@groovy.util.logging.Slf4j @groovy.transform.CompileStatic class BidsParser extends java.lang.Object
Main BIDS dataset parser.
Orchestrates dataset parsing by delegating to LibBidsShWrapper to execute
the libBIDSsh_parse_bids_to_table bash function, then converting the resulting
TSV into nfneuro.plugin.model.BidsFile objects via nfneuro.plugin.util.BidsCsvParser,
and finally assembling them into a nfneuro.plugin.model.BidsDataset.
| Constructor and description |
|---|
BidsParser(nextflow.Session session)Construct a parser bound to the given Nextflow session. |
| Type Params | Return Type | Name and description |
|---|---|---|
|
nfneuro.plugin.model.BidsDataset |
parseToDataset(java.lang.String bidsDir, java.lang.String libBidsShPath, java.lang.Boolean bidsignore, java.lang.Boolean defaultIgnores)Parse BIDS dataset to BidsDataset object |
| 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() |
Construct a parser bound to the given Nextflow session.
session - the active Nextflow session (reserved for future session-scoped configuration)Parse BIDS dataset to BidsDataset object Uses libBIDS.sh to scan BIDS directory and create structured dataset
bidsDir - Path to BIDS dataset directorylibBidsShPath - Path to libBIDS.sh script (optional)