updates

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ec1dc642bb8019421b122b09d33a5ec1
+config: 0c42a34b9f89ccb7b7b7386f626dd2ac
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/index.txt

@@ -8,15 +8,18 @@ The ISB Cancer Genomics Cloud
 
 Welcome to the ISB-CGC Documentation on Read the Docs.
 
-Here you will find information describing the features of the ISB-CGC platform, tips on how to use it, 
-and details about the data that we are hosting on the Google Cloud Platform.
+Here you will find information describing the features of the ISB-CGC platform, 
+tips on how to use it, and details about the data that we are hosting on the 
+Google Cloud Platform.
 
-This documentation is a work-in-progress, please let us know how we can improve it! 
+This documentation is a work-in-progress, please let us know how we can improve 
+it! 
 
-Contents:
+Contents
+--------
 
 .. toctree::
-   :maxdepth: 1 
+   :maxdepth: 2
 
    sections/About-ISB-CGC
    sections/Web-UI
@@ -28,7 +31,7 @@ Contents:
    sections/Other-Useful-Links
 
 Indices and tables
-==================
+------------------
 
 * :ref:`search`
 * :ref:`genindex`

docs/build/html/_sources/sections/About-ISB-CGC.txt

@@ -1,20 +1,24 @@
 About the ISB Cancer Genomics Cloud
 ===================================
 
-The ISB-CGC provides interactive and programmatic access to the TCGA data, leveraging many 
-aspects of the Google Cloud Platform including BigQuery, Compute Engine, App Engine, Cloud
-Datalab and Google Genomics.  Open-access clinical and biospecimen information for all TCGA 
-patients and samples, combined with the Level-3 TCGA data and genomic reference and 
-platform-annotation sources are stored in BigQuery, enabling fast SQL-like queries against 
-the entire dataset.  Controlled-access DNA and RNA sequence data is available to 
-dbGaP-authorized users in the original BAM and FASTQ file formats.
+The ISB-CGC provides interactive and programmatic access to the TCGA data, 
+leveraging many aspects of the Google Cloud Platform including BigQuery, 
+Compute Engine, App Engine, Cloud Datalab and Google Genomics.  
+Open-access clinical and biospecimen information for all TCGA patients 
+and samples, combined with the Level-3 TCGA data and genomic reference and 
+platform-annotation sources are stored in BigQuery, enabling fast SQL-like 
+queries against the entire dataset.  Controlled-access DNA and RNA 
+sequence data is available to dbGaP-authorized users in the original BAM 
+and FASTQ file formats.
 
-The ISB-CGC aims to serve the needs of a broad range of cancer researchers ranging from 
-scientists or clinicians who prefer to use an interactive web-based application to 
-access and explore the rich TCGA dataset, to computational scientists who want to write 
-their own custom scripts using languages such as R or Python, accessing the data through APIs, 
-to algorithm developers who want to spin up thousands of virtual machines to analyze hundreds 
-of terabytes of sequence data.  The ISB-CGC allows scientists to interactively define and 
-compare cohorts, examine the underlying molecular data for specific genes or pathways of 
-interest, and share insights with collaborators around the globe.  
+The ISB-CGC aims to serve the needs of a broad range of cancer researchers 
+ranging from scientists or clinicians who prefer to use an interactive 
+web-based application to access and explore the rich TCGA dataset, to 
+computational scientists who want to write their own custom scripts using 
+languages such as R or Python, accessing the data through APIs, to algorithm 
+developers who want to spin up thousands of virtual machines to rapidly 
+analyze hundreds of terabytes of sequence data.  The ISB-CGC allows scientists 
+to interactively define and compare cohorts, examine the underlying molecular 
+data for specific genes or pathways of interest, and share insights with 
+collaborators around the globe.  
 

docs/build/html/_sources/sections/TCGA-Data.txt

@@ -1,2 +1,10 @@
 About the TCGA Data
 ===================
+
+The ISB-CGC hosts approximately 1 petabyte of TCGA_ data in Google Cloud
+Storage (GCS_) and in BigQuery_.  
+
+.. _TCGA: http://cancergenome.nih.gov/
+.. _GCS: https://cloud.google.com/storage/
+.. _BigQuery: https://cloud.google.com/bigquery/
+

docs/build/html/_sources/sections/Web-UI.txt

@@ -5,7 +5,7 @@ Documentation for the ISB-CGC web app is available from within the web-app.  Aft
 click on the down-arrow next to your name in the upper-right corner and select "Help".
 
 .. toctree::
-  webapp/Releases
+  webapp/releases
   webapp/User-Dashboard
   webapp/Cohorts
   webapp/Visualizations

docs/build/html/_sources/sections/webapp/User-Dashboard.txt

@@ -1,10 +1,11 @@
 User Dashboard
 ==============
 
-*Documentation in progress!*
-
-Create a Cohort
+Create a cohort
 ---------------
+To create a cohort from the User Dashboard, click on the "+Create" button
+and select "New Cohort".  This will take you to the cohort creation page.
+
 To create a cohort from the user dashboard, click on the “+ Create” button and select “New Cohort”. 
 This will take you to the cohort creation page.
 
@@ -32,8 +33,10 @@ be able to select from a list of users that are already registered in the system
 one or more users you wish to share with. Click the “Share Cohort” button when you are done. This is 
 the same for visualizations. 
 
-Users who you share a cohort with will only be able to view and comment on the cohort and not 
-make changes. They will need to clone the cohort before making changes to it.
+When you share a cohort with another user, that user
+will be able to view and comment on the cohort, but will not be able to 
+make changes.  If you want to make changes to a cohort that has been
+shared with you, first clone that cohort.
 
 Set operations on cohorts
 -------------------------

docs/build/html/_static/searchtools.js

@@ -10,7 +10,6 @@
  */
 
 
-/* Non-minified version JS is _stemmer.js if file is provided */ 
 /**
  * Porter Stemmer
  */
@@ -374,7 +373,8 @@ var Search = {
     }
 
     // lookup as search terms in fulltext
-    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
+                     .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
 
     // let the scorer override scores with a custom scoring function
     if (Scorer.score) {
@@ -538,47 +538,23 @@ var Search = {
   /**
    * search for full-text terms in the index
    */
-  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+  performTermsSearch : function(searchterms, excluded, terms, score) {
     var filenames = this._index.filenames;
     var titles = this._index.titles;
 
-    var i, j, file;
+    var i, j, file, files;
     var fileMap = {};
-    var scoreMap = {};
     var results = [];
 
     // perform the search on the required terms
     for (i = 0; i < searchterms.length; i++) {
       var word = searchterms[i];
-      var files = [];
-      var _o = [
-        {files: terms[word], score: Scorer.term},
-        {files: titleterms[word], score: Scorer.title}
-      ];
-
       // no match but word was a required one
-      if ($u.every(_o, function(o){return o.files === undefined;})) {
+      if ((files = terms[word]) === undefined)
         break;
+      if (files.length === undefined) {
+        files = [files];
       }
-      // found search word in contents
-      $u.each(_o, function(o) {
-        var _files = o.files;
-        if (_files === undefined)
-          return
-
-        if (_files.length === undefined)
-          _files = [_files];
-        files = files.concat(_files);
-
-        // set score for the word in each file to Scorer.term
-        for (j = 0; j < _files.length; j++) {
-          file = _files[j];
-          if (!(file in scoreMap))
-            scoreMap[file] = {}
-          scoreMap[file][word] = o.score;
-        }
-      });
-
       // create the mapping
       for (j = 0; j < files.length; j++) {
         file = files[j];
@@ -600,19 +576,14 @@ var Search = {
       // ensure that none of the excluded terms is in the search result
       for (i = 0; i < excluded.length; i++) {
         if (terms[excluded[i]] == file ||
-            titleterms[excluded[i]] == file ||
-            $u.contains(terms[excluded[i]] || [], file) ||
-            $u.contains(titleterms[excluded[i]] || [], file)) {
+          $u.contains(terms[excluded[i]] || [], file)) {
           valid = false;
           break;
         }
       }
 
       // if we have still a valid result we can add it to the result list
       if (valid) {
-        // select one (max) score for the file.
-        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
-        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
         results.push([filenames[file], titles[file], '', null, score]);
       }
     }

docs/build/html/genindex.html

@@ -9,7 +9,7 @@
 
     <title>Index &mdash; ISB Cancer Genomics Cloud 1.0.0 documentation</title>
 
-    <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
@@ -24,13 +24,18 @@
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <link rel="top" title="ISB Cancer Genomics Cloud 1.0.0 documentation" href="index.html" />
-
-
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
-
+    <link rel="top" title="ISB Cancer Genomics Cloud 1.0.0 documentation" href="index.html" /> 
   </head>
-  <body role="document">  
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="nav-item nav-item-0"><a href="index.html">ISB Cancer Genomics Cloud 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
 
     <div class="document">
       <div class="documentwrapper">
@@ -51,13 +56,7 @@ <h1 id="index">Index</h1>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
 
-   <div class="relations">
-<h3>Related Topics</h3>
-<ul>
-  <li><a href="index.html">Documentation overview</a><ul>
-  </ul></li>
-</ul>
-</div>
+
 
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
@@ -76,17 +75,18 @@ <h3>Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="footer">
-      &copy;2015, the ISB-CGC team.
-
-      |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.3</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.7</a>
-
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             >index</a></li>
+        <li class="nav-item nav-item-0"><a href="index.html">ISB Cancer Genomics Cloud 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &copy; Copyright 2015, the ISB-CGC team.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.3.1.
     </div>
-
-
-
-
   </body>
 </html>