LibBidsShWrapper (nf-bids 0.3.0 API)

Summary:
Constructor
Method

| Detail:
Constructor
Method

nfneuro.parser.LibBidsShWrapper

```
@groovy.util.logging.Slf4j
@groovy.transform.CompileStatic
class LibBidsShWrapper
extends java.lang.Object
```
Wrapper for the libBIDS.sh bash library.
Locates the libBIDS.sh script (embedded in the plugin distribution, checked out as a git submodule, or provided explicitly by the caller), then invokes libBIDSsh_parse_bids_to_table to produce a TSV file that is subsequently read by nfneuro.plugin.util.BidsCsvParser.

All user-supplied paths are validated against a shell-metacharacter deny-list before being passed to the subprocess to prevent command injection.

Constructor Summary

Constructors
Constructor and description
`LibBidsShWrapper()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`java.lang.String`	`getLibBidsVersion(java.lang.String scriptPath)` Attempt to extract the version string from a `libBIDS.sh` script.
	`java.io.File`	`parseBidsToTable(java.lang.String bidsDir, java.lang.String libBidsShPath, java.lang.Boolean bidsignore, java.lang.Boolean defaultIgnores)` Parse BIDS directory to TSV table using libBIDS.sh
	`boolean`	`validateLibBidsScript(java.lang.String scriptPath)` Verify that a `libBIDS.sh` script exists, is readable, and contains the expected `libBIDSsh_parse_bids_to_table` function signature.

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll(), java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait()`

- Constructor Detail
  - LibBidsShWrapper()
- Method Detail
  - java.lang.String getLibBidsVersion(java.lang.String scriptPath)
    
    Attempt to extract the version string from a libBIDS.sh script.
    Looks for a VERSION="x.y.z" assignment near the top of the file.
    
    Parameters:
    scriptPath - absolute path to the libBIDS.sh file
    Returns:
    the version string (e.g. "1.2.0"), or "unknown" if not found or on any error
  - java.io.File parseBidsToTable(java.lang.String bidsDir, java.lang.String libBidsShPath, java.lang.Boolean bidsignore, java.lang.Boolean defaultIgnores)
    
    Parse BIDS directory to TSV table using libBIDS.sh Executes the bash script and captures TSV output
    reference:
    libbids_sh_parse process implementation: https://github.com/agahkarakuzu/bids2nf/blob/main/modules/parsers/lib_bids_sh_parser.nf#L1-L28
    
    Parameters:
    bidsDir - Path to BIDS dataset
    libBidsShPath - Path to libBIDS.sh (optional, auto-detects if not provided)
    Returns:
    File containing parsed TSV data
  - boolean validateLibBidsScript(java.lang.String scriptPath)
    
    Verify that a libBIDS.sh script exists, is readable, and contains the expected libBIDSsh_parse_bids_to_table function signature.
    Parameters:
    scriptPath - absolute path to the candidate libBIDS.sh file
    Returns:
    true if the script is usable; false otherwise (errors are logged)

Summary:
Constructor
Method

| Detail:
Constructor
Method

Groovy Documentation