F awi sams

Summary

For #1 (closed). Removes the dependencies on the specifics of the GEOMAR data model and makes things more configurable.

Focus

A lot of functionality is moved into small Python modules in scripting/bin/sample_helpers. They should define a reasonable default behavior for the datamodel in models_and_helper_scripts/sample-management-datamodel.yml and the AWI SAMS datamodel, and should be overwritten by files of the same name in a server profile's custom directory for customization.

Test Environment

So far, only manual testing.

Do round trips for:

• Container registration, export, update
• Sample registration, export, update

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• Up-to-date JSON schema (or not necessary)
• Appropriate user and developer documentation (or not necessary)
  • How do I use the software? Assume "stupid" users.
  • How do I develop or debug the software? Assume novice developers.
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md (or not necessary)
• Appropriate user and developer documentation (or not necessary)
• The test environment setup works and the intended behavior is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?

For further good practices have a look at our review guidelines.

sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml

+#
+# 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/>.
+#
+csv_column_names:
+  entity_id: "LinkAhead ID"
+  custom_label_prop: "Custom Label"
+  start_date_prop: "Start date"
+  end_date_prop: "End date"
+  igsn_doi_prop: "IGSN DOI"
+  locality_description_prop: "Locality description"
+  locality_name_prop: "Locality name"
+  responsible_person_event: "Event responsible"
+  parent_sample_prop: "Parent LinkAhead ID"
+
+csv_column_descriptions:
+  LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
+  container_label: "The label automatically assigned by LinkAhead sample management. Do not change this column."
+  Collection: "Collection(s) to which this container or samples belongs (separated by ';')"
+  Container Contents: "Notes concerning the contents of this container"
+  Container size: "The size of the container (e.g 81 spaces)"
+  Container type: "The type of container. Do not change this column."
+  Custom label: "Any additional custom label you put on the container"
+  Date start: "The start date or datetime in ISO format"
+  Date stop: "The end date or datetime in ISO format"
+  Gear configuration: "How gear is configured, meshsize of the net, filter pore size, what kind of trawl"
+  Latitude start: "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S"
+  Latitude stop: "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S"
+  Longitude start: "Longitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for W"
+  Longitude stop: "Longitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for W"
+  Notes / remarks: "Field for notes"
+  PDFReport: "A PDF containing additional information on the container or sampe contents"
+  PI: "The PI (by abbreviation) of the container or sample"
+  Parent container: "The LinkAhead ID (integer or URL) or name or BIS label of the container where this container is stored."
+  Sampling depth start: "The depth in meters where the sampling started as a positive value, not bottom depth"
+  Sampling depth stop: "The depth in meters where the sampling ended as a positive value,not bottom depth"
+  Storage ID: "LinkAhead ID of the Container that holds this sample"
+  Subevent: "Subevent given by D-Ship in Stationlog. Expl. AL123_14-4"
+  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"
+
+entity_names:
+  abbreviation_prop: abbreviation
+  child_container_prop: "Child_Container"
+  container_label_prop: container_label
+  container_rt: Container
+  container_size_prop: "Container size"
+  containertype_rt: ContainerType
+  custom_label_prop: custom_label
+  end_date_prop: end_date
+  event_rt: Event
+  first_name_prop: first_name
+  igsn_doi_prop: igsn_doi
+  labelcounter_prop: counter
+  labelcounter_rt: LabelCounter
+  last_name_prop: last_name
+  parent_sample_prop: Parent_sample
+  responsible_rt: Responsible
+  start_date_prop: start_date
+  locality_description_prop: locality_description
+  locality_name_prop: locality_name
+  responsible_person_event: Responsible_Person
+
+error_prefix: "Something went wrong:"
+error_suffix: "Please contact your administrator(s)."