Added support for setting task extra volumes at runtime.

services/webapp/code/rosetta/core_app/computing_managers.py

@@ -134,7 +134,10 @@ class LocalComputingManager(ComputingManager):
     
         out = os_shell(stop_command, capture=True)
         if out.exit_code != 0:
-            raise Exception(out.stderr)
+            if 'No such container' in out.stderr:
+                pass
+            else:
+                raise Exception(out.stderr)
  
         # Set task as stopped
         task.status = TaskStatuses.stopped
@@ -194,7 +197,14 @@ class RemoteComputingManager(ComputingManager):
                 bindings = ''
             else:
                 bindings = '-B {}'.format(bindings)
-
+            
+            # Manage task extra volumes
+            if task.extra_volumes:
+                if not bindings:
+                    bindings = '-B {}'.format(task.extra_volumes)
+                else:
+                    bindings += ',{}'.format(task.extra_volumes)
+            
             run_command  = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
             run_command += '/bin/bash -c \'"wget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> /dev/null && export BASE_PORT=\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)
             run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
@@ -345,8 +355,14 @@ class SlurmComputingManager(ComputingManager):
             else:
                 bindings = '-B {}'.format(bindings)
 
-            run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
+            # Manage task extra volumes
+            if task.extra_volumes:
+                if not bindings:
+                    bindings = '-B {}'.format(task.extra_volumes)
+                else:
+                    bindings += ',{}'.format(task.extra_volumes)
 
+            run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
             run_command += '\'bash -c "echo \\"#!/bin/bash\nwget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> \$HOME/{}.log && export BASE_PORT=\\\\\\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)
             run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\\\\\\$BASE_PORT && {} '.format(authstring)
             run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)
@@ -492,6 +508,13 @@ class RemotehopComputingManager(ComputingManager):
             else:
                 bindings = '-B {}'.format(bindings)
 
+            # Manage task extra volumes
+            if task.extra_volumes:
+                if not bindings:
+                    bindings = '-B {}'.format(task.extra_volumes)
+                else:
+                    bindings += ',{}'.format(task.extra_volumes)
+
             run_command  = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
             run_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} /bin/bash -c \''.format(second_user, second_host)
             

services/webapp/code/rosetta/core_app/models.py

@@ -272,6 +272,7 @@ class Task(models.Model):
     port      = models.IntegerField('Task port', blank=True, null=True)
     ip        = models.CharField('Task ip address', max_length=36, blank=True, null=True)
     tunnel_port = models.IntegerField('Task tunnel port', blank=True, null=True)
+    extra_volumes = models.CharField('Extra volumes', max_length=4096, blank=True, null=True)
 
     # Links
     computing = models.ForeignKey(Computing, related_name='+', on_delete=models.CASCADE)

services/webapp/code/rosetta/core_app/templates/components/task.html

@@ -46,10 +46,10 @@
             <td>{{ task.computing }}</td>
            </tr>
 
-           <!-- <tr>
-            <td><b>Task pid</b></td>
-            <td>{{ task.pid}}</td>
-           </tr> -->
+           <tr>
+            <td><b>Extra volumes</b></td>
+            <td>{{ task.extra_volumes }}</td>
+           </tr>  
 
            <tr>
             <td><b>IP</b></td>
@@ -72,7 +72,9 @@
             <td>******</td>
            </tr>
            {% endif %}
-           
+
+
+         
 
            <tr>
             <td><b>Operations</b></td>

services/webapp/code/rosetta/core_app/templates/create_task.html

@@ -135,7 +135,7 @@
             <td valign="top" style="width:180px"><b>Set custom port </b></td>
             <td>
              <input type="text" name="task_base_port" value="" placeholder="" size="23" style="margin-bottom:5px"/><br>
-             <p style="line-height: 0.9"><font size=-1>This container supports dynamic ports and you can thus set a custom port (>5900) to avoid clashes with services already running on the computing resource.</font></p>
+             <p style="line-height: 0.95"><font size=-1>This container supports dynamic ports and you can thus set a custom port (>5900) to avoid clashes with services already running on the computing resource.</font></p>
             </td>
            </tr>
            {% endif %}
@@ -150,6 +150,17 @@
            </tr>
            {% endif %}
 
+
+           {% if data.task_container.type == 'singularity' %}
+           <tr>
+            <td valign="top" style="width:180px"><b>Extra volumes</b></td>
+            <td>
+             <input type="text" name="extra_volumes" value="" placeholder="" size="23" /><br>
+             <p style="line-height: 0.95"><font size=-1>Here you can set extra volume bindings on top of the ones already define by the administrator. Format is <i>host_directory:container_directory</i>, comma separated.</font></p>
+            </td>
+           </tr>
+           {% endif %}
+
            <tr>
             <td><b>Access method</b></td><td>
               <select name="access_method" >
@@ -184,7 +195,7 @@
              
            <tr><td colspan=2>
            <table><tr><td  style="border: 1px solid lightgray;" >
-           I understand that files saved or modified in this container, if not explicitly saved to a persistent storage, will be LOST when the task ends.
+           I understand that files saved or modified in this container, if not explicitly saved to a persistent volume, will be LOST when the task ends.
            </td><td  style="border: 1px solid lightgray;" >
            <input class="form-check-input" type="checkbox" value="" id="invalidCheck" required>
            </td></table>

services/webapp/code/rosetta/core_app/views.py

@@ -553,14 +553,15 @@ def create_task(request):
             if task_base_port:
                 task.port = task_base_port
             
-            # Cheks
+            # Checks
             if task.auth_pass and len(task.auth_pass) < 6:
                 raise ErrorMessage('Task password must be at least 6 chars') 
             
-            # Computing options # TODO: This is hardcoded thinking about Slurm
+            # Computing options # TODO: This is hardcoded thinking about Slurm and Singularity
             computing_cpus = request.POST.get('computing_cpus', None)
             computing_memory = request.POST.get('computing_memory', None)
             computing_partition = request.POST.get('computing_partition', None)
+            extra_volumes = request.POST.get('extra_volumes', None)
             
             computing_options = {}
             if computing_cpus:
@@ -586,6 +587,9 @@ def create_task(request):
             if not task.container.supports_dynamic_ports:
                 if task.container.ports:
                     task.port = task.container.port
+        
+            # Set exttra volumes if any:
+            task.extra_volumes = extra_volumes
 
             # Save the task before starting it, or the computing manager will not be able to work properly
             task.save()