BidsHandler (nf-bids 0.3.0 API)

nfneuro.channel.BidsHandler

```
@groovy.util.logging.Slf4j
@groovy.transform.CompileStatic
class BidsHandler
extends java.lang.Object
```
Fluent builder that orchestrates the full BIDS-to-channel pipeline.
Typical usage (via BidsChannelFactory):
```
 new BidsHandler()
     .withConfig(configPath)
     .withBidsDir(bidsDir)
     .withOpts(options)
     .withParser(new BidsParser(session))
     .ignite(session)
 
```
Internally the handler:
1. Loads and validates the YAML configuration via nfneuro.plugin.config.BidsConfigLoader.
2. Parses the BIDS directory into nfneuro.plugin.model.BidsFile objects via nfneuro.plugin.parser.BidsParser.
3. Routes files to the correct nfneuro.plugin.grouping.BaseSetHandler sub-class (plain / named / sequential / mixed) depending on the configuration analysis.
4. Applies cross-modal broadcasting and emits a flat [meta, data…] map per group.

Constructor Summary

Constructors
Constructor and description
`BidsHandler()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`groovyx.gpars.dataflow.DataflowWriteChannel`	`ignite(nextflow.Session session)` Create the output channel and schedule asynchronous execution.
	`protected void`	`loadConfiguration(java.lang.String configPath)` Load and analyze configuration from file or use defaults
	`BidsHandler`	`perform(boolean async)` Execute the BIDS parsing pipeline, optionally in a background thread.
	`BidsHandler`	`withBidsDir(java.lang.String bidsDir)` Set the path to the BIDS dataset directory.
	`BidsHandler`	`withConfig(java.lang.String configPath)` Load and analyze the YAML configuration file.
	`BidsHandler`	`withOpts(java.util.Map options)` Supply the runtime options map (e.g.
	`BidsHandler`	`withParser(nfneuro.plugin.parser.BidsParser parser)` Inject the nfneuro.plugin.parser.BidsParser to use for dataset parsing.
	`BidsHandler`	`withTarget(groovyx.gpars.dataflow.DataflowWriteChannel target)` Override the output channel (used internally by ignite).

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
  - BidsHandler()
- Method Detail
  - groovyx.gpars.dataflow.DataflowWriteChannel ignite(nextflow.Session session)
    
    Create the output channel and schedule asynchronous execution.
    In DSL2 mode the work is deferred via session.addIgniter; in DSL1 it runs immediately. Either way the returned channel is ready to be consumed by downstream operators before parsing has completed.
    
    Parameters:
    session - the active Nextflow session
    Returns:
    the DataflowWriteChannel that will receive BIDS data items
  - protected void loadConfiguration(java.lang.String configPath)
    
    Load and analyze configuration from file or use defaults
    reference:
    Config loading: https://github.com/agahkarakuzu/bids2nf/blob/main/main.nf#L46-L48
    
    Parameters:
    configPath - Path to YAML configuration file
    Returns:
    Parsed configuration map
  - BidsHandler perform(boolean async)
    
    Execute the BIDS parsing pipeline, optionally in a background thread.
    Parameters:
    async - true to run asynchronously via java.util.concurrent.CompletableFuture (default); false to block the calling thread
    Returns:
    this for method chaining
  - BidsHandler withBidsDir(java.lang.String bidsDir)
    
    Set the path to the BIDS dataset directory.
    Parameters:
    bidsDir - absolute path to the root of the BIDS dataset
    Returns:
    this for method chaining
  - BidsHandler withConfig(java.lang.String configPath)
    
    Load and analyze the YAML configuration file.
    Parameters:
    configPath - path to a bids2nf.yaml configuration file, or null to use defaults
    Returns:
    this for method chaining
  - BidsHandler withOpts(java.util.Map options)
    
    Supply the runtime options map (e.g. libbids_sh, flatten_output).
    Parameters:
    options - map of additional options forwarded from Channel.fromBIDS()
    Returns:
    this for method chaining
  - BidsHandler withParser(nfneuro.plugin.parser.BidsParser parser)
    
    Inject the nfneuro.plugin.parser.BidsParser to use for dataset parsing.
    Parameters:
    parser - pre-constructed parser instance
    Returns:
    this for method chaining
  - BidsHandler withTarget(groovyx.gpars.dataflow.DataflowWriteChannel target)
    
    Override the output channel (used internally by ignite).
    Parameters:
    target - the Dataflow write channel to bind results into
    Returns:
    this for method chaining

Summary:
Constructor
Method

| Detail:
Constructor
Method

Groovy Documentation

[Groovy] Class BidsHandler

Constructor Summary

Methods Summary

Inherited Methods Summary

Constructor Detail

BidsHandler()

Method Detail

groovyx.gpars.dataflow.DataflowWriteChannel ignite(nextflow.Session session)

protected void loadConfiguration(java.lang.String configPath)

BidsHandler perform(boolean async)

BidsHandler withBidsDir(java.lang.String bidsDir)

BidsHandler withConfig(java.lang.String configPath)

BidsHandler withOpts(java.util.Map options)

BidsHandler withParser(nfneuro.plugin.parser.BidsParser parser)

BidsHandler withTarget(groovyx.gpars.dataflow.DataflowWriteChannel target)