From f6e776c1580874639755bd346aa47ab541d5c397 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Mon, 30 Oct 2023 20:48:35 +0100
Subject: [PATCH] move valideInitTableNamePattern into initTable sources
---
jass/models/inittable.py | 3 ++-
jass/models/phenotype.py | 9 +++------
2 files changed, 5 insertions(+), 7 deletions(-)
diff --git a/jass/models/inittable.py b/jass/models/inittable.py
index dc7fc85e..a7cd1b5e 100644
--- a/jass/models/inittable.py
+++ b/jass/models/inittable.py
@@ -5,6 +5,7 @@ Created on Tue Mar 28 09:57:33 2017
@author: vguillem, hjulienne, hmenager
"""
import os
+import re
import glob
import logging
from pandas import HDFStore, DataFrame, read_csv, concat, options, read_hdf
@@ -18,7 +19,7 @@ from functools import reduce
options.mode.chained_assignment = None
warnings.filterwarnings("ignore", category=tables.NaturalNameWarning)
-from pydantic import BaseModel
+valideInitTableNamePattern = re.compile("^([A-Z]*[a-z]*-*\.?[0-9]*)+$")
class InitMeta(object):
def __init__(self, nb_snps, nb_phenotypes):
diff --git a/jass/models/phenotype.py b/jass/models/phenotype.py
index b19bb5d7..d5074302 100644
--- a/jass/models/phenotype.py
+++ b/jass/models/phenotype.py
@@ -3,10 +3,10 @@ from typing import List, Optional
import os
import pandas
-import re
from pydantic import BaseModel, validator
from jass.config import config
+from jass.models.inittable import valideInitTableNamePattern
class Phenotype(BaseModel):
@@ -76,16 +76,13 @@ def get_available_phenotypes(init_file_path: str):
return phenotypes
-_initTableNamePattern = re.compile("^([A-Z]*[a-z]*-*\.?[0-9]*)+$")
-
-
class InitTableNameModel(BaseModel):
initTableName: Optional[str] = "initTable.hdf5"
@validator("initTableName")
def validate_path_injection(cls, value):
- if not _initTableNamePattern.match(value):
- raise ValueError(f"Prohibited char, only \"{_initTableNamePattern.pattern}\" allowed.")
+ if not valideInitTableNamePattern.match(value):
+ raise ValueError(f"Prohibited char, only \"{valideInitTableNamePattern.pattern}\" allowed.")
return value
def get_init_table_path(self):
--
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