From f6e63d3d53a3f4c03c646ccadf718920a0a1095e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 27 Mar 2026 13:15:58 +0100
Subject: Make sure paths are available

---
 more_functions.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

(limited to 'more_functions.py')

diff --git a/more_functions.py b/more_functions.py
index 8162acc..7f12215 100755
--- a/more_functions.py
+++ b/more_functions.py
@@ -175,5 +175,12 @@ def searchArchived(sets, query, filetype,sents, path_user):
         gwas_json+="{ \"id\": \"" + edgeID + "\", \"source\": \"" + query + "\", \"target\": \"" + key + "\", \"sentCnt\": \"" + str(catCnt[key]) + "\",  \"url\":\"/sentences?edgeID=" + edgeID + "\" },\n"
     return(nodes+edges,gwas_json,sn_file)
 
-pubmed_path=os.environ["EDIRECT_PUBMED_MASTER"]
+pubmed_path=os.environ.get("EDIRECT_PUBMED_MASTER", "./minipubmed")
+
+if not os.path.isdir(pubmed_path):
+    print(f"ERROR: EDIRECT_PUBMED_MASTER directory not found: {pubmed_path}")
+    raise SystemExit(1)
+if not os.path.isdir(os.path.join(pubmed_path, "PubMed", "Archive")):
+    print(f"ERROR: PubMed/Archive not found in {pubmed_path}")
+    raise SystemExit(1)
 
-- 
cgit 1.4.1