Update deployment settings and documentation

documentation/deployment_instructions.md

@@ -35,7 +35,8 @@ The full list of settings is as follows:
     | `POSTGRES_PASSWORD` | The password for Postgres access.  This should be set to `'postgres'`. |
     | `POSTGRES_PORT` | The port through which the Postgres is exposed.  This should be set to `5432`. |
     | `API_BASE_URL` | The URL and port by which the QCrBox tool manager can be accessed.  If QCrBox is installed on the same machine as this setup, this should be set to `'http://host.docker.internal:11000'`. |
-    | `API_VISUALISER_PORT` | The port through which the QCrBox_quality visualiser can be accessed.  This should be set to `12008` in most cases. |
+    | `TRAEFIK_HTTP_PORT` | The port through which the Traefik router (which handles GUI routing) is exposed.  For development, this should be set to `12345`. |
+    | `GUI_DOMAIN_PREFIX` | The prefix for GUI subdomains.  This should be set to `.gui.` for default setups. |
     | `MAX_LENGTH_API_LOG` | The maximum length of API output to be saved in the logs.  As some API outputs can be quite long, this gives the option to truncate them in the logs, making the logs more unwieldy at the cost of losing some debug information. |
     | `DJANGO_SUPERUSER_EMAIL` | The email address for the default admin account to be created for the web app. |
     | `DJANGO_SUPERUSER_USERNAME` | The username for the default admin account to be created for the web app. |

environment.env.template

@@ -8,7 +8,8 @@ POSTGRES_PASSWORD='postgres'
 POSTGRES_PORT=5432
 
 API_BASE_URL='http://host.docker.internal:11000'
-API_VISUALISER_PORT='12008'
+TRAEFIK_HTTP_PORT='12345'
+GUI_DOMAIN_PREFIX='.gui.'
 
 MAX_LENGTH_API_LOG=10000
 

qcrbox_frontend/core/settings.py

@@ -211,7 +211,10 @@
 
 # API settings
 API_BASE_URL = os.environ.get('API_BASE_URL', 'http://127.0.0.1:11000')
-API_VISUALISER_PORT = os.environ.get('API_VISUALISER_PORT', '12008')
+
+# Traefik / GUI Routing settings
+TRAEFIK_HTTP_PORT = int(os.environ.get('TRAEFIK_HTTP_PORT', '12345') or 12345)
+GUI_DOMAIN_PREFIX = os.environ.get('GUI_DOMAIN_PREFIX', '.gui.')
 
 # Static files (CSS, JavaScript, Images)
 # https://docs.djangoproject.com/en/3.2/howto/static-files/

qcrbox_frontend/qcrbox/forms.py

@@ -96,7 +96,14 @@ def __init__(self, *args, user, **kwargs):
 
         objs = models.FileMetaData.objects                              # pylint: disable=no-member
         qset = objs.filter(active=True).filter(group__in=permitted_groups)
-        choices = [(f.pk, f.display_filename) for f in qset.all()]
+
+        # Filter to only retain the oldest file in each workflow tree, i.e. files which are
+        # not the output of any process
+        process_objs = models.ProcessStep.objects                       # pylint: disable=no-member
+        process_outfiles = process_objs.all().values_list('outfile', flat=True)
+        qset = qset.exclude(pk__in=process_outfiles)
+
+        choices = [(f.pk, str(f)) for f in qset.all()]
 
         self.fields['file'].choices = choices
 
@@ -377,7 +384,7 @@ def __init__(self, *args, command, dataset, **kwargs):
                 else:
                     ext = 'cif'
 
-                filepath = filepath + f'_{command.name}.{ext}'
+                filepath = filepath + f'.{ext}'
 
                 self.fields[param.name] = forms.CharField(
                     initial=filepath,

qcrbox_frontend/qcrbox/models.py

@@ -55,8 +55,36 @@ class FileMetaData(models.Model):
 
     def __str__(self):
         '''Return the filename when an instance of this is parsed as string'''
+        max_len = 30
 
-        return str(self.display_filename)
+        if len(self.display_filename) < max_len:
+            return str(self.display_filename)
+        return str(str(self.display_filename)[:max_len-3]+'...')
+
+    def get_newest_descendant(self):
+        '''Get the most recently created FileMetaData object which is a direct
+        descendant of this FileMetaData'''
+
+        related_pks = [self.pk]
+        last_gen_pks = [self.pk]
+
+        process_step_objs = ProcessStep.objects                         # pylint: disable=no-member
+
+        # Recursively scan all related process_steps for descendant pks
+        while len(last_gen_pks)>0:
+            gen_processes = process_step_objs.filter(infile__pk__in=last_gen_pks)
+            this_gen_pks = gen_processes.values_list('outfile__pk', flat=True)
+            related_pks += this_gen_pks
+            last_gen_pks = this_gen_pks
+
+        # Fetch the object corresponding to the most recently created related
+        # FileMetaData
+        file_metadata_objs = FileMetaData.objects                       # pylint: disable=no-member
+
+        related_objs = file_metadata_objs.filter(pk__in=related_pks)
+        recent_obj = related_objs.order_by('creation_time').last()
+
+        return recent_obj
 
 
 class Application(models.Model):

qcrbox_frontend/qcrbox/templates/initial.html

@@ -18,7 +18,7 @@
             {{ loadfile_form.as_p }}
             <br/>
             <button type="submit" class="btn btn-primary" id="load-button">
-              <i class="fas fa-download"></i> Load
+              Load&nbsp&nbsp<i class="fas fa-arrow-right"></i>
             </button>
           </form>
         </td>
@@ -28,7 +28,7 @@
             {{ newfile_form.as_p }}
             <br/>
             <button type="submit" class="btn btn-primary" id="upload-button">
-              <i class="fas fa-upload"></i> Upload
+              Upload&nbsp&nbsp<i class="fas fa-upload"></i>
             </button>
           </form>
         </td>

qcrbox_frontend/qcrbox/templates/workflow.html

@@ -23,8 +23,8 @@
 
 </style>
 
-<div class="container">
-  <div class="row justify-content-center">
+<div class="container-fluid">
+  <div class="row">
     <div id="cached-interactive-session-id" title={{app_session_id}}></div>
     <table width=100%>
       <tr>
@@ -38,29 +38,29 @@
               <tr id="ancestor-row">
                 <td align='right'>
                   {% if prior_step.infile.active %}
-                    <a href="{% url 'workflow' prior_step.infile.pk %}" id="workflow-link-{{prior_step.infile.display_filename}}"><i class="fa-regular fa-square"></i></a>
+                    <span title="Load File"><a href="{% url 'workflow' prior_step.infile.pk %}" id="workflow-link-{{prior_step.infile.display_filename}}"><i class="fa-regular fa-square"></i></a></span>
                   {% else %}
                     <i class="fa-regular fa-square"></i>
                   {% endif %}
                 </td>
                 <td align='left' padding=15px>
                   {% if prior_step.infile.active %}
-                    {{prior_step.infile.display_filename}}
+                    {{prior_step.infile}}
                   {% else %}
                     <i>Deleted</i>
                   {% endif %}
                 </td>
                 <td align='left' >
                   {% if prior_step.infile.active %}
-                    <a href="{% url 'download' prior_step.infile.pk %}" id="download-link-{{prior_step.infile.display_filename}}">
+                    <span title="Download File"><a href="{% url 'download' prior_step.infile.pk %}" id="download-link-{{prior_step.infile.display_filename}}">
                       <i class="fas fa-download"></i>
-                    </a>&nbsp 
-                    <a href="{% url 'visualise' prior_step.infile.pk %}" target="_blank" id="visualise-link-{{prior_step.infile.display_filename}}">
+                    </a></span>&nbsp
+                    <span title="Visualise Data"><a href="{% url 'visualise' prior_step.infile.pk %}" target="_blank" id="visualise-link-{{prior_step.infile.display_filename}}">
                       <i class="fas fa-eye"></i>
-                    </a>&nbsp
-                    <a href="{% url 'dataset_history' prior_step.infile.pk %}" id="history-link-{{prior_step.infile.display_filename}}">
+                    </a></span>&nbsp
+                    <span title="Data History"><a href="{% url 'dataset_history' prior_step.infile.pk %}" id="history-link-{{prior_step.infile.display_filename}}">
                       <i class="fas fa-clock"></i>
-                    </a>
+                    </a></span>
                   {% endif %}
                 </td>
               </tr>
@@ -69,7 +69,7 @@
                   <i class="fa-solid fa-arrow-down"></i>
                 </td>
                 <td align='left'>
-                  <i>&nbsp{{prior_step.application.name}}</i>
+                  <i>{{prior_step.command.app.name}}: {{prior_step.command}}</i>
                 </td>
               </tr>
             {% endfor %}
@@ -78,18 +78,18 @@
                 <i class="fa-solid fa-square"></i>
               </td>
               <td align='left'>
-                <b id='current-filename'>{{file.display_filename}}</b>
+                <b id='current-filename'>{{file}}</b>
               </td>
               <td align='left'>
-                <a href="{% url 'download' file.pk %}" id="download-link-current">
+                <span title="Download File"><a href="{% url 'download' file.pk %}" id="download-link-current">
                   <i class="fas fa-download"></i>
-                </a>&nbsp
-                <a href="{% url 'visualise' file.pk %}" target="_blank" id="visualise-link-current">
+                </a></span>&nbsp
+                <span title="Visualise Data"><a href="{% url 'visualise' file.pk %}" target="_blank" id="visualise-link-current">
                   <i class="fas fa-eye"></i>
-                </a>&nbsp
-                <a href="{% url 'dataset_history' file.pk %}" id="history-link-current">
+                </a></span>&nbsp
+                <span title="Data History"><a href="{% url 'dataset_history' file.pk %}" id="history-link-current">
                   <i class="fas fa-clock"></i>
-                </a>
+                </a></span>
               </td>
             </tr>
           </table>
@@ -100,7 +100,7 @@
             {% if not current_command %}
               <h4>Dataset Metadata</h4>
               <ul>
-                <li>Dataset ID: {{file.backend_uuid}}</li>
+                <li>Filename: {{file.display_filename}}</li>
                 <li>Filetype: {{file.filetype}}</li>
               </ul>
               <i>Please select a command from the workflow to continue processing.</i>
@@ -146,13 +146,21 @@ <h5><b><i>Calculation in progress, do not close this tab!</i></b></h5>
             {% endif %}
             {% if session_in_progress or calculation_in_progress %}
             {% else %}
-              <hr>
+              {% if current_command %}
+                </div></div>
+                <br/>
+                <div class="card">
+                <div class="card-body">
+                <h4>Select Different Command</h4>
+              {% else %}
+                <hr>
+              {% endif %}
               <center>
                 <form action="" method="POST" enctype="multipart/form-data">
                   {% csrf_token %}
                   {{ select_command_form.as_p }}
                   <button type="submit" class="btn btn-primary" id="select-app-button">
-                    Select Application
+                    Select Command
                   </button>
                 </form>
               </center>
@@ -168,8 +176,14 @@ <h5><b><i>Calculation in progress, do not close this tab!</i></b></h5>
 {% if current_command.interactive %}
   <script>
     let hostname = window.location.hostname;
+    let appSlug = "{{ current_command.app.slug }}".replace(/_/g, "-");
+    let domainPrefix = "{{ gui_domain_prefix }}";
+    let port = "{{ traefik_port }}";
+    let portSuffix = port ? ":" + port : "";
+
+    let url = `http://${appSlug}${domainPrefix}${hostname}${portSuffix}/`;
 
-    document.getElementById("start-app-button").addEventListener("click", function(){ window.open(`http://${hostname}:{{ current_command.app.port }}/vnc.html?path=vnc&autoconnect=true&resize=remote&reconnect=true&show_dot=true`, '_blank'); }); 
+    document.getElementById("start-app-button").addEventListener("click", function(){ window.open(url, '_blank'); }); 
   </script>
 {% elif calculation_in_progress %}
   <script>

qcrbox_frontend/qcrbox/utility.py

@@ -5,6 +5,7 @@
 
 '''
 
+import re
 import textwrap
 
 from django.core.exceptions import PermissionDenied
@@ -255,3 +256,28 @@ def check_user_view_file_permission(user, load_file):
 
     else:
         raise PermissionDenied
+
+def get_next_valid_filename(filename):
+    ''' Check whether a proposed output filename already exists on record and,
+    if so, modify it to prevent a clash.'''
+
+    file_metas = models.FileMetaData.objects                            # pylint: disable=no-member
+    inv_filenames = file_metas.values_list('filename', flat=True)
+    if not filename in inv_filenames:
+        return filename
+
+    fname_components = filename.split('.')
+    fn_root = fname_components[0]
+    fn_ext = fname_components[-1]
+
+    fn_root = re.sub(r'\(\d+\)$', '', fn_root)
+    if not f'{fn_root}.{fn_ext}' in inv_filenames:
+        return f'{fn_root}.{fn_ext}'
+
+    f_ind = 1
+
+    # Find the next valid pattern 'filename_root(x).ext' which is not already in use
+    while True:
+        if not f'{fn_root}({f_ind}).{fn_ext}' in inv_filenames:
+            return f'{fn_root}({f_ind}).{fn_ext}'
+        f_ind += 1

qcrbox_frontend/qcrbox/views/datasets.py

@@ -225,8 +225,15 @@ def visualise(request, dataset_id):
 
     # Get host name without port, manually prepend http:// to stop django
     # treating this as a relative URL
-    hostname = 'http://' + request.get_host().split(':')[0]
-    v_url = f'{hostname}:{settings.API_VISUALISER_PORT}/retrieve/{visualise_file_meta.backend_uuid}'
+    hostname = request.get_host().split(':')[0]
+
+    # Construct the visualiser domain URL
+    # Format: http://[app-slug].gui.[hostname]:[traefik-port]/
+    visualiser_domain = f'qcrbox-quality{settings.GUI_DOMAIN_PREFIX}{hostname}'
+
+    port_suffix = f':{settings.TRAEFIK_HTTP_PORT}' if settings.TRAEFIK_HTTP_PORT else ''
+
+    v_url = f'http://{visualiser_domain}{port_suffix}/retrieve/{visualise_file_meta.backend_uuid}'
     LOGGER.info(
         'Opening Visualiser at "%s"',
         v_url,

qcrbox_frontend/qcrbox/views/workflows.py

@@ -77,7 +77,11 @@ def initialise_workflow(request):
             ## Handle file loading here.
 
             # If user chose to load pre-existing file, fetch that file's ID
-            redirect_pk = request.POST['file']
+            mod_objs = models.FileMetaData.objects                      # pylint: disable=no-member
+            selected_file = mod_objs.get(pk=request.POST['file'])
+
+            # Find most recently created descendant of selected file
+            redirect_pk = selected_file.get_newest_descendant().pk
 
         else:
 
@@ -224,6 +228,10 @@ def workflow(request, file_id):
     else:
         context['app_session_id'] = None
 
+    # Pass Traefik config to template
+    context['traefik_port'] = settings.TRAEFIK_HTTP_PORT
+    context['gui_domain_prefix'] = settings.GUI_DOMAIN_PREFIX
+
     return render(request, 'workflow.html', context)
 
 

qcrbox_frontend/qcrbox/workflow.py

@@ -704,6 +704,9 @@ def handle_command(request, command, infile):
         output_dtypes = ('QCrBox.output_path','QCrBox.output_cif')
         for i in cps.filter(dtype__in=output_dtypes).values_list('name',flat=True):
             params[i] = params[i].replace('/','_')
+            print(params[i])
+            params[i] = utility.get_next_valid_filename(params[i])
+            print(params[i])
 
         # If the command corresponds to an interactive session, launch it
         if command.interactive: