Initial commit

2026-03-04 00:08:42 +00:00
commit 4d88dc0584
4449 changed files with 1556714 additions and 0 deletions
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+//! Database schema definition and migration
+
+use rusqlite::Connection;
+
+use crate::error::Result;
+
+/// Current schema version
+pub const SCHEMA_VERSION: i32 = 1;
+
+/// Create the database schema
+pub fn create_schema(conn: &Connection) -> Result<()> {
+    conn.execute_batch(SCHEMA_SQL)?;
+
+    // Set schema version
+    conn.execute(
+        "INSERT OR REPLACE INTO schema_version (id, version) VALUES (1, ?1)",
+        [SCHEMA_VERSION],
+    )?;
+
+    Ok(())
+}
+
+/// Check if schema needs migration
+pub fn check_schema_version(conn: &Connection) -> Result<Option<i32>> {
+    // Check if schema_version table exists
+    let exists: bool = conn.query_row(
+        "SELECT COUNT(*) > 0 FROM sqlite_master WHERE type='table' AND name='schema_version'",
+        [],
+        |row| row.get(0),
+    )?;
+
+    if !exists {
+        return Ok(None);
+    }
+
+    let version: i32 = conn.query_row(
+        "SELECT version FROM schema_version WHERE id = 1",
+        [],
+        |row| row.get(0),
+    )?;
+
+    Ok(Some(version))
+}
+
+/// Schema SQL for all tables
+const SCHEMA_SQL: &str = r"
+-- Schema version tracking
+CREATE TABLE IF NOT EXISTS schema_version (
+    id INTEGER PRIMARY KEY,
+    version INTEGER NOT NULL
+);
+
+-- Protocols (top-level container, like a Brainstorm protocol)
+CREATE TABLE IF NOT EXISTS protocols (
+    id TEXT PRIMARY KEY,
+    name TEXT NOT NULL,
+    path TEXT NOT NULL,
+    description TEXT DEFAULT '',
+    created_at TEXT NOT NULL,
+    modified_at TEXT NOT NULL,
+    settings_json TEXT NOT NULL DEFAULT '{}'
+);
+
+-- Subjects within a protocol
+CREATE TABLE IF NOT EXISTS subjects (
+    id TEXT PRIMARY KEY,
+    protocol_id TEXT NOT NULL REFERENCES protocols(id) ON DELETE CASCADE,
+    label TEXT NOT NULL,
+    anatomy_path TEXT,
+    demographics_json TEXT DEFAULT '{}',
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_subjects_protocol ON subjects(protocol_id);
+
+-- Conditions (experimental conditions for grouping)
+CREATE TABLE IF NOT EXISTS conditions (
+    id TEXT PRIMARY KEY,
+    protocol_id TEXT NOT NULL REFERENCES protocols(id) ON DELETE CASCADE,
+    name TEXT NOT NULL,
+    color TEXT DEFAULT '#4A90D9',
+    description TEXT DEFAULT ''
+);
+
+CREATE INDEX IF NOT EXISTS idx_conditions_protocol ON conditions(protocol_id);
+
+-- Recordings (loaded data files)
+CREATE TABLE IF NOT EXISTS recordings (
+    id TEXT PRIMARY KEY,
+    subject_id TEXT REFERENCES subjects(id) ON DELETE SET NULL,
+    condition_id TEXT REFERENCES conditions(id) ON DELETE SET NULL,
+    handle_id TEXT NOT NULL,
+    file_path TEXT NOT NULL,
+    format TEXT NOT NULL,
+    n_channels INTEGER NOT NULL,
+    n_samples INTEGER NOT NULL,
+    sfreq REAL NOT NULL,
+    duration REAL NOT NULL,
+    bad_channels_json TEXT DEFAULT '[]',
+    annotations_json TEXT DEFAULT '[]',
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_recordings_subject ON recordings(subject_id);
+CREATE INDEX IF NOT EXISTS idx_recordings_condition ON recordings(condition_id);
+
+-- Epochs sets
+CREATE TABLE IF NOT EXISTS epochs (
+    id TEXT PRIMARY KEY,
+    recording_id TEXT NOT NULL REFERENCES recordings(id) ON DELETE CASCADE,
+    handle_id TEXT NOT NULL,
+    event_ids_json TEXT NOT NULL,
+    tmin REAL NOT NULL,
+    tmax REAL NOT NULL,
+    baseline_json TEXT,
+    n_epochs INTEGER NOT NULL,
+    n_channels INTEGER NOT NULL,
+    n_times INTEGER NOT NULL,
+    reject_criteria_json TEXT DEFAULT '{}',
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_epochs_recording ON epochs(recording_id);
+
+-- Forward models
+CREATE TABLE IF NOT EXISTS forward_models (
+    id TEXT PRIMARY KEY,
+    recording_id TEXT NOT NULL REFERENCES recordings(id) ON DELETE CASCADE,
+    handle_id TEXT NOT NULL,
+    model_type TEXT NOT NULL,
+    n_sensors INTEGER NOT NULL,
+    n_sources INTEGER NOT NULL,
+    config_json TEXT NOT NULL,
+    gain_matrix_path TEXT,
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_forward_recording ON forward_models(recording_id);
+
+-- Inverse operators
+CREATE TABLE IF NOT EXISTS inverse_operators (
+    id TEXT PRIMARY KEY,
+    forward_id TEXT NOT NULL REFERENCES forward_models(id) ON DELETE CASCADE,
+    handle_id TEXT NOT NULL,
+    method TEXT NOT NULL,
+    lambda2 REAL NOT NULL,
+    n_sources INTEGER NOT NULL,
+    n_channels INTEGER NOT NULL,
+    kernel_path TEXT,
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_inverse_forward ON inverse_operators(forward_id);
+
+-- SSP projectors
+CREATE TABLE IF NOT EXISTS ssp_projectors (
+    id TEXT PRIMARY KEY,
+    recording_id TEXT NOT NULL REFERENCES recordings(id) ON DELETE CASCADE,
+    handle_id TEXT NOT NULL,
+    n_components INTEGER NOT NULL,
+    artifact_type TEXT,
+    explained_var_json TEXT DEFAULT '[]',
+    projector_path TEXT,
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_ssp_recording ON ssp_projectors(recording_id);
+
+-- ICA models
+CREATE TABLE IF NOT EXISTS ica_models (
+    id TEXT PRIMARY KEY,
+    recording_id TEXT NOT NULL REFERENCES recordings(id) ON DELETE CASCADE,
+    handle_id TEXT NOT NULL,
+    n_components INTEGER NOT NULL,
+    method TEXT NOT NULL,
+    excluded_json TEXT DEFAULT '[]',
+    mixing_matrix_path TEXT,
+    unmixing_matrix_path TEXT,
+    created_at TEXT NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_ica_recording ON ica_models(recording_id);
+";
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rusqlite::Connection;
+
+    #[test]
+    fn test_create_schema() {
+        let conn = Connection::open_in_memory().unwrap();
+        create_schema(&conn).unwrap();
+
+        // Verify tables exist
+        let count: i32 = conn
+            .query_row(
+                "SELECT COUNT(*) FROM sqlite_master WHERE type='table'",
+                [],
+                |row| row.get(0),
+            )
+            .unwrap();
+
+        assert!(count >= 10); // At least 10 tables
+    }
+
+    #[test]
+    fn test_schema_version() {
+        let conn = Connection::open_in_memory().unwrap();
+
+        // Before schema creation
+        assert_eq!(check_schema_version(&conn).unwrap(), None);
+
+        // After schema creation
+        create_schema(&conn).unwrap();
+        assert_eq!(check_schema_version(&conn).unwrap(), Some(SCHEMA_VERSION));
+    }
+}