add buckets for arcade, physicell, and readdy outputs, exclude direct…

…ories, and better error feedback
simularium · Sep 24, 2021 · 6a4aad3 · 6a4aad3
1 parent 11a8e11
commit 6a4aad3
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Showing 7 changed files with 114 additions and 11 deletions.
diff --git a/arcade.html b/arcade.html
@@ -0,0 +1,18 @@
+<html>
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+  <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Overpass:wght@200;400;600&display=swap">
+  <link rel="stylesheet" href="main.css">
+</head>
+<body>
+  <a href="index.html">&larr; Back</a>
+  <h1>ARCADE Simularium Library</h1>
+  <div id="listing"></div>
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"></script>
+  <script type="text/javascript">
+    var BUCKET_URL = 'https://arcade-working-bucket.s3.us-west-2.amazonaws.com';
+  </script>
+<script src="list.js"></script>
+</body>
+</html>
+
diff --git a/index.html b/index.html
@@ -6,9 +6,21 @@
 <body>
   <h1 class="title">Simularium Trajectory Libraries</h1>
   <a href="main.html"><div class="bucket">
-    <h2>Main Simularium Library</h2>
+    <h2>Main Library</h2>
     <span>https://aics-simularium-data.s3.us-east-2.amazonaws.com</span>
   </div></a>
+  <a href="readdy.html"><div class="bucket">
+    <h2>AICS ReaDDy Library</h2>
+    <span>https://readdy-working-bucket.s3.us-west-2.amazonaws.com</span>
+  </div></a>
+  <a href="physicell.html"><div class="bucket">
+    <h2>AICS PhysiCell Library</h2>
+    <span>https://physicell-working-bucket.s3.us-west-2.amazonaws.com</span>
+  </div></a>
+  <a href="arcade.html"><div class="bucket">
+    <h2>ARCADE Library</h2>
+    <span>https://arcade-working-bucket.s3.us-west-2.amazonaws.com</span>
+  </div></a>
 </body>
 </html>
 
diff --git a/list.js b/list.js
@@ -4,6 +4,11 @@ jQuery(function($) {
   } else {
     var url = location.protocol + '//' + location.hostname;
   }
+  if (typeof EXCLUDE_DIRS != 'undefined') {
+    var exclude_dirs = EXCLUDE_DIRS;
+  } else {
+    var exclude_dirs = [];
+  }
   $.get(url)
     .done(function(data) {
       var xml = $(data);
@@ -15,10 +20,10 @@ jQuery(function($) {
           Size: item.find('Size').text(),
         }
       });
-      renderTable(files, url);
+      renderTable(files, url, exclude_dirs);
     })
     .fail(function(error) {
-      alert('There was an error');
+      alert(url + ' is not accessible, check that everyone has permission to list files and that the CORS policy allows GET from all origins');
       console.log(error);
     });
 });
@@ -45,22 +50,44 @@ var formatSize = function (str) {
   return ( size / Math.pow(1024, i) ).toFixed(2) * 1 + ' ' + ['B', 'kB', 'MB', 'GB', 'TB'][i];
 }
 
-function renderTable(files, bucket_url) {
+function renderTable(files, bucket_url, exclude_dirs) {
+  var n_files = files.length;
+  var n_files_listed = 0;
   var content = '<h3>' + bucket_url + '</h3>';
-  content += '<div class="instructions">Choose a file to load in the Simularium Viewer.</div>';
+  content += '<div class="instructions">Found ' + n_files + ' file(s) ';
+  if (n_files === 1000)
+  {
+    content += '<span style="color: red;">(This is the maximum listable)</span>';
+  }
+  content += '<br/><br/>Choose a file to load in the Simularium Viewer.</div>';
   $.each(files, function(idx, item) {
     var key = item.Key;
     var ext = getExtension(key);
     if (ext === "simularium")
     {
-      var filename = camalize(getFilename(key));
-      var link = "https://simularium.allencell.org/viewer?trajUrl=" + bucket_url + "/" + key;
-      content += '<a target="_blank" href="' + link + '"><div class="trajectory"><h2>' + filename + '</h2>';
-      content += key + '<br/>';
-      content += '<span class="label">Modified:</span> ' + formatDate(item.LastModified) + '    ',
-      content += '<span class="label">Size:</span> ' + formatSize(item.Size) + '</div></a>';
+      var exclude = false;
+      $.each(exclude_dirs, function(dir) {
+        if (key.includes(exclude_dirs[dir]))
+        {
+          exclude = true;
+        }
+      });
+      if (!exclude)
+      {
+        var filename = camalize(getFilename(key));
+        var link = "https://simularium.allencell.org/viewer?trajUrl=" + bucket_url + "/" + key;
+        content += '<a target="_blank" href="' + link + '"><div class="trajectory"><h2>' + filename + '</h2>';
+        content += key + '<br/>';
+        content += '<span class="label">Modified:</span> ' + formatDate(item.LastModified) + '    ',
+        content += '<span class="label">Size:</span> ' + formatSize(item.Size) + '</div></a>';
+        n_files_listed++;
+      }
     }
   });
+  if (n_files > 0 && n_files_listed === 0)
+  {
+    content += '<div class="error">No .simularium files found in the first 1000 files (alphabetically) that were not in excluded directories.</div>';
+  }
   document.getElementById('listing').innerHTML = '<pre>' + content + '</pre>';
 }
 
diff --git a/main.css b/main.css
@@ -53,6 +53,14 @@ h3 {
     margin-bottom: 40;
 }
 
+.error {
+    font-family: Overpass;
+    font-size: 16px;
+    margin-left: 15;
+    margin-bottom: 40;
+    color: red;
+}
+
 h2 {
     font-family: Overpass;
     margin-bottom: 0;

diff --git a/main.html b/main.html
@@ -1,5 +1,6 @@
 <html>
 <head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
   <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Overpass:wght@200;400;600&display=swap">
   <link rel="stylesheet" href="main.css">
 </head>

diff --git a/physicell.html b/physicell.html
@@ -0,0 +1,18 @@
+<html>
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+  <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Overpass:wght@200;400;600&display=swap">
+  <link rel="stylesheet" href="main.css">
+</head>
+<body>
+  <a href="index.html">&larr; Back</a>
+  <h1>AICS PhysiCell Simularium Library</h1>
+  <div id="listing"></div>
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"></script>
+  <script type="text/javascript">
+    var BUCKET_URL = 'https://physicell-working-bucket.s3.us-west-2.amazonaws.com';
+  </script>
+<script src="list.js"></script>
+</body>
+</html>
+
diff --git a/readdy.html b/readdy.html
@@ -0,0 +1,19 @@
+<html>
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+  <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Overpass:wght@200;400;600&display=swap">
+  <link rel="stylesheet" href="main.css">
+</head>
+<body>
+  <a href="index.html">&larr; Back</a>
+  <h1>AICS ReaDDy Simularium Library</h1>
+  <div id="listing"></div>
+  <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js"></script>
+  <script type="text/javascript">
+    var BUCKET_URL = 'https://readdy-working-bucket.s3.us-west-2.amazonaws.com';
+    var EXCLUDE_DIRS = ['z_archive'];
+  </script>
+<script src="list.js"></script>
+</body>
+</html>
+