Merge branch 'update-build-model' into add-training-data

Author: constantinpape

bioimageio/core/build_spec/build_model.py

@@ -632,7 +632,7 @@ def build_model(
     attachments: Optional[Dict[str, Union[str, List[str]]]] = None,
     packaged_by: Optional[List[str]] = None,
     run_mode: Optional[str] = None,
-    parent: Optional[Tuple[str, str]] = None,
+    parent: Optional[Dict[str, str]] = None,
     config: Optional[Dict[str, Any]] = None,
     dependencies: Optional[Union[Path, str]] = None,
     links: Optional[List[str]] = None,
@@ -709,7 +709,7 @@ def build_model(
         attachments: list of additional files to package with the model.
         packaged_by: list of authors that have packaged this model.
         run_mode: custom run mode for this model.
-        parent: id of the parent model from which this model is derived and sha256 of the corresponding weight file.
+        parent: id of the parent model from which this model is derived and sha256 of the corresponding rdf file.
         config: custom configuration for this model.
         dependencies: relative path to file with dependencies for this model.
         training_data: the training data for this model, either id for a bioimageio dataset or a dataset spec.
@@ -892,7 +892,7 @@ def build_model(
 
     if parent is not None:
         assert len(parent) == 2
-        kwargs["parent"] = {"uri": parent[0], "sha256": parent[1]}
+        kwargs["parent"] = parent
 
     if training_data is not None:
         if "id" in training_data:

example/bioimageio-core-usage.ipynb

@@ -10,19 +10,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c72ba149",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/pape/Work/bioimageio/spec-bioimage-io/bioimageio/spec/shared/_resolve_source.py:326: UserWarning: found cached /tmp/bioimageio_cache/https/raw.githubusercontent.com/bioimage-io/bioimage.io/main/site.config.json. Skipping download of https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/site.config.json.\n",
-      "  warnings.warn(f\"found cached {local_path}. Skipping download of {uri}.\")\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "import hashlib\n",
@@ -39,7 +30,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "74613461",
    "metadata": {},
    "outputs": [],
@@ -69,18 +60,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "2de51dae",
    "metadata": {},
    "outputs": [],
    "source": [
     "# the model can be loaded using different representations:\n",
     "\n",
     "# the doi of the zenodo entry corresponding to the model\n",
-    "rdf_doi = \"10.5281/zenodo.6028056\"\n",
+    "rdf_doi = \"10.5281/zenodo.6287342\"\n",
     "\n",
     "# the url of the yaml file containing the model resource description\n",
-    "rdf_url = \"https://zenodo.org/record/6028056/files/rdf.yaml\"\n",
+    "rdf_url = \"https://zenodo.org/record/6287342/files/rdf.yaml\"\n",
     "\n",
     "# FIXME the model currently does not show up on the website\n",
     "# filepath to the downloaded model (either zipped package or yaml)\n",
@@ -90,70 +81,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "ce884f8c",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "rdf.yaml: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3.20k/3.20k [00:00<00:00, 1.28MiB/s]\n",
-      "/home/pape/Work/bioimageio/spec-bioimage-io/bioimageio/spec/shared/schema.py:46: ValidationWarning: tags: Missing tags for categories: ['dims', 'framework', 'software']\n",
-      "  warnings.warn(msg, category=ValidationWarning)\n"
-     ]
-    },
-    {
-     "ename": "ValidationError",
-     "evalue": "{'_schema': ['Minimal shape [ 1.  2. 32. 32.] of output output0 is too small for halo [0, 0, 16, 16].']}",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mValidationError\u001b[0m                           Traceback (most recent call last)",
-      "\u001b[0;32m/tmp/ipykernel_44819/830282669.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# load model from link to rdf.yaml\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mmodel_resource\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbioimageio\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_resource_description\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrdf_url\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;32m~/Work/bioimageio/core-bioimage-io-python/bioimageio/core/resource_io/io_.py\u001b[0m in \u001b[0;36mload_resource_description\u001b[0;34m(source, weights_priority_order)\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0msource\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     40\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m     \u001b[0mraw_rd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mload_raw_resource_description\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msource\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mupdate_to_format\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"latest\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     43\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mraw_rd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"model\"\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mweights_priority_order\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Work/bioimageio/spec-bioimage-io/bioimageio/spec/io_.py\u001b[0m in \u001b[0;36mload_raw_resource_description\u001b[0;34m(source, update_to_format)\u001b[0m\n\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m     \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msub_spec\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconverters\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmaybe_convert\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 191\u001b[0;31m     \u001b[0mraw_rd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mschema\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    192\u001b[0m     \u001b[0mraw_rd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot_path\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mroot\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    193\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/software/conda/miniconda3/envs/main39/lib/python3.9/site-packages/marshmallow/schema.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(self, data, many, partial, unknown)\u001b[0m\n\u001b[1;32m    717\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0minvalid\u001b[0m \u001b[0mdata\u001b[0m \u001b[0mare\u001b[0m \u001b[0mpassed\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    718\u001b[0m         \"\"\"\n\u001b[0;32m--> 719\u001b[0;31m         return self._do_load(\n\u001b[0m\u001b[1;32m    720\u001b[0m             \u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmany\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmany\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpartial\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpartial\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0munknown\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0munknown\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpostprocess\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    721\u001b[0m         )\n",
-      "\u001b[0;32m~/software/conda/miniconda3/envs/main39/lib/python3.9/site-packages/marshmallow/schema.py\u001b[0m in \u001b[0;36m_do_load\u001b[0;34m(self, data, many, partial, unknown, postprocess)\u001b[0m\n\u001b[1;32m    902\u001b[0m             \u001b[0mexc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mValidationError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merrors\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalid_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mresult\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    903\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhandle_error\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmany\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmany\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpartial\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpartial\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 904\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mexc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    905\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    906\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mValidationError\u001b[0m: {'_schema': ['Minimal shape [ 1.  2. 32. 32.] of output output0 is too small for halo [0, 0, 16, 16].']}"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# load model from link to rdf.yaml\n",
-    "# FIXME need to update the min shape, but can't right now because the model is not on the website\n",
     "model_resource = bioimageio.core.load_resource_description(rdf_url)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "c1230b2d",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "rdf.yaml: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.92k/2.92k [00:00<00:00, 1.02MiB/s]\n"
-     ]
-    },
-    {
-     "ename": "ValidationError",
-     "evalue": "{'_schema': ['Minimal shape [ 1.  2. 32. 32.] of output output is too small for halo [0, 0, 16, 16].']}",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mValidationError\u001b[0m                           Traceback (most recent call last)",
-      "\u001b[0;32m/tmp/ipykernel_44819/725076596.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# load model from doi\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mmodel_resource\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbioimageio\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_resource_description\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrdf_doi\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;32m~/Work/bioimageio/core-bioimage-io-python/bioimageio/core/resource_io/io_.py\u001b[0m in \u001b[0;36mload_resource_description\u001b[0;34m(source, weights_priority_order)\u001b[0m\n\u001b[1;32m     39\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0msource\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     40\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 41\u001b[0;31m     \u001b[0mraw_rd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mload_raw_resource_description\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msource\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mupdate_to_format\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"latest\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     42\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     43\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mraw_rd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtype\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"model\"\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mweights_priority_order\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/Work/bioimageio/spec-bioimage-io/bioimageio/spec/io_.py\u001b[0m in \u001b[0;36mload_raw_resource_description\u001b[0;34m(source, update_to_format)\u001b[0m\n\u001b[1;32m    189\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    190\u001b[0m     \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msub_spec\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconverters\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmaybe_convert\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 191\u001b[0;31m     \u001b[0mraw_rd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mschema\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    192\u001b[0m     \u001b[0mraw_rd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot_path\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mroot\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    193\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m~/software/conda/miniconda3/envs/main39/lib/python3.9/site-packages/marshmallow/schema.py\u001b[0m in \u001b[0;36mload\u001b[0;34m(self, data, many, partial, unknown)\u001b[0m\n\u001b[1;32m    717\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0minvalid\u001b[0m \u001b[0mdata\u001b[0m \u001b[0mare\u001b[0m \u001b[0mpassed\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    718\u001b[0m         \"\"\"\n\u001b[0;32m--> 719\u001b[0;31m         return self._do_load(\n\u001b[0m\u001b[1;32m    720\u001b[0m             \u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmany\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmany\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpartial\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpartial\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0munknown\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0munknown\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpostprocess\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    721\u001b[0m         )\n",
-      "\u001b[0;32m~/software/conda/miniconda3/envs/main39/lib/python3.9/site-packages/marshmallow/schema.py\u001b[0m in \u001b[0;36m_do_load\u001b[0;34m(self, data, many, partial, unknown, postprocess)\u001b[0m\n\u001b[1;32m    902\u001b[0m             \u001b[0mexc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mValidationError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merrors\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalid_data\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mresult\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    903\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhandle_error\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmany\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmany\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpartial\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpartial\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 904\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mexc\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    905\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    906\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mValidationError\u001b[0m: {'_schema': ['Minimal shape [ 1.  2. 32. 32.] of output output is too small for halo [0, 0, 16, 16].']}"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# load model from doi\n",
     "model_resource = bioimageio.core.load_resource_description(rdf_doi)"
@@ -451,13 +393,13 @@
     "\n",
     "# we use the `parent` field to indicate that the new model is created based on\n",
     "# the nucleus segmentation model we have obtained from bioimage.io\n",
-    "# this field is optional and only needs to be given for models that are created based on\n",
-    "# other models from bioimage.io\n",
+    "# this field is optional and only needs to be given for models that are created based on other models from bioimage.io\n",
     "# the parent is specified via it's doi and the hash of its rdf file\n",
-    "rdf_file = os.path.join(model_resource.root_path, \"rdf.yaml\")\n",
+    "model_root_folder = os.path.split(model_resource.weights[\"pytorch_state_dict\"].source)[0]\n",
+    "rdf_file = os.path.join(model_root_folder, \"rdf.yaml\")\n",
     "with open(rdf_file, \"rb\") as f:\n",
-    "    weight_hash = hashlib.sha256(f.read()).hexdigest()\n",
-    "parent = (rdf_doi, weight_hash)\n",
+    "    rdf_hash = hashlib.sha256(f.read()).hexdigest()\n",
+    "parent = {\"uri\": rdf_doi, \"sha256\": rdf_hash}\n",
     "\n",
     "# the name of the new model and where to save the zipped model package\n",
     "name = \"new-model1\"\n",