User Guide: CLI Validator Tool (`signaljourney-validate`)¶

This guide provides comprehensive details on using the signaljourney-validate command-line interface (CLI) to validate signalJourney JSON files.

Installation¶

The CLI tool is installed as part of the signaljourney-validator Python package:

pip install signaljourney-validator

This makes the signaljourney-validate command available in your terminal.

Basic Usage¶

The primary command is validate. It takes the path to a signalJourney JSON file or a directory containing such files as its main argument.

signaljourney-validate [OPTIONS] PATH

PATH: Path to a single *_signalJourney.json file or a directory.

Examples:

Validate a single file:

signaljourney-validate path/to/my_pipeline.signalJourney.json

Output on success:

Validating: path/to/my_pipeline.signalJourney.json ... OK

Output on failure:

Validating: path/to/my_pipeline.signalJourney.json ... FAILED
  - Error at 'pipelineInfo/version': '1.0' is not a 'string' -- Suggestion: Change value type from 'float' to 'string'.
  - Error at 'processingSteps/0/stepId': Required property 'stepId' is missing. -- Suggestion: Ensure required property or properties ('stepId') are present.

Validate all *_signalJourney.json files in a directory (non-recursive):

signaljourney-validate path/to/my_pipelines/

Output:

Scanning directory: path/to/my_pipelines/
Validating: path/to/my_pipelines/pipeline_a.signalJourney.json ... OK
Validating: path/to/my_pipelines/pipeline_b.signalJourney.json ... FAILED
  - Error at ...

Validate recursively through subdirectories:

signaljourney-validate -r path/to/project/
# OR
signaljourney-validate --recursive path/to/project/

Output:

Scanning directory: path/to/project/ recursively
Validating: path/to/project/pipeline1.signalJourney.json ... OK
Validating: path/to/project/derivatives/pipeline2.signalJourney.json ... OK

Options¶

-s, --schema PATH: Validate against a custom JSON schema file instead of the default one bundled with the package.
```
signaljourney-validate -s path/to/custom_schema.json my_file.signalJourney.json
```
-r, --recursive: Recursively search for *_signalJourney.json files in subdirectories when PATH is a directory.
-o, --output-format [text|json]: Specify the output format. Defaults to text (human-readable). Use json for machine-readable output.
```
signaljourney-validate -o json path/to/directory/
```
-v, --verbose: Enable verbose output in text format. Shows more error details, including the specific validator and schema path involved, in addition to the basic message and suggestion.
```
signaljourney-validate -v path/to/invalid_file.signalJourney.json
```
--bids: Enable experimental BIDS context validation checks (see below).

--bids-root PATH: Specify the path to the BIDS dataset root directory. Required if --bids is used.

signaljourney-validate --bids --bids-root /path/to/bids_dataset path/to/bids_dataset/derivatives/...

-h, --help: Show the help message and exit.
--version: Show the version of the signaljourney-validator package and exit.

Output Formats¶

text (Default):
- Prints the validation status (OK or FAILED) for each file.
- On failure, lists errors with the path within the JSON, the error message, and any suggestions.
- If --verbose is used, adds more detail to error messages.

json:

Outputs a single JSON object.
Contains an overall_status ("passed" or "failed").
Contains a files array, where each element is an object representing a validated file.
Each file object includes filepath, status ("passed", "failed", or "error" if processing failed), and an errors array if applicable.
The errors array contains objects with detailed error information: message, path, schema_path, validator, validator_value, instance_value, suggestion.

Example JSON Output Fragment:

{
  "files": [
    {
      "filepath": "path/to/valid_file.signalJourney.json",
      "status": "passed",
      "errors": []
    },
    {
      "filepath": "path/to/invalid_file.signalJourney.json",
      "status": "failed",
      "errors": [
        {
          "message": "'1.0' is not of type 'string'",
          "path": ["pipelineInfo", "version"],
          "schema_path": ["properties", "pipelineInfo", "properties", "version", "type"],
          "validator": "type",
          "validator_value": "string",
          "instance_value": "1.0",
          "suggestion": "Change value type from 'float' to 'string'."
        }
      ]
    }
  ],
  "bids_mode_enabled": false,
  "overall_status": "failed"
}

BIDS Context Validation (`--bids`)¶

This is an experimental feature.

When the --bids flag is used (along with --bids-root), the validator attempts to perform checks relevant to the BIDS standard:

(Planned) Verify the signalJourney file is located appropriately within the BIDS derivatives/ structure.
(Planned) Check if file paths referenced within the signalJourney file (e.g., in inputSources) exist relative to the BIDS root.

Currently, enabling this flag primarily prints an informational message in the underlying library. Full BIDS validation logic will be added in future versions.

Exit Codes¶

The CLI uses the following exit codes, useful for scripting:

0: Validation successful (all files passed, or no *_signalJourney.json files found when using json output).
1: Validation failed (one or more files failed validation or encountered a processing error like file not found/invalid JSON). Also used if no *_signalJourney.json files are found when using text output.
>1: Typically indicates an error with the CLI arguments themselves (handled by click).

User Guide: CLI Validator Tool (signaljourney-validate)¶