From 5b66fbf1050f19cae1e268e4cbfe49787809a902 Mon Sep 17 00:00:00 2001
From: Bryan Brancotte <bryan.brancotte@pasteur.fr>
Date: Mon, 30 Oct 2023 18:12:33 +0100
Subject: [PATCH] move filename to path in a methode of InitTableNameModel
---
jass/models/phenotype.py | 6 ++++++
jass/server.py | 4 ++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/jass/models/phenotype.py b/jass/models/phenotype.py
index f3fbcaae..b19bb5d7 100644
--- a/jass/models/phenotype.py
+++ b/jass/models/phenotype.py
@@ -1,10 +1,13 @@
# coding: utf-8
from typing import List, Optional
+import os
import pandas
import re
from pydantic import BaseModel, validator
+from jass.config import config
+
class Phenotype(BaseModel):
"""
@@ -85,5 +88,8 @@ class InitTableNameModel(BaseModel):
raise ValueError(f"Prohibited char, only \"{_initTableNamePattern.pattern}\" allowed.")
return value
+ def get_init_table_path(self):
+ return os.path.join(config["DATA_DIR"], self.initTableName)
+
class PhenotypeIdList(InitTableNameModel, BaseModel):
phenotypeID: List[str] = []
diff --git a/jass/server.py b/jass/server.py
index 2b6cbb58..66aa31e3 100644
--- a/jass/server.py
+++ b/jass/server.py
@@ -56,14 +56,14 @@ async def read_index():
def phenotypes_list(init_table_name: InitTableNameModel):
"""List phenotypes"""
try:
- return get_available_phenotypes(os.path.join(config["DATA_DIR"], init_table_name.initTableName))
+ return get_available_phenotypes(init_table_name.get_init_table_path())
except FileNotFoundError as e: # initTable does not exists
raise HTTPException(status_code=404, detail=str(e))
@app.post("/api/initmeta")
def inittable_meta(init_table_name: InitTableNameModel):
"""Number of phenotype and SNPs"""
- return get_inittable_meta(os.path.join(config["DATA_DIR"], "initTable.hdf5"))
+ return get_inittable_meta(init_table_name.get_init_table_path())
@app.post("/api/projects", response_model=GlobalProject)
--
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