feat: Add bd repair command for orphaned foreign key refs (hq-2cchm)
When the database has orphaned dependencies or labels, the migration invariant check fails and prevents the database from opening. This creates a chicken-and-egg problem where bd doctor --fix cannot run. The new bd repair command: - Opens SQLite directly, bypassing invariant checks - Deletes orphaned dependencies (issue_id or depends_on_id not in issues) - Deletes orphaned labels (issue_id not in issues) - Runs WAL checkpoint to persist changes - Supports --dry-run to preview what would be cleaned 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Steve Yegge
@@ -281,6 +281,7 @@ var rootCmd = &cobra.Command{
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"powershell",
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"prime",
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"quickstart",
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"repair",
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"setup",
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"version",
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"zsh",
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307
cmd/bd/repair.go
Normal file
307
cmd/bd/repair.go
Normal file
@@ -0,0 +1,307 @@
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package main
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import (
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"database/sql"
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"fmt"
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"os"
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"path/filepath"
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"strings"
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"time"
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_ "github.com/ncruces/go-sqlite3/driver"
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_ "github.com/ncruces/go-sqlite3/embed"
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"github.com/spf13/cobra"
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"github.com/steveyegge/beads/internal/ui"
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)
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var repairCmd = &cobra.Command{
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Use: "repair",
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GroupID: GroupMaintenance,
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Short: "Repair corrupted database by cleaning orphaned references",
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// PreRun disables PersistentPreRun for this command (we open DB directly, bypassing invariants)
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PreRun: func(cmd *cobra.Command, args []string) {},
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Long: `Repair a database that won't open due to orphaned foreign key references.
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When the database has orphaned dependencies or labels, the migration invariant
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check fails and prevents the database from opening. This creates a chicken-and-egg
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problem where 'bd doctor --fix' can't run because it can't open the database.
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This command opens SQLite directly (bypassing invariant checks) and cleans:
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- Orphaned dependencies (issue_id not in issues)
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- Orphaned dependencies (depends_on_id not in issues, excluding external refs)
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- Orphaned labels (issue_id not in issues)
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After repair, normal bd commands should work again.
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Examples:
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bd repair # Repair database in current directory
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bd repair --dry-run # Show what would be cleaned without making changes
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bd repair --path /other/repo # Repair database in another location`,
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Run: runRepair,
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}
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var (
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repairDryRun bool
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repairPath string
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)
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func init() {
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repairCmd.Flags().BoolVar(&repairDryRun, "dry-run", false, "Show what would be cleaned without making changes")
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repairCmd.Flags().StringVar(&repairPath, "path", ".", "Path to repository with .beads directory")
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rootCmd.AddCommand(repairCmd)
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}
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func runRepair(cmd *cobra.Command, args []string) {
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// Find .beads directory
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beadsDir := filepath.Join(repairPath, ".beads")
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if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
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fmt.Fprintf(os.Stderr, "Error: .beads directory not found at %s\n", beadsDir)
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os.Exit(1)
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}
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// Find database file
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dbPath := filepath.Join(beadsDir, "beads.db")
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if _, err := os.Stat(dbPath); os.IsNotExist(err) {
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fmt.Fprintf(os.Stderr, "Error: database not found at %s\n", dbPath)
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os.Exit(1)
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}
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fmt.Printf("Repairing database: %s\n", dbPath)
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if repairDryRun {
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fmt.Println("[DRY-RUN] No changes will be made")
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}
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fmt.Println()
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// Open database directly, bypassing beads storage layer
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db, err := openRepairDB(dbPath)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error opening database: %v\n", err)
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os.Exit(1)
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}
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defer db.Close()
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// Collect repair statistics
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stats := repairStats{}
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// 1. Find and clean orphaned dependencies (issue_id not in issues)
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orphanedIssueID, err := findOrphanedDepsIssueID(db)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error checking orphaned deps (issue_id): %v\n", err)
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os.Exit(1)
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}
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stats.orphanedDepsIssueID = len(orphanedIssueID)
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// 2. Find and clean orphaned dependencies (depends_on_id not in issues)
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orphanedDependsOn, err := findOrphanedDepsDependsOn(db)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error checking orphaned deps (depends_on_id): %v\n", err)
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os.Exit(1)
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}
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stats.orphanedDepsDependsOn = len(orphanedDependsOn)
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// 3. Find and clean orphaned labels
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orphanedLabels, err := findOrphanedLabels(db)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error checking orphaned labels: %v\n", err)
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os.Exit(1)
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}
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stats.orphanedLabels = len(orphanedLabels)
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// Print findings
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if stats.total() == 0 {
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fmt.Printf("%s No orphaned references found - database is clean\n", ui.RenderPass("✓"))
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return
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}
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fmt.Printf("Found %d orphaned reference(s):\n", stats.total())
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if stats.orphanedDepsIssueID > 0 {
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fmt.Printf(" • %d dependencies with missing issue_id\n", stats.orphanedDepsIssueID)
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for _, dep := range orphanedIssueID {
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fmt.Printf(" - %s → %s\n", dep.issueID, dep.dependsOnID)
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}
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}
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if stats.orphanedDepsDependsOn > 0 {
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fmt.Printf(" • %d dependencies with missing depends_on_id\n", stats.orphanedDepsDependsOn)
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for _, dep := range orphanedDependsOn {
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fmt.Printf(" - %s → %s\n", dep.issueID, dep.dependsOnID)
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}
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}
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if stats.orphanedLabels > 0 {
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fmt.Printf(" • %d labels with missing issue_id\n", stats.orphanedLabels)
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for _, label := range orphanedLabels {
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fmt.Printf(" - %s: %s\n", label.issueID, label.label)
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}
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}
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fmt.Println()
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if repairDryRun {
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fmt.Printf("[DRY-RUN] Would delete %d orphaned reference(s)\n", stats.total())
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return
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}
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// Apply repairs
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fmt.Println("Cleaning orphaned references...")
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// Delete orphaned deps (issue_id)
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if len(orphanedIssueID) > 0 {
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result, err := db.Exec(`
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DELETE FROM dependencies
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = dependencies.issue_id)
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`)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error deleting orphaned deps (issue_id): %v\n", err)
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} else {
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deleted, _ := result.RowsAffected()
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fmt.Printf(" %s Deleted %d dependencies with missing issue_id\n", ui.RenderPass("✓"), deleted)
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}
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}
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// Delete orphaned deps (depends_on_id)
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if len(orphanedDependsOn) > 0 {
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result, err := db.Exec(`
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DELETE FROM dependencies
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = dependencies.depends_on_id)
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AND dependencies.depends_on_id NOT LIKE 'external:%'
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`)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error deleting orphaned deps (depends_on_id): %v\n", err)
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} else {
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deleted, _ := result.RowsAffected()
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fmt.Printf(" %s Deleted %d dependencies with missing depends_on_id\n", ui.RenderPass("✓"), deleted)
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}
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}
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// Delete orphaned labels
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if len(orphanedLabels) > 0 {
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result, err := db.Exec(`
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DELETE FROM labels
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = labels.issue_id)
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`)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error deleting orphaned labels: %v\n", err)
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} else {
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deleted, _ := result.RowsAffected()
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fmt.Printf(" %s Deleted %d labels with missing issue_id\n", ui.RenderPass("✓"), deleted)
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}
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}
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// Run WAL checkpoint to persist changes
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fmt.Print(" Running WAL checkpoint... ")
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if _, err := db.Exec("PRAGMA wal_checkpoint(TRUNCATE)"); err != nil {
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fmt.Printf("%s %v\n", ui.RenderFail("✗"), err)
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} else {
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fmt.Printf("%s\n", ui.RenderPass("✓"))
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}
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fmt.Println()
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fmt.Printf("%s Repair complete. Try running 'bd doctor' to verify.\n", ui.RenderPass("✓"))
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}
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// repairStats tracks what was found/cleaned
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type repairStats struct {
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orphanedDepsIssueID int
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orphanedDepsDependsOn int
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orphanedLabels int
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}
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func (s repairStats) total() int {
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return s.orphanedDepsIssueID + s.orphanedDepsDependsOn + s.orphanedLabels
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}
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// orphanedDep represents an orphaned dependency
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type orphanedDep struct {
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issueID string
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dependsOnID string
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}
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// orphanedLabel represents an orphaned label
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type orphanedLabel struct {
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issueID string
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label string
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}
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// openRepairDB opens SQLite directly for repair, bypassing all beads layer code
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func openRepairDB(dbPath string) (*sql.DB, error) {
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// Build connection string with pragmas
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busyMs := int64(30 * time.Second / time.Millisecond)
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if v := strings.TrimSpace(os.Getenv("BD_LOCK_TIMEOUT")); v != "" {
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if d, err := time.ParseDuration(v); err == nil {
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busyMs = int64(d / time.Millisecond)
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}
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}
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connStr := fmt.Sprintf("file:%s?_pragma=busy_timeout(%d)&_pragma=foreign_keys(OFF)&_time_format=sqlite",
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dbPath, busyMs)
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return sql.Open("sqlite3", connStr)
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}
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// findOrphanedDepsIssueID finds dependencies where issue_id doesn't exist
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func findOrphanedDepsIssueID(db *sql.DB) ([]orphanedDep, error) {
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rows, err := db.Query(`
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SELECT d.issue_id, d.depends_on_id
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FROM dependencies d
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = d.issue_id)
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`)
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if err != nil {
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return nil, err
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}
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defer rows.Close()
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var orphans []orphanedDep
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for rows.Next() {
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var dep orphanedDep
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if err := rows.Scan(&dep.issueID, &dep.dependsOnID); err != nil {
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return nil, err
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}
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orphans = append(orphans, dep)
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}
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return orphans, rows.Err()
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}
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// findOrphanedDepsDependsOn finds dependencies where depends_on_id doesn't exist
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func findOrphanedDepsDependsOn(db *sql.DB) ([]orphanedDep, error) {
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rows, err := db.Query(`
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SELECT d.issue_id, d.depends_on_id
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FROM dependencies d
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = d.depends_on_id)
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AND d.depends_on_id NOT LIKE 'external:%'
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`)
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if err != nil {
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return nil, err
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}
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defer rows.Close()
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var orphans []orphanedDep
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for rows.Next() {
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var dep orphanedDep
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if err := rows.Scan(&dep.issueID, &dep.dependsOnID); err != nil {
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return nil, err
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}
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orphans = append(orphans, dep)
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}
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return orphans, rows.Err()
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}
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// findOrphanedLabels finds labels where issue_id doesn't exist
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func findOrphanedLabels(db *sql.DB) ([]orphanedLabel, error) {
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rows, err := db.Query(`
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SELECT l.issue_id, l.label
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FROM labels l
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = l.issue_id)
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`)
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if err != nil {
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return nil, err
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}
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defer rows.Close()
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var labels []orphanedLabel
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for rows.Next() {
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var label orphanedLabel
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if err := rows.Scan(&label.issueID, &label.label); err != nil {
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return nil, err
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}
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labels = append(labels, label)
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}
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return labels, rows.Err()
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}
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201
cmd/bd/repair_orphans_test.go
Normal file
201
cmd/bd/repair_orphans_test.go
Normal file
@@ -0,0 +1,201 @@
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package main
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import (
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"database/sql"
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"os"
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"os/exec"
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"path/filepath"
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"strings"
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"testing"
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_ "github.com/ncruces/go-sqlite3/driver"
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_ "github.com/ncruces/go-sqlite3/embed"
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)
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// runBDRepair runs the repair command with --path flag (bypasses normal db init)
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func runBDRepair(t *testing.T, exe, path string, args ...string) (string, error) {
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t.Helper()
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fullArgs := []string{"repair", "--path", path}
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fullArgs = append(fullArgs, args...)
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cmd := exec.Command(exe, fullArgs...)
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cmd.Dir = path
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cmd.Env = append(os.Environ(), "BEADS_NO_DAEMON=1")
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out, err := cmd.CombinedOutput()
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return string(out), err
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}
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func TestRepairOrphans_DryRun(t *testing.T) {
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requireTestGuardDisabled(t)
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if testing.Short() {
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t.Skip("skipping slow repair test in short mode")
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}
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bdExe := buildBDForTest(t)
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ws := mkTmpDirInTmp(t, "bd-repair-orphans-*")
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dbPath := filepath.Join(ws, ".beads", "beads.db")
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// Initialize with some issues
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if _, err := runBDSideDB(t, bdExe, ws, dbPath, "init", "--prefix", "test", "--quiet"); err != nil {
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t.Fatalf("bd init failed: %v", err)
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}
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if _, err := runBDSideDB(t, bdExe, ws, dbPath, "create", "Issue 1", "-p", "1"); err != nil {
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t.Fatalf("bd create failed: %v", err)
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}
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// Directly insert orphaned data into the database
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db, err := sql.Open("sqlite3", "file:"+dbPath+"?_pragma=foreign_keys(OFF)")
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if err != nil {
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t.Fatalf("open db: %v", err)
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}
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defer db.Close()
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// Insert orphaned dependency (issue_id doesn't exist)
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_, err = db.Exec("INSERT INTO dependencies (issue_id, depends_on_id, type, created_by) VALUES ('nonexistent-1', 'test-xyz', 'blocks', 'test')")
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if err != nil {
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t.Fatalf("insert orphan dep: %v", err)
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}
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// Insert orphaned dependency (depends_on_id doesn't exist)
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_, err = db.Exec("INSERT INTO dependencies (issue_id, depends_on_id, type, created_by) VALUES ('test-xyz', 'deleted-issue', 'blocks', 'test')")
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if err != nil {
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t.Fatalf("insert orphan dep2: %v", err)
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}
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// Insert orphaned label
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_, err = db.Exec("INSERT INTO labels (issue_id, label) VALUES ('gone-issue', 'bug')")
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if err != nil {
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t.Fatalf("insert orphan label: %v", err)
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}
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db.Close()
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// Run repair with --dry-run (use --path, not --db, so repair bypasses normal init)
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out, err := runBDRepair(t, bdExe, ws, "--dry-run")
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if err != nil {
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t.Fatalf("bd repair --dry-run failed: %v\n%s", err, out)
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}
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// Verify it found the orphans
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if !strings.Contains(out, "dependencies with missing issue_id") {
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t.Errorf("expected to find orphaned deps (issue_id), got: %s", out)
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}
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if !strings.Contains(out, "dependencies with missing depends_on_id") {
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t.Errorf("expected to find orphaned deps (depends_on_id), got: %s", out)
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}
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if !strings.Contains(out, "labels with missing issue_id") {
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t.Errorf("expected to find orphaned labels, got: %s", out)
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}
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if !strings.Contains(out, "[DRY-RUN]") {
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t.Errorf("expected DRY-RUN message, got: %s", out)
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}
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// Verify data wasn't actually deleted
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db2, err := sql.Open("sqlite3", "file:"+dbPath+"?_pragma=foreign_keys(OFF)")
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if err != nil {
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t.Fatalf("reopen db: %v", err)
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}
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defer db2.Close()
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var count int
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db2.QueryRow("SELECT COUNT(*) FROM dependencies WHERE issue_id = 'nonexistent-1'").Scan(&count)
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if count != 1 {
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t.Errorf("expected orphan dep to still exist after dry-run, got count=%d", count)
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}
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}
|
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|
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func TestRepairOrphans_Fix(t *testing.T) {
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requireTestGuardDisabled(t)
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|
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if testing.Short() {
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t.Skip("skipping slow repair test in short mode")
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}
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bdExe := buildBDForTest(t)
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ws := mkTmpDirInTmp(t, "bd-repair-fix-*")
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dbPath := filepath.Join(ws, ".beads", "beads.db")
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// Initialize with some issues
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if _, err := runBDSideDB(t, bdExe, ws, dbPath, "init", "--prefix", "test", "--quiet"); err != nil {
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t.Fatalf("bd init failed: %v", err)
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}
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out, err := runBDSideDB(t, bdExe, ws, dbPath, "create", "Issue 1", "-p", "1", "--json")
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if err != nil {
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t.Fatalf("bd create failed: %v\n%s", err, out)
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}
|
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|
||||
// Directly insert orphaned data
|
||||
db, err := sql.Open("sqlite3", "file:"+dbPath+"?_pragma=foreign_keys(OFF)")
|
||||
if err != nil {
|
||||
t.Fatalf("open db: %v", err)
|
||||
}
|
||||
|
||||
// Insert orphaned dependencies and labels
|
||||
db.Exec("INSERT INTO dependencies (issue_id, depends_on_id, type, created_by) VALUES ('orphan-1', 'test-xyz', 'blocks', 'test')")
|
||||
db.Exec("INSERT INTO dependencies (issue_id, depends_on_id, type, created_by) VALUES ('test-xyz', 'deleted-2', 'blocks', 'test')")
|
||||
db.Exec("INSERT INTO labels (issue_id, label) VALUES ('orphan-3', 'wontfix')")
|
||||
db.Close()
|
||||
|
||||
// Run repair (no --dry-run) - use --path to bypass normal db init
|
||||
out, err = runBDRepair(t, bdExe, ws)
|
||||
if err != nil {
|
||||
t.Fatalf("bd repair failed: %v\n%s", err, out)
|
||||
}
|
||||
|
||||
// Verify it cleaned up
|
||||
if !strings.Contains(out, "Deleted") {
|
||||
t.Errorf("expected deletion messages, got: %s", out)
|
||||
}
|
||||
if !strings.Contains(out, "Repair complete") {
|
||||
t.Errorf("expected completion message, got: %s", out)
|
||||
}
|
||||
|
||||
// Verify orphans are gone
|
||||
db2, err := sql.Open("sqlite3", "file:"+dbPath+"?_pragma=foreign_keys(OFF)")
|
||||
if err != nil {
|
||||
t.Fatalf("reopen db: %v", err)
|
||||
}
|
||||
defer db2.Close()
|
||||
|
||||
var depCount, labelCount int
|
||||
db2.QueryRow("SELECT COUNT(*) FROM dependencies WHERE issue_id = 'orphan-1' OR depends_on_id = 'deleted-2'").Scan(&depCount)
|
||||
db2.QueryRow("SELECT COUNT(*) FROM labels WHERE issue_id = 'orphan-3'").Scan(&labelCount)
|
||||
|
||||
if depCount != 0 {
|
||||
t.Errorf("expected orphan deps to be deleted, got count=%d", depCount)
|
||||
}
|
||||
if labelCount != 0 {
|
||||
t.Errorf("expected orphan labels to be deleted, got count=%d", labelCount)
|
||||
}
|
||||
}
|
||||
|
||||
func TestRepairOrphans_CleanDatabase(t *testing.T) {
|
||||
requireTestGuardDisabled(t)
|
||||
|
||||
if testing.Short() {
|
||||
t.Skip("skipping slow repair test in short mode")
|
||||
}
|
||||
|
||||
bdExe := buildBDForTest(t)
|
||||
ws := mkTmpDirInTmp(t, "bd-repair-clean-*")
|
||||
dbPath := filepath.Join(ws, ".beads", "beads.db")
|
||||
|
||||
// Initialize with a clean database
|
||||
if _, err := runBDSideDB(t, bdExe, ws, dbPath, "init", "--prefix", "test", "--quiet"); err != nil {
|
||||
t.Fatalf("bd init failed: %v", err)
|
||||
}
|
||||
if _, err := runBDSideDB(t, bdExe, ws, dbPath, "create", "Issue 1", "-p", "1"); err != nil {
|
||||
t.Fatalf("bd create failed: %v", err)
|
||||
}
|
||||
|
||||
// Run repair on clean database - use --path to bypass normal db init
|
||||
out, err := runBDRepair(t, bdExe, ws)
|
||||
if err != nil {
|
||||
t.Fatalf("bd repair failed: %v\n%s", err, out)
|
||||
}
|
||||
|
||||
// Should report no orphans found
|
||||
if !strings.Contains(out, "No orphaned references found") {
|
||||
t.Errorf("expected clean database message, got: %s", out)
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user