Merge pull request #513 from camicroscope/develop

For 3.9.2

.github/workflows/node.js.yml

@@ -0,0 +1,34 @@
+# This workflow will do a clean install of node dependencies, build the source code and run tests across different versions of node
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions
+
+name: Node.js CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [10.x, 12.x, 14.x, 15.x]
+        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+        node-version: ${{ matrix.node-version }}
+    - run: npm ci
+    - run: npm install
+    - run: npm install jsdom
+    - run: npm install -g http-server
+    - run: npm install -g mocha
+    - run: npm install eslint
+    - run: npm install eslint-config-google
+    - run: http-server -s &
+    - run: npm run build --if-present
+    - run: npm run lint
+    - run: npm test

HISTORY.md

@@ -24,11 +24,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * **Version 1**
     * [1.0.x](#camicroscope-10)
 
-### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.9.0...camicroscope:develop)
+### caMicroscope [Unreleased](https://github.com/camicroscope/camicroscope/compare/v3.9.2...camicroscope:develop)
 ###### TBD
-*
 
-### caMicroscope [3.9.1](https://github.com/camicroscope/camicroscope/compare/v3.8.4...camicroscope:v3.9.0)
+### caMicroscope [3.9.2](https://github.com/camicroscope/camicroscope/compare/v3.9.1...camicroscope:v3.9.2)
+###### 2021-04-07
+* Github action for ci testing [#502](https://github.com/camicroscope/caMicroscope/pull/502)
+* Validate Emails on signup [#501](https://github.com/camicroscope/caMicroscope/pull/501)
+* Image Enhancements [#500](https://github.com/camicroscope/caMicroscope/pull/500)
+* Configurable Toolbar Links [#511](https://github.com/camicroscope/caMicroscope/pull/511)
+* Documentation Improvements [#506](https://github.com/camicroscope/caMicroscope/pull/506)
+
+
+### caMicroscope [3.9.1](https://github.com/camicroscope/camicroscope/compare/v3.8.4...camicroscope:v3.9.1)
 ###### 2021-03-05
 * Bugfix: Annotation Name Filtering
 

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2012-2020, caMicroscope
+Copyright (c) 2012-2021, caMicroscope
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

apps/batchloader/batchLoader.js

@@ -13,8 +13,9 @@ let chunkSize = 5*1024*1024;
 let finishUploadSuccess = false;
 const allowedExtensions = ['svs', 'tif', 'tiff', 'vms', 'vmu', 'ndpi', 'scn', 'mrxs', 'bif', 'svslide'];
 
-
+// call on document ready
 $(document).ready(function() {
+  // fill all current files and slides to existingFiles[] and existingSlides
   $('#files').show(400);
   let store = new Store('../../data/');
   store.findSlide().then((response) => {
@@ -26,7 +27,7 @@ $(document).ready(function() {
   }).catch((error) => {
     console.log(error);
   });
-
+  // display file details when called
   $('#filesInput').change(function() {
     let files = $(this).prop('files');
     let fileNames = $.map(files, function(val) {
@@ -46,7 +47,7 @@ $(document).ready(function() {
     $('#complete').css('display', 'none');
     $('#table').css('display', 'none');
   });
-
+  // called when filenameswitch checkbox changes
   $('#fileNameSwitch').change(function() {
     if ($(this).is(':checked')) {
       $('.fileName').css('opacity', '1');
@@ -70,7 +71,7 @@ $(document).ready(function() {
     $(this).val($(this).val().split(' ').join('_'));
   });
 });
-
+// fuction to add each row (per slide)
 function addbody(rowData) {
   let table = $('table tbody');
   let markup = '<tr><th scope="row">'+rowData.serial+'</th><td><span>'+rowData.fileName+
@@ -88,7 +89,8 @@ function addbody(rowData) {
 
   table.append(markup);
 }
-
+// function called on page load
+// initializes table, adds rows, monitors change or click events and checks for errors in names
 function startTable() {
   slideNames = [];
   fileNames = [];
@@ -185,7 +187,7 @@ function startTable() {
     $('#complete').css('display', 'none');
   }
 }
-
+// checks for erroes in names
 function checkNames() {
   let numErrors = 0;
   for (i=0; i<originalFileNames.length; i++) {
@@ -222,6 +224,7 @@ function checkNames() {
   }
 }
 
+// showSlideInfoX - shows info of slide based on the slide properties
 function showSlideInfo1(index) {
   $('#slideInfoContent').html(`<b>Original Filename:</b> `+originalFileNames[index]+`<br><b>Filename:</b> `+fileNames[index]+
                          `<br><b>Slide name:</b> `+slideNames[index]+`<br><b>Status:</b> Pending Initial Upload`);
@@ -246,7 +249,7 @@ function showSlideInfo5(index) {
                          `<br><b>Slide name:</b> `+slideNames[index]+`<br><b>Token:</b> `+
                          tokens[index]+`<br><b>Status:</b> Posted Successfully`);
 }
-
+// updates the name of the slide after checking if it's not null or duplicated
 function updateSlideName(oldSlideName) {
   $('#confirmUpdateSlideContent').html('Enter the new name for: <br><b>'+oldSlideName+
          '</b><br><br><div class="form-group"><input type="text" id="newSlideName" class="form-control"'+
@@ -276,7 +279,7 @@ function updateSlideName(oldSlideName) {
     }
   });
 }
-
+// updates the name of the file if not null, not duplicated and has the correct file extension
 function updateFileName(oldfileName) {
   $('#confirmUpdateFileContent').html('Enter the new name for: <br><b>'+oldfileName+
          '</b><br><br><div class="form-group"><input type="text" id="newFileName" class="form-control"'+
@@ -323,7 +326,7 @@ function updateFileName(oldfileName) {
   });
 }
 
-
+// function to start batch upload
 function startBatch() {
   tokens = [];
   for (i=0; i<files.length; i++) {
@@ -335,6 +338,7 @@ function startBatch() {
   $('#start').css('display', 'none');
 }
 
+// function to finish batch upload
 function finishBatch() {
   for (i=0; i<fileNames.length; i++) {
     finishUpload(tokens[i], fileNames[i], i);
@@ -359,7 +363,7 @@ async function handleUpload(selectedFile, filename, i) {
   continueUpload(token);
   readFileChunks(selectedFile, token);
 }
-
+// convert to json and POST per file
 async function startUpload(filename) {
   const body = {filename: filename};
   const token = fetch(startUrl, {method: 'POST', body: JSON.stringify(body), headers: {
@@ -380,7 +384,7 @@ function continueUpload(token) {
     }});
   };
 }
-
+// called when upload of a file is finished.
 function finishUpload(token, filename, i) {
 //   let reset = true;
 
@@ -465,13 +469,13 @@ function promiseChunkFileReader(file, part) {
     fr.readAsDataURL(blob);
   });
 }
-
+// checks for all files
 function checkBatch() {
   for (i=0; i<fileNames.length; i++) {
     handleCheck(fileNames[i], i);
   }
 }
-
+// checks if each file doesn't have an error
 function handleCheck(filename, i) {
   fetch(checkUrl + filename, {credentials: 'same-origin'}).then(
       (response) => response.json(), // if the response is a JSON object
@@ -492,13 +496,13 @@ function handleCheck(filename, i) {
       (error) => console.log(error), // Handle the error response object
   );
 }
-
+// upload all files
 function postBatch() {
   for (i=0; i<fileNames.length; i++) {
     handlePost(fileNames[i], slideNames[i], i);
   }
 }
-
+// upload each file with timestamp
 function handlePost(filename, slidename, i) {
   fetch(checkUrl + filename, {credentials: 'same-origin'}).then(
       (response) => response.json(), // if the response is a JSON object
@@ -547,7 +551,7 @@ function handlePost(filename, slidename, i) {
       (error) => console.log(error), // Handle the error response object
   );
 }
-
+// replace certain symbols for proper parsing in html
 function sanitize(string) {
   const map = {
     '&': '&amp;',

apps/landing/landing.html

@@ -95,7 +95,7 @@ <h2>caMicroscope</h2>
                 <a href="../table.html" class="image"><img src="./camic.jpg" alt=""/></a>
                 <div class="content">
                     <h3>caMicroscope</h3>
-                    <p>Use camicroscope to explore and mark slides uploaded.</p>
+                    <p>Use camicroscope to explore and mark slides uploaded. If this is a restricted access deployment, you will be prompted to log in here.</p>
                     <a href="../table.html" class="button">More</a>
                 </div>
             </section>

apps/signup/signup.js

@@ -9,6 +9,12 @@ function addUser(){
   // var attr = document.querySelector('input[name="attr"]:checked').value
   var attrEle = document.getElementById("attr");
   var attr = attrEle.options[attrEle.selectedIndex].value;
+
+  if (!(/^[a-zA-Z0-9.!#$%&'*+/=?^_`{|}~-]+@[a-zA-Z0-9-]+(?:\.[a-zA-Z0-9-]+)*$/.test(email))) {
+    window.alert("Please enter a valid email");
+    return;
+  }
+
   var userType = "Null"
   if (attr == "3"){
     userType = "Admin"