src/jupyter_notebooks/bids/validate_bids_dataset.ipynb

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    "## Validate HED in a BIDS dataset.\n",
    "\n",
    "Validating HED annotations as you develop them makes the annotation process much easier and faster to debug. This notebook validates HED in a BIDS dataset.\n",
    "\n",
    "The tool creates a `BidsDataset` object, which represents the information from a BIDS dataset that is relevant to HED, including the `dataset_description.json`, all `events.tsv` files, and all `events.json` sidecar files.\n",
    "\n",
    "The `validate` method of `BidsDataset` first validates all of the `events.json` sidecars and then assembles the relevant sidecars for each `events.tsv` file and validates it. The validation uses the HED schemas specified in the `HEDVersion` field of the dataset's `dataset_description.json` file.\n",
    "\n",
    "The script does the following steps:\n",
    "\n",
    "1. Set the dataset location (`dataset_path`) to the absolute path of the root of your BIDS dataset.\n",
    "2. Indicates whether to check for warnings during validation (`check_for_warnings`).\n",
    "3. Create a `BidsDataset` for the dataset.\n",
    "4. Validate the dataset and output the issues.\n",
    "\n",
    "**Note:** This validation pertains to event files and HED annotation only. It does not do a full BIDS validation.\n",
    "\n",
    "\n",
    "For validation of a single `events.json` file during annotation development, users often find the [**online sidecar tools**](https://hedtools.ucsd.edu/hed/sidecar) convenient, but the online tool does not provide complete dataset-level validation."
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      "Using HEDTOOLS version: {'date': '2024-02-05T17:04:52-0600', 'dirty': True, 'error': None, 'full-revisionid': '7c05a5461ed273b9a39bddf27d99c2e767ca1aab', 'version': '0.4.0+147.g7c05a54.dirty'}\n",
      "Number of issues: 0\n",
      "No HED validation errors\n"
     ]
    }
   ],
   "source": [
    "from hed.errors import get_printable_issue_string\n",
    "from hed.tools import BidsDataset\n",
    "from hed import _version as vr\n",
    "\n",
    "print(f\"Using HEDTOOLS version: {str(vr.get_versions())}\")\n",
    "\n",
    "## Set the dataset location and the check_for_warnings flag\n",
    "check_for_warnings = True\n",
    "dataset_dir = '../../../datasets/eeg_ds004105s_hed'\n",
    "# outfile = 'temp.txt'\n",
    "outfile = ''\n",
    "\n",
    "## Validate the dataset\n",
    "bids = BidsDataset(dataset_dir)\n",
    "issue_list = bids.validate(check_for_warnings=check_for_warnings)\n",
    "if issue_list:\n",
    "    issue_str = get_printable_issue_string(issue_list, \"HED validation errors: \", skip_filename=False)\n",
    "else:\n",
    "    issue_str = \"No HED validation errors\"\n",
    "# print(issue_str)\n",
    "print(f\"Number of issues: {len(issue_list)}\")\n",
    "if outfile and issue_list:\n",
    "    with open(outfile, 'w') as fp:\n",
    "        fp.write(issue_str)\n",
    "else:\n",
    "    print(f\"{issue_str}\")\n"
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