Add and fix more type hints

Summary

Related to #192 (closed)

Adding more type hints to smaller modules than models.py

Focus

Point the reviewer to the core of the code change. Where should they start reading? What should they focus on (e.g. security, performance, maintainability, user-friendliness, compliance with the specs, finding more corner cases, concrete questions)?

Test Environment

How to set up a test environment for manual testing?

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/linkahead/apiutils.py

@@ -25,11 +25,11 @@
 """API-Utils: Some simplified functions for generation of records etc.
 
 """
-
+from __future__ import annotations
 import logging
 import warnings
 from collections.abc import Iterable
-from typing import Any, Dict, List
+from typing import Any, Dict, List, Union, Optional, Tuple
 
 from .common.datatype import is_reference
 from .common.models import (SPECIAL_ATTRIBUTES, Container, Entity, File,
@@ -47,12 +47,14 @@ class EntityMergeConflictError(LinkAheadException):
     """
 
 
-def new_record(record_type, name=None, description=None,
-               tempid=None, insert=False, **kwargs):
+def new_record(record_type: Union[str],
+               name: Optional[str] = None,
+               description: Optional[str] = None,
+               tempid: Optional[int] = None,
+               insert: bool = False, **kwargs) -> Record:
     """Function to simplify the creation of Records.
 
-    record_type: The name of the RecordType to use for this record.
-                 (ids should also work.)
+    record_type: The name of the RecordType to use for this record.                 
     name: Name of the new Record.
     kwargs: Key-value-pairs for the properties of this Record.
 
@@ -92,19 +94,19 @@ def new_record(record_type, name=None, description=None,
     return r
 
 
-def id_query(ids):
+def id_query(ids: List[int]) -> Container:
     warnings.warn("Please use 'create_id_query', which only creates"
                   "the string.", DeprecationWarning)
 
-    return execute_query(create_id_query(ids))
+    return execute_query(create_id_query(ids))  # type: ignore
 
 
-def create_id_query(ids):
+def create_id_query(ids: List[int]) -> str:
     return "FIND ENTITY WITH " + " OR ".join(
         ["ID={}".format(id) for id in ids])
 
 
-def get_type_of_entity_with(id_):
+def get_type_of_entity_with(id_: int):
     objs = retrieve_entities_with_ids([id_])
 
     if len(objs) == 0:
@@ -127,11 +129,11 @@ def get_type_of_entity_with(id_):
         return Entity
 
 
-def retrieve_entity_with_id(eid):
+def retrieve_entity_with_id(eid: int):
     return execute_query("FIND ENTITY WITH ID={}".format(eid), unique=True)
 
 
-def retrieve_entities_with_ids(entities):
+def retrieve_entities_with_ids(entities: List) -> Container:
     collection = Container()
     step = 20
 
@@ -175,7 +177,10 @@ def getCommitIn(folder):
     return get_commit_in(folder)
 
 
-def compare_entities(old_entity: Entity, new_entity: Entity, compare_referenced_records: bool = False):
+def compare_entities(old_entity: Entity,
+                     new_entity: Entity,
+                     compare_referenced_records: bool = False
+                     ) -> Tuple[Dict[str, Any], Dict[str, Any]]:
     """Compare two entites.
 
     Return a tuple of dictionaries, the first index belongs to additional information for old
@@ -328,7 +333,7 @@ def compare_entities(old_entity: Entity, new_entity: Entity, compare_referenced_
     return (olddiff, newdiff)
 
 
-def empty_diff(old_entity: Entity, new_entity: Entity, compare_referenced_records: bool = False):
+def empty_diff(old_entity: Entity, new_entity: Entity, compare_referenced_records: bool = False) -> bool:
     """Check whether the `compare_entities` found any differences between
     old_entity and new_entity.
 
@@ -357,8 +362,12 @@ def empty_diff(old_entity: Entity, new_entity: Entity, compare_referenced_record
     return True
 
 
-def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_empty_diffs=True,
-                   force=False, merge_id_with_resolved_entity: bool = False):
+def merge_entities(entity_a: Entity,
+                   entity_b: Entity,
+                   merge_references_with_empty_diffs=True,
+                   force=False,
+                   merge_id_with_resolved_entity: bool = False
+                   ) -> Entity:
     """Merge entity_b into entity_a such that they have the same parents and properties.
 
     datatype, unit, value, name and description will only be changed in entity_a
@@ -441,8 +450,12 @@ def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_emp
                         if merge_id_with_resolved_entity is True and attribute == "value":
                             # Do a special check for the case of an id value on the
                             # one hand, and a resolved entity on the other side.
-                            this = entity_a.get_property(key).value
-                            that = entity_b.get_property(key).value
+                            prop_a = entity_a.get_property(key)
+                            assert prop_a is not None, f"Property {key} not found in entity_a"
+                            prop_b = entity_b.get_property(key)
+                            assert prop_b is not None, f"Property {key} not found in entity_b"
+                            this = prop_a.value
+                            that = prop_b.value
                             same = False
                             if isinstance(this, list) and isinstance(that, list):
                                 if len(this) == len(that):
@@ -465,11 +478,13 @@ def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_emp
         else:
             # TODO: This is a temporary FIX for
             #       https://gitlab.indiscale.com/caosdb/src/caosdb-pylib/-/issues/105
-            entity_a.add_property(id=entity_b.get_property(key).id,
-                                  name=entity_b.get_property(key).name,
-                                  datatype=entity_b.get_property(key).datatype,
-                                  value=entity_b.get_property(key).value,
-                                  unit=entity_b.get_property(key).unit,
+            prop_b = entity_b.get_property(key)
+            assert prop_b is not None, f"Property {key} not found in entity_b"
+            entity_a.add_property(id=prop_b.id,
+                                  name=prop_b.name,
+                                  datatype=prop_b.datatype,
+                                  value=prop_b.value,
+                                  unit=prop_b.unit,
                                   importance=entity_b.get_importance(key))
             # entity_a.add_property(
             #     entity_b.get_property(key),