From 82f7f9f7aed405a86a254d547b3fb0d228fde5e3 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Fri, 18 Apr 2025 17:16:30 +0200
Subject: [PATCH] bugfix when removing primers file
---
src/InSillyCloWeb/assemblies/forms.py | 18 +++++++++---------
src/InSillyCloWeb/assemblies/models.py | 8 ++++++--
2 files changed, 15 insertions(+), 11 deletions(-)
diff --git a/src/InSillyCloWeb/assemblies/forms.py b/src/InSillyCloWeb/assemblies/forms.py
index 1197eb8..e7af71e 100644
--- a/src/InSillyCloWeb/assemblies/forms.py
+++ b/src/InSillyCloWeb/assemblies/forms.py
@@ -81,15 +81,15 @@ class PCRModelForm(forms.ModelForm):
#
# 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_PCR_FILENAME
- with open(output_fp, 'wb') as fh:
- for chunk in self.cleaned_data['primers_file'].chunks():
- fh.write(chunk)
- return instance
+ # 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_PCR_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(
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index 066d64b..69d436e 100644
--- a/src/InSillyCloWeb/assemblies/models.py
+++ b/src/InSillyCloWeb/assemblies/models.py
@@ -381,6 +381,10 @@ class SimulatorJob(models.Model):
shutil.copyfileobj(source, dest)
def run_insillyclo(self, request):
+ if self.primers_file.name:
+ primers_file = pathlib.Path(self.primers_file.name)
+ else:
+ primers_file = None
return insillyclo.simulator.compute_all(
observer=InSillyCloDjangoMessageObserver(
request=request,
@@ -393,8 +397,8 @@ 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),
+ primers_file=primers_file,
+ primer_id_pairs=list(self.pcr_pairs) if primers_file else None,
)
@property
--
GitLab