Source Tree Map

Extends nextflow.plugin.BasePlugin. Its sole job is to be discovered by pf4j via the plugin descriptor. It carries no domain logic.

Extends PluginExtensionPoint and declares the public API: the @Factory method fromBIDS() and the three @Operator methods groupTupleBy(), joinBy(), and combineBy(). All factory and operator implementations are delegated to BidsChannelFactory and the *Op classes respectively.

Implements TraceObserverFactory. Its create(Session) method instantiates a BidsObserver and registers it with the Nextflow trace system.

Implements TraceObserver. Currently prints a startup banner on onFlowCreate and a completion message on onFlowComplete. This is the hook point for future workflow-level observability.

Receives the Session at construction and exposes fromBIDS(String bidsDir, String configPath, Map options). It runs pre-flight validation (directory existence, config file existence, optional libbids_sh path) and then constructs a BidsHandler using the fluent builder API.

The stateful orchestrator. It holds the parsed configuration, the list of loopOverEntities, the suffixMapping, and the BidsParser. ignite(Session) creates the DataflowWriteChannel, registers an async igniter for DSL2 execution, and returns the channel. execute() calls parser.parseToDataset(), routes files through the appropriate set-handler subclass, applies cross-modal broadcasting, and emits items onto the channel. The channel is closed with Channel.STOP after all items are emitted.

Groups channel items by a closure-extracted key, accumulating items in a synchronized Map<Object, List> and emitting [key, [items]] tuples.

Performs an inner join between two channels using independent key-extractor closures for left and right sides. Supports remainder and duplicate-handling options, emitting fused join payloads without keys.

Emits the Cartesian product of left and right items within each key group as fused payloads (key omitted). BidsExtension provides three overloads to support a single shared extractor or separate left/right extractors.

Static utility that safely invokes a key-extractor closure on a channel item. It normalises List-valued keys by wrapping them in a CompositeKey so that Map lookups use value equality rather than reference equality.

An @EqualsAndHashCode-annotated wrapper for multi-part keys (e.g., [subject, session]). Without this class, two distinct List instances with identical contents would hash differently in a HashMap.

Orchestrates the two-step parse: calls LibBidsShWrapper.parseBidsToTable() to obtain a TSV file, then passes it to BidsCsvParser (in util). Returns a fully populated BidsDataset.

Bridges Groovy and the external libBIDS.sh bash library. Implements a priority-ordered discovery chain: plugin-embedded lib/libBIDS.sh first, then several relative paths, then system paths (/usr/local/bin, ~/.local/bin). Executes the script using an array-form command (bash -c 'set -euo pipefail && source …​') to prevent shell injection. See The libBIDS.sh Dependency for the full discovery order.

A stub — BIDS validation via bids-validator is deferred to v1.1. The class exists but validate() logs a warning and returns immediately. Validation code in BidsChannelFactory is commented out.

Loads a YAML file with SnakeYAML, rejects the reserved key meta, and delegates structural validation to BidsConfigValidator.

Returns a ValidationResult containing lists of errors and warnings. Validates per-suffix configuration blocks and global keys such as loop_over.

Inspects the loaded config map and returns a boolean analysis map (hasNamedSets, hasSequentialSets, hasMixedSets, hasPlainSets). BidsHandler uses this map to decide which BaseSetHandler subclasses to instantiate. Also extracts the loop_over entity list.

Abstract base providing the process(datasetRoot, bidsFiles, config, loopOverEntities, suffixMapping) template and the static getSetType() helper.

Handles plain_set entries — one file per subject/session/run group per suffix.

Handles named_set entries — multiple acquisition-direction variants collected under a config key (e.g., dwi_ap with ap and pa sub-keys).

Handles sequential_set entries — variable-length sequences such as multi-echo acquisitions, emitted as ordered lists.

Handles mixed_set entries — heterogeneous datasets where the same suffix maps to multiple config keys via suffix_maps_to.

Root container for a parsed dataset. Loads dataset_description.json and participants.tsv on construction.

Represents one file entry from the libBIDS.sh TSV. Carries the path, suffix, associated extensions (.nii.gz, .json, .bval, .bvec, etc.), and a list of BidsEntity objects.

A key-value pair (e.g., subject=sub-01). Holds the canonical long-form entity name and a SHORT_ENTITY_MAPPING that maps long names to BIDS prefix abbreviations.

The transient accumulator used by the set handlers before items are emitted. Stores a Map<String, Object> data (keyed by suffix), a list of raw file paths, and the bidsParentDir. toChannelTuple() converts the accumulator to the [groupingKey, enrichedData] tuple consumed by BidsHandler.

Thin Slf4j wrapper that prefixes every message with a bracketed context tag (e.g., [nf-bids-handler]).

Builds a Map<setType, Map<configKey, actualSuffix>> from suffix_maps_to entries. Used by the set handlers to resolve heterogeneous suffix configurations.

Static helpers for filtering BidsFile lists by entity values and checking entity matches.

Provides tryWithContext() for exception wrapping and createDetailedError() for multi-bullet diagnostic messages.

Parses the TSV produced by libBIDSsh_parse_bids_to_table. The expected column order is derivatives,datatype,subject,template,session,cohort,sample,task,tracksys,acquisition,nucleus,volume,ceagent,tracer,stain,reconstruction,direction,run,modality,echo,flip,inversion,mtransfer,part,processing,hemisphere,space,split,recording,chunk,atlas,segmentation,scale,resolution,density,label,description,suffix,extension,path (tab-separated).