misc flamby integration

- rename FlambyDatasetMetadata to FlambyDatasetMetadataBlock for naming
  homogeneity
- misc proto docstring

fedbiomed/common/data/__init__.py

@@ -9,7 +9,7 @@
 from ._tabular_dataset import TabularDataset
 from ._medical_datasets import NIFTIFolderDataset, MedicalFolderDataset, MedicalFolderBase, MedicalFolderController, \
     MedicalFolderLoadingBlockTypes
-from ._flamby_dataset import FlambyDatasetMetadata, FlambyLoadingBlockTypes, \
+from ._flamby_dataset import FlambyDatasetMetadataBlock, FlambyLoadingBlockTypes, \
     FlambyDataset, discover_flamby_datasets
 from ._data_loading_plan import (DataLoadingBlock,
                                  MapperBlock,
@@ -33,7 +33,7 @@
     "DataLoadingPlan",
     "DataLoadingPlanMixin",
     "SerializationValidation",
-    "FlambyDatasetMetadata",
+    "FlambyDatasetMetadataBlock",
     "FlambyLoadingBlockTypes",
     "FlambyDataset",
     "discover_flamby_datasets"

fedbiomed/common/data/_flamby_dataset.py

@@ -34,7 +34,7 @@ class FlambyLoadingBlockTypes(DataLoadingBlockTypes, Enum):
     FLAMBY_DATASET_METADATA: str = 'flamby_dataset_metadata'
 
 
-class FlambyDatasetMetadata(DataLoadingBlock):
+class FlambyDatasetMetadataBlock(DataLoadingBlock):
     """Metadata about a Flamby Dataset.
 
     Includes information on:
@@ -48,7 +48,7 @@ def __init__(self):
             "flamby_center_id": None
         }
         self._serialization_validator.validation_scheme.update(
-            FlambyDatasetMetadata._extra_validation_scheme())
+            FlambyDatasetMetadataBlock._extra_validation_scheme())
 
     def serialize(self) -> dict:
         """Serializes the class in a format similar to json.
@@ -86,6 +86,9 @@ def apply(self) -> dict:
         Note that the flamby_dataset_name will be the same as the module name required to instantiate the FedClass.
         However, it will not contain the full module path, hence to properly import this module it must be
         prepended with `flamby.datasets`, for example `import flamby.datasets.flamby_dataset_name`
+
+        Returns:
+            this data loading block's metadata
         """
         if any([v is None for v in self.metadata.values()]):
             msg = f"{ErrorNumbers.FB316}. Attempting to read Flamby dataset metadata, but " \
@@ -105,7 +108,7 @@ def _validate_flamby_dataset_name(cls, name: str):
     def _extra_validation_scheme(cls) -> dict:
         return {
             'flamby_dataset_name': {
-                'rules': [str, FlambyDatasetMetadata._validate_flamby_dataset_name],
+                'rules': [str, FlambyDatasetMetadataBlock._validate_flamby_dataset_name],
                 'required': True
             },
             'flamby_center_id': {
@@ -123,7 +126,7 @@ class FlambyDataset(DataLoadingPlanMixin, Dataset):
 
     A FlambyDataset is always created in an empty state, and it **requires** a DataLoadingPlan to be finalized to a
     correct state. The DataLoadingPlan must contain at least the following DataLoadinBlock key-value pair:
-    - FlambyLoadingBlockTypes.FLAMBY_DATASET_METADATA : FlambyDatasetMetadata
+    - FlambyLoadingBlockTypes.FLAMBY_DATASET_METADATA : FlambyDatasetMetadataBlock
 
     The lifecycle of the DataLoadingPlan and the wrapped FedClass are tightly interlinked: when the DataLoadingPlan
     is set, the wrapped FedClass is initialized and instantiated. When the DataLoadingPlan is cleared, the wrapped

fedbiomed/node/cli_utils/_database.py

@@ -6,7 +6,7 @@
 
 from fedbiomed.common.exceptions import FedbiomedDatasetError, FedbiomedDatasetManagerError
 from fedbiomed.common.logger import logger
-from fedbiomed.common.data import MedicalFolderController, DataLoadingPlan, FlambyDatasetMetadata, \
+from fedbiomed.common.data import MedicalFolderController, DataLoadingPlan, FlambyDatasetMetadataBlock, \
     FlambyLoadingBlockTypes
 from fedbiomed.node.cli_utils._medical_folder_dataset import add_medical_folder_dataset_from_cli
 from fedbiomed.node.dataset_manager import DatasetManager
@@ -123,7 +123,7 @@ def add_database(interactive: bool = True,
 
                 # Build the DataLoadingPlan with the selected dataset type and center id
                 data_loading_plan = DataLoadingPlan()
-                metadata_dlb = FlambyDatasetMetadata()
+                metadata_dlb = FlambyDatasetMetadataBlock()
                 metadata_dlb.metadata = {
                     'flamby_dataset_name': available_flamby_datasets[flamby_dataset_index],
                     'flamby_center_id': center_id

tests/test_flamby.py

@@ -6,7 +6,7 @@
 
 from fedbiomed.common.exceptions import FedbiomedDatasetError, FedbiomedDatasetValueError, \
     FedbiomedLoadingBlockValueError, FedbiomedLoadingBlockError
-from fedbiomed.common.data import FlambyDataset, FlambyLoadingBlockTypes, FlambyDatasetMetadata, \
+from fedbiomed.common.data import FlambyDataset, FlambyLoadingBlockTypes, FlambyDatasetMetadataBlock, \
     DataLoadingPlan, discover_flamby_datasets
 from testsupport.testing_data_loading_block import LoadingBlockForTesting, LoadingBlockTypesForTesting
 
@@ -21,7 +21,7 @@ class TestFlamby(unittest.TestCase):
     def test_flamby_01_loading_blocks(self, patched_discover):
         """Test that the custom DataLoadingBlocks for FlambyDataset work as expected."""
         # Base case for FlambyDatasetSelectorLoadingBlock when there are no errors
-        dlb = FlambyDatasetMetadata()
+        dlb = FlambyDatasetMetadataBlock()
         dlb.metadata['flamby_dataset_name'] = 'fed_flamby_test'
         dlb.metadata['flamby_center_id'] = 42
 
@@ -33,28 +33,28 @@ def test_flamby_01_loading_blocks(self, patched_discover):
         self.assertIn('loading_block_class', serialized_dataset_type)
         self.assertIn('loading_block_module', serialized_dataset_type)
         self.assertIn('dlb_id', serialized_dataset_type)
-        _ = FlambyDatasetMetadata().deserialize(serialized_dataset_type)  # assert no errors raised
+        _ = FlambyDatasetMetadataBlock().deserialize(serialized_dataset_type)  # assert no errors raised
 
         # Assert raises when dataset name is of wrong type
         serialized_dataset_type['flamby_dataset_name'] = 0
         with self.assertRaises(FedbiomedLoadingBlockValueError):
-            _ = FlambyDatasetMetadata().deserialize(serialized_dataset_type)
+            _ = FlambyDatasetMetadataBlock().deserialize(serialized_dataset_type)
         # Assert raises when center id is of wrong type
         serialized_dataset_type['flamby_center_id'] = 'a string'
         with self.assertRaises(FedbiomedLoadingBlockValueError):
-            _ = FlambyDatasetMetadata().deserialize(serialized_dataset_type)
+            _ = FlambyDatasetMetadataBlock().deserialize(serialized_dataset_type)
         # Assert raises when dataset name is not one of the flamby datasets
         serialized_dataset_type['flamby_dataset_name'] = 'non-existing name'
         with self.assertRaises(FedbiomedLoadingBlockValueError):
-            _ = FlambyDatasetMetadata().deserialize(serialized_dataset_type)
+            _ = FlambyDatasetMetadataBlock().deserialize(serialized_dataset_type)
         # Assert calling apply gives correct result
         self.assertDictEqual(dlb.apply(),
                              {'flamby_dataset_name': 'fed_flamby_test',
                               'flamby_center_id': 42
                               })
         # Assert exception raised when calling apply on uninitialized loading block
         with self.assertRaises(FedbiomedLoadingBlockError):
-            FlambyDatasetMetadata().apply()
+            FlambyDatasetMetadataBlock().apply()
 
     def test_flamby_02_fed_class_initialization(self):
         """Test that initialization of the FedClass happens correctly.
@@ -70,7 +70,7 @@ def test_flamby_02_fed_class_initialization(self):
             dataset.get_center_id()
 
         # define dlp
-        dlb = FlambyDatasetMetadata()
+        dlb = FlambyDatasetMetadataBlock()
         dlb.metadata = {'flamby_dataset_name': 'fed_flamby_test',
                         'flamby_center_id': 0}
         dlp = DataLoadingPlan({FlambyLoadingBlockTypes.FLAMBY_DATASET_METADATA: dlb})
@@ -136,7 +136,7 @@ def test_flamby_03_transform(self):
                 dataset.init_transform('Wrong type')
 
         # define dlp
-        dlb = FlambyDatasetMetadata()
+        dlb = FlambyDatasetMetadataBlock()
         dlb.metadata = {'flamby_dataset_name': 'fed_flamby_test',
                         'flamby_center_id': 0}
         dlp = DataLoadingPlan({FlambyLoadingBlockTypes.FLAMBY_DATASET_METADATA: dlb})
@@ -187,7 +187,7 @@ def test_flamby_99_discover_flamby_datasets(self):
         dataset = FlambyDataset()
         for flamby_dataset_name in datasets.values():
             # define dlp
-            dlb = FlambyDatasetMetadata()
+            dlb = FlambyDatasetMetadataBlock()
             dlb.metadata = {'flamby_dataset_name': flamby_dataset_name,
                             'flamby_center_id': 0}
             dlp = DataLoadingPlan({FlambyLoadingBlockTypes.FLAMBY_DATASET_METADATA: dlb})