02-patch-metadata-per-category.py

#!/usr/bin/env python
import json
from json import JSONDecodeError

import elabapi_python
from client import api_client

# define which category's items are patched
RESOURCE_CATEGORY_ID = 3

# Synchronize metadata of the item_type with existing items
# See: https://github.com/elabftw/elabftw/issues/3524

# create an instance of Items api
itemsApi = elabapi_python.ItemsApi(api_client)

metadata = {
    "elabftw": {
        "extra_fields_groups": [
            {"id": 1, "name": "Drug settings"},
            {"id": 2, "name": "Mice info"},
        ]
    },
    "extra_fields": {
        "Drug addition": {
            "type": "datetime-local",
            "value": "",
            "group_id": 1,
            "required": True,
            "description": "Time when drug is added",
        },
        "Drug concentration": {
            "type": "number",
            "unit": "mM",
            "units": ["mM", "μM", "nM"],
            "value": "",
            "group_id": 1,
            "required": True,
        },
        "Mouse sex": {
            "type": "select",
            "value": "Male",
            "options": ["Male", "Female"],
            "group_id": 2,
        },
    },
}

for item in itemsApi.read_items(cat=RESOURCE_CATEGORY_ID, limit=9999):
    # skip items with metadata already
    if not item.metadata:
        print(f"Patching item {item.id}")
        try:
            itemsApi.patch_item(item.id, body={"metadata": json.dumps(metadata)})
        except JSONDecodeError as e:
            raise ValueError(
                "'metadata' passed to API request body contains invalid JSON."
            ) from e