adding some TODO statements, speling

beacon-app/arraymap-beacon/v0.4/beacon-query.js

@@ -14,9 +14,9 @@ info['info']['info']['datasets'].forEach(function(dataset){
 });
 
 var referenceMap = {
-    'GRCh38': 'SEGMENTS_HG38',
+    'GRCh36': 'SEGMENTS_HG18',
     'GRCh37': 'SEGMENTS_HG19',
-    'GRCh36': 'SEGMENTS_HG18'
+    'GRCh38': 'SEGMENTS_HG38'
 };
 
 //correspondence to arraymap class
@@ -26,8 +26,8 @@ var alternateBasesMap = {
 };
 
 /*
-  By default doe Maximilien takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt
-  TODO Should it be the same as Maximilen? Is it specified through the Beacon documentaiton?
+  By default doe Maximilian takes Reference 37. https://github.com/maximilianh/ucscBeacon/blob/master/help.txt
+  TODO Should it be the same as Maximilian? Is it specified through the Beacon documentation?
 */
 
 var defaultReference = 'GRCh37';
@@ -64,6 +64,10 @@ function checkPreconditions(params) {
         };
     }
 
+/*
+  TODO: Change method for numeric test, since positions are 0-based.
+*/
+
     if (!Number(params.start)) {
         return {
             hasError: true,

beacon-app/public/js/index.js

@@ -15,7 +15,7 @@ arrayMap.config(['$routeProvider', '$locationProvider',
 
 arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope, $location) {
 
-    $scope.references = ['GRCh38','GRCh37','GRCh36'];
+    $scope.references = ['GRCh36','GRCh37','GRCh38'];
 
     $scope.config = {
         "referenceName": "2",
@@ -66,6 +66,9 @@ arrayMap.controller('BeaconController', ['$scope', '$location', function ($scope
             ((conf.variantClass === "") ? "" : "&variantClass=" + conf.variantClass);
     };
 
+/*
+  TODO: Get datasets from beacon-info.js (or database query).
+*/
 
     $scope.datasets = [
         {
@@ -1681,4 +1684,3 @@ arrayMap.controller('DocumentationCtrl', ['$scope', '$http', function ($scope, $
         $scope.mkText = data;
     });
 }]);
-

beacon-app/public/pages/doc.md

 ## Current implementation
 
-This beacon queries 20K samples coming from ArrayMap from here:
+This beacon queries <60k samples from arrayMap, containing genomic copy number aberration data from cancer samples and associated control experiments.
+
 <a href="http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata">http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata</a>
 
 <img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
@@ -225,7 +226,7 @@ Open questions:
     2. use the property 'variants' to count the number of segments (for instance). - 9 March 2016 - APPROVED.
     3. ask the Beacon team if we can make this optional property.
     4. ask the Beacon team if we can change the property name.
-    
+
 
 --
 
@@ -236,4 +237,4 @@ Open questions:
    4. ask the Beacon team if they can replace the property type by a list of strings (instead of a string).
    5. clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)- OK
      * It's basically a range. See example and our interpretation here: https://github.com/samtools/hts-specs/issues/132
-     * For arrayMap, we need to define that interval for POS and END position. Michael suggested something like 0.5 * average probe distance (would be in order of kB)
\ No newline at end of file
+     * For arrayMap, we need to define that interval for POS and END position. Michael suggested something like 0.5 * average probe distance (would be in order of kB)

mongo-queries/update-beacon-info.sh

-./runquery.sh get-datasets.js | grep -E '[\"\{\}\;]|\[|\]' > /Library/WebServer/Documents/ga4gh-arraymap/beacon-app/arraymap-beacon/v0.4/beacon-info.js
+./runquery.sh build-info.js | grep -E '[\"\{\}\;]|\[|\]' > /Library/WebServer/Documents/ga4gh-arraymap/beacon-app/arraymap-beacon/v0.4/beacon-info.js