Merge pull request #167 from BIH-CEI/165-api-design-with-abc

165 api design with abc

.gitignore

@@ -161,3 +161,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
+
+# VsCode
+*.code-workspace
+.vscode

src/phenopacket_mapper/_api/__init__.py

@@ -0,0 +1,76 @@
+"""
+This package is intended to expose the PhenopacketMapper API to the user.
+"""
+
+import abc
+from typing import Tuple, Iterable, Iterator
+from dataclasses import dataclass
+
+
+class DataModelDefiner(metaclass=abc.ABCMeta):
+    """
+    Take some data model definition and try to load it into :class:`DataModel`.
+
+    E.g. protobuf model "definer".
+    """
+    pass
+
+
+class DataModel(metaclass=abc.ABCMeta):
+    """
+    Value class.
+    The fields:
+     - label, version
+     - a root `DataNode`, it must be there (not `Optional`)
+     - resources (maybe generate dynamically, or keep as a list)
+
+    We want to be able to (de)serialize this.
+    """
+    pass
+
+
+@dataclass
+class DataNode(metaclass=abc.ABCMeta):
+    """
+    This is very much like Jackson (Java) `TreeNode`,
+    because it can be many things.
+
+    The common things may include
+    - label
+    - maybe it knows about the parent (optional) and children
+
+    We want to be able to (de)serialize this.
+    """
+    label: str
+    id: str
+    required: bool
+
+
+class DataInstance:
+    pass
+
+
+class Transformation(metaclass=abc.ABCMeta):
+    """
+
+    """
+    steps: Tuple
+
+
+class Mapper:
+
+    def __init__(
+        self,
+        transformation: Transformation,
+    ):
+        pass
+
+    def transform_dataset(
+        self,
+        data_set: Iterable[DataInstance],
+    ) -> Iterator[DataInstance]:
+        return map(lambda item: self.transform(item), data_set)
+
+    def transform(self, item: DataInstance) -> DataInstance:
+        # TODO: implement based on self.transformation
+        pass

src/phenopacket_mapper/data_standards/data_model.py

@@ -55,6 +55,7 @@ class DataField:
     :ivar required: Required flag of the field
     :ivar ordinal: Ordinal of the field (E.g. 1.1, 1.2, 2.1, etc.)
     """
+    # TODO: change section into path to data
     name: str = field()
     specification: Union[ValueSet, type, List[type]] = field()
     id: str = field(default=None)

src/phenopacket_mapper/mapping/phenopacket_building_block.py

@@ -44,7 +44,7 @@ def map(self, instance: DataModelInstance):
         return self.phenopacket_element(**kwargs)
 
 
-def map_single(key, e, instance, kwargs):
+def map_single(key, e, instance: DataModelInstance, kwargs):
     if isinstance(e, DataField):
         data_field = e
         try: