#14 added custom method to create data dirs

cellxgene_gateway/filecrawl.py

@@ -23,7 +23,7 @@ def recurse_dir(path):
                     x[:-4] if x.endwith('.csv') else x),
                 "path": os.path.join(full_path, x).replace(env.cellxgene_data, ""),
             } for x in os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
-        return [{"name":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
+        return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
 
     def make_entry(el):
         full_path = os.path.join(path, el)
@@ -56,12 +56,14 @@ def render_entries(entries):
 
 def get_url(entry):
     return f"view/{ entry['path'].lstrip('/') }"
+def get_class(entry):
+    return f" class='{entry['class']}'" if 'class' in entry else ''
 
 def render_annotations(entry):
     if len(entry['annotations']) > 0:
-        return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'>{a['name']}</a>" for a in entry['annotations']])
+        return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'{get_class(a)}>{a['name']}</a>" for a in entry['annotations']])
     else:
-        return '';
+        return ''
 
 def render_entry(entry):
     if entry["type"] == "file":

cellxgene_gateway/gateway.py

@@ -17,6 +17,7 @@ import json
 from flask import (
     Flask,
     redirect,
+    make_response,
     render_template,
     request,
     send_from_directory,
@@ -163,11 +164,16 @@ if env.enable_upload:
 def filecrawl():
     entries = recurse_dir(env.cellxgene_data)
     rendered_html = render_entries(entries)
-    return render_template(
+    resp = make_response(render_template(
         "filecrawl.html",
         extra_scripts=get_extra_scripts(),
         rendered_html=rendered_html,
-    )
+    ))
+    resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
+    resp.headers["Pragma"] = "no-cache"
+    resp.headers["Expires"] = "0"
+    resp.headers['Cache-Control'] = 'public, max-age=0'
+    return resp
 
 @app.route("/filecrawl/<path:path>")
 def do_filecrawl(path):

cellxgene_gateway/path_util.py

@@ -28,12 +28,13 @@ def get_key(path):
         if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
             # 1) somedir/dataset.h5ad: a dataset
             return CacheKey(trimmed, trimmed, None)
-        elif trimmed.endswith('.csv') and data_file_exists(trimmed):
+        elif trimmed.endswith('.csv'):
 
-            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
+            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
             annotations_dir = os.path.split(trimmed)[0]
             dataset = make_h5ad(annotations_dir)
             if data_file_exists(dataset):
+                data_dir_ensure(annotations_dir)
                 return CacheKey(trimmed, dataset, trimmed)
         elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
             # 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
@@ -74,6 +75,10 @@ def data_dir_exists(dataset):
     file_path = os.path.join(env.cellxgene_data, dataset)
     validate_is_dir(file_path)
     return True
+def data_dir_ensure(dataset):
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    if not os.path.exists(file_path):
+        os.makedirs(file_path)
 
 def get_file_path(key):
     dataset = key.dataset
@@ -82,12 +87,9 @@ def get_file_path(key):
     return file_path
 
 def get_annotation_file_path(key):
-    print(f"getting annotaiton_file_path for {key.annotation_file}")
     if key.annotation_file is None:
         return None
     if key.annotation_file == '':
         return ''
     file_path = os.path.join(env.cellxgene_data, key.annotation_file)
-    print(f"getting annotaiton_file_path for {key}, file_path {file_path}")
-    validate_is_file(file_path)
     return file_path

cellxgene_gateway/static/js/annotation.js

@@ -0,0 +1,21 @@
+// neandertal javascript
+const new_annotation_callback = (() =>{
+    const chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
+    const pickn = (c, n) => n==0?'':c.substr(Math.random()*c.length,1) + pickn(c,n-1);
+    const suffix = `_${pickn(chars,8)}.csv`;
+    return (e) => {
+        e.preventDefault();
+        const el = $(e.target);
+        const href = el.attr('href');
+        const base = prompt(`Name your annotations collection\nnote: the suffix "${suffix}" will be appended`);
+        if (base !== null && base.length > 0) {
+            if (/^[0-9a-zA-Z_]+$/.test(base)) {
+                window.location = `${href}/${base}${suffix}`;
+            } else {
+                alert("Error: name must match ^[0-9a-zA-Z_]+$\nthat is, only numbers, letters and underscore are allowed")
+            }
+        }
+        return false;
+    }
+})()
+

cellxgene_gateway/templates/filecrawl.html

@@ -16,7 +16,8 @@
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
 	{% for script in extra_scripts %}
 	<script src="{{ script }}"></script>
-	{% endfor %}
+     {% endfor %}
+     <script src="{{ url_for('static', filename='js/annotation.js') }}"></script>
      <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
 </head>
 <body>
@@ -41,5 +42,10 @@
      <li><a href="/">homepage</a></li>
      </ul>
      </p>
+     <script>
+          $(() => {
+               $("a.new").click(new_annotation_callback);
+          })
+     </script>
 </body>
 </html>