From b8403ed3c34c77692a6151d2ca75feb63800d255 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 21 Mar 2025 10:53:40 +0100
Subject: [PATCH] FEAT(export_sample_csv): Export sample names
---
.../caosdb-server/scripting/bin/export_sample_csv.py | 6 ++++++
.../scripting/bin/sample_helpers/default_constants.yml | 2 ++
.../bin/sample_helpers/sample_upload_column_definitions.py | 2 +-
3 files changed, 9 insertions(+), 1 deletion(-)
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 085c839..885fb55 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 +335,11 @@ def extract_event_url(record, key):
return None
+def extract_sample_name(record, key):
+
+ return record.name
+
+
# must include all keys from SPECIAL_TREATMENT
EXTRACTORS = use_custom_names({
"entity_id": lambda record, key: record.id,
@@ -356,6 +361,7 @@ EXTRACTORS = use_custom_names({
"Longitude stop": extract_lng_stop,
"PDFReport": extract_pdf_id,
"PI": extract_person,
+ "sample_name": extract_sample_name,
"Sampling method": default_find,
"Sphere": extract_sphere,
"Start date": extract_start_date,
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 c575cb6..136d9ee 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
@@ -25,6 +25,7 @@ csv_column_names:
locality_name_prop: "Locality name"
responsible_person_event: "Event responsible"
parent_sample_prop: "Parent LinkAhead ID"
+ sample_name: "Sample name"
csv_column_descriptions:
LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
@@ -52,6 +53,7 @@ csv_column_descriptions:
Timezone: "Timezone: Either UTC, CET, .... or in the form +hh[:mm], -hh:[mm]."
Water depth start: "The bottom depth in meters where the sampling started as a positive value"
Water depth stop: "The bottom depth in meters where the sampling ended as a positive value"
+ Sample name: "Name which will be given to the sample entity"
entity_names:
abbreviation_prop: abbreviation
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 0584522..1ad1ade 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
@@ -79,7 +79,6 @@ DATATYPE_DEFINITIONS = use_custom_names({
# Must exist
OBLIGATORY_COLUMNS = use_custom_names([
"entity_id",
- "Start date",
])
OBLIGATORY_COLUMNS_CHILD = use_custom_names([
@@ -118,6 +117,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"PI",
"PDFReport",
"parent_sample_prop",
+ "sample_name",
"Sphere",
"Start date",
"Storage ID",
--
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