Struct Database 

pub struct Database { /* private fields */ }

Manages the SQLite database backing a BidsLayout index.

Stores the complete file index for a BIDS dataset, including:

• Files — Path, filename, directory, file type for every indexed file
• Tags — Entity-value pairs (subject=01, task=rest, etc.) and metadata key-value pairs from JSON sidecars
• Associations — Relationships between files (IntendedFor, Metadata inheritance parent/child, InformedBy)
• Layout info — Root path and config names for database reloading

The database supports both in-memory operation (fast, ephemeral) and on-disk persistence (for caching large dataset indices). It registers a custom REGEXP function for SQLite to support regex-based queries.

Schema

CREATE TABLE files (path TEXT PRIMARY KEY, filename TEXT, dirname TEXT, ...);
CREATE TABLE tags (file_path TEXT, entity_name TEXT, value TEXT, ...);
CREATE TABLE associations (src TEXT, dst TEXT, kind TEXT, ...);
CREATE TABLE layout_info (root TEXT PRIMARY KEY, config TEXT, ...);

Implementations

impl Database

pub fn in_memory() -> Result<Self>

Create a new in-memory database.

pub fn open(path: &Path) -> Result<Self>

Open or create a database at the given path.

pub fn exists(path: &Path) -> bool

Check if a database file exists.

pub fn begin_transaction(&self) -> Result<()>

Begin an explicit transaction for bulk operations.

Wrapping many inserts in a single transaction avoids per-statement fsyncs, giving ~100× better insert throughput on large datasets.

pub fn commit_transaction(&self) -> Result<()>

Commit the current transaction.

pub fn rollback_transaction(&self) -> Result<()>

Roll back the current transaction.

pub fn insert_file(&self, file: &BidsFile) -> Result<()>

Insert a file into the database.

pub fn insert_tag( &self, file_path: &str, entity_name: &str, value: &str, dtype: &str, is_metadata: bool, ) -> Result<()>

Insert a tag (entity-value pair for a file).

pub fn insert_association(&self, src: &str, dst: &str, kind: &str) -> Result<()>

Insert a file association.

pub fn set_layout_info(&self, root: &str, config: &str) -> Result<()>

Store layout info.

pub fn get_layout_info(&self) -> Result<Option<(String, String)>>

Get layout info (root, config).

pub fn all_file_paths(&self) -> Result<Vec<String>>

Query all file paths.

pub fn get_tags( &self, file_path: &str, ) -> Result<Vec<(String, String, String, bool)>>

Get tags for a specific file.

pub fn get_unique_entity_values(&self, entity_name: &str) -> Result<Vec<String>>

Get all unique values for a given entity.

pub fn get_entity_names(&self) -> Result<Vec<String>>

Get all unique entity names.

pub fn query_files( &self, filters: &[(String, Vec<String>, bool)], ) -> Result<Vec<String>>

Query files with advanced filtering including Query::None/Any and regex.

Filter types:

• Normal: (entity, values, false) — entity must match one of values
• Regex: (entity, [pattern], true) — entity must match regex
• Query::None: (entity, [“NONE”], false) — entity must NOT exist
• Query::Any: (entity, [“ANY”], false) — entity must exist (any value)

pub fn query_directories( &self, target_entity: &str, filters: &[(String, Vec<String>, bool)], ) -> Result<Vec<String>>

Get distinct directories for files matching filters and having a target entity.

pub fn get_associations( &self, src: &str, kind: Option<&str>, ) -> Result<Vec<(String, String)>>

Get associated files for a given source file.

pub fn file_count(&self) -> Result<usize>

Get the total number of indexed files.

pub fn save_to(&self, path: &Path) -> Result<()>

Save the current in-memory database to a file.