feat: bd repair - add comments/events orphan detection and --json flag
- Check comments table for orphaned issue_id references - Check events table for orphaned issue_id references - Delete orphaned comments/events in repair transaction - Add --json flag for machine-readable output with: - orphan_counts by type (dependencies, labels, comments, events) - orphan_details with full reference info - status (success, no_orphans, dry_run, error) - backup_path when applicable (bd-2wm2, bd-ie7j) 🤖 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
357
cmd/bd/repair.go
357
cmd/bd/repair.go
@@ -2,6 +2,7 @@ package main
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import (
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"database/sql"
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"encoding/json"
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"fmt"
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"os"
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"path/filepath"
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@@ -30,31 +31,53 @@ 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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- Orphaned comments (issue_id not in issues)
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- Orphaned events (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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bd repair --path /other/repo # Repair database in another location
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bd repair --json # Output results as JSON`,
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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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repairJSON bool
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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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repairCmd.Flags().BoolVar(&repairJSON, "json", false, "Output results as JSON")
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rootCmd.AddCommand(repairCmd)
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}
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// outputJSONAndExit outputs the repair result as JSON and exits
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func outputJSONAndExit(result repairResult, exitCode int) {
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data, err := json.MarshalIndent(result, "", " ")
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if err != nil {
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fmt.Fprintf(os.Stderr, `{"error": "failed to marshal JSON: %v"}`, err)
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os.Exit(1)
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}
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fmt.Println(string(data))
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os.Exit(exitCode)
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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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if repairJSON {
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outputJSONAndExit(repairResult{
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Status: "error",
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Error: fmt.Sprintf(".beads directory not found at %s", beadsDir),
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}, 1)
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}
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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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@@ -62,19 +85,34 @@ func runRepair(cmd *cobra.Command, args []string) {
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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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if repairJSON {
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outputJSONAndExit(repairResult{
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Status: "error",
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Error: fmt.Sprintf("database not found at %s", dbPath),
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}, 1)
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}
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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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if !repairJSON {
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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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}
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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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if repairJSON {
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outputJSONAndExit(repairResult{
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DatabasePath: dbPath,
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Status: "error",
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Error: fmt.Sprintf("opening database: %v", err),
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}, 1)
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}
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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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@@ -107,53 +145,146 @@ func runRepair(cmd *cobra.Command, args []string) {
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}
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stats.orphanedLabels = len(orphanedLabels)
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// Print findings
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// 4. Find and clean orphaned comments
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orphanedCommentsList, err := findOrphanedComments(db)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error checking orphaned comments: %v\n", err)
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os.Exit(1)
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}
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stats.orphanedComments = len(orphanedCommentsList)
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// 5. Find and clean orphaned events
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orphanedEventsList, err := findOrphanedEvents(db)
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if err != nil {
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fmt.Fprintf(os.Stderr, "Error checking orphaned events: %v\n", err)
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os.Exit(1)
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}
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stats.orphanedEvents = len(orphanedEventsList)
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// Build JSON result structure (used for both JSON output and tracking)
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jsonResult := repairResult{
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DatabasePath: dbPath,
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DryRun: repairDryRun,
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OrphanCounts: repairOrphanCounts{
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DependenciesIssueID: stats.orphanedDepsIssueID,
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DependenciesDependsOn: stats.orphanedDepsDependsOn,
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Labels: stats.orphanedLabels,
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Comments: stats.orphanedComments,
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Events: stats.orphanedEvents,
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Total: stats.total(),
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},
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}
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// Build orphan details
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for _, dep := range orphanedIssueID {
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jsonResult.OrphanDetails.DependenciesIssueID = append(jsonResult.OrphanDetails.DependenciesIssueID,
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repairDepDetail{IssueID: dep.issueID, DependsOnID: dep.dependsOnID})
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}
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for _, dep := range orphanedDependsOn {
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jsonResult.OrphanDetails.DependenciesDependsOn = append(jsonResult.OrphanDetails.DependenciesDependsOn,
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repairDepDetail{IssueID: dep.issueID, DependsOnID: dep.dependsOnID})
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}
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for _, label := range orphanedLabels {
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jsonResult.OrphanDetails.Labels = append(jsonResult.OrphanDetails.Labels,
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repairLabelDetail{IssueID: label.issueID, Label: label.label})
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}
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for _, comment := range orphanedCommentsList {
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jsonResult.OrphanDetails.Comments = append(jsonResult.OrphanDetails.Comments,
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repairCommentDetail{ID: comment.id, IssueID: comment.issueID, Author: comment.author})
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}
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for _, event := range orphanedEventsList {
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jsonResult.OrphanDetails.Events = append(jsonResult.OrphanDetails.Events,
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repairEventDetail{ID: event.id, IssueID: event.issueID, EventType: event.eventType})
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}
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// Handle no orphans case
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if stats.total() == 0 {
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if repairJSON {
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jsonResult.Status = "no_orphans"
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outputJSONAndExit(jsonResult, 0)
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}
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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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// Print findings (text mode)
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if !repairJSON {
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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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}
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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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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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}
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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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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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if stats.orphanedComments > 0 {
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fmt.Printf(" • %d comments with missing issue_id\n", stats.orphanedComments)
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for _, comment := range orphanedCommentsList {
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fmt.Printf(" - %s (by %s)\n", comment.issueID, comment.author)
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}
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}
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if stats.orphanedEvents > 0 {
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fmt.Printf(" • %d events with missing issue_id\n", stats.orphanedEvents)
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for _, event := range orphanedEventsList {
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fmt.Printf(" - %s: %s\n", event.issueID, event.eventType)
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}
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}
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fmt.Println()
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}
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fmt.Println()
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// Handle dry-run
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if repairDryRun {
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if repairJSON {
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jsonResult.Status = "dry_run"
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outputJSONAndExit(jsonResult, 0)
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}
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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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// Create backup before destructive operations
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backupPath := dbPath + ".pre-repair"
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fmt.Printf("Creating backup: %s\n", filepath.Base(backupPath))
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if !repairJSON {
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fmt.Printf("Creating backup: %s\n", filepath.Base(backupPath))
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}
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if err := copyFile(dbPath, backupPath); err != nil {
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if repairJSON {
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jsonResult.Status = "error"
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jsonResult.Error = fmt.Sprintf("creating backup: %v", err)
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outputJSONAndExit(jsonResult, 1)
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}
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fmt.Fprintf(os.Stderr, "Error creating backup: %v\n", err)
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fmt.Fprintf(os.Stderr, "Aborting repair. Fix backup issue and retry.\n")
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os.Exit(1)
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}
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fmt.Printf(" %s Backup created\n\n", ui.RenderPass("✓"))
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jsonResult.BackupPath = backupPath
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if !repairJSON {
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fmt.Printf(" %s Backup created\n\n", ui.RenderPass("✓"))
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}
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// Apply repairs in a transaction
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fmt.Println("Cleaning orphaned references...")
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if !repairJSON {
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fmt.Println("Cleaning orphaned references...")
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}
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tx, err := db.Begin()
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if err != nil {
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if repairJSON {
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jsonResult.Status = "error"
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jsonResult.Error = fmt.Sprintf("starting transaction: %v", err)
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outputJSONAndExit(jsonResult, 1)
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}
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fmt.Fprintf(os.Stderr, "Error starting transaction: %v\n", err)
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os.Exit(1)
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}
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@@ -171,7 +302,7 @@ func runRepair(cmd *cobra.Command, args []string) {
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`)
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if err != nil {
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repairErr = fmt.Errorf("deleting orphaned deps (issue_id): %w", err)
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} else {
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} else if !repairJSON {
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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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@@ -191,7 +322,7 @@ func runRepair(cmd *cobra.Command, args []string) {
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`)
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if err != nil {
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repairErr = fmt.Errorf("deleting orphaned deps (depends_on_id): %w", err)
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} else {
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} else if !repairJSON {
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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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@@ -206,15 +337,50 @@ func runRepair(cmd *cobra.Command, args []string) {
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`)
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if err != nil {
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repairErr = fmt.Errorf("deleting orphaned labels: %w", err)
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} else {
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} else if !repairJSON {
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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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// Delete orphaned comments
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if len(orphanedCommentsList) > 0 && repairErr == nil {
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// Comments reference non-existent issues, so no dirty marking needed
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result, err := tx.Exec(`
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DELETE FROM comments
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = comments.issue_id)
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`)
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if err != nil {
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repairErr = fmt.Errorf("deleting orphaned comments: %w", err)
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} else if !repairJSON {
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deleted, _ := result.RowsAffected()
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fmt.Printf(" %s Deleted %d comments with missing issue_id\n", ui.RenderPass("✓"), deleted)
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}
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}
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// Delete orphaned events
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if len(orphanedEventsList) > 0 && repairErr == nil {
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// Events reference non-existent issues, so no dirty marking needed
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result, err := tx.Exec(`
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DELETE FROM events
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WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = events.issue_id)
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`)
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if err != nil {
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repairErr = fmt.Errorf("deleting orphaned events: %w", err)
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} else if !repairJSON {
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deleted, _ := result.RowsAffected()
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fmt.Printf(" %s Deleted %d events with missing issue_id\n", ui.RenderPass("✓"), deleted)
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}
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}
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// Commit or rollback
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if repairErr != nil {
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_ = tx.Rollback()
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if repairJSON {
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jsonResult.Status = "error"
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jsonResult.Error = repairErr.Error()
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outputJSONAndExit(jsonResult, 1)
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}
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fmt.Fprintf(os.Stderr, "\n%s Error: %v\n", ui.RenderFail("✗"), repairErr)
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fmt.Fprintf(os.Stderr, "Transaction rolled back. Database unchanged.\n")
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fmt.Fprintf(os.Stderr, "Backup available at: %s\n", backupPath)
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@@ -222,19 +388,34 @@ func runRepair(cmd *cobra.Command, args []string) {
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}
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if err := tx.Commit(); err != nil {
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if repairJSON {
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jsonResult.Status = "error"
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jsonResult.Error = fmt.Sprintf("committing transaction: %v", err)
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outputJSONAndExit(jsonResult, 1)
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}
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fmt.Fprintf(os.Stderr, "\n%s Error committing transaction: %v\n", ui.RenderFail("✗"), err)
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fmt.Fprintf(os.Stderr, "Backup available at: %s\n", backupPath)
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os.Exit(1)
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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 !repairJSON {
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fmt.Print(" Running WAL checkpoint... ")
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}
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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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if !repairJSON {
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fmt.Printf("%s %v\n", ui.RenderFail("✗"), err)
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}
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} else if !repairJSON {
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fmt.Printf("%s\n", ui.RenderPass("✓"))
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}
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// Final output
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if repairJSON {
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jsonResult.Status = "success"
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outputJSONAndExit(jsonResult, 0)
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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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fmt.Printf("Backup preserved at: %s\n", filepath.Base(backupPath))
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@@ -245,10 +426,12 @@ 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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orphanedComments int
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orphanedEvents 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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return s.orphanedDepsIssueID + s.orphanedDepsDependsOn + s.orphanedLabels + s.orphanedComments + s.orphanedEvents
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}
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// orphanedDep represents an orphaned dependency
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@@ -263,6 +446,70 @@ type orphanedLabel struct {
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label string
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}
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// orphanedComment represents an orphaned comment
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type orphanedComment struct {
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id int
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issueID string
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author string
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}
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// orphanedEvent represents an orphaned event
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type orphanedEvent struct {
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id int
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issueID string
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eventType string
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}
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// repairResult is the JSON output structure
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type repairResult struct {
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DatabasePath string `json:"database_path"`
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DryRun bool `json:"dry_run"`
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OrphanCounts repairOrphanCounts `json:"orphan_counts"`
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OrphanDetails repairOrphanDetails `json:"orphan_details"`
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Status string `json:"status"` // "success", "no_orphans", "dry_run", "error"
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BackupPath string `json:"backup_path,omitempty"`
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Error string `json:"error,omitempty"`
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}
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type repairOrphanCounts struct {
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DependenciesIssueID int `json:"dependencies_issue_id"`
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DependenciesDependsOn int `json:"dependencies_depends_on"`
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Labels int `json:"labels"`
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Comments int `json:"comments"`
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Events int `json:"events"`
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Total int `json:"total"`
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}
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type repairOrphanDetails struct {
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DependenciesIssueID []repairDepDetail `json:"dependencies_issue_id,omitempty"`
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||||
DependenciesDependsOn []repairDepDetail `json:"dependencies_depends_on,omitempty"`
|
||||
Labels []repairLabelDetail `json:"labels,omitempty"`
|
||||
Comments []repairCommentDetail `json:"comments,omitempty"`
|
||||
Events []repairEventDetail `json:"events,omitempty"`
|
||||
}
|
||||
|
||||
type repairDepDetail struct {
|
||||
IssueID string `json:"issue_id"`
|
||||
DependsOnID string `json:"depends_on_id"`
|
||||
}
|
||||
|
||||
type repairLabelDetail struct {
|
||||
IssueID string `json:"issue_id"`
|
||||
Label string `json:"label"`
|
||||
}
|
||||
|
||||
type repairCommentDetail struct {
|
||||
ID int `json:"id"`
|
||||
IssueID string `json:"issue_id"`
|
||||
Author string `json:"author"`
|
||||
}
|
||||
|
||||
type repairEventDetail struct {
|
||||
ID int `json:"id"`
|
||||
IssueID string `json:"issue_id"`
|
||||
EventType string `json:"event_type"`
|
||||
}
|
||||
|
||||
// openRepairDB opens SQLite directly for repair, bypassing all beads layer code
|
||||
func openRepairDB(dbPath string) (*sql.DB, error) {
|
||||
// Build connection string with pragmas
|
||||
@@ -349,3 +596,49 @@ func findOrphanedLabels(db *sql.DB) ([]orphanedLabel, error) {
|
||||
return labels, rows.Err()
|
||||
}
|
||||
|
||||
// findOrphanedComments finds comments where issue_id doesn't exist
|
||||
func findOrphanedComments(db *sql.DB) ([]orphanedComment, error) {
|
||||
rows, err := db.Query(`
|
||||
SELECT c.id, c.issue_id, c.author
|
||||
FROM comments c
|
||||
WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = c.issue_id)
|
||||
`)
|
||||
if err != nil {
|
||||
return nil, err
|
||||
}
|
||||
defer rows.Close()
|
||||
|
||||
var comments []orphanedComment
|
||||
for rows.Next() {
|
||||
var comment orphanedComment
|
||||
if err := rows.Scan(&comment.id, &comment.issueID, &comment.author); err != nil {
|
||||
return nil, err
|
||||
}
|
||||
comments = append(comments, comment)
|
||||
}
|
||||
return comments, rows.Err()
|
||||
}
|
||||
|
||||
// findOrphanedEvents finds events where issue_id doesn't exist
|
||||
func findOrphanedEvents(db *sql.DB) ([]orphanedEvent, error) {
|
||||
rows, err := db.Query(`
|
||||
SELECT e.id, e.issue_id, e.event_type
|
||||
FROM events e
|
||||
WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = e.issue_id)
|
||||
`)
|
||||
if err != nil {
|
||||
return nil, err
|
||||
}
|
||||
defer rows.Close()
|
||||
|
||||
var events []orphanedEvent
|
||||
for rows.Next() {
|
||||
var event orphanedEvent
|
||||
if err := rows.Scan(&event.id, &event.issueID, &event.eventType); err != nil {
|
||||
return nil, err
|
||||
}
|
||||
events = append(events, event)
|
||||
}
|
||||
return events, rows.Err()
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user