Commented a lot of functions. Tried to get jsDoc and/or docco to work

.gitignore

@@ -1,3 +1,5 @@
+.idea/
+docs/
 .meteor/local
 .meteor/meteorite
 node_modules

LesionTracker/client/routes.js

@@ -1,4 +1,3 @@
-tabs = new Meteor.Collection(null);
 Session.setDefault('ViewerData', {});
 
 // Re-add any tab data saved in the Session
@@ -8,7 +7,7 @@ Object.keys(ViewerData).forEach(function(contentId) {
         title: tabData.title,
         contentid: tabData.contentid,
     };
-    tabs.insert(data);
+    WorklistTabs.insert(data);
 });
 
 Router.configure({
@@ -34,7 +33,7 @@ Router.route('/viewer/:_id', {
         
         // Check if this study is already loaded in a tab
         // If it is, stop here so we don't keep adding tabs on hot-code reloads
-        var tab = tabs.find({'studyInstanceUid' : studyInstanceUid}).fetch();
+        var tab = WorklistTabs.find({'studyInstanceUid' : studyInstanceUid}).fetch();
         if (tab) {
             return;
         }

Makefile

@@ -0,0 +1,13 @@
+docs:
+	mkdir -p docs
+	rm docs/* || true
+	
+	# Make jsdoc3 documentation
+	jsdoc . -c conf.json -r -d docs -R README.md
+
+	# Make docco documentation (not sure if we will keep this)
+	mkdir -p docs/docco
+	docco {Packages,Viewer,LesionTracker}/{**/*,*} -o docs/docco -l parallel
+
+# Force rebuild even if the docs exist
+.PHONY: docs

OHIFViewer/.gitignore

@@ -1,3 +1,4 @@
+.idea
 .meteor/local
 .meteor/meteorite
 node_modules

OHIFViewer/.meteor/versions

@@ -58,6 +58,7 @@ minifiers@1.1.7
 minimongo@1.0.10
 mobile-experience@1.0.1
 mobile-status-bar@1.0.6
+momentjs:moment@2.8.4
 mongo@1.1.3
 mongo-id@1.0.1
 mrt:moment@2.8.1

OHIFViewer/client/routes.js

@@ -1,4 +1,3 @@
-tabs = new Meteor.Collection(null);
 Session.setDefault('ViewerData', {});
 
 // Re-add any tab data saved in the Session
@@ -8,7 +7,7 @@ Object.keys(ViewerData).forEach(function(contentId) {
         title: tabData.title,
         contentid: tabData.contentid,
     };
-    tabs.insert(data);
+    WorklistTabs.insert(data);
 });
 
 Router.configure({
@@ -34,7 +33,7 @@ Router.route('/viewer/:_id', {
         
         // Check if this study is already loaded in a tab
         // If it is, stop here so we don't keep adding tabs on hot-code reloads
-        var tab = tabs.find({studyInstanceUid: studyInstanceUid}).fetch();
+        var tab = WorklistTabs.find({studyInstanceUid: studyInstanceUid}).fetch();
         if (tab) {
             return;
         }

Packages/cornerstone/client/hangingProtocol.js

@@ -1,5 +1,16 @@
 var hangingProtocol;
 
+/**
+ * This is an example of a hanging protocol
+ * It takes in a set of studies, as well as the
+ * number of rows and columns in the layout.
+ *
+ * It returns an array of objects, one for each viewport, detailing
+ * which series should be loaded in the viewport.
+ *
+ * @param inputData
+ * @returns {Array}
+ */
 function defaultHangingProtocol(inputData) {
     var studies = inputData.studies;
     var viewportRows = inputData.viewportRows;

Packages/dicomweb/lib/findIndexOfString.js

@@ -0,0 +1,49 @@
+/**
+ * Converts a String to a UInt8 array of character codes
+ * @param {String} str Input string
+ * @returns {Uint8Array} Uint8 Array of character codes
+ */
+function stringToUint8Array(str) {
+    var uint=new Uint8Array(str.length);
+    for(var i=0,j=str.length;i<j;i++){
+        uint[i]=str.charCodeAt(i);
+    }
+    return uint;
+}
+
+function checkToken(token, data, dataOffset) {
+    if(dataOffset + token.length > data.length) {
+        //console.log('dataOffset >> ', dataOffset);
+        return false;
+    }
+
+    for(var i = 0; i < token.length; i++) {
+        if(token[i] !== data[endIndex++]) {
+            if(endIndex > 520000) {
+                console.log('token=',uint8ArrayToString(token));
+                console.log('data=', uint8ArrayToString(data, dataOffset, endIndex-dataOffset));
+                console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(data[endIndex]), endIndex);
+                console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(token[endIndex]), endIndex);
+            }
+            return false;
+        }
+    }
+    return true;
+}
+
+
+findIndexOfString = function(data, str, offset) {
+    offset = offset || 0;
+
+    var token = stringToUint8Array(str);
+
+    for(var i=offset; i < data.length; i++) {
+        if(data[i] === token[0]) {
+            //console.log('match @', i);
+            if(checkToken(token, data, i)) {
+                return i;
+            }
+        }
+    }
+    return -1;
+};

Packages/dicomweb/lib/uint8ArrayToString.js

@@ -0,0 +1,17 @@
+/**
+ * Converts a Uint8 array to a string
+ * @param data
+ * @param offset
+ * @param length
+ * @returns {string}
+ */
+uint8ArrayToString = function(data, offset, length) {
+    offset = offset || 0;
+    length = length || data.length - offset;
+    var str = "";
+
+    for(var i=offset; i < offset + length; i++) {
+        str += String.fromCharCode(data[i]);
+    }
+    return str;
+};

Packages/dicomweb/package.js

@@ -7,6 +7,7 @@ Package.describe({
 Package.onUse(function (api) {
     api.use('http');
 
+    // DICOMWeb API functions
     api.addFiles('server/namespace.js', 'server');
     api.addFiles('server/getImageFrame.js', 'server');
     api.addFiles('server/getJSON.js', 'server');
@@ -14,6 +15,10 @@ Package.onUse(function (api) {
     api.addFiles('server/getNumber.js', 'server');
     api.addFiles('server/getString.js', 'server');
 
+    // Helper functions
+    api.addFiles('lib/findIndexOfString.js', 'server');
+    api.addFiles('lib/uint8ArrayToString.js', 'server');
+
     api.export("DICOMWeb", 'server');
 });
 

Packages/viewerbase/components/viewer/imageViewerViewport/imageViewerViewport.js

@@ -190,9 +190,11 @@ function loadSeriesIntoViewport(data) {
         // Add stack state managers for the stack tool, CINE tool, and reference lines
         cornerstoneTools.addStackStateManager(element, [ 'stack', 'playClip', 'referenceLines' ]);
 
-        // Enable orientation markers, if applicable
+        // Get the current viewport settings
         var viewport = cornerstone.getViewport(element);
-        updateOrientationMarkers(element, viewport);
+
+        // Enable orientation markers, if applicable
+        updateOrientationMarkers(element);
 
         // Clear any old stack data
         cornerstoneTools.clearToolState(element, 'stack');

Packages/viewerbase/components/viewer/layoutChooser/layoutChooser.js

@@ -1,3 +1,10 @@
+/**
+ * Adds the 'hover' class to cells above and to the left of the current cell
+ * This is used to "fill in" the grid that the user will change the layout to,
+ * if they click on a specific table cell.
+ *
+ * @param currentCell
+ */
 function highlightCells(currentCell) {
     var cells = $('.layoutChooser table td');
     cells.removeClass('hover');

Packages/viewerbase/components/viewer/viewportOrientationMarkers/viewportOrientationMarkers.js

@@ -1,5 +1,13 @@
-updateOrientationMarkers = function(element, viewport) {
-    // Updates the orientation labels on the viewport
+/**
+ * Updates the orientation labels on a Cornerstone-enabled Viewport element
+ * when the viewport settings change (e.g. when a horizontal flip or a rotation occurs)
+ *
+ * @param element The DOM element of the Cornerstone viewport
+ */
+updateOrientationMarkers = function(element) {
+    // Get the current viewport settings
+    var viewport = cornerstone.getViewport(element);
+
     var enabledElement = cornerstone.getEnabledElement(element);
     var imagePlane = cornerstoneTools.metaData.get('imagePlane', enabledElement.image.imageId);
     

Packages/viewerbase/lib/createStacks.js

@@ -1,7 +1,22 @@
+/**
+ * Creates a set of series to be placed in the Study Browser
+ * The series that appear in the Study Browser must represent
+ * imaging modalities.
+ *
+ * Furthermore, for drag/drop functionality,
+ * it is easiest if the stack objects also contain information about
+ * which study they are linked to.
+ *
+ * @param study The study instance to be used
+ * @returns {Array} An array of series to be placed in the Study Browser
+ */
 createStacks = function(study) {
+    // Define an empty array of stacks
     var stacks = [];
+
     // TODO: Split by multi-frame, modality, image size, etc
     study.seriesList.forEach(function(series) {
+        // If the series has no instanced, skip it
         if (!series.instances) {
             return;
         }
@@ -13,7 +28,10 @@ createStacks = function(study) {
             return;
         }
 
+        // Include the study instance Uid for drag/drop purposes
         series.studyInstanceUid = study.studyInstanceUid;
+
+        // Add this series to the list of stacks
         stacks.push(series);
     });
     return stacks;

Packages/viewerbase/lib/docking-container.js

@@ -1,6 +1,4 @@
 (function($) {
-
-
     //Collapse the container
     function collapseContainer ( container ) {
         container.toggleClass("collapseHorizontal");

Packages/viewerbase/lib/encodeQueryData.js

@@ -8,10 +8,11 @@
 encodeQueryData = function(data)
 {
   var ret = [];
+
   for (var d in data) {
-    if(data[d]) {
-      ret.push(encodeURIComponent(d) + "=" + encodeURIComponent(data[d]));
-    }
+      if(data[d]) {
+         ret.push(encodeURIComponent(d) + "=" + encodeURIComponent(data[d]));
+      }
   }
   return ret.join("&");
 };

Packages/viewerbase/lib/findIndexOfString.js

@@ -1,39 +0,0 @@
-function checkToken(token, data, dataOffset) {
-
-  if(dataOffset + token.length > data.length) {
-    //console.log('dataOffset >> ', dataOffset);
-    return false;
-  }
-
-  var endIndex = dataOffset;
-
-  for(var i = 0; i < token.length; i++) {
-    if(token[i] !== data[endIndex++]) {
-      if(endIndex > 520000) {
-        console.log('token=',uint8ArrayToString(token));
-        console.log('data=', uint8ArrayToString(data, dataOffset, endIndex-dataOffset));
-        console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(data[endIndex]), endIndex);
-        console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(token[endIndex]), endIndex);
-      }
-      return false;
-    }
-  }
-  return true;
-}
-
-findIndexOfString = function(data, str, offset) {
-
-  offset = offset || 0;
-
-  var token = stringToUint8Array(str);
-
-  for(var i=offset; i < data.length; i++) {
-    if(token[0] === data[i]) {
-      //console.log('match @', i);
-      if(checkToken(token, data, i)) {
-        return i;
-      }
-    }
-  }
-  return -1;
-}

Packages/viewerbase/lib/getActiveViewportElement.js

@@ -1,5 +0,0 @@
-getActiveViewportElement = function() {
-    // TODO: Fix this, just hardcoded for now
-    var element = $('.imageViewerViewport').get(0);
-    return element;
-};

Packages/viewerbase/lib/getImageId.js

@@ -1,3 +1,9 @@
+/**
+ * Obtain an imageId for Cornerstone from an image instance
+ *
+ * @param instance
+ * @returns {string} The imageId to be used by Cornerstone
+ */
 getImageId = function(instance) {
     if (!instance) {
         return;

Packages/viewerbase/lib/getWADORSImageId.js

@@ -1,3 +1,10 @@
+/**
+ * Obtain an imageId for Cornerstone based on the WADO-RS scheme
+ *
+ * @param instance
+ * @returns {string} The imageId to be used by Cornerstone
+ */
+
 getWADORSImageId = function(instance) {
     var columnPixelSpacing = 1.0;
     var rowPixelSpacing = 1.0;

Packages/viewerbase/lib/helpers/formatDA.js

@@ -1,9 +1,11 @@
+/**
+ * A global Blaze UI helper function to format DICOM Dates using the Moment library
+ */
 UI.registerHelper('formatDA', function (context, format, options) {
     if (!context) {
         return undefined;
     }
-    var date = context;
-    var dateAsMoment = moment(date, "YYYYMMDD");
+    var dateAsMoment = moment(context, "YYYYMMDD");
     var strFormat = "MMM D, YYYY";
     if (options) {
         strFormat = format;

Packages/viewerbase/lib/helpers/formatNumberPrecision.js

@@ -1,4 +1,7 @@
-UI.registerHelper('formatNumberPrecision', function(context, precision, options) {
+/**
+ * A global Blaze UI helper to format a float value to a specified precision
+ */
+UI.registerHelper('formatNumberPrecision', function(context, precision) {
     if (context) {
         return parseFloat(context).toFixed(precision);
     }

Packages/viewerbase/lib/helpers/formatPN.js

@@ -1,7 +1,9 @@
-UI.registerHelper('formatPN', function (context, format, options) {
+/**
+ * A global Blaze UI helper to format a patient name for display purposes
+ */
+UI.registerHelper('formatPN', function (context) {
     if (!context) {
         return undefined;
     }
-    var patientName = context.replace('^', ', ');
-    return patientName;
+    return context.replace('^', ', ');
 });

Packages/viewerbase/lib/helpers/formatTM.js

@@ -1,13 +1,14 @@
-UI.registerHelper('formatTM', function(context, format, options) {
+/**
+ * A global Blaze UI helper to format a DICOM Time for display using the Moment library
+ */
+UI.registerHelper('formatTM', function(context, format) {
     if (!context) {
         return undefined;
     }
-    var date = context;
-    var dateAsMoment = moment(date);
+    var dateAsMoment = moment(context);
     var strFormat = "HH:mm:ss";
     if (options) {
         strFormat = format;
     }
-
     return dateAsMoment.format(strFormat);
 });

Packages/viewerbase/lib/isTouchDevice.js

@@ -1,3 +1,11 @@
+/**
+ * Helper function to determine if the current client devices
+ * is touch-capable. This can be used to modify certain aspects of the UI.
+ *
+ * The check may not work on all devices!
+ *
+ * @returns {boolean} true if the client device is touch-capable, false otherwise
+ */
 isTouchDevice = function() {
     return (('ontouchstart' in window)  ||
         (navigator.MaxTouchPoints > 0) ||

Packages/viewerbase/lib/metaDataProvider.js

@@ -1,5 +1,17 @@
 var metaDataLookup = {};
 
+/**
+ * Cornerstone MetaData provider to store image meta data
+ * Data from instances, series, and studies are associated with
+ * imageIds to facilitate usage of this information by Cornerstone's Tools
+ *
+ * e.g. the imagePlane metaData object contains instance information about
+ * row/column pixel spacing, patient position, and patient orientation. It
+ * is used in CornerstoneTools to position reference lines and orientation markers.
+ *
+ * @param {String} imageId The Cornerstone ImageId
+ * @param {Object} data An object containing instance, series, and study metaData
+ */
 addMetaData = function(imageId, data) {
     var instanceMetaData = data.instance;
     var seriesMetaData = data.series;
@@ -72,6 +84,15 @@ addMetaData = function(imageId, data) {
     metaDataLookup[imageId] = metaData;
 };
 
+/**
+ * Looks up metaData for Cornerstone Tools given a specified type and imageId
+ * A type may be, e.g. 'study', or 'patient', or 'imagePlane'. These types
+ * are keys in the stored metaData objects.
+ *
+ * @param type
+ * @param imageId
+ * @returns {Object} Relevant metaData of the specified type
+ */
 function provider(type, imageId) {
     var imageMetaData = metaDataLookup[imageId];
     if (!imageMetaData) {

Packages/viewerbase/lib/rerenderViewportWithNewSeries.js

@@ -1,5 +1,5 @@
 /**
- * This function destroys and rerenders the imageViewerViewport template.
+ * This function destroys and re-renders the imageViewerViewport template.
  * It uses the data provided (object containing seriesIndex and studyIndex) to
  * load a new series into the produced viewport.
  *
@@ -7,8 +7,12 @@
  * @param data An object containing a seriesIndex and studyIndex for a study to load into this viewport
  */
 rerenderViewportWithNewSeries = function(element, data) {
+    // Get the container and index of the current viewport.
+    // The parent container is identified because it is later removed from the DOM
     var container = $(element).parents('.viewportContainer').get(0);
     var viewportIndex = $(container).index();
+
+    // Record the current viewportIndex so this can be passed into the re-rendering call
     data.viewportIndex = viewportIndex;
 
     // Update the dictionary of loaded series for the specified viewport

Packages/viewerbase/lib/sortStudy.js

@@ -1,3 +1,9 @@
+/**
+ * Sorts the series and instances inside a study instance by their series
+ * and instance numbers in ascending order.
+ *
+ * @param {Object} study The study instance
+ */
 sortStudy = function(study) {
     if (!study) {
         return;

Packages/viewerbase/lib/stringToUint8Array.js

@@ -1,7 +1 @@
-stringToUint8Array = function(str) {
-  var uint=new Uint8Array(str.length);
-  for(var i=0,j=str.length;i<j;i++){
-    uint[i]=str.charCodeAt(i);
-  }
-  return uint;
-};
+

Packages/viewerbase/lib/uint8ArrayToString.js

@@ -1,9 +0,0 @@
-uint8ArrayToString = function(data, offset, length) {
-  offset = offset || 0;
-  length = length || data.length - offset;
-  var str = "";
-  for(var i=offset; i < offset + length; i++) {
-    str += String.fromCharCode(data[i]);
-  }
-  return str;
-};

Packages/viewerbase/lib/updateOrientationMarkers.js

@@ -1,5 +1,13 @@
-updateOrientationMarkers = function(element, viewport) {
-    // Updates the orientation labels on the viewport
+/**
+ * Updates the orientation labels on a Cornerstone-enabled Viewport element
+ * when the viewport settings change (e.g. when a horizontal flip or a rotation occurs)
+ *
+ * @param element The DOM element of the Cornerstone viewport
+ */
+updateOrientationMarkers = function(element) {
+    // Get the current viewport settings
+    var viewport = cornerstone.getViewport(element);
+
     var enabledElement = cornerstone.getEnabledElement(element);
     var imagePlane = cornerstoneTools.metaData.get('imagePlane', enabledElement.image.imageId);
     
@@ -14,7 +22,7 @@ updateOrientationMarkers = function(element, viewport) {
 
     var markers = {
         top: oppositeColumnString,
-        left: oppositeRowString,
+        left: oppositeRowString
     };
 
     // If any vertical or horizontal flips are applied, change the orientation strings ahead of

Packages/viewerbase/log.js

@@ -1,3 +1,3 @@
 // Create package logger using loglevel
 // https://atmospherejs.com/spacejamio/loglevel
-log = loglevel.createPackageLogger('viewerbase', defaultLevel = 'warn');
+log = loglevel.createPackageLogger('viewerbase', defaultLevel = 'info');

Packages/viewerbase/package.js

@@ -95,33 +95,24 @@ Package.onUse(function (api) {
     api.addFiles('lib/accountsConfig.js', 'client');
     api.addFiles('lib/createStacks.js', 'client');
     api.addFiles('lib/encodeQueryData.js', ['client', 'server']);
-    api.addFiles('lib/findIndexOfString.js', 'client');
-    api.addFiles('lib/getActiveViewportElement.js', 'client');
     api.addFiles('lib/getImageId.js', 'client');
     api.addFiles('lib/getWADORSImageId.js', 'client');
     api.addFiles('lib/isTouchDevice.js', 'client');
     api.addFiles('lib/metaDataProvider.js', 'client');
     api.addFiles('lib/rerenderViewportWithNewSeries.js', 'client');
     api.addFiles('lib/sortStudy.js', 'client');
-    api.addFiles('lib/stringToUint8Array.js', 'client');
     api.addFiles('lib/toolManager.js', 'client');
-    api.addFiles('lib/uint8ArrayToString.js', 'client');
-    api.addFiles('lib/updateOrientationMarkers.js', 'client');
 
     //api.export('accountsConfig', 'client');
     api.export('createStacks', 'client');
     api.export('encodeQueryData', ['client', 'server']);
-    api.export('findIndexOfString', 'client');
-    api.export('getActiveViewportElement', 'client');
     api.export('getImageId', 'client');
     api.export('getWADORSImageId', 'client');
     api.export('isTouchDevice', 'client');
     api.export('metaDataProvider', 'client');
     api.export('rerenderViewportWithNewSeries', 'client');
     api.export('sortStudy', 'client');
-    api.export('stringToUint8Array', 'client');
     api.export('toolManager', 'client');
-    api.export('uint8ArrayToString', 'client');
     api.export('updateOrientationMarkers', 'client');
 
     // UI Helpers

Packages/viewerbase/server/methods/getStudyMetadata.js

@@ -1,10 +1,15 @@
 Meteor.methods({
-  'GetStudyMetadata' : function(studyInstanceUid) {
-    log.info('GetStudyMetadata(%s)', studyInstanceUid);
+    /**
+     * Retrieves Study metadata given a Study Instance UID
+     * This Meteor method is available from both the client and the server
+     */
+    'GetStudyMetadata' : function(studyInstanceUid) {
+        log.info('GetStudyMetadata(%s)', studyInstanceUid);
 
-    var server = Meteor.settings.dicomWeb.endpoints[0];
+        // Get the server data. This is user-defined in the
+        // config.json files used to run the Meteor server
+        var server = Meteor.settings.dicomWeb.endpoints[0];
 
-    //return Services.QIDO.Instances(server, studyInstanceUid);
-    return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
-  }
+        return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
+    }
 });

Packages/viewerbase/server/methods/worklistSearch.js

@@ -1,6 +1,13 @@
 Meteor.methods({
-  'WorklistSearch' : function(filter) {
-    var server = Meteor.settings.dicomWeb.endpoints[0];
-    return Services.QIDO.Studies(server, filter);
-  }
+    /**
+     * Use the specified filter to conduct a search from the DICOM server
+     * @param filter
+     */
+    'WorklistSearch': function(filter) {
+        // Get the server data. This is user-defined in the
+        // config.json files used to run the Meteor server
+        var server = Meteor.settings.dicomWeb.endpoints[0];
+
+        return Services.QIDO.Studies(server, filter);
+    }
 });

Packages/viewerbase/server/services/qido/instances.js

@@ -1,59 +1,83 @@
+/**
+ * Creates a QIDO URL given the server settings and a study instance UID
+ * @param server
+ * @param studyInstanceUid
+ * @returns {string} URL to be used for QIDO calls
+ */
 function buildUrl(server, studyInstanceUid) {
-
-  var url = server.qidoRoot + '/studies/' + studyInstanceUid + '/instances';
-
-  return url;
+    return server.qidoRoot + '/studies/' + studyInstanceUid + '/instances';
 }
 
+/**
+ * Parses data returned from a QIDO search and transforms it into
+ * an array of series that are present in the study
+ *
+ * @param server The DICOM server
+ * @param studyInstanceUid
+ * @param resultData
+ * @returns {Array} Series List
+ */
 function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
-  var seriesMap = {};
-  var seriesList = [];
-  resultData.forEach(function(instance) {
-    var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
-    var series = seriesMap[seriesInstanceUid];
-    if(!series) {
-      series = {
-        seriesInstanceUid : seriesInstanceUid,
-        seriesNumber : DICOMWeb.getString(instance['00200011']),
-        instances: []
-      };
-      seriesMap[seriesInstanceUid] = series;
-      seriesList.push(series);
-    }
+    var seriesMap = {};
+    var seriesList = [];
 
-    // The uri for the dicomweb
-    // NOTE: DCM4CHEE seems to return the data zipped
-    // NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
-    //       know how to parse yet
-    //var uri = DICOMWeb.getString(instance['00081190']);
-    //uri = uri.replace('wado-rs', 'dicom-web');
+    resultData.forEach(function(instance) {
+        // Use seriesMap to cache series data
+        // If the series instance UID has already been used to
+        // process series data, continue using that series
+        var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
+        var series = seriesMap[seriesInstanceUid];
 
-    // manually create a WADO-URI from the UID's
-    // NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
-    var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
-    var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
+        // If no series data exists in the seriesMap cache variable,
+        // process any available series data
+        if(!series) {
+            series = {
+                seriesInstanceUid : seriesInstanceUid,
+                seriesNumber : DICOMWeb.getString(instance['00200011']),
+                instances: []
+            };
 
-    series.instances.push({
-      sopClassUid: DICOMWeb.getString(instance['00080016']),
-      sopInstanceUid: sopInstanceUid,
-      uri: uri,
-      instanceNumber: DICOMWeb.getString(instance['00200013'])
-    });
+            // Save this data in the seriesMap cache variable
+            seriesMap[seriesInstanceUid] = series;
+            seriesList.push(series);
+        }
+
+        // The uri for the dicomweb
+        // NOTE: DCM4CHEE seems to return the data zipped
+        // NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
+        //       know how to parse yet
+        //var uri = DICOMWeb.getString(instance['00081190']);
+        //uri = uri.replace('wado-rs', 'dicom-web');
+
+        // manually create a WADO-URI from the UIDs
+        // NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
+        var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
+        var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
+
+        // Add this instance to the current series
+        series.instances.push({
+            sopClassUid: DICOMWeb.getString(instance['00080016']),
+            sopInstanceUid: sopInstanceUid,
+            uri: uri,
+            instanceNumber: DICOMWeb.getString(instance['00200013'])
+        });
   });
   return seriesList;
 }
 
+/**
+ * Retrieve a set of instances using a QIDO call
+ * @param server
+ * @param studyInstanceUid
+ * @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
+ */
 Services.QIDO.Instances = function(server, studyInstanceUid) {
+    var url = buildUrl(server, studyInstanceUid);
+    var result = DICOMWeb.getJSON(url, server.requestOptions);
 
-  var url = buildUrl(server, studyInstanceUid);
-
-  var result = DICOMWeb.getJSON(url, server.requestOptions);
-  
-  var study = {
-    wadoUriRoot: server.wadoUriRoot,
-    studyInstanceUid: studyInstanceUid,
-    seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
-  };
-
-  return study;
+    return {
+        wadoUriRoot: server.wadoUriRoot,
+        studyInstanceUid: studyInstanceUid,
+        seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
+    };
 };

Packages/viewerbase/server/services/qido/studies.js

@@ -1,45 +1,56 @@
+/**
+ * Produces a QIDO URL given server details and a set of specified search filter
+ * items
+ *
+ * @param server
+ * @param filter
+ * @returns {string} The URL with encoded filter query data
+ */
 function filterToQIDOURL(server, filter) {
-  var parameters = {
-    PatientName : filter.patientName,
-    PatientID: filter.patientId,
-    AccessionNumber : filter.accessionNumber,
-    limit : filter.limit || 20,
-    includefield : server.qidoSupportsIncludeField ? 'all' : undefined
-  };
-  var url = server.qidoRoot + '/studies?' + encodeQueryData(parameters);
-  return url;
+    var parameters = {
+        PatientName : filter.patientName,
+        PatientID: filter.patientId,
+        AccessionNumber : filter.accessionNumber,
+        limit : filter.limit || 20,
+        includefield : server.qidoSupportsIncludeField ? 'all' : undefined
+    };
+    return server.qidoRoot + '/studies?' + encodeQueryData(parameters);
 }
 
+/**
+ * Parses resulting data from a QIDO call into a set of Study MetaData
+ *
+ * @param resultData
+ * @returns {Array} An array of Study MetaData objects
+ */
 function resultDataToStudies(resultData) {
-  var studies = [];
-  resultData.forEach(function(study) {
-    studies.push({
-      studyInstanceUid: DICOMWeb.getString(study['0020000D']),
-      // 00080005 = SpecificCharacterSet
-      studyDate: DICOMWeb.getString(study['00080020']),
-      studyTime: DICOMWeb.getString(study['00080030']),
-      accessionNumber: DICOMWeb.getString(study['00080050']),
-      referringPhysicianName: DICOMWeb.getString(study['00080090']),
-      // 00081190 = URL
-      patientName: DICOMWeb.getName(study['00100010']),
-      patientId: DICOMWeb.getString(study['00100020']),
-      patientBirthdate: DICOMWeb.getString(study['00100030']),
-      patientSex: DICOMWeb.getString(study['00100040']),
-      imageCount: DICOMWeb.getString(study['00201208']),
-      studyId: DICOMWeb.getString(study['00200010']),
-      studyDescription: DICOMWeb.getString(study['00081030']),
-      modalities: DICOMWeb.getString(study['00080061'])
-      //url : server.wadoRoot + '/studies/' + DICOMWeb.getString(study['0020000D']) + '/metadata'
+    var studies = [];
+
+    resultData.forEach(function(study) {
+        studies.push({
+          studyInstanceUid: DICOMWeb.getString(study['0020000D']),
+          // 00080005 = SpecificCharacterSet
+          studyDate: DICOMWeb.getString(study['00080020']),
+          studyTime: DICOMWeb.getString(study['00080030']),
+          accessionNumber: DICOMWeb.getString(study['00080050']),
+          referringPhysicianName: DICOMWeb.getString(study['00080090']),
+          // 00081190 = URL
+          patientName: DICOMWeb.getName(study['00100010']),
+          patientId: DICOMWeb.getString(study['00100020']),
+          patientBirthdate: DICOMWeb.getString(study['00100030']),
+          patientSex: DICOMWeb.getString(study['00100040']),
+          imageCount: DICOMWeb.getString(study['00201208']),
+          studyId: DICOMWeb.getString(study['00200010']),
+          studyDescription: DICOMWeb.getString(study['00081030']),
+          modalities: DICOMWeb.getString(study['00080061'])
+        });
     });
-  });
-  return studies;
+    return studies;
 }
 
+
 Services.QIDO.Studies = function(server, filter) {
-
-  var url = filterToQIDOURL(server, filter);
-
-  var result = DICOMWeb.getJSON(url, server.requestOptions);
-
-  return resultDataToStudies(result.data);
+    var url = filterToQIDOURL(server, filter);
+    var result = DICOMWeb.getJSON(url, server.requestOptions);
+    return resultDataToStudies(result.data);
 };

Packages/viewerbase/server/services/wado/retrieveMetadata.js

@@ -1,8 +1,22 @@
+/**
+ * Creates a URL for a WADO search
+ *
+ * @param server
+ * @param studyInstanceUid
+ * @returns {string}
+ */
 function buildUrl(server, studyInstanceUid) {
-    var url = server.wadoRoot + '/studies/' + studyInstanceUid + '/metadata';
-    return url;
+    return server.wadoRoot + '/studies/' + studyInstanceUid + '/metadata';
 }
 
+/**
+ * Parses the SourceImageSequence, if it exists, in order
+ * to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
+ * is used to refer to this image in any accompanying DICOM-SR documents.
+ *
+ * @param instance
+ * @returns {String} The ReferenceSOPInstanceUID
+ */
 function getSourceImageInstanceUid(instance) {
     // TODO= Parse the whole Source Image Sequence
     // This is a really poor workaround for now.
@@ -13,6 +27,16 @@ function getSourceImageInstanceUid(instance) {
     }
 }
 
+/**
+ * Parses result data from a WADO search into Study MetaData
+ * Returns an object populated with study metadata, including the
+ * series list.
+ *
+ * @param server
+ * @param studyInstanceUid
+ * @param resultData
+ * @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
+ */
 function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
     var seriesMap = {};
     var seriesList = [];
@@ -92,6 +116,12 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
     return studyData;
 }
 
+/**
+ * Retrieved Study MetaData from a DICOM server using a WADO call
+ * @param server
+ * @param studyInstanceUid
+ * @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
+ */
 Services.WADO.RetrieveMetadata = function(server, studyInstanceUid) {
     var url = buildUrl(server, studyInstanceUid);
 

Packages/worklist/components/tabTitle/tabTitle.js

@@ -1,19 +1,46 @@
 Template.tabTitle.events({
+    /**
+     * Closes a tab when the close button is pressed in the title
+     * The next tab to the left is loaded if the current tab is closed
+     *
+     * @param e The click event used to close the tab
+     */
     'click .close': function(e) {
+        // Identify the tab title DOM node
         var tab = $(e.currentTarget).parents('a[data-toggle="tab"]').eq(0);
+
+        // Get the relevent contentId that this tab title represents
+        // Replace any hash marks (#) that were required by Bootstrap's tab switching
         var contentId = tab.data("target").replace("#", "");
+    
+        // Check if we are closing the active tab. If we are, prepare to switch
+        // to the next tab to the left.    
+        var activeContentId = Session.get('activeContentId');
+        if (activeContentId === contentId) {
+            // Find the index of the tab that is being closed
+            var tabIndex = tab.parent('li').index();
 
-        var tabIndex = tab.parent('li').index();
-        var newActiveTabIndex = Math.max(tabIndex - 1, 0);
-        var newActiveTab = $(".tabTitle").eq(newActiveTabIndex);
-        var newActiveTabLink = newActiveTab.find("a[data-toggle=tab]");
-        var newContentId = newActiveTabLink.data("target").replace("#", "");
+            // Find the index the tab to its left
+            var newActiveTabIndex = Math.max(tabIndex - 1, 0);
 
-        switchToTab(newContentId);
-        
-        var tabObjectId = tabs.find({contentid: contentId}).fetch()[0]._id;
-        tabs.remove(tabObjectId);
+            // Find the DOM node of the tab that will be activated
+            var newActiveTab = $(".tabTitle").eq(newActiveTabIndex);
 
+            // Find the content ID of the tab that will be switched to
+            var newActiveTabLink = newActiveTab.find("a[data-toggle=tab]");
+            var newContentId = newActiveTabLink.data("target").replace("#", "");
+
+            // Switch to this tab
+            switchToTab(newContentId);   
+        }
+
+        // Find the tab to be closed in the Tabs collection
+        var tabObjectId = WorklistTabs.findOne({contentid: contentId})._id;
+
+        // Remove this tab from the Tabs collection so it is no longer rendered
+        WorklistTabs.remove(tabObjectId);
+
+        // Remove any stored data related to this tab from the global ViewerData structure
         delete ViewerData[contentId];
     }
 });

Packages/worklist/components/worklist.html

@@ -3,7 +3,7 @@
         <li role="presentation" class="tabTitle active">
             <a data-target="#worklistTab" role="tab" data-toggle="tab">Study List</a>
         </li>
-        {{ #each tabs }}
+        {{ #each worklistTabs }}
             {{ >tabTitle }}
         {{ /each }}
     </ul>
@@ -14,7 +14,7 @@
                 {{> worklistResult }}
             </div>
         </div>
-        {{ #each tabs }}
+        {{ #each worklistTabs }}
             {{ >tabContent }}
         {{ /each }}
     </div>

Packages/worklist/components/worklist.js

@@ -1,31 +1,78 @@
-ViewerData = Session.get('ViewerData') || {};
-StudyMetaData = {};
+/**
+ * Template: Worklist
+ *
+ * This is the main component of the Worklist package
+ */
 
+// Define the ViewerData global object
+// If there is currently any Session data for this object,
+// use this to repopulate the variable
+ViewerData = Session.get('ViewerData') || {};
+
+// Define the StudyMetaData object. This is used as a cache
+// to store study meta data information to prevent unnecessary
+// calls to the server
+var StudyMetaData = {};
+
+// Create the WorklistTabs collection
+WorklistTabs = new Meteor.Collection(null);
+
+/**
+* Retrieves study metadata using a server call, and fires a callback
+* when completed.
+*
+* @params {string} studyInstanceUid The UID of the Study to be retrieved
+* @params {function} doneCallback The callback function to be executed when the study retrieval has finished
+*/
 getStudyMetadata = function(studyInstanceUid, doneCallback) {
     log.info('worklistStudy getStudyMetadata');
 
-    if (StudyMetaData.hasOwnProperty(studyInstanceUid) && StudyMetaData[studyInstanceUid]) {
-        var study = StudyMetaData[studyInstanceUid];
+    // If the StudyMetaData cache already has data related to this
+    // studyInstanceUid, then we should fire the doneCallback with this data
+    // and stop here.
+    var study = StudyMetaData[studyInstanceUid];
+    if (study) {
         doneCallback(study);
         return;
     }
 
+    // If no study metadata is in the cache variable, we need to retrieve it from
+    // the server with a call.
     Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
+        // Once we have retrieved the data, we sort the series' by series
+        // and instance number in ascending order
         sortStudy(study);
-        
+
+        // Then we store this data in the cache variable
         StudyMetaData[studyInstanceUid] = study;
 
+        // Finally, we fire the doneCallback with this study meta data
         doneCallback(study);
     });
 };
 
+/**
+ *  Switches to a new tab in the tabbed worklist container
+ *  This function renders either the Worklist or the Viewer template with new data.
+ *
+ * @param contentId The unique ID of the tab to be switched to
+ */
 switchToTab = function(contentId) {
     log.info("Switching to tab: " + contentId);
 
+    // Use Bootstrap's Tab JavaScript to show the contents of the current tab
+    // Unless it is the worklist, it is currently an empty div
     $('.tabTitle a[data-target="#' + contentId + '"]').tab('show');
 
+    // Remove any previous Viewers from the DOM
     $("#viewer").remove();
 
+    // Update the 'activeContentId' variable in Session
+    Session.set("activeContentId", contentId);
+
+    // If we are switching to the Worklist tab, reset any CSS styles
+    // that have been applied to prevent scrolling in the Viewer.
+    // Then stop here, since nothing needs to be re-rendered.
     if (contentId === 'worklistTab') {
         document.body.style.overflow = null;
         document.body.style.height = null;
@@ -34,30 +81,44 @@ switchToTab = function(contentId) {
         return;
     }
 
-    // Set active tab
-    Session.set("activeContentId", contentId);
-
-    // Get tab content container
+    // Get tab content container given the contentId string
+    // If no such container exists, stop here because something is wrong
     var container = $('.tab-content').find("#" + contentId).get(0);
     if (!container) {
+        log.warn('No container present with the contentId: ' + contentId);
         return;
     }
-    
+
+    // Use the stored ViewerData global object to retrieve the studyInstanceUid
+    // related to this tab
     var studyInstanceUid = ViewerData[contentId].studyInstanceUid;
+
+    // Attempt to retrieve the meta data (it might be cached)
     getStudyMetadata(studyInstanceUid, function(study) {
+
+        // Once we have the study data, store it in a structure with
+        // any other saved data about this tab (e.g. layout structure)
         var data = {
             viewportRows: ViewerData[contentId].viewportRows,
             viewportColumns: ViewerData[contentId].viewportColumns,
             contentId: contentId,
-            studies: [study],
+            studies: [study]
         };
 
+        // Update the Session variable with the loaded studies
         Session.set('studies', data.studies);
 
-        // Remove the loading text template that is inside by default
+        // Remove the loading text template that is inside the tab container by default
         container.innerHTML = "";
+
+        // Use Blaze to render the Viewer Template into the container
         UI.renderWithData(Template.viewer, data, container);
+
+        // Retrieve the DOM element of the viewer
         var imageViewer = $("#viewer");
+
+        // If it is present in the DOM (it should be), then apply
+        // styles to prevent page scrolling and overscrolling on mobile devices
         if (imageViewer) {
             document.body.style.overflow = "hidden";
             document.body.style.height = '100%';
@@ -68,20 +129,34 @@ switchToTab = function(contentId) {
     });
 };
 
-
+/**
+ * Opens a new tab in the tabbed worklist environment using
+ * a given study and new tab title.
+ *
+ * @param studyInstanceUid The UID of the Study to be opened
+ * @param title The title to be used for the tab heading
+ */
 openNewTab = function(studyInstanceUid, title) {
+    // Generate a unique ID to represent this tab
+    // We can't just use the Mongo entry ID because
+    // then it will change after hot-reloading.
     var contentid = generateUUID();
-    var data = {
+
+    // Create a new entry in the WorklistTabs Collection
+    WorklistTabs.insert({
         title: title,
         contentid: contentid,
-    };
-    tabs.insert(data);
+        active: false
+    });
 
+    // Update the ViewerData global object
     ViewerData[contentid] = {
         title: title,
         contentid: contentid,
         studyInstanceUid: studyInstanceUid
     };
+
+    // Switch to the new tab
     switchToTab(contentid);
 };
 
@@ -96,9 +171,12 @@ Template.worklist.onRendered(function() {
 
 
 Template.worklist.helpers({
-    'tabs': function() {
-        log.info('Updating tabs');
-        return tabs.find();
+    /**
+     * Returns the current set of Worklist Tabs
+     * @returns Meteor.Collection The current state of the WorklistTabs Collection
+     */
+    'worklistTabs': function() {
+        return WorklistTabs.find();
     }
 });
 

Packages/worklist/components/worklistResult/worklistResult.js

@@ -1,6 +1,13 @@
+// Define the Studies Collection
+// This is a client-side only Collection which
+// Stores the list of studies in the Worklist
 Studies = new Mongo.Collection(null);
 
 Template.worklistResult.helpers({
+    /**
+     * Returns a sorted instance of the Studies Collection
+     * by Patient name and Study Date in Ascending order.
+     */
     studies : function() {
         return Studies.find({}, {sort: {patientName : 1, studyDate : 1}});
     }

Packages/worklist/components/worklistSearch/worklistSearch.js

@@ -1,4 +1,4 @@
-//Get all studies
+// Retrieve all studies
 search();
 
 var studyDateFrom;
@@ -6,6 +6,13 @@ var studyDateTo;
 var checkFrom = false;
 var checkTo = false;
 
+/**
+ * Transforms an input string into a search filter for
+ * the Worklist Search call
+ *
+ * @param filter The input string to be searched for
+ * @returns {*}
+ */
 function getFilter(filter) {
     if(filter && filter.length && filter.substr(filter.length - 1) !== '*') {
         filter += '*';
@@ -13,16 +20,19 @@ function getFilter(filter) {
     return filter;
 }
 
-//Search value
+/**
+ * Search for a value in a string
+ */
 function isIndexOf(mainVal, searchVal) {
-    if(mainVal === undefined || mainVal === '' || mainVal.indexOf(searchVal) > -1){
+    if (mainVal === undefined || mainVal === '' || mainVal.indexOf(searchVal) > -1){
         return true;
     }
-
     return false;
 }
 
-//Replace object is undefined
+/**
+ * Replace object if undefined
+ */
 function replaceUndefinedColumnValue (text) {
     if (text == undefined || text === "undefined") {
         return "";
@@ -31,94 +41,96 @@ function replaceUndefinedColumnValue (text) {
     }
 }
 
-//Convert string to study date
+/**
+ * Convert string to study date
+ */
 function convertStringToStudyDate (dateStr) {
     var y = dateStr.substring(0,4);
     var m = dateStr.substring(4,6);
     var d = dateStr.substring(6,8);
     var newDateStr = y+"/"+m+"/"+d;
-    var date_ = new Date(newDateStr);
-    return date_;
+    return new Date(newDateStr);
 }
 
+/**
+ * Runs a search for studies matching the worklist query parameters
+ * Inserts the identified studies into the Studies Collection
+ */
 function search() {
+    // Create the filters to be used for the Worklist Search
     var filter = {
         patientName: getFilter($('#patientName').val()),
         patientId: getFilter($('#patientId').val()),
         accessionNumber: getFilter($('#patientAccessionNumber').val())
     };
 
+    // Make sure that modality has a reasonable value, since it is occasionally
+    // returned as 'undefined'
     var modality = replaceUndefinedColumnValue($('#modality').val());
 
+    // Clear all current studies
     Studies.remove({});
+
     Meteor.call('WorklistSearch', filter, function(error, studies) {
-        if (studies) {
-            studies.forEach(function(study) {
-
-                if(isIndexOf(study.modalities, modality) &&
-                    (new Date(studyDateFrom).setHours(0,0,0,0) <= convertStringToStudyDate(study.studyDate) || !checkFrom) &&
-                    (convertStringToStudyDate(study.studyDate) <= new Date(studyDateTo).setHours(0,0,0,0) || !checkTo)) {
-
-                    Studies.insert(study);
-                }
-            });
+        if (!studies) {
+            return;
         }
+
+        // Loop through all identified studies
+        studies.forEach(function(study) {
+
+            // Search the rest of the parameters that aren't done via the server call
+            if(isIndexOf(study.modalities, modality) &&
+                (new Date(studyDateFrom).setHours(0,0,0,0) <= convertStringToStudyDate(study.studyDate) || !checkFrom) &&
+                (convertStringToStudyDate(study.studyDate) <= new Date(studyDateTo).setHours(0,0,0,0) || !checkTo)) {
+
+                // Insert any matching studies into the Studies Collection
+                Studies.insert(study);
+            }
+        });
     });
 
 }
 
 Template.worklistSearch.events({
-
-    //Search
+    /**
+     * Searches for studies given the current state of the form controls
+     */
     'click button#btnSearch' :function(event) {
         studyDateFrom = $('#studyDateFrom').val();
         studyDateTo = $('#studyDateTo').val();
         checkFrom = $('#checkFrom').is(':checked');
         checkTo = $('#checkTo').is(':checked');
         search();
-
-        return false;
     },
-
-    //Today
+    /**
+     * Searches for studies with a study date equal to Today
+     */
     'click button#btnToday' :function(event) {
         studyDateTo = new Date();
         studyDateFrom =  studyDateTo;
         checkFrom = true;
         checkTo = true;
-
         search();
-
-        return false;
     },
 
-    //Clear
-    'click button#btnClear' :function(event) {
-        $("#patientId").val("");
-        $("#patientName").val("");
-        $("#patientAccessionNumber").val("");
-        $("#studyDescription").val("");
-        $("#referringPhysician").val("");
-        $("#studyDateFrom").val("");
-        $("#studyDateTo").val("");
-        $("#modality").val("");
-        $('#checkFrom').prop('checked', false);
-        $('#checkTo').prop('checked', false);
-
-    },
-
-    //Last 7 Days
-    'click button#btnLastSevenDays' :function(event) {
+    /**
+     * Searches for studies in the Last 7 Days
+     */
+    'click button#btnLastSevenDays' :function() {
         studyDateTo = new Date();
         studyDateFrom =  new Date();
         studyDateFrom.setDate(studyDateFrom.getDate()-7);
         checkFrom = true;
         checkTo = true;
-
         search();
-
-        return false;
+    },
+    /**
+     * Clears all input data in the study search panel
+     */
+    'click button#btnClear' :function(event) {
+        $("#searchPanel .form-control").val("");
+        $('#checkFrom').prop('checked', false);
+        $('#checkTo').prop('checked', false);
     }
-
-
 });

Packages/worklist/lib/generateUUID.js

@@ -1,4 +1,7 @@
-//Generate UUID to create unique tabs
+/**
+ *
+ * @returns {string}
+ */
 generateUUID = function() {
     var d = new Date().getTime();
     var uuid = 'xxxxxxxx'.replace(/[xy]/g, function(c) {

Packages/worklist/package.js

@@ -14,9 +14,12 @@ Package.onUse(function (api) {
 
     api.use('practicalmeteor:loglevel');
 
-    // Our custom package
+    // Our custom packages
     api.use('dicomweb');
 
+    // This sets the default logging level of the package using the
+    // loglevel package. It can be overridden in the JavaScript
+    // console for debugging purposes
     api.addFiles('log.js', 'client');
 
     // Components
@@ -46,10 +49,15 @@ Package.onUse(function (api) {
     api.addFiles('lib/generateUUID.js', 'client');
     api.export('generateUUID', 'client');
 
+    // Export Worklist helper functions for usage in Routes
     api.export('getStudyMetadata', 'client');
     api.export('openNewTab', 'client');
     api.export('switchToTab', 'client');
-    
+
+    // Export the global ViewerData object
     api.export('ViewerData', 'client');
+
+    // Export the WorklistTabs Collection
+    api.export('WorklistTabs', 'client');
 });
 

conf.json

@@ -0,0 +1,37 @@
+// Run with jsdoc . -r -c conf.json -d docs
+{
+    "tags": {
+        "allowUnknownTags": true,
+        "dictionaries": ["jsdoc"]
+    },
+    "source": {
+        "include": ["Packages", "OHIFViewer", "LesionTracker"],
+        "includePattern": ".+\\.js(doc)?$",
+        "excludePattern": "(^|\\/|\\\\)_",
+        "exclude": ["Packages/cornerstone/", "node_modules", "docs", "etc"]
+    },
+    "plugins": ["plugins/markdown"],
+    "templates": {
+        "logoFile": "",
+        "cleverLinks": false,
+        "monospaceLinks": false,
+        "dateFormat": "ddd MMM Do YYYY",
+        "outputSourceFiles": false,
+        "outputSourcePath": false,
+        "systemName": "OHIF Meteor Packages",
+        "footer": "OHIF",
+        "copyright": "Copyright © 2015 Open Health Imaging Foundation",
+        "navType": "vertical",
+        "theme": "flatly",
+        "linenums": true,
+        "collapseSymbols": false,
+        "inverseNav": true,
+        "highlightTutorialCode": true,
+        "protocol": "html://",
+        "methodHeadingReturns": false
+    },
+    "markdown": {
+        "parser": "gfm",
+        "hardwrap": true
+    }
+}