diff --git a/src/InSillyCloWeb/assemblies/forms.py b/src/InSillyCloWeb/assemblies/forms.py
index 4234daeba1655fe447ad3250bf674298799fa441..55ce365fbd577d9dcf90940d6c255a18b3706ed3 100644
--- a/src/InSillyCloWeb/assemblies/forms.py
+++ b/src/InSillyCloWeb/assemblies/forms.py
@@ -59,18 +59,30 @@ class PCRModelForm(forms.ModelForm):
class Meta:
model = SimulatorJob
fields = ('pcr_pairs_str',)
+ widgets = {'pcr_pairs_str': forms.Textarea(attrs={'rows': 2})}
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 \";\".'),
+ # widget=forms.ClearableFileInput(attrs={'multiple': False}),
)
+ # def __init__(self, *args, **kwargs):
+ # # files=kwargs.pop('files', dict())
+ # initial=kwargs.pop('initial', dict())
+ # instance = kwargs.pop('instance', None)
+ # if instance:
+ # # files['primer_file'] =instance.primer_file
+ # initial['primers_file'] =instance.primer_file
+ #
+ # super().__init__(initial=initial,instance=instance,*args, **kwargs)
+
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
+ output_fp = instance.job_dir / insillyclo.main.DEFAULT_PCR_FILENAME
with open(output_fp, 'wb') as fh:
for chunk in self.cleaned_data['primers_file'].chunks():
fh.write(chunk)
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index 3ab9c88f02a82f4fca6e82c618948fc792ff06ec..d22d772e95c307d74073bb63e73255a738bb134f 100644
--- a/src/InSillyCloWeb/assemblies/models.py
+++ b/src/InSillyCloWeb/assemblies/models.py
@@ -1,6 +1,7 @@
import json
import pathlib
import re
+from functools import cached_property
from io import BytesIO
from tempfile import NamedTemporaryFile
from typing import List, Tuple
@@ -21,6 +22,7 @@ from .insillyclo_impl import InSillyCloDjangoMessageObserver
import insillyclo.data_source
+import insillyclo.main
import insillyclo.models
import insillyclo.template_generator
import insillyclo
@@ -294,6 +296,28 @@ class SimulatorJob(models.Model):
#########################################################################
# Function and methods
#########################################################################
+
+ # PCR
+ @property
+ def pcr_pairs(self) -> List[Tuple[str, str]]:
+ if not self.pcr_pairs_str:
+ return []
+ for line in self.pcr_pairs_str.splitlines():
+ forward, rev = line.split(',')
+ yield forward, rev
+
+ @property
+ def primer_file(self) -> pathlib.Path:
+ return self.job_dir / insillyclo.main.DEFAULT_PCR_FILENAME
+
+ @cached_property
+ def pcr_image_url(self) -> str:
+ file = self.results_dir / 'pcr.png'
+ if file.exists():
+ return settings.MEDIA_URL / file.relative_to(settings.MEDIA_ROOT)
+ return ''
+
+ # Others
def save(self, *args, **kwargs):
self.job_dir.mkdir(parents=True, exist_ok=True)
self.results_dir.mkdir(parents=True, exist_ok=True)
@@ -344,6 +368,8 @@ class SimulatorJob(models.Model):
gb_plasmids=self.genbank_dir.glob('**/*.gb'),
output_dir=self.results_dir,
data_source=insillyclo.data_source.DataSourceHardCodedImplementation(),
+ primers_file=self.primer_file,
+ primer_id_pairs=list(self.pcr_pairs),
)
@property
diff --git a/src/InSillyCloWeb/assemblies/static/theme.scss b/src/InSillyCloWeb/assemblies/static/theme.scss
index ad1d00e79693b906d39fad6cf67888277f9fd10e..a520313c33977d3bed0fcc0b1b76accf0f3dbf6a 100644
--- a/src/InSillyCloWeb/assemblies/static/theme.scss
+++ b/src/InSillyCloWeb/assemblies/static/theme.scss
@@ -534,6 +534,13 @@ $nav-pills-link-active-bg:$secondary;
text-transform: uppercase !important;
font-weight: $headings-font-weight;
}
+.context-simulator .form-label {
+ color: $color-tarocco;
+}
+.border-simulator {
+ --#{$prefix}border-color: #{$color-tarocco};
+ --#{$prefix}modal-header-border-color: #{$color-tarocco};
+}
legend>.asteriskField,
label>.asteriskField{
color:$color-orange-crayola;
@@ -635,4 +642,31 @@ label>.asteriskField{
background-position-x: -10vw;
background-position-y: -5vw;
background-size: 50vw;
+}
+.card-result{
+ border-color: $simulator;
+}
+.card-result .card-header{
+ text-align: left !important;
+ color: $color-orange-crayola;
+ padding-bottom: 0;
+}
+.card-result .card-header+.card-body:not(.collapsing):not(.collapse){
+ padding-top: 0;
+}
+.card-result .card-body.collapsing,
+.card-result .card-body.collapse{
+ border-top-color: $simulator !important;
+ border-top: 1px;
+ border-top-style: solid;
+}
+.btn.btn-auto[data-bs-toggle="collapse"]{
+ padding: 0 5px 0 5px;
+ float: right;
+}
+.btn.btn-auto.collapsed .is-expended{
+ display: none;
+}
+.btn.btn-auto:not(.collapsed) .is-collapsed{
+ display: none;
}
\ 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
index ab1b344ba42ed14bd274b476bf72573afebfc23c..5b7bb3d88e813fb8a450463eb2eda448b76436ac 100644
--- a/src/InSillyCloWeb/assemblies/templates/assemblies/simulatorjob_detail.html
+++ b/src/InSillyCloWeb/assemblies/templates/assemblies/simulatorjob_detail.html
@@ -36,4 +36,70 @@
<h1 class="col-12 text-center">
TODO
</h1>
+<div class="col-12">
+ <div class="card card-result context-simulator">
+ <div class="card-header">
+ Simulate Verification
+ <a class="btn btn-auto {%if not object.pcr_image_url%}collapsed{%endif%}" data-bs-toggle="collapse" href="#verification" role="button"
+ aria-expanded="false"
+ aria-controls="verification">
+ <i class="bi bi-chevron-down is-collapsed fs-6"></i>
+ <i class="bi bi-chevron-up is-expended fs-6"></i>
+ </a>
+ </div>
+ <div class="card-body">
+ Simulate the agarose gel obtained after a PCR or a restriction digestion reaction.
+ </div>
+ <div class="{%if not object.pcr_image_url%}collapse{%endif%} border-top border-simulator" id="verification">
+ {%if object.pcr_image_url%}
+ <div class="card-header">
+ PCR gel simulation
+ <a href="#" data-bs-toggle="modal" data-bs-target="#pcrModal">
+ <i class="bi bi-pencil text-simulator"></i>
+ </a>
+ <!-- Modal -->
+ <div class="modal fade" id="pcrModal" tabindex="-1" aria-labelledby="pcrModalLabel" aria-hidden="true">
+ <div class="modal-dialog border-simulator">
+ <div class="modal-content">
+ <div class="modal-header">
+ <h1 class="modal-title fs-5" id="pcrModalLabel">Modal title</h1>
+ <button type="button" class="btn-close" data-bs-dismiss="modal"
+ aria-label="Close"></button>
+ </div>
+ <form method="post" enctype="multipart/form-data"
+ action="{%url 'assemblies:simulator-pcr-edit' object.pk %}">
+ <div class="modal-body">
+ {% csrf_token %}
+ {{form_pcr|crispy}}
+ </div>
+ <div class="modal-footer">
+ <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close
+ </button>
+ <button type="submit" class="btn btn-auto">Run simulation</button>
+ </div>
+ </form>
+ </div>
+ </div>
+ </div>
+ </div>
+ <div class="card-body text-center">
+ <img class="w-auto" src="{{object.pcr_image_url}}"/>
+ </div>
+ {%else%}
+ <div class="card-body">
+ <div class="card card-result">
+ <form class="card-body" method="post" enctype="multipart/form-data"
+ action="{%url 'assemblies:simulator-pcr-edit' object.pk %}">
+ {% csrf_token %}
+ {{form_pcr|crispy}}
+ <div class="text-center">
+ <button type="submit" class="btn btn-auto">Run simulation</button>
+ </div>
+ </form>
+ </div>
+ </div>
+ {%endif%}
+ </div>
+ </div>
+</div>
{%endblock content %}
\ No newline at end of file
diff --git a/src/InSillyCloWeb/assemblies/views.py b/src/InSillyCloWeb/assemblies/views.py
index c2c15d54646ad06d881d69f44619a9cceb053237..81f4c88ffa644c5aba572773e207057f69b2b5f6 100644
--- a/src/InSillyCloWeb/assemblies/views.py
+++ b/src/InSillyCloWeb/assemblies/views.py
@@ -119,6 +119,7 @@ class JobSimulatorResult(DetailView):
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
+ context['form_pcr'] = forms.PCRModelForm(instance=self.object)
return context
@@ -139,8 +140,9 @@ class SimulatorJobEdit(
return form
def form_valid(self, form):
+ ret = super().form_valid(form)
self.object.run_insillyclo(self.request)
- return super().form_valid(form)
+ return ret
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)