From fafe57c6ae590f80640ae574672ad6f343e6279f Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 11 May 2021 21:23:33 +0200
Subject: [PATCH] fix filepath for upload_from_galaxy_fs()
---
gga_load_data.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 8a1408c..0584632 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
+import re
import bioblend
import argparse
@@ -183,7 +184,8 @@ class LoadData(speciesData.SpeciesData):
logging.info("Skipping useless file '%s'" % single_file)
continue
- single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file)
+ single_file_relative_path = re.sub(data_dir_root, CONTAINER_DATA_DIR_ROOT, single_file)
+ single_file_path_in_container=os.path.join(CONTAINER_DATA_DIR_ROOT, single_file_relative_path)
logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file_path_in_container, ftype, clean_name))
datasets = prj_lib.upload_from_galaxy_fs(
--
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