From 047df9c4a01f860f76c5c8c605780009e3e3ce03 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/gemma.py          |  2 +-
 gn3/api/rqtl.py           |  2 +-
 gn3/computations/gemma.py | 13 +------------
 gn3/fs_helpers.py         |  9 +++++++++
 4 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index c862d91..2dd53ea 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -10,7 +10,7 @@ from flask import request
 from gn3.commands import queue_cmd
 from gn3.commands import run_cmd
 from gn3.fs_helpers import cache_ipfs_file
-from gn3.fs_helpers import jsonfile_to_dict
+from gn3.fs_helpers import jsonfile_to_dict, assert_paths_exist
 from gn3.computations.gemma import generate_gemma_cmd
 from gn3.computations.gemma import assert_paths_exist
 
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index bfb191e..3893275 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -8,7 +8,7 @@ from flask import request
 
 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 5a2616b..2c367ff 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -8,7 +8,7 @@ from typing import Optional, Dict
 from typing import List
 from typing import ValuesView
 from gn3.commands import compose_gemma_cmd
-from gn3.fs_helpers import get_hash_of_files
+from gn3.fs_helpers import get_hash_of_files, assert_paths_exist
 
 
 def generate_hash_of_string(unhashed_str: str) -> str:
@@ -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 e7366ac..6b0a00a 100644
--- a/gn3/fs_helpers.py
+++ b/gn3/fs_helpers.py
@@ -11,6 +11,15 @@ from typing import Dict
 from typing import List
 from werkzeug.utils import secure_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
 
 def get_hash_of_files(files: List[str]) -> str:
     """Given a list of valid of FILES, return their hash as a string"""
-- 
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