rbbt-views 1.0.1 → 2.0.0

data/share/views/partials/layout/_coda.haml

@@ -0,0 +1,10 @@
+= serve_js(params[:debug_js].nil?)
+
+:javascript
+  function deffer(func){func.call()}
+  $(defferred_execution).each(function(pos,func){
+    func.call();
+  })
+  rbbt_setup_layout();
+
+

data/share/views/partials/layout/_details.haml

@@ -0,0 +1,25 @@
+#details_controls
+  %span.entity_type
+  %ul
+    %li
+      %a.button(href="#" id="hide_details") hide
+    %li
+      %a.button(href="#" id="toggle_expand_details") toggle
+    %li
+      %a.button(href="#" id="back_details") back
+    %li
+      %a.button(href="#" id="reload_details") reload
+    %li
+      %a.button(href="#" id="link_details") link
+    %li.save
+      %a.button(href="#" id="save_details") save
+      in list:
+      %select.loaded_lists(name="other_list" type="NONE")
+        %option.keep(value='temp') temp
+    %li.select
+      %a.button.select_list(href="#select_list" attr-list-type="" attr-list="") select
+
+
+#details
+
+

data/share/views/partials/layout/_head.haml

@@ -0,0 +1,22 @@
+- if defined? @rbbt_refresh and Fixnum === @rbbt_refresh and @rbbt_refresh > 0
+  %meta(http-equiv="refresh" content=@rbbt_refresh)
+
+%title
+  = title
+%link{:rel => "shortcut icon", :type => "image/png", :href => "/favicon.gif"}/
+
+%meta{'http-equiv'=>"Content-Type", :content=>"text/html; charset=UTF-8"}/
+%meta{'http-equiv'=>"Content-Language", :content=>"en-us"}/
+
+:javascript
+  var defferred_execution = [];
+  function deffer(func){
+    defferred_execution.push(func);
+  }
+  var cytoscape_visualizations = {};
+
+= workflow_partial('partials/layout/_resources')
+
+= serve_css
+
+

data/share/views/partials/layout/_header.haml

@@ -0,0 +1,29 @@
+#header
+  %h1
+    %a(href="/")= title
+  #controls
+    %span.wide
+      %a(href="#") <=>
+    %span.centered
+      %a.hide(href="#") >=<
+    %span.login
+      - if session[:user]
+        ==Logged in as: 
+        %span.user== #{session[:user]}
+        \. 
+        %a(href="/logout") logout
+      - else
+        Not logged in
+        %a(href="/login") login
+    %span.add_gene_list
+      %a(href='/add_gene_list') Add Gene List
+    %span.list_dropdown
+      %a(href='#lists') Entity Lists
+    %span.reload_page
+      %a(href='#') Reload
+    %span.notes
+      %a(href='#') Notes
+  %span.find
+    = workflow_partial('find.haml') if settings.respond_to? :finder
+
+

data/share/views/partials/layout/_menu.haml

@@ -0,0 +1,20 @@
+#menu
+  - if session.include?(:context) and Hash === session[:context] and session[:context].collect{|w,t| t.values}.flatten.any?
+    #context
+      %h2 Context Jobs
+      = workflow_partial('partials/_context_control', nil, nil, locals)
+
+    %h2 Workflows
+
+  - WorkflowREST.workflows.each do |workflow|
+    %h3.workflow_title(target=workflow)= workflow.to_s
+    %div.workflow_menu(id=workflow)
+      %a.replace(href="/#{workflow.to_s}")
+  #footer
+    %p Structural Computational Biology Group
+
+    %p Structural Biology and BioComputing Programme
+
+    %p Spanish National Cancer Research Centre (CNIO). C/ Melchor Fernández Almagro, 3, E-28029 Madrid Spain 
+
+

data/share/views/partials/layout/_resources.haml

@@ -0,0 +1,41 @@
+
+- %w(layout app).each do |css_file|
+  - record_css File.join('/stylesheets', css_file)
+
+- record_js File.join('/js', 'json2')
+
+- %w(jquery-1.8.0.min jquery.cookie jquery.form).each do |jquery_file|
+  - record_js File.join('/plugins/jquery/js/', jquery_file)
+
+- record_js File.join('/plugins/jquery-ui/js/', 'jquery-ui-1.8.14.custom.min.js')
+
+-#{{{ HITAREA
+- record_js '/plugins/wz_jsgraphics.js'
+- record_js '/plugins/jquery-ui.hitarea.js'
+
+-#{{{ JMOL
+- record_js '/plugins/jmol/Jmol'
+
+-#{{{ CYTOSCAPE
+- record_js '/plugins/cytoscape-web/js/AC_OETags'
+- record_js '/plugins/cytoscape-web/js/cytoscapeweb'
+
+-#{{{ FANCYBOX
+-# record_js '/plugins/fancybox/js/jquery.fancybox'
+-# record_css "/plugins/fancybox/css/jquery.fancybox.css"
+
+-#{{{ ImageView
+-# record_js '/plugins/jquery-imageView/js/jquery.imageView'
+
+-#{{{ TABLE SORTER
+- record_js '/plugins/tablesorter/jquery.tablesorter.min.js'
+- record_js '/js/fix_tablesorter_scientific.js'
+
+-#{{{ Feature Image Zoom
+- record_css '/plugins/featuredimagezoomer/css/featuredimagezoomer'
+- record_js '/plugins/featuredimagezoomer/js/featuredimagezoomer'
+
+- %w(_basic _action_setup _dom_updates _workflow _details _embedded _cytoscape _lists _table _images _layout app).each do |js_file|
+  - record_js File.join('/js', js_file)
+
+

data/share/views/public/plugins/cytoscape-web/LICENSE.txt

@@ -0,0 +1,504 @@
+          GNU LESSER GENERAL PUBLIC LICENSE
+               Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+                Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
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+specially designated software packages--typically libraries--of the
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+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+  When we speak of free software, we are referring to freedom of use,
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+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+             END OF TERMS AND CONDITIONS
+
+           How to Apply These Terms to Your New Libraries
+
+  If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change.  You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+  To apply these terms, attach the following notices to the library.  It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the library's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This library is free software; you can redistribute it and/or
+    modify it under the terms of the GNU Lesser General Public
+    License as published by the Free Software Foundation; either
+    version 2.1 of the License, or (at your option) any later version.
+
+    This library is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+    Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public
+    License along with this library; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the
+  library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+  <signature of Ty Coon>, 1 April 1990
+  Ty Coon, President of Vice
+
+That's all there is to it!
+
+