Merge pull request #131 from SciCatProject/fix-default-field-values

Dont init wrong fields in download

docs/conf.py

@@ -40,9 +40,10 @@
 
 intersphinx_mapping = {
     "fabric": ("https://docs.fabfile.org/en/latest", None),
-    "hypothesis": ("https://hypothesis.readthedocs.io/en/latest/", None),
-    "python": ("https://docs.python.org/3", None),
+    "hypothesis": ("https://hypothesis.readthedocs.io/en/latest", None),
     "paramiko": ("https://docs.paramiko.org/en/latest", None),
+    "pydantic": ("https://docs.pydantic.dev/latest", None),
+    "python": ("https://docs.python.org/3", None),
 }
 
 # autodocs includes everything, even irrelevant API internals. autosummary

docs/release-notes.rst

@@ -50,6 +50,8 @@ Breaking changes
 Bugfixes
 ~~~~~~~~
 
+* Fields of derived datasets are no longer initialized when downloading raw datasets and vice versa.
+
 Documentation
 ~~~~~~~~~~~~~
 

pyproject.toml

@@ -82,6 +82,7 @@ warn_unreachable = true
 [[tool.mypy.overrides]]
 module = "tests.*"
 disallow_untyped_defs = false
+disallow_untyped_calls = false
 
 [tool.ruff]
 line-length = 88

src/scitacean/_base_model.py

@@ -86,6 +86,31 @@ def _delete_ignored_args(self, args: Dict[str, Any]) -> None:
         for key in self._masked_fields:
             args.pop(key, None)
 
+    @classmethod
+    def user_model_type(cls) -> Optional[type]:
+        """Return the user model type for this model.
+
+        Returns ``None`` if there is no user model, e.g., for ``Dataset``
+        where there is a custom class instead of a plain model.
+        """
+        return None
+
+    @classmethod
+    def upload_model_type(cls) -> Optional[type]:
+        """Return the upload model type for this model.
+
+        Returns ``None`` if the model cannot be uploaded or this is an upload model.
+        """
+        return None
+
+    @classmethod
+    def download_model_type(cls) -> Optional[type]:
+        """Return the download model type for this model.
+
+        Returns ``None`` if this is a download model.
+        """
+        return None
+
     if is_pydantic_v1():
 
         @classmethod
@@ -143,7 +168,23 @@ def _upload_model_dict(self) -> Dict[str, Any]:
 
     @classmethod
     def from_download_model(cls, download_model: Any) -> BaseUserModel:
-        raise NotImplementedError()
+        raise NotImplementedError("Function does not exist for BaseUserModel")
+
+    @classmethod
+    def upload_model_type(cls) -> Optional[type]:
+        """Return the upload model type for this user model.
+
+        Returns ``None`` if the model cannot be uploaded.
+        """
+        return None
+
+    @classmethod
+    def download_model_type(cls) -> type:
+        """Return the download model type for this user model."""
+        # There is no sensible default value here as there always exists a download
+        # model.
+        # All child classes must implement this function.
+        raise NotImplementedError("Function does not exist for BaseUserModel")
 
 
 def construct(
@@ -159,6 +200,7 @@ def construct(
     -------
     If the model is created without validation, no fields will be converted
     to their proper type but will simply be whatever arguments are passed.
+    See ``model_construct`` or :class:`pydantic.BaseModel` for more information.
 
     A warning will be emitted in this case.
 

src/scitacean/_dataset_fields.py

@@ -12,7 +12,7 @@
 from __future__ import annotations
 
 from datetime import datetime, timezone
-from typing import Any, Dict, List, Literal, Optional, Tuple, Union
+from typing import Any, Dict, List, Literal, Optional, Tuple, Type, Union
 
 import dateutil.parser
 
@@ -21,7 +21,11 @@
 from .datablock import OrigDatablock
 from .filesystem import RemotePath
 from .model import (
+    construct,
+    BaseModel,
+    BaseUserModel,
     DownloadDataset,
+    DownloadLifecycle,
     Lifecycle,
     Relationship,
     Technique,
@@ -1062,12 +1066,44 @@ def _prepare_fields_from_download(
                 init_args[field.name] = getattr(download_model, field.scicat_name)
 
         init_args["meta"] = download_model.scientificMetadata
-        DatasetBase._convert_readonly_fields_in_place(read_only)
+        _convert_download_fields_in_place(init_args, read_only)
 
         return init_args, read_only
 
     @staticmethod
-    def _convert_readonly_fields_in_place(read_only: Dict[str, Any]) -> Dict[str, Any]:
-        if "_pid" in read_only:
-            read_only["_pid"] = _parse_pid(read_only["_pid"])
-        return read_only
+    def _convert_readonly_fields_in_place(read_only: Dict[str, Any]) -> None:
+        if (pid := read_only.get("_pid")) is not None:
+            read_only["_pid"] = _parse_pid(pid)
+
+
+def _convert_download_fields_in_place(
+    init_args: Dict[str, Any], read_only: Dict[str, Any]
+) -> None:
+    for mod, key in ((Technique, "techniques"), (Relationship, "relationships")):
+        init_args[key] = _list_field_from_download(mod, init_args.get(key))
+
+    DatasetBase._convert_readonly_fields_in_place(read_only)
+    if (lifecycle := read_only.get("_lifecycle")) is not None:
+        read_only["_lifecycle"] = Lifecycle.from_download_model(
+            _as_model(DownloadLifecycle, lifecycle)
+        )
+
+
+def _list_field_from_download(
+    mod: Type[BaseUserModel], value: Optional[List[Any]]
+) -> Optional[List[BaseUserModel]]:
+    if value is None:
+        return None
+    return [
+        mod.from_download_model(_as_model(mod.download_model_type(), item))
+        for item in value
+    ]
+
+
+# If validation fails, sub models are not converted automatically by Pydantic.
+def _as_model(
+    mod: Type[BaseModel], value: Union[BaseModel, Dict[str, Any]]
+) -> BaseModel:
+    if isinstance(value, dict):
+        return construct(mod, **value, _strict_validation=False)
+    return value

src/scitacean/dataset.py

@@ -25,12 +25,9 @@
 from .datablock import OrigDatablock
 from .file import File
 from .model import (
-    BaseUserModel,
     DatasetType,
     DownloadDataset,
     DownloadOrigDatablock,
-    Relationship,
-    Technique,
     UploadDerivedDataset,
     UploadOrigDatablock,
     UploadRawDataset,
@@ -60,8 +57,6 @@ def from_download_models(
             A new Dataset instance.
         """
         init_args, read_only = DatasetBase._prepare_fields_from_download(dataset_model)
-        for mod, key in ((Technique, "techniques"), (Relationship, "relationships")):
-            init_args[key] = _list_field_from_download(mod, init_args[key])
         dset = cls(**init_args)
         for key, val in read_only.items():
             setattr(dset, key, val)
@@ -459,11 +454,3 @@ def _list_field_for_upload(value: Optional[List[Any]]) -> Optional[List[Any]]:
     if value is None:
         return None
     return [item.make_upload_model() for item in value]
-
-
-def _list_field_from_download(
-    mod: Type[BaseUserModel], value: Optional[List[Any]]
-) -> Optional[List[Any]]:
-    if value is None:
-        return None
-    return [mod.from_download_model(item) for item in value]