#2 added link to relaunch server on process error page

cellxgene_gateway/cache_entry.py

@@ -6,6 +6,7 @@
 # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
+import psutil
 from flask import make_response, request
 from requests import get, post, put
 
@@ -73,7 +74,8 @@ class CacheEntry:
         else:
             self.all_output += output
 
-    def terminate(self, process):
+    def terminate(self):
+        pid = self.pid
         if pid != None and self.status != "terminated":
             p = psutil.Process(pid)
             p.terminate()

cellxgene_gateway/gateway.py

@@ -48,6 +48,7 @@ def handle_invalid_usage(error):
             "cellxgene_error.html",
             extra_scripts=get_extra_scripts(),
             message=message,
+            path=error.path
         ),
         error.http_status,
     )
@@ -67,7 +68,11 @@ def handle_invalid_process(error):
         render_template(
             "process_error.html",
             extra_scripts=get_extra_scripts(),
-            message=message,
+            message=error.message,
+            http_status=error.http_status,
+            stdout=error.stdout,
+            stderr=error.stderr,
+            dataset=error.dataset,
         ),
         error.http_status,
     )
@@ -180,7 +185,7 @@ def do_view(path):
             "loading.html", launchtime=launch_time, all_output=match.all_output
         )
     elif match.status == "error":
-        raise ProcessException.from_pid_object(match)
+        raise ProcessException.from_cache_entry(match)
 
 @app.route("/cache_status", methods=["GET"])
 def do_GET_status():
@@ -195,7 +200,7 @@ def do_relaunch(path):
     match = cache.check_entry(dataset)
     if not match is None:
         match.terminate()
-    return redirect(url_for('view', path=path), code=301)
+    return redirect(url_for('do_view', path=path), code=302)
 
 def main():
     env.validate()

cellxgene_gateway/process_exception.py

@@ -9,18 +9,20 @@
 
 
 class ProcessException(Exception):
-    def __init__(self, message, stdout, stderr, http_status):
+    def __init__(self, message, stdout, stderr, http_status, dataset):
         Exception.__init__(self)
         self.message = message
         self.stdout = stdout
         self.stderr = stderr
         self.http_status = http_status
+        self.dataset = dataset
 
     @classmethod
-    def from_pid_object(cls, pid_object):
+    def from_cache_entry(cls, cache_entry):
         return cls(
-            pid_object.message,
+            cache_entry.message,
-            pid_object.all_output,
+            cache_entry.all_output,
-            pid_object.stderr,
+            cache_entry.stderr,
-            pid_object.http_status,
+            cache_entry.http_status,
+            cache_entry.dataset,
         )

cellxgene_gateway/prune_process_cache.py

@@ -9,8 +9,6 @@
 
 import time
 
-import psutil
-
 from cellxgene_gateway.util import current_time_stamp
 from cellxgene_gateway.env import ttl
 

cellxgene_gateway/subprocess_backend.py

@@ -62,7 +62,7 @@ class SubprocessBackend:
                 cache_entry.status = "error"
                 cache_entry.set_error(message, stderr, http_status)
 
-                raise ProcessException.from_pid_object(cache_entry)
+                raise ProcessException.from_cache_entry(cache_entry)
             else:
                 cache_entry.append_output(output)
 

cellxgene_gateway/templates/cache_status.html

@@ -31,7 +31,7 @@
                <th>dataset</th>
                <th>port</th>
                <th>launchtime</th>
-               <th>timestamp</th>
+               <th>last access</th>
                <th>status</th>
                <th>message</th>
                <th>http_status</th>
@@ -43,8 +43,8 @@
                <td>{{ entry.pid }}</td>
                <td>{{ entry.dataset }}</td>
                <td>{{ entry.port }}</td>
-               <td>{{ entry.launchtime }}</td>
+               <td class="timestamp">{{ entry.launchtime }}</td>
-               <td>{{ entry.timestamp }}</td>
+               <td class="timestamp">{{ entry.timestamp }}</td>
                <td>{{ entry.status }}</td>
                <td>{{ entry.message }}</td>
                <td>{{ entry.http_status }}</td>
@@ -52,5 +52,15 @@
      {% endfor %}
      </tbody>
      </table>
+     <script>
+          $(() => {
+               $(".timestamp").each(function(){
+                    const el = $(this);
+                    const ts = el.text();
+                    const dt = new Date(parseInt(ts * 1000));
+                    el.html(`${dt.toISOString()}<br>(${ts})`);
+               });
+          })
+     </script>
 </body>
 </html>

cellxgene_gateway/templates/index.html

@@ -39,6 +39,11 @@
 		  <u>File Crawler: Allows you to view all uploaded data.</u></a>
 		  
 	</div>
+	<div class="list-group" style="width:50%;padding-left:65px">
+		<a href="/cache_status" class="list-group-item list-group-item-action">
+			<u>Cache Status: view status of launched cellxgene servers.</u></a>
+	</div>
+	
 	<br>
 
 	<h1 style="padding-left:35px">
@@ -103,9 +108,5 @@ scp -r pbmc3k.h5ad ec2-user@{{ ip }}:{{ cellxgene_data }}/USER/DATA/</pre>
 		<li>Take a look at your data using the file crawler link above</li>
 	</ol>	
 
-	<ul>
-		<li><a href="/cache_status.html">Cache Status<</a>  - view status of currently loaded datasets</li>
-	</ul>
-
 </body>
 </html>

cellxgene_gateway/templates/process_error.html

@@ -25,19 +25,27 @@
      </header>
      <br>
      <div style="margin-left:20px">
-          
+     <h4>Error Details</h4>
-     <h4>{{ message[0] }}</h4>
+     <table>
-     <h4>{{ message[1] }}</h4>
+          <tr><th>Message</th><td>{{ message }}</td></tr>
-     <h4>{{ message[2] }}</h4>
+          <tr><th>Status</th><td>{{ http_status }}</td></tr>
-     <h4>{{ message[3] }}</h4>
+          <tr><th>Stdout</th><td>{{ stdout }}</td></tr>
-
+          <tr><th>Stderr</th><td>{{ stderr }}</td></tr>
-     <a href="/filecrawl.html">
+     </table>
-          Please click here to be redirected to the file directory.
+<br>
-     </a>
+<h4>Options</h4>
-     <br>
+     Please choose one of the following, or use the back button:
-     <a href="/">
+     <ul>
-          Please click here to return to the homepage.
+          <li><a href="{{url_for('do_relaunch', path=dataset)}}">
-     </a>
+                    Attempt to relaunch the cellxgene server.
-     </div>
+               </a></li>
+          <li><a href="/filecrawl.html">
+               Return to the file directory.
+          </a></li>
+          <li><a href="/">
+               Return to the homepage.
+          </a></li>
+     </ul>
+     
 </body>
 </html>