From aaf057af48008bde561a18f0d7a6f23339382886 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Fri, 21 Mar 2025 14:23:26 +0100
Subject: [PATCH] FEAT: add columns required for event insertion automatically
---
.../scripting/bin/register_new_samples.py | 6 +-
.../sample_registration_check_column_names.py | 68 +++++++++++++++++++
2 files changed, 72 insertions(+), 2 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_check_column_names.py
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index 15e22bd..a320c0d 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -13,6 +13,7 @@ from bis_utils import (create_email_with_link_text,
get_options_row, send_mail_with_defaults)
from sample_helpers.sample_registration_get_person_identifier import get_person_identifier
from sample_helpers.sample_registration_post_processing import post_process_samples
+from sample_helpers.sample_registration_check_column_names import check_column_names
from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
ERROR_PREFIX = CONSTANTS["error_prefix"]
@@ -34,8 +35,9 @@ def get_column_names(data):
other_names = data["required_column_names"].split(',') + data["column_names"]
starting_names.extend([name.strip()
for name in other_names if name.strip() not in starting_names])
- return [get_column_header_name(name) for name in starting_names]
-
+ cnames = [get_column_header_name(name) for name in starting_names]
+ check_column_names(cnames)
+ return cnames
def create_sample_entities(data):
responsible_person_id = int(data["responsible_person"])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_check_column_names.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_check_column_names.py
new file mode 100644
index 0000000..79f62dd
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_check_column_names.py
@@ -0,0 +1,68 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Henrik tom Wörden <h.tomwoerden@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import logging
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import CONSTANTS, get_column_header_name, get_entity_name
+from .sample_upload_column_definitions import use_custom_names
+
+logger = logging.getLogger("caosadvancedtools")
+
+def check_column_names(names: list[str]) -> None:
+ event_and_position_properties = use_custom_names([
+ "Campaign",
+ "Biome",
+ "Device",
+ "Elevation start",
+ "Elevation stop",
+ "End date",
+ "responsible_person_event",
+ "igsn_doi_prop",
+ "Latitude start",
+ "Latitude stop",
+ "Level",
+ "locality_description_prop",
+ "locality_name_prop",
+ "Longitude start",
+ "Longitude stop",
+ "Sphere",
+ "Start date",
+ ])
+ needs_events = False
+ for name in names:
+ if name in event_and_position_properties:
+ needs_events = True
+ appended = []
+ if needs_events:
+ for name in use_custom_names([
+ "Longitude start",
+ "Latitude start",
+ "Elevation start",
+ "Start date",
+ ]):
+ if name not in names:
+ names.append(name)
+ appended.append(name)
+
+ if appended:
+ logger.warning(
+ "The following columns were added in order to allow consitent data insertion:\n"
+ f"{', '.join(appended)}"
+ )
--
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