Revert "Revert "Merge branch 'f-extend-yaml-model' into 'dev'""

Summary

For #72 (closed). Repairs the previous MR which introduced the role and value keywords into the yaml model.

Focus

For the actual changes after the reversion of the revert, have a look at https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/merge_requests/36/diffs?diff_id=5835&start_sha=619c25e6214aaeb5f91f10252a8dda104b0e46b5. Note that role: File is postponed until later (#74), as is the implementation of the valued_properties keyword (#75).

Test Environment

New unit tests and integration tests (use with the debug profile of caosdb-deploy as described in README_SETUP.md). Depending on your level of paranoia, you can also test it with the AWI server profile:

1. Check out server-profile in local-testing-main and update (and init, if necessary) the integration test submodule.
2. Run integration-tests/tests/test.sh

Check List for the Author

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• All automated tests pass
• Reference related issues
• Up-to-date CHANGELOG.md (or not necessary)
• 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)
• 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/models/parser.py

@@ -25,7 +25,8 @@ import yaml
 from .data_model import DataModel
 
 # Keywords which are allowed in data model descriptions.
-KEYWORDS = ["parent",  # TODO: can we remove that, see: #36
+KEYWORDS = ["parent",  # deprecated, use inherit_from_* instead:
+                       # https://gitlab.com/caosdb/caosdb-advanced-user-tools/-/issues/36
             "importance",
             "datatype",  # for example TEXT, INTEGER or REFERENCE
             "unit",
@@ -37,7 +38,8 @@ KEYWORDS = ["parent",  # TODO: can we remove that, see: #36
             "inherit_from_suggested",
             "inherit_from_obligatory",
             "role",
-            "value", ]
+            "value",
+            ]
 
 # TODO: check whether it's really ignored
 # These KEYWORDS are not forbidden as properties, but merely ignored.
@@ -112,9 +114,9 @@ def parse_model_from_string(string):
 
 class Parser(object):
     def __init__(self):
-        """
-        Initialize an empty parer object and initialize
-        the dictionary of entities and the list of treated elements.
+        """Initialize an empty parser object and initialize the dictionary of entities and the list of
+        treated elements.
+
         """
         self.model = {}
         self.treated = []
@@ -311,7 +313,25 @@ class Parser(object):
                     raise
 
     def _add_to_recordtype(self, ent_name, props, importance):
-        """Add properties to a RecordType."""
+        """Add properties to a RecordType.
+
+        Parameters
+        ----------
+        ent_name : str
+          The name of the entity to which the properties shall be added.
+
+        props : dict [str -> dict or :doc:`Entity`]
+          The properties, indexed by their names.  Properties may be given as :doc:`Entity` objects
+          or as dictionaries.
+
+        importance
+          The importance as used in :doc:`Entity.add_property`.
+
+        Returns
+        -------
+        None
+
+        """
 
         for n, e in props.items():
             if n in KEYWORDS:
@@ -326,9 +346,10 @@ class Parser(object):
 
             if isinstance(e, dict):
                 if "datatype" in e and _get_listdatatype(e["datatype"]) is not None:
+                    # Reuse the existing datatype for lists.
                     datatype = db.LIST(_get_listdatatype(e["datatype"]))
                 else:
-                    # ignore a possible e["datatype"] here if it's not a list
+                    # Ignore a possible e["datatype"] here if it's not a list
                     # since it has been treated in the definition of the
                     # property (entity) already
                     datatype = None