diff --git a/src/InSillyCloWeb/assemblies/admin.py b/src/InSillyCloWeb/assemblies/admin.py
index 00babc05bdf75ee4b6a5514a31ce817c8e08277d..8faea5da85085b18408a80aefec6871fb9d76567 100644
--- a/src/InSillyCloWeb/assemblies/admin.py
+++ b/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",)
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index 46546f89bab49ba8bb483e04c00740245ff7fbd7..ab336f3247bd5a1039e22e61bb9724da83672a40 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):
@@ -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:
diff --git a/src/InSillyCloWeb/assemblies/templates/assemblies/simulator_results.html b/src/InSillyCloWeb/assemblies/templates/assemblies/simulator_results.html
new file mode 100644
index 0000000000000000000000000000000000000000..424f371cd0f8b4d1013b1429b15ca3f761941860
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/simulator_results.html
@@ -0,0 +1,35 @@
+{% 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
diff --git a/src/InSillyCloWeb/assemblies/views.py b/src/InSillyCloWeb/assemblies/views.py
index 641be61ee6032a6ad908c28f75be67a50a09a6a6..7c6ed1998fa60fda94101638a03ee7795cb76962 100644
--- a/src/InSillyCloWeb/assemblies/views.py
+++ b/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
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):