From 1d3df5795cc432e606aff3839e0929a0dee8aa5a Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 21 Mar 2025 15:21:27 +0100
Subject: [PATCH] FEAT: Raise error when identifying event properties are
missing
---
.../sample_upload_column_definitions.py | 2 +-
.../bin/sample_helpers/sample_upload_get_event.py | 15 +++++++++++++++
.../scripting/bin/upload_sample_template.py | 7 +++----
3 files changed, 19 insertions(+), 5 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
index 3bd2b85..251f5f1 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -91,7 +91,7 @@ COLUMN_CONVERTER = use_custom_names({
"Collector": semicolon_separated_list,
"Curator": semicolon_separated_list,
"Embargo": _embargo_converter,
- "Event responsible": semicolon_separated_list,
+ "responsible_person_event": semicolon_separated_list,
"Sphere": semicolon_separated_list,
})
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
index 1949541..3bc4947 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -15,6 +15,7 @@
# 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 pandas as pd
@@ -85,6 +86,20 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
# only add if there was any event data at all:
if len(event.properties) > 0:
+ # Start date and position are identifying event properties
+ if event.get_property(get_entity_name("start_date_prop")) is None:
+ raise DataInconsistencyError(
+ f"Sample with {get_column_header_name('entity_id')} {sample.id} has an "
+ f"{get_entity_name('event_rt')} but is missing a {
+ get_column_header_name('start_date_prop')} "
+ "which is required."
+ )
+ if event.get_property(get_entity_name(position_prop.name)) is None:
+ raise DataInconsistencyError(
+ f"Sample with {get_column_header_name('entity_id')} {sample.id} has an "
+ f"{get_entity_name('event_rt')} but is missing start position information "
+ "which is required."
+ )
sample = update_property(sample, event_rt.id, event, property_name=event_rt.name)
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 db9aa64..1e25408 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
@@ -40,8 +40,7 @@ from caosadvancedtools.serverside import helper
from caosadvancedtools.table_importer import CSVImporter
from caoscrawler.logging import configure_server_side_logging
-from bis_utils import (replace_entity_urls_by_ids,
- whitespace_cleanup_in_df)
+from bis_utils import (replace_entity_urls_by_ids)
from sample_helpers.sample_upload_column_definitions import (
COLUMN_CONVERTER, DATATYPE_DEFINITIONS,
OBLIGATORY_COLUMNS, OBLIGATORY_COLUMNS_CHILD, SPECIAL_TREATMENT_SAMPLE)
@@ -96,8 +95,8 @@ def read_data_from_file(filename):
)
raise DataInconsistencyError("There was a problem with the CSV upload.")
- # strip leading and trailing whitespaces
- return whitespace_cleanup_in_df(df)
+ # TODO: strip leading and trailing whitespaces
+ return df
def _get_converter_from_property_datatype(dt):
--
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