diff --git a/src/InSillyCloWeb/assemblies/admin.py b/src/InSillyCloWeb/assemblies/admin.py
index 0594370ee63ef80c7edeb1e74e3253117cb86e91..ca777ec808a8c5c02294d5f036f2f9eaca365304 100644
--- a/src/InSillyCloWeb/assemblies/admin.py
+++ b/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',
)
-
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index f319b3df26c701d6d0b4cd587dd0f8619c95a522..3e5c22a7c3edfc985400cbac100bc52b150261e8 100644
--- a/src/InSillyCloWeb/assemblies/models.py
+++ b/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)}'
diff --git a/src/InSillyCloWeb/assemblies/urls.py b/src/InSillyCloWeb/assemblies/urls.py
index dacaaedf7f4b4b1064d16c9456b42d0a4dc3d170..47aea977137b4bf766d72b55605941e5919e4c2d 100644
--- a/src/InSillyCloWeb/assemblies/urls.py
+++ b/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'),
diff --git a/src/InSillyCloWeb/assemblies/views.py b/src/InSillyCloWeb/assemblies/views.py
index ce4c963440fc218d098ffebab0471638b31a8523..56fa3b3f0d3dc6e1fa72cce0fcc7bde68b689378 100644
--- a/src/InSillyCloWeb/assemblies/views.py
+++ b/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,
+ ),
+ )
diff --git a/src/InSillyCloWeb/assemblies/wizard_views.py b/src/InSillyCloWeb/assemblies/wizard_views.py
index f0c7d1b3681667495d57e4500dc08cc79ef9e6e7..88ef0daa38d5af1a36851c331c221726ec28ae34 100644
--- a/src/InSillyCloWeb/assemblies/wizard_views.py
+++ b/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):