diff --git a/src/InSillyCloWeb/assemblies/admin.py b/src/InSillyCloWeb/assemblies/admin.py
index 35d97a12c4ece73a8b39ab7cf78790e665bdd22f..00babc05bdf75ee4b6a5514a31ce817c8e08277d 100644
--- a/src/InSillyCloWeb/assemblies/admin.py
+++ b/src/InSillyCloWeb/assemblies/admin.py
@@ -49,3 +49,40 @@ class UserAdmin(auth_admin.UserAdmin):
'is_staff',
'is_superuser',
)
+
+
+@admin.register(models.SimulatorJob)
+class JobAdmin(
+ ViewOnSiteModelAdmin,
+):
+ ordering = ("created_at",)
+ date_hierarchy = 'created_at'
+ list_display = (
+ 'uuid',
+ 'status',
+ 'created_at',
+ 'updated_at',
+ )
+ search_fields = (
+ 'uuid',
+ 'name',
+ )
+ actions = [
+ "re_run_job",
+ "delete_id_media_is_missing",
+ ]
+
+ @admin.action(description="Re-run task")
+ def re_run_job(self, request, queryset):
+ for job in queryset:
+ job.run_simulator()
+
+ @admin.action(description="Delete selected jobs if run_dir is missing/empty")
+ def delete_id_media_is_missing(self, request, queryset):
+ for job in queryset:
+ if not job.job_dir.exists():
+ job.delete()
+
+ def delete_queryset(self, request, queryset):
+ for o in queryset:
+ o.delete()
diff --git a/src/InSillyCloWeb/assemblies/forms.py b/src/InSillyCloWeb/assemblies/forms.py
index bd3cd4ca24398f51f194cf43342011a90ed3bdaf..4234daeba1655fe447ad3250bf674298799fa441 100644
--- a/src/InSillyCloWeb/assemblies/forms.py
+++ b/src/InSillyCloWeb/assemblies/forms.py
@@ -1,11 +1,12 @@
+import insillyclo.main
from crispy_forms import layout
from crispy_forms.helper import FormHelper
from django import forms
-from django.forms import modelformset_factory
+from django.forms import modelformset_factory, modelform_factory
from django.utils.safestring import mark_safe
from django.utils.translation import gettext as _
-from assemblies.models import Assembly, InputPart
+from assemblies.models import Assembly, InputPart, SimulatorJob
SEP_CHOICES = (
(".", "Dot"),
@@ -14,6 +15,74 @@ SEP_CHOICES = (
)
+class MultipleFileInput(forms.ClearableFileInput):
+ allow_multiple_selected = True
+
+
+class MultipleFileField(forms.FileField):
+ def __init__(self, *args, **kwargs):
+ kwargs.setdefault("widget", MultipleFileInput())
+ super().__init__(*args, **kwargs)
+
+ def clean(self, data, initial=None):
+ single_file_clean = super().clean
+ if isinstance(data, (list, tuple)):
+ result = [single_file_clean(d, initial) for d in data]
+ else:
+ result = single_file_clean(data, initial)
+ return result
+
+
+class SimulatorAssemblyTypeForm(forms.Form):
+ input_file = forms.FileField(
+ label="Load your assembly file",
+ required=True,
+ widget=forms.ClearableFileInput(attrs={'multiple': False}),
+ )
+
+
+class SimulatorDataForm(forms.Form):
+ sequence_file = forms.FileField(
+ label="Load your sequence file",
+ required=True,
+ widget=forms.ClearableFileInput(attrs={'multiple': False}),
+ )
+
+ db_ip_files = forms.FileField(
+ label="Load your db ip files",
+ required=True,
+ widget=forms.ClearableFileInput(attrs={'multiple': False}),
+ )
+
+
+class PCRModelForm(forms.ModelForm):
+ class Meta:
+ model = SimulatorJob
+ fields = ('pcr_pairs_str',)
+
+ primers_file = forms.FileField(
+ required=False,
+ label=_('Primers file'),
+ help_text=_('A CSV file where the header is \"primerId;sequence\".\nNote that the separator is \";\".'),
+ )
+
+ def save(self, commit=True):
+ instance: SimulatorJob = super().save(commit=commit)
+ if not commit or self.cleaned_data['primers_file'] is None:
+ return instance
+ output_fp = instance.job_dir / insillyclo.main.DEFAULT_CONCENTRATIONS_FILENAME
+ with open(output_fp, 'wb') as fh:
+ for chunk in self.cleaned_data['primers_file'].chunks():
+ fh.write(chunk)
+ return instance
+
+
+RestrictionEnzymeModelForm = modelform_factory(
+ model=SimulatorJob,
+ fields=('restriction_enzyme_gel',),
+)
+
+
class AssemblyForm(forms.ModelForm):
class Meta:
model = Assembly
diff --git a/src/InSillyCloWeb/assemblies/migrations/0007_simulatorjob.py b/src/InSillyCloWeb/assemblies/migrations/0007_simulatorjob.py
new file mode 100644
index 0000000000000000000000000000000000000000..08e83cff557b86f7f0d119c54adaeb2efc28fadb
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/migrations/0007_simulatorjob.py
@@ -0,0 +1,44 @@
+# Generated by Django 5.1.4 on 2025-04-17 08:17
+
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('assemblies', '0006_alter_inputpart_options_and_more'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='SimulatorJob',
+ fields=[
+ (
+ 'uuid',
+ models.UUIDField(
+ default=uuid.uuid4, editable=False, primary_key=True, serialize=False, unique=True
+ ),
+ ),
+ ('name', models.CharField(blank=True, max_length=255, null=True)),
+ (
+ 'status',
+ models.IntegerField(
+ choices=[
+ (None, '(Unknown)'),
+ (0, 'New'),
+ (1, 'Queued'),
+ (5, 'Fetching'),
+ (10, 'Running'),
+ (15, 'Done'),
+ (16, 'Error'),
+ (17, 'Canceled'),
+ ],
+ default=0,
+ ),
+ ),
+ ('created_at', models.DateTimeField(auto_now_add=True)),
+ ('updated_at', models.DateTimeField(auto_now=True)),
+ ],
+ ),
+ ]
diff --git a/src/InSillyCloWeb/assemblies/migrations/0008_simulatorjob_pcr_pairs_str_and_more.py b/src/InSillyCloWeb/assemblies/migrations/0008_simulatorjob_pcr_pairs_str_and_more.py
new file mode 100644
index 0000000000000000000000000000000000000000..395250ba8ce2d8c821fd940da126bc9b93ddc137
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/migrations/0008_simulatorjob_pcr_pairs_str_and_more.py
@@ -0,0 +1,33 @@
+# Generated by Django 5.1.8 on 2025-04-17 14:02
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('assemblies', '0007_simulatorjob'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='simulatorjob',
+ name='pcr_pairs_str',
+ field=models.TextField(
+ blank=True,
+ default='',
+ help_text='In a CSV-like format where you have one pair per line, the forward primer first, then the reverse primer.',
+ verbose_name='PCR Pairs to use',
+ ),
+ ),
+ migrations.AddField(
+ model_name='simulatorjob',
+ name='restriction_enzyme_gel',
+ field=models.TextField(
+ blank=True,
+ default='',
+ help_text='Enzyme used to produce digestion gel',
+ verbose_name='Restriction enzyme',
+ ),
+ ),
+ ]
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index d2dd6116506cb0d0dce7dceeb328b25080e56001..86de26538dc163613e27e3f1378a80a075c241ec 100644
--- a/src/InSillyCloWeb/assemblies/models.py
+++ b/src/InSillyCloWeb/assemblies/models.py
@@ -4,6 +4,11 @@ import re
from io import BytesIO
from tempfile import NamedTemporaryFile
from typing import List, Tuple
+import uuid
+import os
+import zipfile
+from pathlib import Path
+import shutil
from django.contrib.auth import models as auth_models
from django.contrib.sessions.models import Session
@@ -11,10 +16,15 @@ from django.db import models
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):
@@ -231,3 +241,146 @@ class Assembly(models.Model):
def get_absolute_url(self):
return reverse("assemblies:assembly-detail", args=[self.id])
+
+
+class JobStatus(models.IntegerChoices):
+ NEW = 0, _("New")
+ QUEUED = 1, _("Queued")
+ FETCHING = 5, _("Fetching")
+ RUNNING = 10, _("Running")
+ DONE = 15, _("Done")
+ ERROR = 16, _("Error")
+ CANCELED = 17, _("Canceled")
+
+ __empty__ = "(Unknown)"
+
+
+class SimulatorJob(models.Model):
+ #########################################################################
+ # Job attributs and parameters
+ #########################################################################
+ uuid = models.UUIDField(
+ primary_key=True,
+ default=uuid.uuid4,
+ editable=False,
+ unique=True,
+ )
+ name = models.CharField(
+ max_length=255,
+ null=True,
+ blank=True,
+ )
+ status = models.IntegerField(choices=JobStatus.choices, default=JobStatus.NEW)
+ created_at = models.DateTimeField(auto_now_add=True)
+ updated_at = models.DateTimeField(auto_now=True)
+
+ #########################################################################
+ # InSillyClo simulator attributs and parameters
+ #########################################################################
+ pcr_pairs_str = models.TextField(
+ default='',
+ blank=True,
+ verbose_name="PCR Pairs to use",
+ help_text="In a CSV-like format where you have one pair per line, "
+ "the forward primer first, then the reverse primer.",
+ )
+ restriction_enzyme_gel = models.TextField(
+ default='',
+ blank=True,
+ verbose_name="Restriction enzyme",
+ help_text="Enzyme used to produce digestion gel",
+ )
+
+ #########################################################################
+ # Function and methods
+ #########################################################################
+ def save(self, *args, **kwargs):
+ self.job_dir.mkdir(parents=True, exist_ok=True)
+
+ super().save(*args, **kwargs)
+
+ def add_design_to_dir(self, design_file):
+ file_name = os.path.join(self.job_dir, 'design_file.xlsx')
+
+ with open(file_name, 'wb+') as f:
+ for chunk in design_file.chunks():
+ f.write(chunk)
+
+ def add_gb_to_dir(self, gb_file):
+ if not os.path.isdir(self.genbank_dir):
+ os.mkdir(self.genbank_dir)
+
+ with zipfile.ZipFile(gb_file, 'r') as zip:
+ for member in zip.namelist():
+ 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:
+ shutil.copyfileobj(source, dest)
+
+ def add_db_ip_to_dir(self, db_ip_file):
+ if not os.path.isdir(self.dbip_dir):
+ os.mkdir(self.dbip_dir)
+
+ with zipfile.ZipFile(db_ip_file, 'r') as zip:
+ for member in zip.namelist():
+ 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:
+ return pathlib.Path(settings.MEDIA_ROOT) / 'jobs' / str(self.uuid)
+
+ @property
+ def uuid_short(self):
+ return str(self.uuid)[:8]
+
+ @property
+ def genbank_dir(self):
+ return os.path.join(self.job_dir, 'genbank')
+
+ @property
+ 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 delete(self, *args, **kwargs):
+ try:
+ shutil.rmtree(self.job_dir)
+ except OSError as e:
+ print("Error: %s - %s." % (e.filename, e.strerror))
+ return super().delete(*args, **kwargs)
+
+ def get_absolute_url(self):
+ return reverse("assemblies:simulator-detail", args=[self.uuid])
+
+ def __str__(self):
+ return f'{str(self.uuid)[:8]} - {str(self.created_at)}'
diff --git a/src/InSillyCloWeb/assemblies/templates/assemblies/index.html b/src/InSillyCloWeb/assemblies/templates/assemblies/index.html
index be1d4ae4b4090020fc827c38faa99c1fcf5b4f10..43b1a1e96bd19fe06b9b5567065f56ea302aeaa1 100644
--- a/src/InSillyCloWeb/assemblies/templates/assemblies/index.html
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/index.html
@@ -29,7 +29,7 @@
{%trans "Assembly simulator subtitle"%}
</div>
<div class="ma-body">
- <a role="button" class="btn btn-auto">
+ <a role="button" class="btn btn-auto" href="{% url 'assemblies:simulator-create' %}">
{%trans "Start assembly simulator"%}
</a>
</div>
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/templates/assemblies/simulator_summary.html b/src/InSillyCloWeb/assemblies/templates/assemblies/simulator_summary.html
new file mode 100644
index 0000000000000000000000000000000000000000..3ac70fb832f72832e498ac89271b6b47d9d3d269
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/simulator_summary.html
@@ -0,0 +1,108 @@
+{% 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 %}{{ title }}{% endblock %}
+{% block page_title %}{{ page_title|default:title }}{% 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%}">
+ <form method="post" enctype="multipart/form-data">
+ {% csrf_token %}
+ {{ wizard.form.media }}
+ {{ wizard.management_form }}
+
+ {%if form_title %}
+ <h3 class="card-header {{form_title_class}}">
+ {{form_title}}
+ </h3>
+ {%endif%}
+ {%if step_message %}
+ <div class="card-body">
+ {{ step_message|default:"" }}
+ </div>
+ {%endif%}
+
+ <div class="row mb-4">
+ <div class="col-6">
+ <div class="card">
+ <div class="card-header">Input plasmid</div>
+ <table class="table table-striped">
+ </table>
+ </div>
+ </div>
+
+ <div class="col-6">
+ <div class="card">
+ <div class="card-header">Plasmid repository</div>
+ <table class="table table-striped">
+ </table>
+ </div>
+ </div>
+ </div>
+
+ <div class="card">
+ <div class="card-header">Output plasmid</div>
+ <table class="table table-striped">
+ <thead>
+ <tr>
+ <th scope="col">pID</th>
+ <th scope="col">Output part type</th>
+ <th scope="col">Input plasmid 1</th>
+ <th scope="col">Input plasmid 2</th>
+ <th scope="col">Input plasmid 3</th>
+ <th scope="col">Input plasmid 4</th>
+ <th scope="col">Input plasmid 5</th>
+ <th scope="col">Input plasmid 6</th>
+ <th scope="col">Input plasmid 7</th>
+ <th scope="col">Input plasmid 8</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for plasmid in plasmids %}
+ <tr>
+ <td>{{ plasmid.plasmid_id }}</td>
+ <td>{{ plasmid.output_type }}</td>
+ {% for part in plasmid.parts %}
+ <td colspan="{{ part.1.part_types|length }}">{{ part.0 }}</td>
+ {% endfor %}
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+
+ <div class="text-center mt-3">
+ <a class="" role="button" href="../?reset">
+ {% trans "clear form" %}
+ </a>
+ </div>
+ <button class=" btn btn-auto {{btn_classes}}" name="submit" type="submit">
+ {{submit_text|default:"OK" }}
+ </button>
+ </form>
+</div>
+{% endblock content %}
\ No newline at end of file
diff --git a/src/InSillyCloWeb/assemblies/templates/assemblies/simulatorjob_detail.html b/src/InSillyCloWeb/assemblies/templates/assemblies/simulatorjob_detail.html
new file mode 100644
index 0000000000000000000000000000000000000000..009b9939a5ded555bf6ef8b02a4e2d9eefef71f1
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/simulatorjob_detail.html
@@ -0,0 +1,17 @@
+{% extends "assemblies/base.html" %}
+{% load assemblies_tags %}
+{% load i18n %}
+
+
+{% block title %}Job: {{object.uuid_short}}{% endblock %}
+{% block page_title %}Assembly simulator{% endblock %}
+{% block page_sub_title %}Assembly simulator{% endblock %}
+
+{%block content %}
+<h6 class="col-12 text-center">
+ Run on {{object.updated_at}}
+</h6>
+<h1 class="col-12 text-center">
+ TODO
+</h1>
+{%endblock content %}
\ No newline at end of file
diff --git a/src/InSillyCloWeb/assemblies/templates/assemblies/wizard_view_form_simulator_data.html b/src/InSillyCloWeb/assemblies/templates/assemblies/wizard_view_form_simulator_data.html
new file mode 100644
index 0000000000000000000000000000000000000000..8ea79ca93a5360732135f5d71f9eaf7cbdca7cd2
--- /dev/null
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/wizard_view_form_simulator_data.html
@@ -0,0 +1,116 @@
+{% 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 %}{{ title }}{% endblock %}
+{% block page_title %}{{ page_title|default:title }}{% 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%}">
+ <form method="post" enctype="multipart/form-data">
+ {% csrf_token %}
+ {{ wizard.form.media }}
+ {{ wizard.management_form }}
+
+ {%if form_title %}
+ <h3 class="card-header {{form_title_class}}">
+ {{form_title}}
+ </h3>
+ {%endif%}
+ {%if step_message %}
+ <div class="card-body">
+ {{ step_message|default:"" }}
+ </div>
+ {%endif%}
+
+ <div class="card card-auto mb-4">
+ <div class="card-body">
+ Name of the assembly: {{ assembly.name }}
+ <hr>
+ Separator: {{ assembly.separator }}
+ Enzyme: {{ assembly.enzyme }}
+ </div>
+ </div>
+
+ {% if wizard.form.forms is not None %}
+ {{ wizard.form.management_form }}
+ <div class="card card-auto mb-4">
+ <div class="card-body">
+ {% for form in wizard.form.forms %}
+ <div class="formset-row" data-formset-prefix="{{ wizard.form.prefix }}">
+ {% crispy form %}
+ {% if formset.can_delete %}
+ {{ form.DELETE }}
+ {% endif %}
+ </div>
+ {% endfor %}
+ {% if can_add_new != False %}
+ <div class="formset-new-item pb-4 text-center">
+ <input type="button"
+ class="btn btn-auto"
+ value="{{add_new_item_to_formset_text}}"/>
+ </div>
+ {% endif %}
+ </div>
+ </div>
+ {% else %}
+ {% crispy wizard.form %}
+ {% endif %}
+ <div class="text-center mt-3">
+ <a class="" role="button" href="../?reset">
+ {% trans "clear form" %}
+ </a>
+ </div>
+ <div class="text-center mt-5">
+ {% if wizard.steps.prev and not hide_step_button%}
+ {% if not hide_first_step_button%}
+ <a class="btn btn-secondary" role="button" href="../{{ wizard.steps.first }}">
+ <i class="bi-chevron-double-left"></i>
+ <span class="d-none d-sm-inline">{% trans "first step" %}</span>
+ </a>
+ {% endif %}
+ <a class="btn btn-secondary" role="button" href="../{{ wizard.steps.prev }}">
+ <i class="bi-chevron-left"></i>
+ <span class="d-none d-sm-inline">{% trans "prev step" %}</span>
+ </a>
+ {% endif %}
+ <button class=" btn btn-auto {{btn_classes}}" name="submit" type="submit">
+ {{submit_text|default:"OK" }}
+ </button>
+ </div>
+ </form>
+ <div class="d-none empty_form" data-prefix="{{wizard.form.prefix}}">
+ {% block emptyform %}
+ {% if wizard.form.forms is not None %}
+ <div class="formset-row" data-formset-prefix="{{ wizard.form.prefix }}">
+ {% crispy wizard.form.empty_form %}
+ </div>
+ {% endif %}
+ {% endblock emptyform%}
+ </div>
+</div>
+{% endblock %}
+
diff --git a/src/InSillyCloWeb/assemblies/urls.py b/src/InSillyCloWeb/assemblies/urls.py
index 4790a451d35c5cc602180f7d4185a8ab12ad9757..c35bd48462323108cd696c597131f6d945065663 100644
--- a/src/InSillyCloWeb/assemblies/urls.py
+++ b/src/InSillyCloWeb/assemblies/urls.py
@@ -7,6 +7,9 @@ designer_wizard = wizard_views.AssemblyDesignerNotProtected.as_view(
url_name='assemblies:designer-create-step',
)
+simulator_wizard = wizard_views.AssemblySimulatorNotProtected.as_view(
+ url_name='assemblies:simulator-create-step',
+)
designer_edition_wizard = wizard_views.AssemblyDesignerEdition.as_view(
url_name='assemblies:designer-edit-step',
)
@@ -62,6 +65,16 @@ urlpatterns = [
path('', views.index, name='assembly-simulator'),
path('assembly/', views.AssemblyListView.as_view(), name='assembly-list'),
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/<slug:uuid>/', views.JobSimulatorResult.as_view(), name='simulator-detail'),
+ path('assembly-simulator/<uuid:uuid>/results/', views.JobSimulatorResult.as_view(), name='simulator-results'),
+ path('assembly-simulator/<slug:uuid>/pcr-edit/', views.JobPCREdit.as_view(), name='simulator-pcr-edit'),
+ path(
+ 'assembly-simulator/<slug:uuid>/enzyme-edit/',
+ views.JobRestrictionEnzymeEdit.as_view(),
+ name='simulator-enzyme-edit',
+ ),
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/utils.py b/src/InSillyCloWeb/assemblies/utils.py
index 3ca48c5857efda6fa98efc11cf0237f2005d1f07..b2c1d2a023ff4270977beb7f736ba961d9507e82 100644
--- a/src/InSillyCloWeb/assemblies/utils.py
+++ b/src/InSillyCloWeb/assemblies/utils.py
@@ -1,4 +1,5 @@
import os
+import glob
from zipfile import ZipFile
from Bio import SeqIO
from Bio.Seq import Seq
@@ -56,3 +57,17 @@ def get_fragments(part, enzyme=None, site_for='GGTCTC', site_rev='GAGACC', inter
(out_part, in_part) = get_in_out_part(reorder_seq(seq, site_for), site_rev)
return get_sens_antisens(in_part, out_part, inter_s)
+
+
+def get_files(path, extension, recursive=False):
+ """
+ A generator of filepaths for each file into path with the target extension.
+ If recursive, it will loop over subfolders as well.
+ """
+ if not recursive:
+ for file_path in glob.iglob(path + "/*." + extension):
+ yield file_path
+ else:
+ for root, dirs, files in os.walk(path):
+ for file_path in glob.iglob(root + "/*." + extension):
+ yield file_path
diff --git a/src/InSillyCloWeb/assemblies/views.py b/src/InSillyCloWeb/assemblies/views.py
index ce4c963440fc218d098ffebab0471638b31a8523..63f83a511ab6650a7dbd0dc0c69079bccb7ae867 100644
--- a/src/InSillyCloWeb/assemblies/views.py
+++ b/src/InSillyCloWeb/assemblies/views.py
@@ -1,13 +1,15 @@
import traceback
+from abc import ABC, abstractmethod
from io import BytesIO
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
+from django.views.generic import ListView, DetailView, View, DeleteView, UpdateView
from django.views.generic.detail import SingleObjectMixin
from . import mixins
@@ -108,3 +110,64 @@ class AssemblyDeleteView(
def form_valid(self, form):
messages.info(self.request, _(f"Assembly {self.object} deleted"))
return super().form_valid(form)
+
+
+class JobSimulatorResult(DetailView):
+ model = models.SimulatorJob
+ slug_field = 'uuid'
+ slug_url_kwarg = 'uuid'
+
+ template_name = "assemblies/simulator_results.html"
+
+ def get_context_data(self, **kwargs):
+ context = super().get_context_data(**kwargs)
+ context['simulation'] = self.object
+ return context
+
+
+class SimulatorJobEdit(
+ ABC,
+ UpdateView,
+):
+ model = models.SimulatorJob
+ slug_field = 'uuid'
+ slug_url_kwarg = 'uuid'
+ template_name = "assemblies/form_host.html"
+
+ def get_form(self, form_class=None):
+ form = super().get_form()
+ if not hasattr(form, 'helper'):
+ form.helper = crispy_forms.helper.FormHelper()
+ form.helper.form_tag = False
+ return form
+
+ def form_valid(self, form):
+ self.object.run_insillyclo(self.request)
+ return super().form_valid(form)
+
+ def get_context_data(self, **kwargs):
+ context = super().get_context_data(**kwargs)
+ context["title"] = self.get_title()
+ return context
+
+ @abstractmethod
+ def get_title(self):
+ pass
+
+
+class JobPCREdit(
+ SimulatorJobEdit,
+):
+ form_class = forms.PCRModelForm
+
+ def get_title(self):
+ return _("PCR primers to use for gel simulation")
+
+
+class JobRestrictionEnzymeEdit(
+ SimulatorJobEdit,
+):
+ form_class = forms.RestrictionEnzymeModelForm
+
+ def get_title(self):
+ return _("Restriction enzyme to use for gel simulation")
diff --git a/src/InSillyCloWeb/assemblies/wizard_views.py b/src/InSillyCloWeb/assemblies/wizard_views.py
index b65ec445d4cfae4e01e89339da93bb8f6ea5147e..88ef0daa38d5af1a36851c331c221726ec28ae34 100644
--- a/src/InSillyCloWeb/assemblies/wizard_views.py
+++ b/src/InSillyCloWeb/assemblies/wizard_views.py
@@ -1,15 +1,119 @@
+import insillyclo.parser
from crispy_forms.helper import FormHelper
from django.contrib.sessions.models import Session
from django.db import transaction
-from django.shortcuts import redirect
+from django.shortcuts import render, redirect
+from django.conf import settings
from django.template.loader import render_to_string
from django.urls import reverse
from django.utils.safestring import mark_safe
from django.utils.translation import gettext as _
from django.views.generic.detail import SingleObjectMixin
from formtools.wizard import views as wizard_views
+from django.core.files.storage import FileSystemStorage
+
+import pathlib
+
+import insillyclo
+import insillyclo.simulator
+import os
from assemblies import forms, models, mixins
+from .models import SimulatorJob
+from .utils import get_files
+from .insillyclo_impl import InSillyCloDjangoMessageObserver
+
+
+class AssemblySimulatorNotProtected(wizard_views.NamedUrlSessionWizardView):
+ file_storage = FileSystemStorage(location=os.path.join(settings.MEDIA_ROOT, 'assemblytype'))
+
+ form_list = [
+ ("Intro", forms.AgreeForm),
+ ("InputFile", forms.SimulatorAssemblyTypeForm),
+ ("Data", forms.SimulatorDataForm),
+ ("Summary", forms.AgreeForm),
+ ]
+
+ TEMPLATES = {
+ "Intro": 'wizard_view_form_host.html',
+ "InputFile": 'wizard_view_form_host.html',
+ "Data": 'assemblies/wizard_view_form_simulator_data.html',
+ "Summary": 'assemblies/simulator_summary.html',
+ }
+
+ is_edition = False
+ condition_dict = dict()
+
+ def get_context_data(self, form, step=None, **kwargs):
+ context = super().get_context_data(form=form, step=step, **kwargs)
+ context["submit_text"] = _("Next")
+ context["title"] = _("SimulatorDesignerWizard.title")
+ context["custom_css_width"] = "col-12 context-simulator"
+ context["form_title_class"] = "text-primary"
+ context["custom_container_class"] = "context-simulator"
+ context["hide_first_step_button"] = True
+ if step is None:
+ step = self.steps.current
+ if step == "Intro":
+ context["form_title_class"] = "h1"
+ context["title"] = ""
+ context["form_title"] = _("SimulatorDesignerWizard.Intro.form_title")
+ context["step_message"] = mark_safe(_("SimulatorDesignerWizard.Intro.step_message"))
+ elif step == "Data":
+ context['assembly'], context["plasmids"] = insillyclo.parser.parse_assembly_and_plasmid_from_template(
+ self.get_cleaned_data_for_step("InputFile")["input_file"],
+ input_part_factory=insillyclo.models.InputPartDataClassFactory(),
+ assembly_factory=insillyclo.models.AssemblyDataClassFactory(),
+ plasmid_factory=insillyclo.models.PlasmidDataClassFactory(),
+ observer=InSillyCloDjangoMessageObserver,
+ )
+ elif step == "Summary":
+ context["submit_text"] = _("Run assembly")
+ context["form_title"] = _("SimulatorDesignerWizard.Summary.form_title")
+
+ context['assembly'], context["plasmids"] = insillyclo.parser.parse_assembly_and_plasmid_from_template(
+ self.get_cleaned_data_for_step("InputFile")["input_file"],
+ input_part_factory=insillyclo.models.InputPartDataClassFactory(),
+ assembly_factory=insillyclo.models.AssemblyDataClassFactory(),
+ plasmid_factory=insillyclo.models.PlasmidDataClassFactory(),
+ observer=InSillyCloDjangoMessageObserver,
+ )
+ return context
+
+ def get_template_names(self):
+ return [self.TEMPLATES[self.steps.current]]
+
+ def get_form_initial(self, step):
+ return super().get_form_initial(step)
+
+ def get_form_kwargs(self, step=None):
+ d = super().get_form_kwargs(step=step)
+ return d
+
+ def get_form(self, *args, **kwargs):
+ form = super().get_form(*args, **kwargs)
+ if not hasattr(form, 'helper'):
+ helper = FormHelper()
+ helper.form_tag = False
+ form.helper = helper
+ return form
+
+ def done(self, form_list, form_dict=None, **kwargs):
+
+ sjob = SimulatorJob.objects.create()
+ sjob.save()
+
+ 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"],
+ )
+
+ return redirect('assemblies:simulator-results', uuid=sjob.uuid)
class AssemblyDesignerNotProtected(wizard_views.NamedUrlSessionWizardView):
diff --git a/src/InSillyCloWeb/insillycloweb/settings.py b/src/InSillyCloWeb/insillycloweb/settings.py
index cb7b56ba4b36153cdcc0f2c7e500e1745192e706..be6e99c3a26589c3abf7f6cdeb2c31f851c0613c 100644
--- a/src/InSillyCloWeb/insillycloweb/settings.py
+++ b/src/InSillyCloWeb/insillycloweb/settings.py
@@ -12,11 +12,9 @@ https://docs.djangoproject.com/en/5.1/ref/settings/
import logging
import os
-import os
-from pathlib import Path
from pathlib import Path
from socket import gethostname, gethostbyname
-from socket import gethostname, gethostbyname
+
from decouple import config