From bbca8fe96bd2176f300cab8746dace6fd2323320 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 24 Mar 2024 09:36:33 +0100
Subject: Change behavior of do_paths_exist to actually throw useful error

---
 gn3/api/rqtl.py           |  2 +-
 gn3/computations/gemma.py | 11 +++++++++++
 2 files changed, 12 insertions(+), 1 deletion(-)

(limited to 'gn3')

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 36bc3da..0a380a4 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.fs_helpers import assert_paths_exist
+from gn3.computations.gemma import assert_paths_exist
 
 rqtl = Blueprint("rqtl", __name__)
 
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 2c367ff..f97fa6d 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -41,6 +41,17 @@ 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,
-- 
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