From 6615797ac35de3feac9419fa3872ca4f8c63fb56 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 31 Jan 2025 12:00:34 +0100
Subject: [PATCH] ENH: Make get_person customizable in sample upload
---
.../scripting/bin/crawl_sample_data_async.py | 45 +-----------
.../sample_upload_get_person.py | 70 +++++++++++++++++++
2 files changed, 72 insertions(+), 43 deletions(-)
create mode 100644 sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
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 7d99c3a..3c3c093 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
@@ -47,8 +47,9 @@ 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_person import get_person
from sample_helpers.sample_upload_post_processing import post_process_samples
-from sample_helpers.utils import get_column_header_name
+from sample_helpers.utils import get_column_header_name, get_entity_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -396,48 +397,6 @@ def get_nagoya_case(data):
return nagoya_case
-def get_person(text) -> db.Record:
- """
- Return the BIS ID of the person that is specifed as 'Main User' or 'Sampling Person' in data.
-
- If the Person is not present in the database, an Exception is raised. Creating new Person Reconrds can only be done by a priviledged user.
- """
- # Check in which format the person is identified:
- person_identifier = text.split(", ")
- if len(person_identifier) == 1:
- person = _get_person_by_abbreviation(person_identifier[0])
- else:
- person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
-
- return person
-
-
-def _get_person_by_fullname(first_name, last_name):
- # seach for person in db
- res = db.execute_query(
- "FIND RECORD Person WITH 'First name' = '{}' AND 'Last name' = '{}'".format(first_name, last_name))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no person Record with 'First name' = '{}' AND 'Last name' = '{}' in the database. ".format(
- first_name, last_name)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
-def _get_person_by_abbreviation(abbreviation):
- # seach for person in db
- res = db.execute_query("FIND RECORD Person WITH 'Abbreviation' = '{}'".format(abbreviation))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no Person Record with Abbreviation = '{}'".format(abbreviation)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
def synchroize(records, additional_property_ents, htmluserlog_public):
crawler = Crawler(securityMode=SecurityMode.UPDATE)
identifiables_definition_file = os.path.expanduser("~/identifiables.yml")
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
new file mode 100644
index 0000000..49c34f6
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -0,0 +1,70 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# 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
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+
+def get_person(text: str) -> db.Record:
+ """Return the Person Record that is specifed as 'Main User' or
+ 'Sampling Person' in data.
+
+ If the Person is not present in the database, an Exception is
+ raised. Creating new Person Reconrds can only be done by a
+ priviledged user.
+
+ """
+ # Check in which format the person is identified:
+ person_identifier = text.split(", ")
+ if len(person_identifier) == 1:
+ person = _get_person_by_id(person_identifier[0])
+ else:
+ person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
+
+ return person
+
+
+def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
+ # seach for person in db
+ res = db.execute_query(
+ f"FIND '{get_entity_name('Person')}' WITH '{
+ get_entity_name('first_name_prop')}'='{first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}'='{last_name}'"
+ )
+ # if person doesn't exist in database...
+ if len(res) == 0:
+ # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
+ error_msg = (
+ f"There is no person Record with '{get_entity_name('first_name_prop')}' = '{
+ first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}' = '{last_name}' in the database. ")
+ raise DataInconsistencyError(error_msg)
+ else:
+ 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:
+ raise DataInconsistencyError(
+ f"Could not find a {get_entity_name('Person')} with ID {eid}."
+ )
--
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