package lib

import (
	"bytes"
	"encoding/json"
	"fmt"
	"image"
	"image/color"
	"image/png"
	"os"
	"path/filepath"
	"sort"
	"strings"
	"time"
)

// ============================================================================
// V2 API - Clean data layer using Store
// ============================================================================
//
// RBAC ENFORCEMENT:
// All data access functions take AccessContext as first parameter.
// Permission checks happen HERE at the lowest level - there is NO WAY to bypass.
//
// Rules:
// - ctx == nil or ctx.IsSystem → allow (for internal/system operations)
// - ctx.AccessorID == dossierID → allow (owner)
// - Otherwise → check access grants in database
//
// ============================================================================

// accessorIDFromContext extracts accessorID from AccessContext for RBAC checks
// Returns SystemAccessorID for system context (explicit backdoor with audit trail)
func accessorIDFromContext(ctx *AccessContext) string {
	if ctx == nil || ctx.IsSystem {
		return SystemAccessorID
	}
	return ctx.AccessorID
}

// --- ENTRY ---

type EntryFilter struct {
	DossierID string
	Type      string
	Value     string
	SearchKey string
	FromDate  int64
	ToDate    int64
	Limit     int
}

// EntryWrite creates/updates entries. Requires write permission on parent.
func EntryWrite(ctx *AccessContext, entries ...*Entry) error {
	if len(entries) == 0 {
		return nil
	}

	// RBAC: Check write permission for each entry
	for _, e := range entries {
		if e.DossierID == "" {
			return fmt.Errorf("entry missing dossier_id")
		}
		// Check write on parent (or root if no parent)
		if err := checkAccess(accessorIDFromContext(ctx), e.DossierID, e.ParentID, e.Category, 'w'); err != nil {
			return err
		}
	}

	for _, e := range entries {
		if e.EntryID == "" {
			e.EntryID = NewID()
		}
	}
	if len(entries) == 1 {
		return dbSave("entries", entries[0])
	}
	return dbSave("entries", entries)
}

// EntryRemove deletes entries. Requires delete permission.
func EntryRemove(ctx *AccessContext, ids ...string) error {
	// RBAC: Check delete permission for each entry
	for _, id := range ids {
		e, err := entryGetRaw(id)
		if err != nil {
			continue // Entry doesn't exist, skip
		}
		if err := checkAccess(accessorIDFromContext(ctx), e.DossierID, id, e.Category, 'd'); err != nil {
			return err
		}
	}
	return deleteByIDs("entries", "entry_id", ids)
}

// EntryRemoveByDossier removes all entries for a dossier. Requires delete permission on dossier root.
func EntryRemoveByDossier(ctx *AccessContext, dossierID string) error {
	// RBAC: Check delete permission on dossier root
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", 0, 'd'); err != nil {
		return err
	}

	var entries []*Entry
	if err := dbQuery("SELECT entry_id FROM entries WHERE dossier_id = ?", []any{dossierID}, &entries); err != nil {
		return err
	}
	for _, e := range entries {
		if err := dbDelete("entries", "entry_id", e.EntryID); err != nil {
			return err
		}
	}
	return nil
}

// EntryGet retrieves an entry. Requires read permission.
func EntryGet(ctx *AccessContext, id string) (*Entry, error) {
	e, err := entryGetRaw(id)
	if err != nil {
		return nil, err
	}

	// RBAC: Check read permission
	if err := checkAccess(accessorIDFromContext(ctx), e.DossierID, id, e.Category, 'r'); err != nil {
		return nil, err
	}

	return e, nil
}

// entryGetRaw retrieves an entry without permission check (internal use only)
func entryGetRaw(id string) (*Entry, error) {
	e := &Entry{}
	return e, dbLoad("entries", id, e)
}

// EntryList retrieves entries. Requires read permission on parent/dossier.
// accessorID: who is asking (SystemAccessorID = internal operations)
// dossierID comes from f.DossierID
func EntryList(accessorID string, parent string, category int, f *EntryFilter) ([]*Entry, error) {
	// RBAC: Determine dossier and check read permission
	dossierID := ""
	if f != nil {
		dossierID = f.DossierID
	}
	if dossierID == "" && parent != "" {
		// Get dossier from parent entry
		if p, err := entryGetRaw(parent); err == nil {
			dossierID = p.DossierID
		}
	}
	if dossierID != "" {
		if err := checkAccess(accessorID, dossierID, parent, category, 'r'); err != nil {
			return nil, err
		}
	}

	q := "SELECT * FROM entries WHERE 1=1"
	args := []any{}

	if category > 0 {
		q += " AND category = ?"
		args = append(args, category)
	}

	if parent == "" {
		q += " AND (parent_id IS NULL OR parent_id = '')"
	} else {
		q += " AND parent_id = ?"
		args = append(args, parent)
	}

	if f != nil {
		if f.DossierID != "" {
			q += " AND dossier_id = ?"
			args = append(args, f.DossierID)
		}
		if f.Type != "" {
			q += " AND type = ?"
			args = append(args, CryptoEncrypt(f.Type))
		}
		if f.Value != "" {
			q += " AND value = ?"
			args = append(args, CryptoEncrypt(f.Value))
		}
		if f.SearchKey != "" {
			q += " AND search_key = ?"
			args = append(args, CryptoEncrypt(f.SearchKey))
		}
		if f.FromDate > 0 {
			q += " AND timestamp >= ?"
			args = append(args, f.FromDate)
		}
		if f.ToDate > 0 {
			q += " AND timestamp < ?"
			args = append(args, f.ToDate)
		}
	}

	q += " ORDER BY ordinal"

	if f != nil && f.Limit > 0 {
		q += fmt.Sprintf(" LIMIT %d", f.Limit)
	}

	var result []*Entry
	err := dbQuery(q, args, &result)
	return result, err
}

// --- DOSSIER ---

type DossierFilter struct {
	EmailHash   string
	DateOfBirth string
	Limit       int
}

// DossierWrite creates/updates dossiers. Requires manage permission (or nil ctx for system).
func DossierWrite(ctx *AccessContext, dossiers ...*Dossier) error {
	if len(dossiers) == 0 {
		return nil
	}

	// RBAC: For existing dossiers, check manage permission
	for _, d := range dossiers {
		if d.DossierID != "" {
			// Update - need manage permission (unless creating own or system)
			if err := checkAccess(accessorIDFromContext(ctx), d.DossierID, "", 0, 'm'); err != nil {
				return err
			}
		}
		// New dossiers (no ID) are allowed - they'll get assigned an ID
	}

	for _, d := range dossiers {
		if d.DossierID == "" {
			d.DossierID = NewID()
		}
		// Format DOB to encrypted string
		if !d.DOB.IsZero() {
			d.DateOfBirth = d.DOB.Format("2006-01-02")
		}
	}
	if len(dossiers) == 1 {
		return dbSave("dossiers", dossiers[0])
	}
	return dbSave("dossiers", dossiers)
}

// DossierRemove deletes dossiers. Requires manage permission.
func DossierRemove(ctx *AccessContext, ids ...string) error {
	// RBAC: Check manage permission for each dossier
	for _, id := range ids {
		if err := checkAccess(accessorIDFromContext(ctx), id, "", 0, 'm'); err != nil {
			return err
		}
	}
	return deleteByIDs("dossiers", "dossier_id", ids)
}

// DossierGet retrieves a dossier. Requires read permission.
func DossierGet(ctx *AccessContext, id string) (*Dossier, error) {
	// RBAC: Check read permission
	if err := checkAccess(accessorIDFromContext(ctx), id, "", 0, 'r'); err != nil {
		return nil, err
	}

	return dossierGetRaw(id)
}

// dossierGetRaw retrieves a dossier without permission check (internal use only)
func dossierGetRaw(id string) (*Dossier, error) {
	d := &Dossier{}
	if err := dbLoad("dossiers", id, d); err != nil {
		return nil, err
	}
	// Parse DOB from encrypted string
	if d.DateOfBirth != "" {
		d.DOB, _ = time.Parse("2006-01-02", d.DateOfBirth)
	}
	return d, nil
}

// DossierList retrieves dossiers. System only (for security - lists all dossiers).
func DossierList(ctx *AccessContext, f *DossierFilter) ([]*Dossier, error) {
	// RBAC: Only system context can list all dossiers
	if ctx != nil && !ctx.IsSystem {
		return nil, ErrAccessDenied
	}

	q := "SELECT * FROM dossiers WHERE 1=1"
	args := []any{}

	if f != nil {
		if f.EmailHash != "" {
			q += " AND email_hash = ?"
			args = append(args, f.EmailHash)
		}
		if f.DateOfBirth != "" {
			q += " AND date_of_birth = ?"
			args = append(args, CryptoEncrypt(f.DateOfBirth))
		}
		if f.Limit > 0 {
			q += fmt.Sprintf(" LIMIT %d", f.Limit)
		}
	}

	var result []*Dossier
	err := dbQuery(q, args, &result)
	return result, err
}

// DossierGetByEmail retrieves a dossier by email. System only (auth flow).
func DossierGetByEmail(ctx *AccessContext, email string) (*Dossier, error) {
	// RBAC: Only system context can lookup by email (for auth)
	if ctx != nil && !ctx.IsSystem {
		return nil, ErrAccessDenied
	}

	email = strings.ToLower(strings.TrimSpace(email))
	if email == "" {
		return nil, fmt.Errorf("empty email")
	}
	q := "SELECT * FROM dossiers WHERE email = ? LIMIT 1"
	var result []*Dossier
	if err := dbQuery(q, []any{CryptoEncrypt(email)}, &result); err != nil {
		return nil, err
	}
	if len(result) == 0 {
		return nil, fmt.Errorf("not found")
	}
	return result[0], nil
}

// DossierGetBySessionToken retrieves a dossier by session token. No RBAC (auth flow).
func DossierGetBySessionToken(token string) *Dossier {
	if token == "" {
		return nil
	}
	q := "SELECT * FROM dossiers WHERE session_token = ? LIMIT 1"
	var result []*Dossier
	if err := dbQuery(q, []any{CryptoEncrypt(token)}, &result); err != nil {
		return nil
	}
	if len(result) == 0 {
		return nil
	}
	return result[0]
}

// --- LEGACY ACCESS (dossier_access table) ---
// TODO: Migrate to new RBAC access table

type AccessFilter struct {
	AccessorID string
	TargetID   string
	Status     *int
}

func AccessWrite(records ...*DossierAccess) error {
	if len(records) == 0 {
		return nil
	}
	for _, r := range records {
		if r.AccessID == "" {
			r.AccessID = NewID()
		}
	}
	if len(records) == 1 {
		return dbSave("dossier_access", records[0])
	}
	return dbSave("dossier_access", records)
}

func AccessRemove(accessorID, targetID string) error {
	access, err := AccessGet(accessorID, targetID)
	if err != nil {
		return err
	}
	return dbDelete("dossier_access", "access_id", access.AccessID)
}

func AccessGet(accessorID, targetID string) (*DossierAccess, error) {
	q := "SELECT * FROM dossier_access WHERE accessor_dossier_id = ? AND target_dossier_id = ?"
	var result []*DossierAccess
	if err := dbQuery(q, []any{accessorID, targetID}, &result); err != nil {
		return nil, err
	}
	if len(result) == 0 {
		return nil, fmt.Errorf("not found")
	}
	return result[0], nil
}

func AccessList(f *AccessFilter) ([]*DossierAccess, error) {
	q := "SELECT * FROM dossier_access WHERE 1=1"
	args := []any{}

	if f != nil {
		if f.AccessorID != "" {
			q += " AND accessor_dossier_id = ?"
			args = append(args, f.AccessorID)
		}
		if f.TargetID != "" {
			q += " AND target_dossier_id = ?"
			args = append(args, f.TargetID)
		}
		if f.Status != nil {
			q += " AND status = ?"
			args = append(args, *f.Status)
		}
	}

	var result []*DossierAccess
	err := dbQuery(q, args, &result)
	return result, err
}

// --- AUDIT ---

type AuditFilter struct {
	ActorID  string
	TargetID string
	Action   string
	FromDate int64
	ToDate   int64
	Limit    int
}

func AuditWrite(entries ...*AuditEntry) error {
	if len(entries) == 0 {
		return nil
	}
	for _, a := range entries {
		if a.AuditID == "" {
			a.AuditID = NewID()
		}
	}
	if len(entries) == 1 {
		return dbSave("audit", entries[0])
	}
	return dbSave("audit", entries)
}

func AuditList(f *AuditFilter) ([]*AuditEntry, error) {
	q := "SELECT * FROM audit WHERE 1=1"
	args := []any{}

	if f != nil {
		if f.ActorID != "" {
			q += " AND actor1_id = ?"
			args = append(args, f.ActorID)
		}
		if f.TargetID != "" {
			q += " AND target_id = ?"
			args = append(args, f.TargetID)
		}
		if f.Action != "" {
			q += " AND action = ?"
			args = append(args, CryptoEncrypt(f.Action))
		}
		if f.FromDate > 0 {
			q += " AND timestamp >= ?"
			args = append(args, f.FromDate)
		}
		if f.ToDate > 0 {
			q += " AND timestamp < ?"
			args = append(args, f.ToDate)
		}
	}

	q += " ORDER BY timestamp DESC"

	if f != nil && f.Limit > 0 {
		q += fmt.Sprintf(" LIMIT %d", f.Limit)
	}

	var result []*AuditEntry
	err := dbQuery(q, args, &result)
	return result, err
}

// --- PROMPT ---

type TrackerFilter struct {
	DossierID  string
	Category   string
	Type       string
	ActiveOnly bool
	Limit      int
}

func TrackerWrite(trackers ...*Tracker) error {
	if len(trackers) == 0 {
		return nil
	}
	for _, p := range trackers {
		if p.TrackerID == "" {
			p.TrackerID = NewID()
		}
	}
	if len(trackers) == 1 {
		return dbSave("trackers", trackers[0])
	}
	return dbSave("trackers", trackers)
}

func TrackerRemove(ids ...string) error {
	return deleteByIDs("trackers", "tracker_id", ids)
}

func TrackerList(f *TrackerFilter) ([]*Tracker, error) {
	q := "SELECT * FROM trackers WHERE 1=1"
	args := []any{}

	if f != nil {
		if f.DossierID != "" {
			q += " AND dossier_id = ?"
			args = append(args, f.DossierID)
		}
		if f.Category != "" {
			q += " AND category = ?"
			args = append(args, CryptoEncrypt(f.Category))
		}
		if f.Type != "" {
			q += " AND type = ?"
			args = append(args, CryptoEncrypt(f.Type))
		}
		if f.ActiveOnly {
			q += " AND active = 1 AND dismissed = 0"
		}
	}

	q += " ORDER BY active DESC, time_of_day, created_at"

	if f != nil && f.Limit > 0 {
		q += fmt.Sprintf(" LIMIT %d", f.Limit)
	}

	var result []*Tracker
	err := dbQuery(q, args, &result)
	return result, err
}

// --- IMAGE ---

type ImageOpts struct {
	WC, WW     float64 // window center/width (0 = defaults)
	Zoom       float64 // unused
	PanX, PanY float64 // unused
}

// ImageGet retrieves an image. Requires read permission.
func ImageGet(ctx *AccessContext, id string, opts *ImageOpts) ([]byte, error) {
	e, err := entryGetRaw(id)
	if err != nil {
		return nil, err
	}

	// RBAC: Check read permission
	if err := checkAccess(accessorIDFromContext(ctx), e.DossierID, id, e.Category, 'r'); err != nil {
		return nil, err
	}

	var data struct {
		WindowCenter     float64 `json:"window_center"`
		WindowWidth      float64 `json:"window_width"`
		PixelMin         int     `json:"pixel_min"`
		PixelMax         int     `json:"pixel_max"`
		RescaleSlope     float64 `json:"rescale_slope"`
		RescaleIntercept float64 `json:"rescale_intercept"`
	}
	json.Unmarshal([]byte(e.Data), &data)

	slope := data.RescaleSlope
	if slope == 0 {
		slope = 1
	}

	center, width := data.WindowCenter, data.WindowWidth
	if data.RescaleIntercept != 0 {
		center = (center - data.RescaleIntercept) / slope
		width = width / slope
	}
	if center == 0 && width == 0 {
		center = float64(data.PixelMin+data.PixelMax) / 2
		width = float64(data.PixelMax - data.PixelMin)
		if width == 0 {
			width = 1
		}
	}

	if opts != nil {
		if opts.WC != 0 {
			center = opts.WC
		}
		if opts.WW != 0 {
			width = opts.WW
		}
	}

	dec, err := objectReadRaw(e.DossierID, id)
	if err != nil {
		return nil, err
	}

	img, err := png.Decode(bytes.NewReader(dec))
	if err != nil {
		return nil, err
	}
	g16, ok := img.(*image.Gray16)
	if !ok {
		return nil, fmt.Errorf("not 16-bit grayscale")
	}

	low, high := center-width/2, center+width/2
	lut := make([]uint8, 65536)
	for i := range lut {
		if float64(i) <= low {
			lut[i] = 0
		} else if float64(i) >= high {
			lut[i] = 255
		} else {
			lut[i] = uint8((float64(i) - low) * 255 / width)
		}
	}

	bounds := g16.Bounds()
	out := image.NewGray(bounds)
	for y := bounds.Min.Y; y < bounds.Max.Y; y++ {
		for x := bounds.Min.X; x < bounds.Max.X; x++ {
			out.SetGray(x, y, color.Gray{Y: lut[g16.Gray16At(x, y).Y]})
		}
	}

	var buf bytes.Buffer
	png.Encode(&buf, out)
	return buf.Bytes(), nil
}

// --- OBJECT STORAGE ---

// ObjectWrite encrypts and writes data to the object store. Requires write permission.
func ObjectWrite(ctx *AccessContext, dossierID, entryID string, data []byte) error {
	// RBAC: Check write permission
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, entryID, 0, 'w'); err != nil {
		return err
	}

	path := ObjectPath(dossierID, entryID)
	if err := os.MkdirAll(filepath.Dir(path), 0755); err != nil {
		return err
	}
	encrypted := CryptoEncryptBytes(data)
	return os.WriteFile(path, encrypted, 0644)
}

// ObjectRead reads and decrypts data from the object store. Requires read permission.
func ObjectRead(ctx *AccessContext, dossierID, entryID string) ([]byte, error) {
	// RBAC: Check read permission
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, entryID, 0, 'r'); err != nil {
		return nil, err
	}

	raw, err := os.ReadFile(ObjectPath(dossierID, entryID))
	if err != nil {
		return nil, err
	}
	return CryptoDecryptBytes(raw)
}

// objectReadRaw reads object without permission check (internal use only, e.g. ImageGet)
func objectReadRaw(dossierID, entryID string) ([]byte, error) {
	raw, err := os.ReadFile(ObjectPath(dossierID, entryID))
	if err != nil {
		return nil, err
	}
	return CryptoDecryptBytes(raw)
}

// ObjectRemove deletes an object from the store. Requires delete permission.
func ObjectRemove(ctx *AccessContext, dossierID, entryID string) error {
	// RBAC: Check delete permission
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, entryID, 0, 'd'); err != nil {
		return err
	}
	return os.Remove(ObjectPath(dossierID, entryID))
}

// ObjectRemoveByDossier removes all objects for a dossier. Requires delete permission.
func ObjectRemoveByDossier(ctx *AccessContext, dossierID string) error {
	// RBAC: Check delete permission on dossier root
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", 0, 'd'); err != nil {
		return err
	}
	return os.RemoveAll(filepath.Join(ObjectDir, dossierID))
}

// DossierListAccessible is now in access.go with RBAC enforcement

// DossierGetByEmailHash returns a dossier by email_hash. System only.
func DossierGetByEmailHash(ctx *AccessContext, emailHash string) (*Dossier, error) {
	dossiers, err := DossierList(ctx, &DossierFilter{EmailHash: emailHash, Limit: 1})
	if err != nil {
		return nil, err
	}
	if len(dossiers) == 0 {
		return nil, fmt.Errorf("not found")
	}
	return dossiers[0], nil
}

// DossierGetFirst returns the first dossier (for dev/test purposes only). System only.
func DossierGetFirst(ctx *AccessContext) (*Dossier, error) {
	dossiers, err := DossierList(ctx, &DossierFilter{Limit: 1})
	if err != nil {
		return nil, err
	}
	if len(dossiers) == 0 {
		return nil, fmt.Errorf("no dossiers")
	}
	return dossiers[0], nil
}

// AccessListByTargetWithNames returns access records with accessor names joined from dossiers
func AccessListByTargetWithNames(targetID string) ([]map[string]interface{}, error) {
	// Get access records via store.go
	accessList, err := AccessList(&AccessFilter{TargetID: targetID})
	if err != nil {
		return nil, err
	}

	var result []map[string]interface{}
	for _, a := range accessList {
		name := ""
		if d, err := DossierGet(nil, a.AccessorDossierID); err == nil && d != nil {
			name = d.Name
		}

		result = append(result, map[string]interface{}{
			"accessor_id":      a.AccessorDossierID,
			"name":             name,
			"relation":         a.Relation,
			"is_care_receiver": a.IsCareReceiver,
			"can_edit":         a.CanEdit,
		})
	}
	return result, nil
}

// TrackerDistinctTypes returns distinct category/type pairs for a dossier's active trackers
func TrackerDistinctTypes(dossierID string) (map[string][]string, error) {
	var trackers []*Tracker
	if err := dbQuery("SELECT * FROM trackers WHERE dossier_id = ? AND active = 1", []any{dossierID}, &trackers); err != nil {
		return nil, err
	}

	// Extract distinct category/type pairs
	seen := make(map[string]bool)
	result := make(map[string][]string)
	for _, p := range trackers {
		key := p.Category + "|" + p.Type
		if !seen[key] && p.Category != "" && p.Type != "" {
			seen[key] = true
			result[p.Category] = append(result[p.Category], p.Type)
		}
	}
	return result, nil
}

// --- RBAC PERMISSIONS ---

type PermissionFilter struct {
	DossierID string // whose data
	GranteeID string // who has access
	EntryID   string // specific entry
	Role      string // filter by role name
}

// AccessWrite saves one or more access grants
func AccessGrantWrite(grants ...*Access) error {
	if len(grants) == 0 {
		return nil
	}
	for _, a := range grants {
		if a.AccessID == "" {
			a.AccessID = NewID()
		}
		if a.CreatedAt == 0 {
			a.CreatedAt = time.Now().Unix()
		}
	}
	if len(grants) == 1 {
		return dbSave("access", grants[0])
	}
	return dbSave("access", grants)
}

// AccessGrantRemove removes access grants by ID
func AccessGrantRemove(ids ...string) error {
	for _, id := range ids {
		if err := dbDelete("access", "access_id", id); err != nil {
			return err
		}
	}
	return nil
}

// MigrateOldAccess converts dossier_access entries to access grants (one-time migration)
func MigrateOldAccess() int {
	type oldAccess struct {
		AccessorID    string `db:"accessor_dossier_id"`
		TargetID      string `db:"target_dossier_id"`
		CanEdit       int    `db:"can_edit"`
	}
	var entries []oldAccess
	err := dbQuery("SELECT accessor_dossier_id, target_dossier_id, can_edit FROM dossier_access WHERE status = 1", nil, &entries)
	if err != nil {
		return 0
	}

	migrated := 0
	for _, e := range entries {
		// Skip self-references (owner access is automatic)
		if e.AccessorID == e.TargetID {
			continue
		}
		// Skip if grant already exists
		existing, _ := AccessGrantList(&PermissionFilter{DossierID: e.TargetID, GranteeID: e.AccessorID})
		if len(existing) > 0 {
			continue
		}
		// Create root-level grant
		ops := "r"
		if e.CanEdit == 1 {
			ops = "rwdm"
		}
		AccessGrantWrite(&Access{
			DossierID: e.TargetID,
			GranteeID: e.AccessorID,
			EntryID:   "",
			Role:      "Migrated",
			Ops:       ops,
		})
		migrated++
	}
	return migrated
}

// MigrateStudiesToCategoryRoot moves orphan studies (parent_id="") under their
// imaging category_root entry. Idempotent — skips studies already parented.
func MigrateStudiesToCategoryRoot() int {
	// Find all imaging entries with empty parent_id, filter to studies in Go
	var all []*Entry
	err := dbQuery(
		"SELECT * FROM entries WHERE category = ? AND (parent_id IS NULL OR parent_id = '')",
		[]any{CategoryImaging}, &all)
	if err != nil {
		return 0
	}
	var studies []*Entry
	for _, e := range all {
		if e.Type == "study" {
			studies = append(studies, e)
		}
	}
	if len(studies) == 0 {
		return 0
	}

	migrated := 0
	catRoots := map[string]string{} // dossier_id → category_root entry_id

	for _, s := range studies {
		rootID, ok := catRoots[s.DossierID]
		if !ok {
			rootID, err = EnsureCategoryRoot(s.DossierID, CategoryImaging)
			if err != nil {
				continue
			}
			catRoots[s.DossierID] = rootID
		}

		s.ParentID = rootID
		if err := dbSave("entries", s); err == nil {
			migrated++
		}
	}
	return migrated
}

// AccessGrantGet retrieves a single access grant by ID
func AccessGrantGet(id string) (*Access, error) {
	a := &Access{}
	return a, dbLoad("access", id, a)
}

// AccessGrantList retrieves access grants with optional filtering
func AccessGrantList(f *PermissionFilter) ([]*Access, error) {
	q := "SELECT * FROM access WHERE 1=1"
	args := []any{}

	if f != nil {
		if f.DossierID != "" {
			q += " AND dossier_id = ?"
			args = append(args, f.DossierID)
		}
		if f.GranteeID != "" {
			q += " AND grantee_id = ?"
			args = append(args, f.GranteeID)
		}
		if f.EntryID != "" {
			q += " AND entry_id = ?"
			args = append(args, f.EntryID)
		}
		if f.Role != "" {
			q += " AND role = ?"
			args = append(args, CryptoEncrypt(f.Role))
		}
	}

	q += " ORDER BY created_at DESC"

	var result []*Access
	err := dbQuery(q, args, &result)
	return result, err
}

// AccessGrantsForGrantee returns all grants for a specific grantee, grouped by dossier
func AccessGrantsForGrantee(granteeID string) (map[string][]*Access, error) {
	grants, err := AccessGrantList(&PermissionFilter{GranteeID: granteeID})
	if err != nil {
		return nil, err
	}

	result := make(map[string][]*Access)
	for _, g := range grants {
		result[g.DossierID] = append(result[g.DossierID], g)
	}
	return result, nil
}

// AccessRoleTemplates returns role templates (grantee_id is null) for a dossier
// Pass empty dossierID for system-wide templates
func AccessRoleTemplates(dossierID string) ([]*Access, error) {
	q := "SELECT * FROM access WHERE grantee_id IS NULL OR grantee_id = ''"
	args := []any{}

	if dossierID != "" {
		q += " AND (dossier_id = ? OR dossier_id IS NULL OR dossier_id = '')"
		args = append(args, dossierID)
	} else {
		q += " AND (dossier_id IS NULL OR dossier_id = '')"
	}

	q += " ORDER BY role, entry_id"

	var result []*Access
	err := dbQuery(q, args, &result)
	return result, err
}

// AccessGrantRole copies role template entries for a specific grantee
func AccessGrantRole(dossierID, granteeID, role string) error {
	// Get template entries for this role
	templates, err := AccessRoleTemplates(dossierID)
	if err != nil {
		return err
	}

	var grants []*Access
	for _, t := range templates {
		if t.Role != role {
			continue
		}
		grants = append(grants, &Access{
			DossierID: dossierID,
			GranteeID: granteeID,
			EntryID:   t.EntryID,
			Role:      role,
			Ops:       t.Ops,
		})
	}

	if len(grants) == 0 {
		// No template found, create default read-only grant
		grants = append(grants, &Access{
			DossierID: dossierID,
			GranteeID: granteeID,
			Role:      role,
			Ops:       "r",
		})
	}

	return AccessGrantWrite(grants...)
}

// AccessRevokeAll removes all access grants for a grantee to a specific dossier
func AccessRevokeAll(dossierID, granteeID string) error {
	// Query for matching grants, then delete each by PK
	grants, err := AccessGrantList(&PermissionFilter{DossierID: dossierID, GranteeID: granteeID})
	if err != nil {
		return err
	}
	for _, g := range grants {
		if err := dbDelete("access", "access_id", g.AccessID); err != nil {
			return err
		}
	}
	return nil
}

// AccessRevokeEntry removes a specific entry grant for a grantee
func AccessRevokeEntry(dossierID, granteeID, entryID string) error {
	grants, err := AccessGrantList(&PermissionFilter{DossierID: dossierID, GranteeID: granteeID, EntryID: entryID})
	if err != nil {
		return err
	}
	for _, g := range grants {
		if err := dbDelete("access", "access_id", g.AccessID); err != nil {
			return err
		}
	}
	return nil
}

// --- GENOME QUERIES ---
// Note: These functions use nil ctx for internal operations. When called from
// API handlers, the API should perform its own RBAC check first.

// GenomeGetExtraction returns the extraction entry for genome data
func GenomeGetExtraction(ctx *AccessContext, dossierID string) (*Entry, error) {
	entries, err := EntryList(accessorIDFromContext(ctx), "", CategoryGenome, &EntryFilter{
		DossierID: dossierID,
		Type:      "extraction",
		Limit:     1,
	})
	if err != nil || len(entries) == 0 {
		return nil, fmt.Errorf("no genome data")
	}
	return entries[0], nil
}

// GenomeTier represents a genome category tier
type GenomeTier struct {
	TierID   string
	Category string
}

// GenomeGetTiers returns all tier entries for a genome extraction
func GenomeGetTiers(ctx *AccessContext, dossierID, extractionID string) ([]GenomeTier, error) {
	entries, err := EntryList(accessorIDFromContext(ctx), extractionID, CategoryGenome, &EntryFilter{
		DossierID: dossierID,
		Type:      "tier",
	})
	if err != nil {
		return nil, err
	}

	var tiers []GenomeTier
	for _, e := range entries {
		tiers = append(tiers, GenomeTier{
			TierID:   e.EntryID,
			Category: e.Value, // Value holds category name
		})
	}
	return tiers, nil
}

// GenomeGetTierByCategory returns a specific tier by category name
func GenomeGetTierByCategory(ctx *AccessContext, dossierID, extractionID, category string) (*GenomeTier, error) {
	entries, err := EntryList(accessorIDFromContext(ctx), extractionID, CategoryGenome, &EntryFilter{
		DossierID: dossierID,
		Type:      "tier",
		Value:     category,
		Limit:     1,
	})
	if err != nil || len(entries) == 0 {
		return nil, fmt.Errorf("tier not found")
	}
	return &GenomeTier{
		TierID:   entries[0].EntryID,
		Category: entries[0].Value,
	}, nil
}

// GenomeVariant represents a genome variant with its metadata
type GenomeVariant struct {
	EntryID     string
	RSID        string
	Genotype    string
	Gene        string
	Magnitude   float64
	Repute      string
	Summary     string
	Subcategory string
	TierID      string
}

// GenomeGetVariants returns variants for specified tier IDs
func GenomeGetVariants(ctx *AccessContext, dossierID string, tierIDs []string) ([]GenomeVariant, error) {
	if len(tierIDs) == 0 {
		return nil, nil
	}

	// Query entries for each tier and deduplicate by type (rsid)
	seen := make(map[string]bool)
	var variants []GenomeVariant

	for _, tierID := range tierIDs {
		entries, err := EntryList(accessorIDFromContext(ctx), tierID, CategoryGenome, &EntryFilter{DossierID: dossierID})
		if err != nil {
			continue
		}

		for _, e := range entries {
			// Deduplicate by type (rsid)
			if seen[e.Type] {
				continue
			}
			seen[e.Type] = true

			var data struct {
				Mag float64 `json:"mag"`
				Rep string  `json:"rep"`
				Sum string  `json:"sum"`
				Sub string  `json:"sub"`
			}
			json.Unmarshal([]byte(e.Data), &data)

			variants = append(variants, GenomeVariant{
				EntryID:     e.EntryID,
				RSID:        e.Type,
				Genotype:    e.Value,
				Gene:        e.Tags,
				Magnitude:   data.Mag,
				Repute:      data.Rep,
				Summary:     data.Sum,
				Subcategory: data.Sub,
				TierID:      tierID,
			})
		}
	}
	return variants, nil
}

// GenomeGetVariantsByTier returns variants for a specific tier
func GenomeGetVariantsByTier(ctx *AccessContext, dossierID, tierID string) ([]GenomeVariant, error) {
	entries, err := EntryList(accessorIDFromContext(ctx), tierID, CategoryGenome, &EntryFilter{DossierID: dossierID})
	if err != nil {
		return nil, err
	}

	var variants []GenomeVariant
	for _, e := range entries {
		var data struct {
			Mag float64 `json:"mag"`
			Rep string  `json:"rep"`
			Sum string  `json:"sum"`
			Sub string  `json:"sub"`
		}
		json.Unmarshal([]byte(e.Data), &data)

		variants = append(variants, GenomeVariant{
			EntryID:     e.EntryID,
			RSID:        e.Type,
			Genotype:    e.Value,
			Gene:        e.Tags,
			Magnitude:   data.Mag,
			Repute:      data.Rep,
			Summary:     data.Sum,
			Subcategory: data.Sub,
			TierID:      tierID,
		})
	}
	return variants, nil
}

// GenomeMatch represents a single genome query result
type GenomeMatch struct {
	RSID        string   `json:"rsid"`
	Genotype    string   `json:"genotype"`
	Gene        string   `json:"gene,omitempty"`
	Magnitude   *float64 `json:"magnitude,omitempty"`
	Repute      string   `json:"repute,omitempty"`
	Summary     string   `json:"summary,omitempty"`
	Categories []string `json:"categories,omitempty"`
}

// GenomeQueryResult is the response from GenomeQuery
type GenomeQueryResult struct {
	Matches  []GenomeMatch `json:"matches"`
	Returned int           `json:"returned"`
	Total    int           `json:"total"`
}

// GenomeQueryOpts are the filter/sort/pagination options for GenomeQuery
type GenomeQueryOpts struct {
	Category      string
	Search        string
	Gene          string   // comma-separated
	RSIDs         []string
	MinMagnitude  float64
	Repute        string // filter by repute (Good, Bad, Clear)
	IncludeHidden bool
	Sort          string // "magnitude" (default), "gene", "rsid"
	Offset        int
	Limit         int
	AccessorID    string // who is querying (for audit logging)
}

// GenomeQuery queries genome variants for a dossier. Requires read permission on genome data.
// Fast path: gene/rsid use indexed search_key/type columns (precise SQL queries).
// Slow path: search/min_magnitude load all variants and filter in memory.
func GenomeQuery(ctx *AccessContext, dossierID string, opts GenomeQueryOpts) (*GenomeQueryResult, error) {
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", CategoryGenome, 'r'); err != nil {
		return nil, err
	}

	if opts.IncludeHidden {
		var details []string
		if opts.Gene != "" {
			details = append(details, "gene="+opts.Gene)
		}
		if len(opts.RSIDs) > 0 {
			details = append(details, "rsids="+strings.Join(opts.RSIDs, ","))
		}
		if opts.Search != "" {
			details = append(details, "search="+opts.Search)
		}
		if opts.Category != "" {
			details = append(details, "category="+opts.Category)
		}
		AuditLog(opts.AccessorID, "genome_reveal_hidden", dossierID, strings.Join(details, " "))
	}

	limit := opts.Limit
	if limit <= 0 {
		limit = 100
	}
	if limit > 500 {
		limit = 500
	}

	// Fast path: gene or rsid — use indexed columns
	if opts.Gene != "" || len(opts.RSIDs) > 0 {
		return genomeQueryFast(dossierID, opts, limit)
	}

	// Slow path: search/min_magnitude — load all, filter in memory
	return genomeQuerySlow(dossierID, opts, limit)
}

// genomeQueryFast uses indexed search_key (gene) and type (rsid) columns.
func genomeQueryFast(dossierID string, opts GenomeQueryOpts, limit int) (*GenomeQueryResult, error) {
	var entries []Entry

	if opts.Gene != "" {
		// Split comma-separated genes, query each via indexed search_key
		genes := strings.Split(opts.Gene, ",")
		for i := range genes {
			genes[i] = strings.TrimSpace(genes[i])
		}

		// Build gene IN clause
		genePlaceholders := make([]string, len(genes))
		args := []any{dossierID, CategoryGenome}
		for i, gene := range genes {
			genePlaceholders[i] = "?"
			args = append(args, CryptoEncrypt(gene))
		}
		sql := "SELECT * FROM entries WHERE dossier_id = ? AND category = ? AND search_key IN (" + strings.Join(genePlaceholders, ",") + ")"

		// Add rsid filter if specified
		if len(opts.RSIDs) > 0 {
			rsidPlaceholders := make([]string, len(opts.RSIDs))
			for i, rsid := range opts.RSIDs {
				rsidPlaceholders[i] = "?"
				args = append(args, CryptoEncrypt(rsid))
			}
			sql += " AND type IN (" + strings.Join(rsidPlaceholders, ",") + ")"
		}

		dbQuery(sql, args, &entries)
	} else if len(opts.RSIDs) > 0 {
		// rsid only, no gene — single IN query
		placeholders := make([]string, len(opts.RSIDs))
		args := []any{dossierID, CategoryGenome}
		for i, rsid := range opts.RSIDs {
			placeholders[i] = "?"
			args = append(args, CryptoEncrypt(rsid))
		}
		sql := "SELECT * FROM entries WHERE dossier_id = ? AND category = ? AND type IN (" + strings.Join(placeholders, ",") + ")"
		dbQuery(sql, args, &entries)
	}

	// Look up tier categories for parent_ids (single IN query)
	tierCategories := make(map[string]string)
	tierIDSet := make(map[string]bool)
	for _, e := range entries {
		tierIDSet[e.ParentID] = true
	}
	if len(tierIDSet) > 0 {
		placeholders := make([]string, 0, len(tierIDSet))
		args := make([]any, 0, len(tierIDSet))
		for id := range tierIDSet {
			placeholders = append(placeholders, "?")
			args = append(args, id)
		}
		var tierEntries []Entry
		dbQuery("SELECT * FROM entries WHERE entry_id IN ("+strings.Join(placeholders, ",")+")", args, &tierEntries)
		for _, t := range tierEntries {
			tierCategories[t.EntryID] = t.Value
		}
	}

	return genomeEntriesToResult(entries, tierCategories, opts, limit)
}

// genomeQuerySlow loads all variants and filters in memory (for search/min_magnitude).
func genomeQuerySlow(dossierID string, opts GenomeQueryOpts, limit int) (*GenomeQueryResult, error) {
	sysCtx := &AccessContext{IsSystem: true}

	extraction, err := GenomeGetExtraction(sysCtx, dossierID)
	if err != nil {
		return nil, fmt.Errorf("GENOME_NO_EXTRACTION: %w", err)
	}

	tiers, _ := GenomeGetTiers(sysCtx, dossierID, extraction.EntryID)
	if len(tiers) == 0 {
		return &GenomeQueryResult{Matches: []GenomeMatch{}}, nil
	}

	tierCategories := make(map[string]string)
	tierIDs := make([]string, len(tiers))
	for i, t := range tiers {
		tierIDs[i] = t.TierID
		tierCategories[t.TierID] = t.Category
	}

	variants, err := GenomeGetVariants(sysCtx, dossierID, tierIDs)
	if err != nil {
		return nil, fmt.Errorf("GENOME_VARIANT_QUERY_FAILED: %w", err)
	}

	// Convert to entries for shared result builder
	var entries []Entry
	for _, v := range variants {
		dataJSON, _ := json.Marshal(struct {
			Mag float64 `json:"mag,omitempty"`
			Rep string  `json:"rep,omitempty"`
			Sum string  `json:"sum,omitempty"`
			Sub string  `json:"sub,omitempty"`
		}{v.Magnitude, v.Repute, v.Summary, v.Subcategory})

		entries = append(entries, Entry{
			EntryID:  v.EntryID,
			ParentID: v.TierID,
			Type:     v.RSID,
			Value:    v.Genotype,
			Tags:     v.Gene,
			Data:     string(dataJSON),
		})
	}

	return genomeEntriesToResult(entries, tierCategories, opts, limit)
}

// genomeEntriesToResult converts raw entries to GenomeQueryResult with filtering/sorting.
func genomeEntriesToResult(entries []Entry, tierCategories map[string]string, opts GenomeQueryOpts, limit int) (*GenomeQueryResult, error) {
	targeted := opts.Gene != "" || len(opts.RSIDs) > 0

	// Dedup by rsid, merge categories
	seen := make(map[string]*GenomeMatch)
	var order []string

	for _, e := range entries {
		var data struct {
			Mag float64 `json:"mag"`
			Rep string  `json:"rep"`
			Sum string  `json:"sum"`
			Sub string  `json:"sub"`
		}
		if e.Data != "" {
			json.Unmarshal([]byte(e.Data), &data)
		}

		if opts.Search != "" {
			sl := strings.ToLower(opts.Search)
			if !strings.Contains(strings.ToLower(e.Tags), sl) &&
				!strings.Contains(strings.ToLower(data.Sum), sl) &&
				!strings.Contains(strings.ToLower(data.Sub), sl) &&
				!strings.Contains(strings.ToLower(e.Type), sl) &&
				!strings.Contains(strings.ToLower(e.Value), sl) {
				continue
			}
		}

		if opts.Category != "" && tierCategories[e.ParentID] != opts.Category {
			continue
		}

		if opts.MinMagnitude > 0 && data.Mag < opts.MinMagnitude {
			continue
		}

		if opts.Repute != "" && !strings.EqualFold(data.Rep, opts.Repute) {
			continue
		}

		isHidden := data.Mag > 4.0 || strings.EqualFold(data.Rep, "bad")
		if isHidden && !opts.IncludeHidden && !targeted {
			continue
		}

		cat := tierCategories[e.ParentID]

		if m, ok := seen[e.Type]; ok {
			// Already seen this rsid — add category if not duplicate
			if cat != "" {
				dup := false
				for _, c := range m.Categories {
					if c == cat {
						dup = true
						break
					}
				}
				if !dup {
					m.Categories = append(m.Categories, cat)
				}
			}
			continue
		}

		redact := isHidden && !opts.IncludeHidden
		match := &GenomeMatch{
			RSID: e.Type,
			Gene: e.Tags,
		}
		if cat != "" {
			match.Categories = []string{cat}
		}
		if redact {
			match.Genotype = "hidden"
			match.Summary = "Sensitive variant hidden. Query with include_hidden=true to reveal."
		} else {
			match.Genotype = e.Value
			if data.Sum != "" {
				match.Summary = data.Sum
			}
		}
		if data.Mag > 0 {
			mag := data.Mag
			match.Magnitude = &mag
		}
		if data.Rep != "" {
			match.Repute = data.Rep
		}

		seen[e.Type] = match
		order = append(order, e.Type)
	}

	total := len(order)
	var matches []GenomeMatch
	for i, rsid := range order {
		if i < opts.Offset {
			continue
		}
		if len(matches) >= limit {
			break
		}
		matches = append(matches, *seen[rsid])
	}

	// Sort
	switch opts.Sort {
	case "gene":
		sort.Slice(matches, func(i, j int) bool {
			return matches[i].Gene < matches[j].Gene
		})
	case "rsid":
		sort.Slice(matches, func(i, j int) bool {
			return matches[i].RSID < matches[j].RSID
		})
	default:
		sort.Slice(matches, func(i, j int) bool {
			mi, mj := float64(0), float64(0)
			if matches[i].Magnitude != nil {
				mi = *matches[i].Magnitude
			}
			if matches[j].Magnitude != nil {
				mj = *matches[j].Magnitude
			}
			return mi > mj
		})
	}

	return &GenomeQueryResult{
		Matches:  matches,
		Returned: len(matches),
		Total:    total,
	}, nil
}

// --- RBAC-CHECKED QUERY HELPERS ---

// EntryCategoryCounts returns entry counts by category for a dossier.
func EntryCategoryCounts(ctx *AccessContext, dossierID string) (map[string]int, error) {
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", 0, 'r'); err != nil {
		return nil, err
	}
	var counts []struct {
		Category int `db:"category"`
		Count    int `db:"cnt"`
	}
	if err := dbQuery("SELECT category, COUNT(*) as cnt FROM entries WHERE dossier_id = ? AND category > 0 GROUP BY category", []any{dossierID}, &counts); err != nil {
		return nil, err
	}
	result := make(map[string]int)
	for _, c := range counts {
		name := CategoryName(c.Category)
		if name != "unknown" {
			result[name] = c.Count
		}
	}
	return result, nil
}

// EntryCount returns entry count for a dossier by category and optional type.
func EntryCount(ctx *AccessContext, dossierID string, category int, typ string) (int, error) {
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", category, 'r'); err != nil {
		return 0, err
	}
	if typ != "" {
		return dbCount("SELECT COUNT(*) FROM entries WHERE dossier_id = ? AND category = ? AND type = ?",
			dossierID, category, CryptoEncrypt(typ))
	}
	return dbCount("SELECT COUNT(*) FROM entries WHERE dossier_id = ? AND category = ?",
		dossierID, category)
}

// EntryListByDossier returns all entries for a dossier ordered by category and timestamp.
func EntryListByDossier(ctx *AccessContext, dossierID string) ([]*Entry, error) {
	if err := checkAccess(accessorIDFromContext(ctx), dossierID, "", 0, 'r'); err != nil {
		return nil, err
	}
	var entries []*Entry
	return entries, dbQuery("SELECT * FROM entries WHERE dossier_id = ? ORDER BY category, timestamp", []any{dossierID}, &entries)
}

// LabTestList returns all lab tests (reference data, no RBAC needed).
func LabTestList() ([]LabTest, error) {
	var tests []LabTest
	return tests, dbQuery("SELECT loinc_id, name FROM lab_test", nil, &tests)
}

// LabEntryListForIndex returns lab entries with data for building search indexes.
func LabEntryListForIndex() ([]*Entry, error) {
	var entries []*Entry
	return entries, dbQuery("SELECT entry_id, data FROM entries WHERE category = ? AND parent_id != ''",
		[]any{CategoryLab}, &entries)
}

// LabRefListBySource returns lab references matching a source pattern in ref_id.
func LabRefListBySource(source string) ([]LabReference, error) {
	var refs []LabReference
	return refs, dbQuery("SELECT * FROM lab_reference WHERE ref_id LIKE ?", []any{"%|" + source + "|%"}, &refs)
}

// LabRefDeleteByID deletes a lab reference by ref_id.
func LabRefDeleteByID(refID string) error {
	return dbDelete("lab_reference", "ref_id", refID)
}

// --- HELPERS ---

func deleteByIDs(table, col string, ids []string) error {
	for _, id := range ids {
		if err := dbDelete(table, col, id); err != nil {
			return err
		}
	}
	return nil
}