Filling XLSX: Everything except multiple choice.

Summary

For caosdb/customers/dimr/management#219:

Filling XLSX templates from JSON works now.

Focus

• Correct handling of foreign keys
• Correct handling of other lists

Test Environment

Run the unit tests.

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.

src/caosadvancedtools/cfoods/h5.py

 #!/usr/bin/env python3
 
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
 #
 # Copyright (C) 2020,2021 IndiScale GmbH <www.indiscale.com>
-# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
+# Copyright (C) 2020-2025 Daniel Hornung <d.hornung@indiscale.com>
 # Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
 # Copyright (C) 2021 Alexander Kreft
 # Copyright (C) 2021 Laboratory for Fluid Physics and Biocomplexity,
@@ -33,19 +33,14 @@ attributes. Groups and datasets are mapped to Records and attributes to
 Properties.
 """
 
-import re
 from copy import deepcopy
 
 import caosdb as db
 import h5py
 import numpy as np
 from caosadvancedtools.cfood import fileguide
-from caosdb.common.datatype import is_reference
-from caosdb.common.utils import uuid
 
-from ..cfood import (AbstractFileCFood, assure_has_description,
-                     assure_has_parent, assure_has_property,
-                     assure_property_is)
+from ..cfood import AbstractFileCFood
 from ..structure_mapping import (EntityMapping, collect_existing_structure,
                                  update_structure)
 
@@ -100,8 +95,7 @@ def h5_attr_to_property(val):
         if hasattr(val, 'ndim'):
             if not isinstance(val, np.ndarray) and val.ndim != 0:
                 print(val, val.ndim)
-                raise Exception(
-                    "Implementation assumes that only np.arrays have ndim.")
+                raise RuntimeError("Implementation assumes that only np.arrays have ndim.")
 
         return val, dtype
 
@@ -127,6 +121,8 @@ class H5CFood(AbstractFileCFood):
         self.identifiable_root = None
         self.root_name = "root"
         self.hdf5Container = db.Container()
+        self.to_be_inserted = db.Container()
+        self.structure = db.Container()
         self.em = EntityMapping()
 
     def collect_information(self):
@@ -165,7 +161,8 @@ class H5CFood(AbstractFileCFood):
 
         """
 
-        self.structure._cuid = "root element"
+        # TODO Why do we need a protected member here?
+        self.structure._cuid = "root element"  # pylint: disable=protected-access
         self.em.add(self.structure, self.identifiable_root)
         collect_existing_structure(self.structure, self.identifiable_root,
                                    self.em)
@@ -282,7 +279,7 @@ class H5CFood(AbstractFileCFood):
         return rec
 
     def insert_missing_structure(self, target_structure: db.Record):
-        if target_structure._cuid not in self.em.to_existing:
+        if target_structure._cuid not in self.em.to_existing:  # pylint: disable=protected-access
             self.to_be_inserted.append(target_structure)
 
         for prop in target_structure.get_properties():