From 6cde3c3117108be3af05b6c289479610f847bfbe Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 6 Feb 2025 18:09:04 +0100
Subject: [PATCH] ENH: Use separate event-adding module
---
.../scripting/bin/crawl_sample_data_async.py | 22 ++-----------------
.../sample_helpers/sample_upload_get_event.py | 2 +-
2 files changed, 3 insertions(+), 21 deletions(-)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index e538e64..063b153 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,6 +47,7 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_get_event import add_event_to_sample
from sample_helpers.sample_upload_get_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
from sample_helpers.utils import get_column_header_name, get_entity_name
@@ -383,30 +384,10 @@ def update_sample_records(data, htmluserlog_public):
sample = _update_property(entity=sample, property_id=db.get_entity_by_name("PI").id,
property_name="PI",
value=get_person(row["PI"]))
- if "Nagoya case number" in row and return_value_if_not_none(row["Nagoya case number"]) is not None:
- sample = _update_property(entity=sample, property_id=nagoya_case_property_id,
- property_name="NagoyaCase",
- value=get_nagoya_case(row))
if "Storage ID" in row and return_value_if_not_none(row["Storage ID"]) is not None:
sample = _update_property(entity=sample, property_id=container_property_id,
property_name="Container",
value=get_container(row))
- if "Collection" in row and return_value_if_not_none(row["Collection"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Collection").id,
- property_name="Collection",
- datatype=db.LIST("Collection"),
- value=[db.Record(name=el)
- .add_parent(name="Collection")
- for el in row["Collection"]])
- if "Sphere" in row and return_value_if_not_none(row["Sphere"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Sphere").id,
- property_name="Sphere",
- datatype=db.LIST("Sphere"),
- value=[db.Record(name=el)
- .add_parent(name="Sphere")
- for el in row["Sphere"]])
if "PDFReport" in data.columns:
sample = _update_property(
@@ -435,6 +416,7 @@ def update_sample_records(data, htmluserlog_public):
entity=sample, property_id=additional_property_ids[property_name],
value=value, property_name=property_name)
+ sample = add_event_to_sample(sample, row)
samples.append(sample)
samples = post_process_samples(samples, data)
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 a149876..aa62498 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
@@ -31,7 +31,7 @@ def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
"""
_perform_sanity_checks(sample, data)
-
+ # TODO Add event-specific columns
return sample
--
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