
 - public/js/jquery.activity.js
 - public/js/sequenceserver.blast.js
@@ -103,9 +104,11 @@ files:
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
+- tests/ui.specs.todo
 - config.ru
 - example.config.yml
 - LICENSE.txt
+- LICENSE.Apache.txt
 - README.txt
 - Gemfile
 - sequenceserver.gemspec