From a57564ab27e3d6936f560977c5034127f6d4dae5 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Mon, 24 Mar 2025 12:56:50 +0100
Subject: [PATCH] FEAT(sample_upload): Allow event names in registration,
upload, and expor
---
.../src/ext/js/ext_samplemanagement.js | 1 +
.../scripting/bin/export_sample_csv.py | 15 ++++++++++++++-
.../bin/sample_helpers/default_constants.yml | 1 +
.../sample_upload_column_definitions.py | 2 ++
.../bin/sample_helpers/sample_upload_get_event.py | 15 +++++++++++----
5 files changed, 29 insertions(+), 5 deletions(-)
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index acf9a18..88fcefe 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -54,6 +54,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Elevation start",
"Elevation stop",
"End date",
+ "Event name",
"Event responsible",
"IGSN DOI",
"Latitude stop",
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index e97cdf5..7273f00 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -335,6 +335,17 @@ def extract_event_url(record, key):
return None
+def extract_event_name(record, key):
+
+ events = retrieve_event(record)
+ if not events:
+ return None
+ if len(events) == 1:
+ return events[0].name
+ logger.debug(f"Sample {record.id} has multiple events.")
+ return None
+
+
def extract_sample_name(record, key):
return record.name
@@ -353,6 +364,7 @@ EXTRACTORS = use_custom_names({
"Elevation stop": extract_ele_stop,
"Embargo": default_find,
"End date": extract_end_date,
+ "event_name": extract_event_name,
"Latitude start": extract_lat_start,
"Latitude stop": extract_lat_stop,
"Level": extract_level,
@@ -397,7 +409,8 @@ ADDITIONAL_EXPORTS = use_custom_names([
"LinkAhead URL",
"parent_sample_prop",
"Storage chain",
- "sample_name"
+ "sample_name",
+ "event_name"
])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
index 8761cae..77791d4 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -26,6 +26,7 @@ csv_column_names:
responsible_person_event: "Event responsible"
parent_sample_prop: "Parent LinkAhead ID"
sample_name: "Sample name"
+ event_name: "Event name"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
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 251f5f1..963470e 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
@@ -63,6 +63,7 @@ DATATYPE_DEFINITIONS = use_custom_names({
"Elevation start": float,
"Elevation stop": float,
"End date": str,
+ "event_name": str,
"Latitude start": float,
"Latitude stop": float,
"Longitude start": float,
@@ -105,6 +106,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"Elevation stop",
"Embargo",
"End date",
+ "event_name",
"responsible_person_event",
"igsn_doi_prop",
"Latitude start",
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 b726a66..598117a 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
@@ -35,6 +35,10 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
event_rt = db.get_entity_by_name(get_entity_name("event_rt"), role="RECORDTYPE")
event = db.Record().add_parent(event_rt)
+ # Event name. Replace with empty if cell is empty.
+ if get_column_header_name("event_name") in data:
+ event.name = return_value_if_not_none(data[get_column_header_name("event_name")])
+
# We performed the sanity checks so we can assume that if the
# Start/Stop Latitude exists, all start/stop data exist.
positions = []
@@ -134,8 +138,11 @@ def _perform_sanity_checks(sample, data):
)
for name in ["start", "stop"]:
- bool_list = [get_column_header_name(f"{val} {name}") in data for val in [
- "Latitude", "Longitude", "Elevation"]]
+ bool_list = [
+ ((get_column_header_name(f"{val} {name}") in data) and
+ (return_value_if_not_none(data[get_column_header_name(f"{val} {name}")]) is not None))
+ for val in ["Latitude", "Longitude", "Elevation"]
+ ]
raise_error = False
if any(bool_list):
if not all(bool_list):
@@ -155,9 +162,9 @@ def _perform_sanity_checks(sample, data):
if (get_column_header_name("Latitude stop") in data and
return_value_if_not_none(data[get_column_header_name("Latitude stop")]) is not None):
if (get_column_header_name("Latitude start") not in data or
- return_value_if_not_none(data[get_column_header_name("Latitude start")]) is not None):
+ return_value_if_not_none(data[get_column_header_name("Latitude start")]) is None):
raise DataInconsistencyError(
- f"Sample with {get_entity_name('entity_id')} {sample.id} has a "
+ f"Sample with {get_column_header_name('entity_id')} {sample.id} has a "
f"{get_entity_name('StopPosition')} but no valid "
f"{get_entity_name('StartPosition')}."
)
--
GitLab