put call to insillyclo cli inside simulatorjob model

src/InSillyCloWeb/assemblies/admin.py

@@ -37,6 +37,7 @@ class InputPartAdmin(ViewOnSiteModelAdmin, admin.ModelAdmin):
         'is_in_output_plasmid_name',
     )
 
+
 @admin.register(models.SimulatorJob)
 class SimulatorJobAdmin(ViewOnSiteModelAdmin, admin.ModelAdmin):
     date_hierarchy = 'created_at'
@@ -54,4 +55,3 @@ class UserAdmin(auth_admin.UserAdmin):
         'is_staff',
         'is_superuser',
     )
-

src/InSillyCloWeb/assemblies/models.py

@@ -17,11 +17,14 @@ from django.db.models.functions import Upper
 from django.urls import reverse
 from django.utils.translation import gettext_lazy as _
 from django.conf import settings
+from .insillyclo_impl import InSillyCloDjangoMessageObserver
 
 
 import insillyclo.data_source
 import insillyclo.models
 import insillyclo.template_generator
+import insillyclo
+import insillyclo.simulator
 
 
 class UserManager(auth_models.UserManager):
@@ -269,11 +272,11 @@ class SimulatorJob(models.Model):
     updated_at = models.DateTimeField(auto_now=True)
 
     def save(self, *args, **kwargs):
-        if not self.uuid:
-            super().save(*args, **kwargs)
-
         if not os.path.isdir(self.job_dir):
             os.mkdir(self.job_dir)
+            os.mkdir(self.results_dir)
+
+        super().save(*args, **kwargs)
 
     def add_design_to_dir(self, design_file):
         file_name = os.path.join(self.job_dir, 'design_file.xlsx')
@@ -288,7 +291,7 @@ class SimulatorJob(models.Model):
 
         with zipfile.ZipFile(gb_file, 'r') as zip:
             for member in zip.namelist():
-                if Path(member).suffix == '.gb':
+                if Path(member).suffix == '.gb' and not Path(member).stem.startswith('.'):
                     source = zip.open(member)
                     new_filename = os.path.join(self.genbank_dir, Path(member).stem + '.gb')
                     with open(new_filename, 'wb') as dest:
@@ -300,10 +303,33 @@ class SimulatorJob(models.Model):
 
         with zipfile.ZipFile(db_ip_file, 'r') as zip:
             for member in zip.namelist():
-                source = zip.open(member)
-                new_filename = os.path.join(self.dbip_dir, Path(member).stem + Path(member).suffix)
-                with open(new_filename, 'wb') as dest:
-                    shutil.copyfileobj(source, dest)
+                if not Path(member).stem.startswith('.'):
+                    source = zip.open(member)
+                    new_filename = os.path.join(self.dbip_dir, Path(member).stem + Path(member).suffix)
+                    with open(new_filename, 'wb') as dest:
+                        shutil.copyfileobj(source, dest)
+
+    def run_insillyclo(self, request):
+        return insillyclo.simulator.compute_all(
+            observer=InSillyCloDjangoMessageObserver(
+                request=request,
+                debug=False,
+                fail_on_error=False,
+            ),
+            input_template_filled=os.path.join(self.job_dir, 'design_file.xlsx'),
+            input_parts_files=self.db_ip_files,
+            gb_plasmids=self.genbank_files,
+            output_dir=Path(self.results_dir),
+            data_source=insillyclo.data_source.DataSourceHardCodedImplementation(),
+        )
+
+    @property
+    def db_ip_files(self):
+        return [os.path.join(self.dbip_dir, file) for file in os.listdir(self.dbip_dir)]
+
+    @property
+    def genbank_files(self):
+        return [Path(os.path.join(self.genbank_dir, file)) for file in os.listdir(self.genbank_dir)]
 
     @property
     def job_dir(self):
@@ -317,5 +343,9 @@ class SimulatorJob(models.Model):
     def dbip_dir(self):
         return os.path.join(self.job_dir, 'db_ip')
 
+    @property
+    def results_dir(self):
+        return os.path.join(self.job_dir, 'results')
+
     def __str__(self):
         return f'{str(self.uuid)[:8]} - {str(self.created_at)}'

src/InSillyCloWeb/assemblies/urls.py

@@ -67,6 +67,7 @@ urlpatterns = [
     path('assembly/<int:pk>/', views.AssemblyDetailView.as_view(), name='assembly-detail'),
     path('assembly-simulator/create/<str:step>/', simulator_wizard, name='simulator-create-step'),
     path('assembly-simulator/create/', simulator_wizard, name='simulator-create'),
+    path('assembly-simulator/<uuid:uuid>/results/', views.simulator_results, name='simulator-results'),
     path('assembly/<int:pk>/download/', views.AssemblyDetailDownloadView.as_view(), name='assembly-download'),
     path('assembly/<int:pk>/delete/', views.AssemblyDeleteView.as_view(), name='assembly-delete'),
     path('fragment', views.show_fragment, name='fragment'),

src/InSillyCloWeb/assemblies/views.py

@@ -4,7 +4,7 @@ from typing import Tuple
 
 from django.contrib import messages
 from django.http import HttpResponse
-from django.shortcuts import render, redirect
+from django.shortcuts import render, redirect, get_object_or_404
 from django.urls import reverse_lazy
 from django.utils.translation import gettext_lazy as _
 from django.views.generic import ListView, DetailView, View, DeleteView
@@ -108,3 +108,20 @@ class AssemblyDeleteView(
     def form_valid(self, form):
         messages.info(self.request, _(f"Assembly {self.object} deleted"))
         return super().form_valid(form)
+
+
+def simulator_results(request, uuid):
+    """
+    This view is used to display the results of the assembly simulation.
+    """
+    simulation = get_object_or_404(models.SimulatorJob, uuid=uuid)
+
+    simulation.run_insillyclo(request)
+
+    return render(
+        request,
+        template_name='assemblies/simulator_results.html',
+        context=dict(
+            simulation=simulation,
+        ),
+    )

src/InSillyCloWeb/assemblies/wizard_views.py

@@ -20,8 +20,8 @@ import os
 
 from assemblies import forms, models, mixins
 from .models import SimulatorJob
-from .insillyclo_impl import InSillyCloDjangoMessageObserver
 from .utils import get_files
+from .insillyclo_impl import InSillyCloDjangoMessageObserver
 
 
 class AssemblySimulatorNotProtected(wizard_views.NamedUrlSessionWizardView):
@@ -103,38 +103,17 @@ class AssemblySimulatorNotProtected(wizard_views.NamedUrlSessionWizardView):
         sjob = SimulatorJob.objects.create()
         sjob.save()
 
-        print(sjob.uuid)
-
-        sjob.add_design_to_dir(self.get_cleaned_data_for_step("InputFile")["input_file"])
-
-        sjob.add_gb_to_dir(self.get_cleaned_data_for_step("Data")["sequence_file"])
-
-        sjob.add_db_ip_to_dir(self.get_cleaned_data_for_step("Data")["db_ip_files"])
-
-        """
-        results = insillyclo.simulator.compute_all(
-            observer = InSillyCloDjangoMessageObserver(
-                request=self.request,
-                debug=False,
-                fail_on_error=False,
-            ),
-            input_template_filled = input_template,
-            input_parts_files = db_ip_files,
-            gb_plasmids = gb_files,
-            output_dir = pathlib.Path(output_directory),
-            data_source = insillyclo.data_source.DataSourceHardCodedImplementation(),
+        sjob.add_design_to_dir(
+            self.get_cleaned_data_for_step("InputFile")["input_file"],
         )
-
-        print(results)
-        """
-
-        return render(
-            self.request,
-            'simple_message_page.html',
-            context=dict(
-                sub_message="test results",
-            ),
+        sjob.add_gb_to_dir(
+            self.get_cleaned_data_for_step("Data")["sequence_file"],
         )
+        sjob.add_db_ip_to_dir(
+            self.get_cleaned_data_for_step("Data")["db_ip_files"],
+        )
+
+        return redirect('assemblies:simulator-results', uuid=sjob.uuid)
 
 
 class AssemblyDesignerNotProtected(wizard_views.NamedUrlSessionWizardView):