From 7abd6eb267adfc4935ccaa162ce6e6f179a849ad Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Mon, 23 Mar 2026 15:56:09 +0100
Subject: [PATCH] Use wget/python instead of curl for MinIO download (curl not
 in image)

---
 main.nf | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index b8094f0..53b88a8 100644
--- a/main.nf
+++ b/main.nf
@@ -56,32 +56,40 @@ process POCKETMINER {
             fi
         fi
 
-        # Method 3: Download from MinIO via curl (no auth needed for public)
+        # Method 3: Download from MinIO via wget
         if [ -z "\$PDB_FILE" ]; then
             S3_PATH="\$(echo '${pdb_path}' | sed 's|^s3://||')"
             MINIO_URL="http://datalake-hl.datalake.svc.cluster.local:9000/\$S3_PATH"
             echo "Downloading from MinIO: \$MINIO_URL" >> run.log
-            curl -sf "\$MINIO_URL" -o input.pdb 2>> run.log
+            wget -q "\$MINIO_URL" -O input.pdb 2>> run.log || true
             if [ -f input.pdb ] && [ -s input.pdb ]; then
                 echo "Downloaded from MinIO (\$(wc -c < input.pdb) bytes)" >> run.log
                 PDB_FILE="input.pdb"
             else
-                echo "MinIO download failed or empty" >> run.log
+                echo "wget download failed, trying python..." >> run.log
                 rm -f input.pdb
             fi
         fi
 
-        # Method 4: Download from MinIO using AWS env vars
-        if [ -z "\$PDB_FILE" ] && [ -n "\${AWS_ACCESS_KEY_ID:-}" ]; then
+        # Method 4: Download from MinIO using python urllib
+        if [ -z "\$PDB_FILE" ]; then
             S3_PATH="\$(echo '${pdb_path}' | sed 's|^s3://||')"
             ENDPOINT="\${AWS_ENDPOINT_URL:-http://datalake-hl.datalake.svc.cluster.local:9000}"
-            echo "Downloading with AWS creds from: \$ENDPOINT/\$S3_PATH" >> run.log
-            curl -sf -u "\${AWS_ACCESS_KEY_ID}:\${AWS_SECRET_ACCESS_KEY}" "\$ENDPOINT/\$S3_PATH" -o input.pdb 2>> run.log
+            echo "Downloading with python from: \$ENDPOINT/\$S3_PATH" >> run.log
+            python -c "
+import urllib.request
+url = '\$ENDPOINT/\$S3_PATH'
+try:
+    urllib.request.urlretrieve(url, 'input.pdb')
+    print(f'Downloaded from {url}')
+except Exception as e:
+    print(f'Failed: {e}')
+" >> run.log 2>&1
             if [ -f input.pdb ] && [ -s input.pdb ]; then
-                echo "Downloaded with AWS creds (\$(wc -c < input.pdb) bytes)" >> run.log
+                echo "Downloaded via python (\$(wc -c < input.pdb) bytes)" >> run.log
                 PDB_FILE="input.pdb"
             else
-                echo "AWS cred download failed" >> run.log
+                echo "Python download failed" >> run.log
                 rm -f input.pdb
             fi
         fi