From dc1aebc50160698295b53ef9d7b4e280e7a2194e Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Wed, 29 Jan 2025 15:15:31 +0100
Subject: [PATCH] ENH: Addapt upload sample script to configurable column names
---
.../caosdb-server/scripting/bin/upload_sample_template.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index 7d71282..484e651 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -42,7 +42,7 @@ from caoscrawler.logging import configure_server_side_logging
from bis_utils import (replace_entity_urls_by_ids,
SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
-from sample_helpers.utils import CONSTANTS
+from sample_helpers.utils import CONSTANTS, get_column_header_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -66,7 +66,7 @@ def get_parser():
def _is_child_sample_table(filename):
tmp_data = pd.read_csv(filename, sep=',')
if 'Parent BIS ID' in tmp_data.columns:
- return not tmp_data["Parent BIS ID"].isnull().all()
+ return not tmp_data[get_column_header_name("Parent LinkAhead ID")].isnull().all()
return False
@@ -171,7 +171,8 @@ def main():
OBLIGATORY_COLUMNS.append(property_name)
try:
data = read_data_from_file(path)
- data = replace_entity_urls_by_ids(data, ["BIS ID", "Storage ID", "Parent BIS ID"])
+ data = replace_entity_urls_by_ids(data, [get_column_header_name(name) for name in [
+ "entity_id", "Storage ID", "Parent LinkAhead ID"]])
pickle_out = NamedTemporaryFile(delete=False, suffix=".pkl")
data.to_pickle(pickle_out.name)
except DataInconsistencyError as err:
--
GitLab