Merge pull request #568 from camicroscope/develop

For 3.10.0
camicroscope · Oct 25, 2022 · 00e86f1 · 00e86f1
2 parents 9df777b + 83a43e9
commit 00e86f1
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diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml
@@ -12,7 +12,7 @@ jobs:
 
     strategy:
       matrix:
-        node-version: [10.x, 12.x, 14.x, 15.x]
+        node-version: [14.x, 16.x, 18.x]
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:

diff --git a/apps/port/export.html b/apps/port/export.html
@@ -0,0 +1,41 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <script src="../../core/Store.js"></script>
+  <title>Export Results [caMicroscope]</title>
+  <link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-iYQeCzEYFbKjA/T2uDLTpkwGzCiq6soy8tYaI1GyVh/UjpbCx/TYkiZhlZB6+fzT" crossorigin="anonymous">
+  <style>
+    body{
+      padding:20px;
+    }
+    #output{
+      padding: 20px;
+    }
+    span{
+      display:inline-block;
+    }
+    .form-check-input{
+      padding:5px !important;
+    }
+    </style>
+</head>
+<body>
+
+  <h1>Export Results</h1>
+  <div class="form">
+  <label for="slide_id">Slide Ids (exact matches, comma delimited):</label>
+  <input type="text" id="slide_id" name="slide_id"><br>
+
+  <button id="populate_btn" onclick="populateList()" type="button">Get List of Results</button>
+
+  </div>
+  <br><br>
+  <h3>Select Results</h3>
+  <div id="output"></div>
+  <button id="convert_btn" onclick="downloadResults()" type="button">Download Selected Results</button>
+  <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-u1OknCvxWvY5kfmNBILK2hRnQC3Pr17a+RTT6rIHI7NnikvbZlHgTPOOmMi466C8" crossorigin="anonymous"></script>
+  <script src="//code.jquery.com/jquery.min.js"></script>
+  <script src="./tree_table.js"></script>
+  <script src="./export.js"></script>
+</body>
+</html>
diff --git a/apps/port/export.js b/apps/port/export.js
@@ -0,0 +1,158 @@
+const store = new Store('../../data/');
+
+async function populateList() {
+  // clear any previous
+  document.getElementById('output').innerHTML = '';
+  console.log('populating list...');
+  nameField = 'name';
+  // get slide and associated result information
+  let slides = [];
+  let results = {};
+  let slideList = document.getElementById('slide_id').value;
+  slideList = slideList.replace(/\s+/g, '');
+  slideList = slideList.split(',');
+  for (let id of slideList) {
+    let slide = await store.getSlide(id);
+    slide = slide[0];
+    if (slide && slide['_id']) {
+      let s = {'id': slide['_id']['$oid'], 'name': slide['name'], 'type': 'slide', 'raw': slide};
+      console.log(s);
+      slides.push(s);
+      // get associated result types
+      r = [];
+      for (let a of await store.findMarkTypes(slide['_id']['$oid'], 'computer')) {
+        console.log(a);
+        r.push({'id': a['execution_id'], 'name': a['name'], 'type': 'computer mark'});
+      }
+      for (let a of await store.findMarkTypes(slide['_id']['$oid'], 'human')) {
+        console.log(a);
+        r.push({'id': a['_id']['analysis']['execution_id'], 'name': a['_id']['analysis']['name'], 'type': 'human mark'});
+      }
+      // todo -- is this right for heatmapType results?
+      for (let a of await store.findHeatmapType(slide['_id']['$oid'])) {
+        r.push({'id': a['provenance']['analysis']['execution_id'],
+          'name': a['provenance']['analysis']['execution_id'], 'type': 'heatmap'});
+      }
+      results[slide['_id']['$oid']] = r;
+    }
+  }
+
+  let headers = ['name', 'id', 'type'];
+  let t = document.createElement('table');
+  t.id = 'tree-table';
+  t.classList.add('table', 'table-hover', 'table-bordered');
+  // add headers
+  let table = document.createElement('tbody');
+  let headerTr = document.createElement('tr');
+  for (let z of headers) {
+    let th = document.createElement('th');
+    th.innerText = z || '?';
+    headerTr.appendChild(th);
+  }
+  // add select header special
+  let selectTh = document.createElement('th');
+  selectTh.innerText = 'Select';
+  headerTr.appendChild(selectTh);
+  table.append(headerTr);
+  // populate results
+  for (let x of slides) {
+    let parent = document.createElement('tr');
+    parent.setAttribute('data-id', x.id);
+    parent.setAttribute('data-parent', 0);
+    parent.setAttribute('data-level', 1);
+    for (let z of headers) {
+      let d = document.createElement('td');
+      d.innerText = x[z] || '?';
+      if (z==nameField) {
+        d.setAttribute('data-column', 'name');
+      }
+      parent.appendChild(d);
+    }
+    // add special checkbox
+    parentCheck = document.createElement('input');
+    parentCheck.classList.add('form-check-input');
+    parentCheck.type = 'checkbox';
+    parentCheck.indeterminate = true; // cool!
+    // TODO -- finish this. you'd want to add logic that sets this checkbox to true, false or indeterminate
+    //         depending on children selection. also select/deselect all children on change of this.
+    // parent.appendChild(parentCheck);
+    table.appendChild(parent);
+    for (let y of results[x.id]) {
+      console.log(x.raw);
+      let child = document.createElement('tr');
+      child.setAttribute('data-id', x.id+'-'+y.id);
+      child.setAttribute('data-parent', x.id);
+      child.setAttribute('data-level', 2);
+      for (let z of headers) {
+        let d = document.createElement('td');
+        d.innerText = y[z] || '?';
+        if (z==nameField) {
+          d.setAttribute('data-column', 'name');
+        }
+        child.appendChild(d);
+      }
+      // special checkbox
+      childCheck = document.createElement('input');
+      childCheck.type = 'checkbox';
+      childCheck.classList.add('form-check-input');
+      childCheck.classList.add('result');
+      childCheck.setAttribute('data-target', x.id);
+      childCheck.setAttribute('data-self', y.id);
+      childCheck.setAttribute('data-slideInfo', JSON.stringify(x.raw));
+      childCheck.setAttribute('data-type', y.type);
+      childCheck.checked = true;
+      child.appendChild(childCheck);
+      table.appendChild(child);
+    }
+  }
+  t.appendChild(table);
+  document.getElementById('output').appendChild(t);
+  makeTreeTable('tree-table');
+}
+
+async function downloadResults() {
+  let checks = document.querySelectorAll('.result:checked');
+  let marks = [];
+  let heatmaps = [];
+  for (let c of checks) {
+    console.log(c.dataset);
+    let parentSlide = JSON.parse(checks[0].dataset.slideinfo);
+    if (c.dataset.type == 'human mark' || c.dataset.type == 'human mark') {
+      let mark = await store.getMarkByIds([c.dataset.self], c.dataset.target);
+      for (m of mark) {
+        m.provenance.image = parentSlide;
+        marks.push(m);
+      }
+      console.log(mark);
+    } else if (c.dataset.type == 'heatmap' ) {
+      let hm = await store.getHeatmap(c.dataset.parent, c.dataset.target);
+      for (h of hm) {
+        h.provenance.image = parentSlide;
+        heatmaps.push(h);
+      }
+    }
+  }
+  console.log(marks, heatmaps);
+  if (marks.length) {
+    var element = document.createElement('a');
+    element.setAttribute('href', 'data:application/json;charset=utf-8,' + encodeURIComponent(JSON.stringify(marks)));
+    element.setAttribute('download', 'camic_export_marks.json');
+    element.style.display = 'none';
+    document.body.appendChild(element);
+    element.click();
+    document.body.removeChild(element);
+  }
+  if (heatmaps.length) {
+    var element = document.createElement('a');
+    element.setAttribute('href', 'data:application/json;charset=utf-8,' + encodeURIComponent(JSON.stringify(heatmaps)));
+    element.setAttribute('download', 'camic_export_heatmaps.json');
+    element.style.display = 'none';
+    document.body.appendChild(element);
+    element.click();
+    document.body.removeChild(element);
+  }
+  // tell the user that data is missing
+  if (!heatmaps.length && !marks.length) {
+    alert('No data selected for download.');
+  }
+}
diff --git a/apps/port/index.html → apps/port/import.html b/apps/port/index.html → apps/port/import.html
@@ -2,7 +2,7 @@
 <html>
 <head>
   <script src="../../core/Store.js"></script>
-  <script src="./port.js"></script>
+  <script src="./import.js"></script>
   <script src="./xml2geo.js"></script>
   <link rel="stylesheet" href="./style.css">
   <title>Import and Export [caMicroscope]</title>

diff --git a/apps/port/port.js → apps/port/import.js b/apps/port/port.js → apps/port/import.js
diff --git a/apps/port/tree_table.js b/apps/port/tree_table.js
@@ -0,0 +1,64 @@
+function makeTreeTable(id) {
+  var
+    $table = $('#' + id);
+  var rows = $table.find('tr');
+
+  rows.each(function(index, row) {
+    var
+      $row = $(row);
+    var level = $row.data('level');
+    var id = $row.data('id');
+    var $columnName = $row.find('td[data-column="name"]');
+    var children = $table.find('tr[data-parent="' + id + '"]');
+
+    if (children.length) {
+      var expander = $columnName.prepend('' +
+                '<span class="treegrid-expander glyphicon glyphicon-chevron-right">&#9660;</span>' +
+                '');
+
+      children.hide();
+
+      expander.on('click', function(e) {
+        var $target = $(e.target);
+        if ($target.hasClass('glyphicon-chevron-right')) {
+          $target
+              .removeClass('glyphicon-chevron-right')
+              .addClass('glyphicon-chevron-down');
+
+          children.show();
+        } else {
+          $target
+              .removeClass('glyphicon-chevron-down')
+              .addClass('glyphicon-chevron-right');
+
+          reverseHide($table, $row);
+        }
+      });
+    }
+
+    $columnName.prepend('' +
+            '<span class="treegrid-indent" style="width:' + 25 * level + 'px"></span>' +
+            '');
+  });
+
+  // Reverse hide all elements
+  reverseHide = function(table, element) {
+    var
+      $element = $(element);
+    var id = $element.data('id');
+    var children = table.find('tr[data-parent="' + id + '"]');
+
+    if (children.length) {
+      children.each(function(i, e) {
+        reverseHide(table, e);
+      });
+
+      $element
+          .find('.glyphicon-chevron-down')
+          .removeClass('glyphicon-chevron-down')
+          .addClass('glyphicon-chevron-right');
+
+      children.hide();
+    }
+  };
+}
diff --git a/apps/table.html b/apps/table.html
@@ -64,6 +64,9 @@
 						<li class="nav-item link">
 							<a class="nav-link" href="./dev-workbench/workbench.html"> <i class="fas fa-pencil-ruler"></i> Workbench</a>
 						</li>
+						<li class="nav-item link">
+							<a class="nav-link" href="./port/export.html"> <i class="fas fa-solid fa-file-export"></i> Export</a>
+						</li>
 						<li class="nav-item link" style="font-family: sans-serif;">
 							<a class="nav-link" href="./signup/signup.html"> <i class="fas fa-user-plus"></i> Signup</a>
 						</li>
@@ -136,7 +139,7 @@ <h1 class="h1">caMicroscope</h1>
                         onclick="(()=>{location.reload();return false;})()"> <i class="fas fa-sync-alt"></i>
                         Reload</button>
                 </div>
-                <div> 
+                <div>
 			    <div id="slideUploadButton" class="btn-group float-right pl-md-2 pt-2">
 				    <button type="button" class="btn btn-primary " data-bs-toggle="modal"
 			data-bs-target="#upload-dialog" onclick="hidePostButton(); hideCheckButton(); resetUploadForm();" > <i class="fas fa-upload"></i> Upload</button>
@@ -149,12 +152,12 @@ <h1 class="h1">caMicroscope</h1>
                 </div>
             </div>
         </div>
-            
+
 
 		</div>
 		</div>
 	</div>
-		
+
 
 
         <div class="modal fade" id="upload-dialog" tabindex="-1" role="dialog"
@@ -285,7 +288,7 @@ <h5 class="modal-title" id="slideNameChangeModalLabel">Slide name change confirm
 			</div>
 		</div>
 		</div>
-	<!-- popup -->	
+	<!-- popup -->
 	<div id="popup-container"></div>
 </div>
 
@@ -295,7 +298,7 @@ <h5 class="modal-title" id="slideNameChangeModalLabel">Slide name change confirm
 <footer class="text-center text-white bg-dark p-3">
 	<p class="p">Copyright © 2021 caMicroscope</p>
 </footer>
-	
+
 <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js" integrity="sha384-p34f1UUtsS3wqzfto5wAAmdvj+osOnFyQFpp4Ua3gs/ZVWx6oOypYoCJhGGScy+8" crossorigin="anonymous"></script>
 <script src="./table.js"></script>
 </body>

diff --git a/apps/viewer/init.js b/apps/viewer/init.js
@@ -167,7 +167,7 @@ function initCore() {
       if ($D.params.retry) {
         $UI.message.addError(e.message);
         // can't reach Slide and return to home page
-        if (e.isServiceError) redirect($D.pages.table, e.message, 0);
+        if (e.isServiceError) redirect($D.pages.table, e.message, 1);
       } else {
         // If this is our first attempt, try one more time.
         let params = new URLSearchParams(window.location.search);

diff --git a/common/PathdbMods.js b/common/PathdbMods.js
@@ -1,7 +1,7 @@
-function PathDbMods() {
+async function PathDbMods() {
   console.log("PathDbMods()...");
   // determine if user is authenicated
-  fetch("/user/login_status?_format=json", {credentials: 'include'})
+  await fetch("/user/login_status?_format=json", {credentials: 'include'})
     .then(response => response.json())
     .then(function(data) {
       if (data!=0) {
@@ -11,6 +11,7 @@ function PathDbMods() {
               console.log(x)
               if (x.hasOwnProperty('token') && x.token) {
                 document.cookie = "token=" + x.token + ";"
+                console.log("set cookie, is now:" , document.cookie)
               }
            })
       } else {
@@ -49,9 +50,9 @@ function PathDbMods() {
       x.mpp = x.mpp_x
     }
     if (data.field_iip_path && data.field_iip_path.length >= 1) {
-      x.location = data.field_iip_path[0].value;
-      //x.location = "pathdb*" + pathdbid;
-      x.url = "../../img/IIP/raw/?DeepZoom=" + x.location + ".dzi";
+      //x.location = data.field_iip_path[0].value;
+      x.location = "pathdb*" + pathdbid;
+      x.url = "../../img/IIP/raw/?DeepZoom=pathdb*" + pathdbid + ".dzi";
     } else {
       throw "no iip path in pathdb data"
     }

diff --git a/common/dynamicLoadScript.js b/common/dynamicLoadScript.js
@@ -6,14 +6,15 @@ const params = getUrlVars();
 let file;
 if (params.mode && params.mode==="pathdb"){
     ImgloaderMode = 'iip';
-    PathDbMods()
+    PathDbMods().then(x=>{IsPackageLoading = true})
 }
 else if(params.slideId&&params.id&&params.slideId==="local"&&params.id.includes('http://localhost:8888')){
     ImgloaderMode = 'imgbox';
     NanoBorbMods()
     init_LocalStore()
+    IsPackageLoading = true;
 }else{
     ImgloaderMode = 'iip';
+    IsPackageLoading = true;
     // no mods to perform as of now
 }
-IsPackageLoading=true;