From 7208a7a94ccad39dd47e6e1aa4486c6735020acb Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Tue, 11 May 2021 20:56:59 +0200
Subject: [PATCH] fix filepath for upload_from_galaxy_fs()
---
gga_load_data.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/gga_load_data.py b/gga_load_data.py
index 22fbd35..b77f1da 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -141,7 +141,7 @@ class LoadData(speciesData.SpeciesData):
for fname, files in folders.items():
if fname and files:
- folder_name = fname[len(data_dir_root) + 1:]
+ folder_name = fname[len(CONTAINER_DATA_DIR_ROOT) + 1:]
logging.info("Creating folder: %s" % folder_name)
folder = self.create_deep_folder(prj_lib, folder_name)
@@ -183,11 +183,9 @@ class LoadData(speciesData.SpeciesData):
logging.info("Skipping useless file '%s'" % single_file)
continue
- single_file_path=os.path.join(CONTAINER_DATA_DIR_ROOT,single_file)
-
logging.info("Adding file '%s' with type '%s' and name '%s'" % (single_file, ftype, clean_name))
datasets = prj_lib.upload_from_galaxy_fs(
- single_file_path,
+ single_file,
folder=folder,
link_data_only='link_to_files',
file_type=ftype,
--
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