Merge branch 'release'

.gitignore

@@ -10,3 +10,9 @@
 .DS_Store
 .DS_Store/*
 
+# Test node modules
+node_modules
+node_modules/*
+test/node_modules
+test/node_modules/*
+test/package-lock.json

.travis.yml

@@ -0,0 +1,21 @@
+sudo: required
+services:
+    - nodejs
+language: php
+node_js:
+   - "8"
+before_install:
+    - mkdir ../js
+    - cp test/__config.js ../js/config.js
+    - touch ../authenticate.php
+    - which php
+install:
+    - npm install
+    - npm install -g mocha
+before_script:
+    - cd test
+    - node test_server.js &
+    - cd ..
+script:
+    - mocha js/Helpers/test --recursive
+    - mocha test/functional_tests.js

README.md

@@ -1,82 +1,45 @@
-
-caMicroscope - A Web Based Annotation and Visualization Platform for Digitized Whole Slide Images
+# caMicroscope 
+## A Web Based Annotation and Visualization Platform for Digitized Whole Slide Images
 
-Ameen Kazerouni <[email protected]>
-
-Ashish Sharma <[email protected]>
-
-[Ganesh Iyer](http://ganeshiyer.net) <[email protected]>
-
-Sanjay Agravat <[email protected]>
-
-Shaohuan Li <[email protected]> 
-
-============
-
-About
--------
-GSOC Bio-medical Image Viewer Project is a HTML5 image viewer optimized for large bio-medical image data viewing. 
+#### Develop branch build status:
+[![Build Status](https://travis-ci.org/camicroscope/caMicroscope.svg?branch=develop)](https://travis-ci.org/camicroscope/caMicroscope)
 
-The Image Viewer server is based on the IIPImage server(http://iipimage.sourceforge.net/) which is an Fast CGI modeule written in C++ and IIPMooviewer-2.0(https://github.com/ruven/iipmooviewer) which is a HTML5 Ajax-based javascript image streaming client developed by Ruven.
 
-This project forcuses on SVG annotation development, HTML5 canvas implementation and database design for viewing large Bio-Medical image data.
+## About
 
-Prerequisite
---------
-The IIPImage server(http://iipimage.sourceforge.net/) will have to be installed in the server. 
+caMicroscope is a HTML5 image viewer optimized for large bio-medical image data viewing, with a strong emphasis on cancer pathology.
 
-Apache or lighttpd web server will need to be installed as well.
+The Image Viewer server is based on [IIPImage server](http://iipimage.sourceforge.net/) which is a Fast CGI module and [OpenSeaDragon](https://openseadragon.github.io/) which is a deep zoom image viewer.
 
-PHP5 will be needed to handle the annotation saving function.
 
-Features
---------
+## Usage
 
-*HTML5 Canvas Markup Drawing. Rectangle tool,ellipse tool, pencil tool, polyline tool, measurement tool and magnifying tool have been developed.
+caMicroscope should be deployed as part of a stack; for further information see the [caMicroscope distribution repository](https://github.com/camicroscope/Distro).
 
-*SVG Markup Displaying. The image markups are displayed as SVG(Scalable Vector Graphics) images which preserve good resolutions for different sizes of views
+## Core Features
 
-*Annotation/Markup data saving. The markups/annotations will be saved to the database using PHP scripts via Ajax calls.
+* Variable resolution browser rendering of slide images of multiple formats
 
-Specifications
---------------
+* Segmentation analysis on user-selected regions
 
-js/annotools.js is the main outcome of this project. It is an independent annotation module which allows users to draw markups/annotations on the image viewer.The annotation annotools object will need to be associated with a div tag id and a container id to run the tools smoothly. 
-An example would be like http://170.140.138.125/view.html. The annotools only work for HTML5 enabled browsers. 
+* Annotation drawing and sharing
 
-css/annotools.css and the svg imges in the images folder are associated with the annotools.js.
 
-js/iipmooviewer-2.0.js is the orignial IIPMooViewer with some customization. One big change is to add a displayAnnotation funciton in the requestImages function inside the IIPMooViewer class. Some small changes would be like the adjustment of the navigation window size.
-
-js/mootools-more.js and mootools-core.js would be the latest mootools framework.
-
-js/main.js is the image meta data handler. js/moreImages.js is the bottom slider which will display the image meta data more conveniently.
-
-api/annot.php is for saving and getting annotation meta.
-api/annot.txt is the file storing the annotation data. This file has to be set as readable/writable to the public.
-
-api/image.php is the php script to get the image information from the database
-api/annotation.php is the PHP script to get the annotation info from the database
-api/state.php is to save the state of the viewer. The developers would be using zoomTo(zoom) and moveTo(left,top) to navigate to the saved state.
-
-view.html is for annotation saving without connecting to the database.You may test it here:http://170.140.138.125/view.html
-
-index.html and viewer.html is for the image viewer which is connected to the database. You may test it here.http://170.140.138.125
+## Contributors
+Ameen Kazerouni <[email protected]>
 
-schema.sql is the database schema
+Alina Jasniewski
 
-Database Module
----------------
+Ashish Sharma <[email protected]>
 
-One approach for saving annotations is to use databases. As the annotations will be associated with a particular image, the annotations will have to contain one foreign key referencing the image id.
+Feiqiao "Bridge" Wang
 
+[Ganesh Iyer](http://ganeshiyer.net) <[email protected]>
 
-Image MetaData Viewing Module
------------------------------
+[Ryan Birmingham](http://rbirm.us) <[email protected]>
 
-The metadata is displayed as unsorted list on the bottom of the image viewer. This utilizes the tween function in Mootools. One example can be shown in viewer.html
+Sanjay Agravat <[email protected]>
 
-Image Uploading Module
------------------------------
-This is handled by uploader.html and uploader.php. The images will by default be saved to the /usr/share/iip folder.
+Shaohuan Li <[email protected]>
 
+Tammy DiPrima

api/Configuration/config.php

@@ -1,10 +1,28 @@
 <?php
 
-$baseUrl = "http://quip-data:9099";
-$kueUrl = "http://quip-jobs:3000";
+if (file_exists('../../../config.php')) {
+    $config = require '../../../config.php';
+}
+else {
+    $config = ['dataHost' => 'quip-data:9099',
+               'kueHost' => 'quip-jobs:3000'];
+}
+
+
+$baseUrl = "http://" . $config['dataHost'];
+$kueUrl = "http://" . $config['kueHost'];
 
 $serviceUrl     = "$baseUrl/services/Camicroscope_DataLoader";
 $annotationsUrl = "$baseUrl/services/Camicroscope_Annotations";
+
+if (isset($_SESSION['db_name']) && !empty($_SESSION['db_name'])) {
+
+    if ($_SESSION["db_name"] == "quip_comp"){
+        $serviceUrl     = "$baseUrl/services/Camicroscope_DataLoader_comp";
+        $annotationsUrl = "$baseUrl/services/Camicroscope_Annotations_comp";
+    }
+}
+
 $u24_userUrl    = "$baseUrl/services/u24_user";
 $imageUrl       = "$serviceUrl/DataLoader";
 $lymphocyteUrl = "$baseUrl/services/Camicroscope_Lymphocyte";
@@ -28,6 +46,7 @@
     /*
      * temp
      */
+    'getOverlayTiles' => "$baseUrl/services/TileOverlay/Tiles/query/getTileLocation?",
     'algorithmsForImage' => "$annotationsUrl/MarkupsForImages/query/MarkupsAvilableForImage?",
     'getMultipleAnnotations' => "$annotationsUrl/MarkupLoader/query/getMultipleMarkups?",
     'getROI' => "$annotationsUrl/MarkupLoader/query/getROI", //Featurescape URL.
@@ -53,6 +72,8 @@
     'postDataForLymphocytes' => "$lymphocyteUrl/DataForLymphocytes/submit/json?",
     'getLymphocyteData' => "$lymphocyteUrl/DataForLymphocytes/query/getLymphocytes?",
     'getLymphocyteDataByCaseId' => "$lymphocyteUrl/DataForLymphocytes/query/getLymphocytesByCaseId?",
+    'postDataForHeatmap' => "$lymphocyteUrl/HeatmapData/submit/json?",
+    'getHeatmapData' => "$lymphocyteUrl/HeatmapData/query/getQualHeatmapByCaseidExecid?",
 
     /* Lymphocyte Superusers */
     'postSuperuserForLymphocytes' => "$lymphocyteUrl/LymphocyteUsers/submit/json?",
@@ -77,26 +98,35 @@
 
     /* Template */
     'retrieveTemplate'      => "$templateUrl/AnnotationTemplate/query/retrieveTemplate",
-    'retrieveTemplateClone' => "$templateUrl/AnnotationTemplate/query/retrieveTemplateClone",
+    'retrieveTemplateByName' => "$templateUrl/AnnotationTemplate/query/retrieveTemplateByName",
 
     /* u24_user */
     'findUserByName'   => "$u24_userUrl/user_data/query/findUserByName?",
     'findUserByEmail'  => "$u24_userUrl/user_data/query/findUserByEmail?",
+    'findUser'         => "$u24_userUrl/user_data/query/findUser?",
     'findAdmin'        => "$u24_userUrl/user_data/query/findAdmin?",
     'findAllBindaasUsers'=>"$u24_userUrl/user_data/query/findAllBindaasUsers?",
+    'findSuperUserCount'=>"$u24_userUrl/user_data/query/findSuperUserCount?",
+
     'deleteUserByName' => "$u24_userUrl/user_data/delete/deleteUserByName?",
     'deleteUserByEmail'=> "$u24_userUrl/user_data/delete/deleteUserByEmail?",
     'postUser'         => "$u24_userUrl/user_data/submit/json",
+    'setUserType'      => "$u24_userUrl/user_data/delete/setUserType?",
 
 
     /* Image */
     'getDimensions' => "$imageUrl/query/getDimensionsByIID?api_key=",
     'getFileLocation' => "$imageUrl/query/getFileLocationByIID?api_key=",
+    //'getTileLocation' => "$imageUrl/query/getTileLocationByIID?api_key=",
     'getMPP' => "$imageUrl/query/getMPPByIID?api_key=",
     'getImageInfoByCaseID'=> "$imageUrl/query/getImageInfoByCaseID?api_key=",
-    'fastcgi_server' => "../fcgi-bin/iipsrv.fcgi",
+    'fastcgi_server' => "/fcgi-bin/iipsrv.fcgi",
+    'imageStatusUpdate'=> "$imageUrl/delete/imageStatusUpdate?",
+    'getImageStatus'=> "$imageUrl/query/getImageStatusByCaseID?api_key=",
+    'getImageAssignTo'=> "$imageUrl/query/getImageAssignToByCaseID?api_key=",
+    'imageAssignTo'=> "$imageUrl/delete/imageAssignTo?",
 
-	 /* Dynamic Services */
+    /* Dynamic Services */
     'postWorkOrder' => "$dynamicServices/WorkOrders/submit/json",
     'kueUrl' => $kueUrl
 );

api/Data/CamicUtils.php

@@ -1,40 +1,64 @@
 <?php
+
 class CamicUtils
 {
-	public $CONFIG;
-	public $api_key;
-	function __construct($Session)
-	{
-		include_once("RestRequest.php");
-		$this->CONFIG = require '../Configuration/config.php';
-		$this->api_key = $Session['api_key'];
-	}
+    public $CONFIG;
+    public $api_key;
+
+    function __construct($Session)
+    {
+        include_once("RestRequest.php");
+        $this->CONFIG = require '../Configuration/config.php';
+        $this->api_key = trim($Session['api_key']);
+    }
+
+    function getImageDimensions($tissueId)
+    {
+        $dimensionsUrl = $this->CONFIG['getDimensions'] . $this->api_key . "&TCGAId=" . $tissueId;
+        $getDimensionRequest = new RestRequest($dimensionsUrl, 'GET');
+        $getDimensionRequest->execute();
+        $dimensionList = json_decode($getDimensionRequest->responseBody);
+        $finalDimensions;
 
-	function getImageDimensions($tissueId)
+        foreach ($dimensionList as $singleDimension) {
+            $finalDimensions = $singleDimension;
+            break;
+        }
+        return $finalDimensions;
+    }
+
+    function retrieveImageLocation($tissueId)
+    {
+        $fileUrl = $this->CONFIG['getFileLocation'] . $this->api_key . "&TCGAId=" . $tissueId;
+        $fileUrl = str_replace(" ", "%20", $fileUrl);
+        $getFileLocationRequest = new RestRequest($fileUrl, 'GET');
+        $getFileLocationRequest->execute();
+        $location = json_decode($getFileLocationRequest->responseBody);
+        return $location;
+    }
+
+        function retrieveImageStatus($tissueId)
 	{
-		$dimensionsUrl = $this->CONFIG['getDimensions'] .  $this->api_key . "&TCGAId=" . $tissueId;
-		$getDimensionRequest = new RestRequest($dimensionsUrl, 'GET');
-		$getDimensionRequest->execute();
-		$dimensionList = json_decode($getDimensionRequest->responseBody);
-		$finalDimensions;
-		foreach($dimensionList as $singleDimension)
-		{
-			$finalDimensions = $singleDimension;
-			break;
-		}
-		return $finalDimensions;
+		$statusUrl = $this->CONFIG['getImageStatus'] . $this->api_key . "&TCGAId=" . $tissueId;
+		$statusUrl = str_replace(" ","%20",$statusUrl);
+		$getImageStatusRequest = new RestRequest($statusUrl,'GET');
+		$getImageStatusRequest->execute();
+		$status = json_decode($getImageStatusRequest->responseBody);
+		return $status;
 	}
-	function retrieveImageLocation($tissueId)
+
+        function retrieveImageAssignTo($tissueId)
 	{
-		$fileUrl = $this->CONFIG['getFileLocation'] . $this->api_key . "&TCGAId=" . $tissueId;
-		$fileUrl = str_replace(" ","%20",$fileUrl);
-		$getFileLocationRequest = new RestRequest($fileUrl,'GET');
-		$getFileLocationRequest->execute();
-		$location = json_decode($getFileLocationRequest->responseBody);
-		return $location;
+		$statusUrl = $this->CONFIG['getImageAssignTo'] . $this->api_key . "&TCGAId=" . $tissueId;
+		//print_r($statusUrl);
+                $statusUrl = str_replace(" ","%20",$statusUrl);
+		$getImageAssignToRequest = new RestRequest($statusUrl,'GET');
+		$getImageAssignToRequest->execute();
+		$AssignTo = json_decode($getImageAssignToRequest->responseBody);
+		//print_r($AssignTo);
+                return $AssignTo;
 	}
 
-
 	function retrieveMpp($tissueId)
 	{
 	    $mppUrl = $this->CONFIG['getMPP'] . $this->api_key . "&TCGAId=" . $tissueId;
@@ -49,46 +73,41 @@ function retrieveMpp($tissueId)
 		break;
 	    }
 
-	    return $finalMPP;
-	}
+        return $finalMPP;
+    }
 
-	function setUpSymLinks($fileLocation)
-	{
-		foreach($fileLocation[0] as $key => $value)
-		{
-			$path = "/tmp/symlinks/" . session_id();
-			if(!is_dir($path))
-			{
-				mkdir($path);
-			}
-			$file = strrchr($value, '/');
-			$fileNameWithoutExtension = substr($file,0,-5);
-			if(is_dir($path . $fileNameWithoutExtension))
-			{
-				$link = $path . $fileNameWithoutExtension . $file . ".dzi";
-			}
-
-			else
-			{
-				mkdir($path . $fileNameWithoutExtension);
-				$file = $path . $fileNameWithoutExtension . $file;
-				symlink($value, $file);
-				symlink($file, $file . ".dzi");
-				$link = $file . ".dzi";
-			}
-		}
-
-		return $link;
-	}
+    function setUpSymLinks($fileLocation)
+    {
+        foreach ($fileLocation[0] as $key => $value) {
+            $path = "/tmp/symlinks/" . session_id();
+            if (!is_dir($path)) {
+                mkdir($path);
+            }
 
-	function setUpSVSImage($fileLocation)
-	{
-	    foreach($fileLocation[0] as $key => $value)
-	    {
-		$link = str_replace("tiff","svs",$value);
-		$link = $link . ".dzi";
-	    }
+            $file = strrchr($value, '/');
+            $fileNameWithoutExtension = substr($file, 0, -5);
 
-	    return $link;
-	}
+            if (is_dir($path . $fileNameWithoutExtension)) {
+                $link = $path . $fileNameWithoutExtension . $file . ".dzi";
+            } else {
+                mkdir($path . $fileNameWithoutExtension);
+                $file = $path . $fileNameWithoutExtension . $file;
+                symlink($value, $file);
+                symlink($file, $file . ".dzi");
+                $link = $file . ".dzi";
+            }
+        }
+
+        return $link;
+    }
+
+    function setUpSVSImage($fileLocation)
+    {
+        foreach ($fileLocation[0] as $key => $value) {
+            $link = str_replace("tiff", "svs", $value);
+            $link = $link . ".dzi";
+        }
+
+        return $link;
+    }
 }