From 1264410b515a755eb3a683510ad37125668aa741 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 24 Mar 2024 09:41:55 +0100
Subject: Move assert_paths_exist into fs_helpers

---
 gn3/api/rqtl.py           |  2 +-
 gn3/computations/gemma.py | 11 -----------
 gn3/fs_helpers.py         | 17 ++++++-----------
 3 files changed, 7 insertions(+), 23 deletions(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 0a380a4..36bc3da 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -9,7 +9,7 @@ from flask import request
 from gn3.debug import __pk__
 from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \
                                   process_rqtl_pairscan, process_perm_output
-from gn3.computations.gemma import assert_paths_exist
+from gn3.fs_helpers import assert_paths_exist
 
 rqtl = Blueprint("rqtl", __name__)
 
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index f97fa6d..2c367ff 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -41,17 +41,6 @@ def generate_pheno_txt_file(trait_filename: str,
     return f"{tmpdir}/gn2/{trait_filename}"
 
 
-def assert_paths_exist(paths: ValuesView) -> bool:
-    """Given a list of PATHS, throw error if any of them do not exist."""
-    for path in paths:
-        if not os.path.isfile(path):
-            if throw_error:
-                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
-            else:
-                return False
-    return True
-
-
 # pylint: disable=R0913
 def generate_gemma_cmd(gemma_cmd: str,
                        output_dir: str,
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py
index 845c48b..c2c240c 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -13,19 +13,14 @@ from typing import List
 from typing import ValuesView
 from werkzeug.utils import secure_filename
 
-def assert_path_exists(path: str, throw_error: bool = True) -> bool:
-    """Throw error if any of them do not exist."""
-    if not os.path.isfile(path):
-        if throw_error:
-            raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
-        else:
-            return False
-    return True
-
-def assert_paths_exist(paths: ValuesView, throw_error: bool = True) -> bool:
+def assert_paths_exist(paths: ValuesView) -> bool:
     """Given a list of PATHS, throw error if any of them do not exist."""
     for path in paths:
-        assert_path_exists(path,throw_error)
+        if not os.path.isfile(path):
+            if throw_error:
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
+            else:
+                return False
     return True
 
 def get_hash_of_files(files: List[str]) -> str:
-- 
cgit v1.2.3