Updater 0.1 -> 0.2

src/dgbowl_schemas/tomato/payload_0_1/__init__.py

@@ -3,11 +3,15 @@
 from .tomato import Tomato
 from .sample import Sample
 from .method import Method
+from ..payload_0_2 import Payload as NewPayload
 
+import logging
 from pathlib import Path
 import yaml
 import json
 
+logger = logging.getLogger(__name__)
+
 
 class Payload(BaseModel, extra=Extra.forbid):
     version: Literal["0.1"]
@@ -46,3 +50,10 @@ def extract_methodfile(cls, values):  # pylint: disable=E0213
             assert "method" in method
             values["method"] = method["method"]
         return values
+
+    def update(self):
+        logger.info("Updating from Payload-0.1 to Payload-0.2")
+        md = self.dict(exclude_defaults=True, exclude_none=True)
+        md["version"] = "0.2"
+
+        return NewPayload(**md)

src/dgbowl_schemas/tomato/payload_0_2/tomato.py

@@ -1,5 +1,5 @@
 from pydantic.v1 import BaseModel, Extra, Field
-from typing import Literal
+from typing import Literal, Optional
 
 
 class Tomato(BaseModel, extra=Extra.forbid):
@@ -33,5 +33,5 @@ class Snapshot(BaseModel, extra=Extra.forbid):
     output: Output = Field(default_factory=Output)
     """Options for final FAIR data output."""
 
-    snapshot: Snapshot = None
+    snapshot: Optional[Snapshot] = None
     """Options for periodic snapshotting."""

tests/test_payload.py

@@ -27,3 +27,24 @@ def test_payload_yml(inpath, datadir):
     with open(f"ref.{inpath.replace('yml','json')}", "r") as ofile:
         ref = json.load(ofile)
     assert ret == ref
+
+
+@pytest.mark.parametrize(
+    "inpath",
+    [
+        "ts0.yml",  # 0.1
+        "ts1.yml",  # 0.1
+        "ts2.yml",  # 0.1
+        "ts3.yml",  # 0.1
+        "ts4.yml",  # 0.1
+    ],
+)
+def test_payload_update_chain(inpath, datadir):
+    os.chdir(datadir)
+    with open(inpath, "r") as infile:
+        indict = yaml.safe_load(infile)
+    ret = to_payload(**indict)
+    while hasattr(ret, "update"):
+        ret = ret.update()
+    print(f"{ret=}")
+    assert ret.version == "0.2"