Merge branch 'simulator' into edit-view-job

src/InSillyCloWeb/assemblies/admin.py

@@ -38,6 +38,12 @@ class InputPartAdmin(ViewOnSiteModelAdmin, admin.ModelAdmin):
     )
 
 
+@admin.register(models.SimulatorJob)
+class SimulatorJobAdmin(ViewOnSiteModelAdmin, admin.ModelAdmin):
+    date_hierarchy = 'created_at'
+    search_fields = ('uuid',)
+
+
 @admin.register(models.User)
 class UserAdmin(auth_admin.UserAdmin):
     ordering = ("email",)

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):
@@ -292,11 +295,11 @@ class SimulatorJob(models.Model):
     # Function and methods
     #########################################################################
     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')
@@ -311,7 +314,7 @@ 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:
@@ -323,10 +326,33 @@ 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) -> pathlib.Path:
@@ -344,8 +370,9 @@ class SimulatorJob(models.Model):
     def dbip_dir(self):
         return os.path.join(self.job_dir, 'db_ip')
 
-    def run_simulator(self):
-        pass
+    @property
+    def results_dir(self):
+        return os.path.join(self.job_dir, 'results')
 
     def delete(self, *args, **kwargs):
         try:

src/InSillyCloWeb/assemblies/templates/assemblies/simulator_results.html

+{% extends "base.html" %}
+{% load crispy_forms_tags %}
+{% load sstatic %}
+{% load i18n %}
+
+{% block extra_js %}
+{{block.super}}
+{% if extra_js_file %}
+<script src="{% sstatic extra_js_file %}"></script>
+{% endif%}
+{% for extra_js_file in extra_js_files %}
+<script src="{% sstatic extra_js_file %}"></script>
+{% endfor%}
+{% endblock %}
+
+{% block extra_css %}
+{{block.super}}
+{% if extra_css_file %}
+<link rel="stylesheet" href="{% sstatic extra_css_file %}"/>
+{% endif%}
+{% for extra_css_file in extra_css_files %}
+<link rel="stylesheet" href="{% sstatic extra_css_file %}"/>
+{% endfor%}
+{% endblock %}
+
+{% block container_class %}{{block.super}} {{ custom_container_class }}{% endblock %}
+
+{% block title %}Results{% endblock %}
+{% block page_title %}Results{% endblock %}
+
+{% block content %}
+<div class="formset-container col-12 col-xs-12 {%if custom_css_width %}{{custom_css_width}}{%else%}{%if not medium_width%}col-sm-10 col-sm-offset-1 offset-sm-1 col-md-8 col-md-offset-2 offset-md-2 col-lg-6 col-lg-offset-3 offset-lg-3 col-xl-4 col-xl-offset-4 offset-xl-4 col-xxl-2 col-xxl-offset-5{%endif%}{%if medium_width%}col-md-10 col-md-offset-1 offset-md-1 col-lg-8 col-lg-offset-2 offset-lg-2 col-xl-6 col-xl-offset-3 offset-xl-3 col-xxl-4 col-xxl-offset-4 col-xxxl-2 col-xxxl-offset-5{%endif%}{%endif%}">
+    {{ simulation.uuid }}
+</div>
+{% endblock content %}
\ No newline at end of file

src/InSillyCloWeb/assemblies/views.py

@@ -6,7 +6,7 @@ from typing import Tuple
 import crispy_forms.helper
 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, UpdateView

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):