From 715a8085bf70962b6b12e7b49445161ff304550e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Wed, 12 Mar 2025 09:12:35 +0100
Subject: [PATCH] FIX: in consistencies in csv treatment
---
README.md | 15 ++++++++++++-
.../sample-management-datamodel.yml | 2 +-
.../src/ext/js/ext_samplemanagement.js | 5 ++++-
.../bin/sample_helpers/default_constants.yml | 2 +-
.../sample_upload_add_special_properties.py | 6 ++++++
.../sample_upload_column_definitions.py | 4 +++-
.../sample_upload_get_person.py | 21 +++++++++++++------
7 files changed, 44 insertions(+), 11 deletions(-)
diff --git a/README.md b/README.md
index 724f519..71abb5a 100644
--- a/README.md
+++ b/README.md
@@ -66,6 +66,19 @@ stored in LinkAhead
You can create a filled CSV template with the information about Containers as
it is currently stored in LinkAhead.
+### Extensibility
+The registration, update and export does not only work with RecordTypes and
+Properties that are defined within this module, but the data model can be
+extended by users of the system: Any Property that is added to the Sample
+RecordType can also be used within the workflow. Once an additional Property
+was added to the RecordType (say "width"), you can select a corresponding
+column during registration with the same name and also upload CSV templates
+that have this column. The Sample records will be created or updated to also
+have this ("width") column.
+
+If the Property that is added is a RecordType, it must be kind of an enum, i.e.
+it should be uniquely identified either by its name or by a sole property.
+
## Usage
**TODO**: Add explanations, screenshots, ec. to explain the sample
@@ -132,7 +145,7 @@ allow to change those.
This is the central RecordType for the sample management and used to represent
samples of various types
-#### `Parent_Sample` (`$parent_sample_prop`)
+#### `Parent_sample` (`$parent_sample_prop`)
references the sample from which the sample at hand originated (for example by
cutting the parent sample into multiple pieces0
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index 4d12dc6..aef3b68 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -83,7 +83,7 @@ Sample:
recommended_properties:
Container:
SampleType:
- Parent_Sample:
+ Parent_sample:
datatype: Sample
Main User:
datatype: Person
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 ba4dcb4..e8e46e0 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
@@ -42,6 +42,7 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
"Latitude start",
"Longitude start",
"Elevation start",
+ "Start date",
"Storage ID",
"Device"
];
@@ -73,8 +74,10 @@ const ext_samplemanagement = function($, navbar, log, form_elements, form_panel,
const unused_property_names = [
"Main User",
+ "Event",
+ "Container",
'NagoyaCase',
- "Parent_Sample",
+ "Parent_sample",
]
const upload_sample_template_form_config = {
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 f752180..c575cb6 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
@@ -68,7 +68,7 @@ entity_names:
labelcounter_prop: counter
labelcounter_rt: LabelCounter
last_name_prop: last_name
- parent_sample_prop: Parent_Sample
+ parent_sample_prop: Parent_sample
responsible_rt: Responsible
start_date_prop: start_date
locality_description_prop: locality_description
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
index 5c559d4..9ec2fff 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -33,10 +33,16 @@ def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
"""
main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
+ pi_prop = db.get_entity_by_name(get_entity_name("PI"))
container_rt = db.get_entity_by_name(get_entity_name("container_rt"))
device_rt = db.get_entity_by_name(get_entity_name("Device"))
parent_sample_prop = db.get_entity_by_name(get_entity_name("parent_sample_prop"))
+ if (get_column_header_name("PI") in data and
+ return_value_if_not_none(data[get_column_header_name("PI")]) is not None):
+ pi_user = get_person(return_value_if_not_none(data[get_column_header_name("PI")]))
+ sample = update_property(sample, pi_prop.id, pi_user, property_name=pi_prop.name)
+
if (get_column_header_name("Main User") in data and
return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))
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 5535863..0584522 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
@@ -79,6 +79,7 @@ DATATYPE_DEFINITIONS = use_custom_names({
# Must exist
OBLIGATORY_COLUMNS = use_custom_names([
"entity_id",
+ "Start date",
])
OBLIGATORY_COLUMNS_CHILD = use_custom_names([
@@ -114,6 +115,7 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
"Longitude start",
"Longitude stop",
"Main User",
+ "PI",
"PDFReport",
"parent_sample_prop",
"Sphere",
@@ -124,6 +126,6 @@ SPECIAL_TREATMENT_SAMPLE = use_custom_names([
IGNORED_COLUMN_NAMES_SAMPLE = use_custom_names([
"LinkAhead URL",
- "Parent Sample",
+ "Parent_sample",
"Storage chain",
])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
index 1872f62..3e94780 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -21,6 +21,7 @@ from caosadvancedtools.datainconsistency import DataInconsistencyError
from .utils import get_entity_name
+from linkahead.cached import cached_get_entity_by, cached_query as cquery
def get_person(text: str) -> db.Record:
"""Return the Person Record that is specifed as 'Main User' or
@@ -60,11 +61,19 @@ def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
return res[0]
-def _get_person_by_id(eid: str) -> db.Record:
-
- try:
- return db.get_entity_by_id(eid, role=get_entity_name("Person"))
- except db.EmptyUniqueQueryError:
+def _get_person_by_id(ident: str) -> db.Record:
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH ID='{ident}' ")
+ if len(options)==1:
+ return options[0]
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH "
+ f"'{get_entity_name('abbreviation_prop')}'='{ident}' ")
+ if len(options) == 1:
+ return options[0]
+ elif len(options) == 0:
+ raise DataInconsistencyError(
+ f"Could not find a {get_entity_name('Person')} with ID {ident}."
+ )
+ else:
raise DataInconsistencyError(
- f"Could not find a {get_entity_name('Person')} with ID {eid}."
+ f"Found multiple {get_entity_name('Person')} with {get_entity_name('abbreviation_prop')}={ident}."
)
--
GitLab