From e9e5e9e365132a1576c5154c3e7e1de77a5734d7 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Fri, 18 Apr 2025 15:56:49 +0200
Subject: [PATCH] use pathlib
---
src/InSillyCloWeb/assemblies/models.py | 24 ++++++++++--------------
1 file changed, 10 insertions(+), 14 deletions(-)
diff --git a/src/InSillyCloWeb/assemblies/models.py b/src/InSillyCloWeb/assemblies/models.py
index d42bf67..3ab9c88 100644
--- a/src/InSillyCloWeb/assemblies/models.py
+++ b/src/InSillyCloWeb/assemblies/models.py
@@ -338,21 +338,17 @@ class SimulatorJob(models.Model):
debug=False,
fail_on_error=False,
),
- input_template_filled=os.path.join(self.job_dir, 'design_file.xlsx'),
+ input_template_filled=self.job_dir / 'design_file.xlsx',
settings=None,
input_parts_files=self.db_ip_files,
- gb_plasmids=self.genbank_files,
- output_dir=Path(self.results_dir),
+ gb_plasmids=self.genbank_dir.glob('**/*.gb'),
+ output_dir=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)]
+ return [self.dbip_dir / file for file in os.listdir(self.dbip_dir)]
@property
def job_dir(self) -> pathlib.Path:
@@ -363,16 +359,16 @@ class SimulatorJob(models.Model):
return str(self.uuid)[:8]
@property
- def genbank_dir(self):
- return os.path.join(self.job_dir, 'genbank')
+ def genbank_dir(self) -> pathlib.Path:
+ return self.job_dir / 'genbank'
@property
- def dbip_dir(self):
- return os.path.join(self.job_dir, 'db_ip')
+ def dbip_dir(self) -> pathlib.Path:
+ return self.job_dir / 'db_ip'
@property
- def results_dir(self):
- return os.path.join(self.job_dir, 'results')
+ def results_dir(self) -> pathlib.Path:
+ return self.job_dir / 'results'
def delete(self, *args, **kwargs):
try:
--
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