Add migration to remove output field which was incorrectly set in the frontend in UploadedFileSource

README.md

@@ -28,8 +28,6 @@ And you can skip the backup (simply edit in place):
 python -m opencloning_linkml.migrations.migrate file.json --no-backup
 ```
 
-
-
 ## Developer Documentation
 
 The python package can be installed from PyPI:
@@ -45,6 +43,23 @@ Use the `make` command to generate project artefacts:
 * `make deploy`: deploys site
 </details>
 
+### Creating a migration
+
+To add a migration from version `X.Y.Z` to a new version `A.B.C`, follow these steps:
+
+1. **Archive the current model**: Save a copy of the current Pydantic model to `src/opencloning_linkml/migrations/model_archive/vA_B_C.py`. This file should contain the complete model classes for version `A.B.C` (typically copied from `src/opencloning_linkml/datamodel/_models.py` after generating the new version).
+
+2. **Create the transformation file**: Create a new file `src/opencloning_linkml/migrations/transformations/vX_Y_Z_to_vA_B_C.py` with a migration function
+
+3. **Register the migration**: Add the migration to `src/opencloning_linkml/migrations/__init__.py`:
+   - Import the migration function: `from .transformations.vX_Y_Z_to_vA_B_C import migrate_X_Y_Z_to_A_B_C`
+   - Add it to the `load_migrations()` return dictionary: `("X.Y.Z", "A.B.C"): migrate_X_Y_Z_to_A_B_C`
+
+4. **Add a test**: Add a test to `tests/test_migration.py` to ensure the migration works as expected.
+
+**Example**: See `v0_2_8_to_v0_2_9.py` for a simple transformation example, or `v0_2_9_to_v_0_4_0.py` for a more complex migration with ID remapping and structural changes.
+
+
 ## Credits
 
 This project was made with

project/jsonld/opencloning_linkml.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2025-10-20T16:29:26",
+      "generation_date": "2025-11-17T18:53:28",
       "source": "opencloning_linkml.yaml"
    },
    "@context": {

project/jsonld/opencloning_linkml.jsonld

@@ -3542,9 +3542,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "opencloning_linkml.yaml",
-  "source_file_date": "2025-10-20T16:11:45",
+  "source_file_date": "2025-11-17T18:34:01",
   "source_file_size": 26051,
-  "generation_date": "2025-10-20T16:29:26",
+  "generation_date": "2025-11-17T18:53:29",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/opencloning_linkml.context.jsonld",

project/python/opencloning_linkml.py

@@ -1,5 +1,5 @@
 # Auto generated from opencloning_linkml.yaml by pythongen.py version: 0.0.1
-# Generation date: 2025-10-20T16:29:27
+# Generation date: 2025-11-17T18:53:30
 # Schema: OpenCloning_LinkML
 #
 # id: https://opencloning.github.io/OpenCloning_LinkML

src/opencloning_linkml/migrations/__init__.py

@@ -19,11 +19,13 @@ def load_migrations() -> MigrationDict:
     from .transformations.v0_2_6_1_to_v_0_2_8 import migrate_0_2_6_1_to_0_2_8  # noqa: F401
     from .transformations.v0_2_8_to_v0_2_9 import migrate_0_2_8_to_0_2_9  # noqa: F401
     from .transformations.v0_2_9_to_v_0_4_0 import migrate_0_2_9_to_0_4_0  # noqa: F401
+    from .transformations.v0_4_0_to_v0_4_6 import migrate_0_4_0_to_0_4_6  # noqa: F401
 
     return {
         ("0.2.6.1", "0.2.8"): migrate_0_2_6_1_to_0_2_8,
         ("0.2.8", "0.2.9"): migrate_0_2_8_to_0_2_9,
         ("0.2.9", "0.4.0"): migrate_0_2_9_to_0_4_0,
+        ("0.4.0", "0.4.6"): migrate_0_4_0_to_0_4_6,
     }