Add bd repair-deps command (bd-58)

- Scans all issues for dependencies pointing to non-existent issues
- Reports orphaned dependencies with issue ID, depends_on ID, and type
- --fix flag automatically removes all orphaned dependencies
- --interactive mode prompts for each orphan before removal
- Uses direct SQL deletion to avoid foreign key errors on missing issues
- JSON output support with --json flag
- 4 comprehensive tests covering scan, fix, and multiple dependency types

Amp-Thread-ID: https://ampcode.com/threads/T-942a3e75-f90b-45b4-9f88-c7f1b8298cef
Co-authored-by: Amp <amp@ampcode.com>
This commit is contained in:
Steve Yegge
2025-10-29 12:56:51 -07:00
parent 0c06900956
commit da9773c31b
3 changed files with 513 additions and 107 deletions

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@@ -1,3 +1,4 @@
// Package main implements the bd CLI dependency repair command.
package main
import (
@@ -5,158 +6,170 @@ import (
"fmt"
"os"
"github.com/fatih/color"
"github.com/spf13/cobra"
"github.com/steveyegge/beads/internal/storage/sqlite"
"github.com/steveyegge/beads/internal/types"
)
var repairDepsCmd = &cobra.Command{
Use: "repair-deps",
Short: "Find and fix orphaned dependency references",
Long: `Find issues that reference non-existent dependencies and optionally remove them.
This command scans all issues for dependency references (both blocks and related-to)
that point to issues that no longer exist in the database.
Example:
bd repair-deps # Show orphaned dependencies
bd repair-deps --fix # Remove orphaned references
bd repair-deps --json # Output in JSON format`,
Run: func(cmd *cobra.Command, _ []string) {
// Check daemon mode - not supported yet (uses direct storage access)
if daemonClient != nil {
fmt.Fprintf(os.Stderr, "Error: repair-deps command not yet supported in daemon mode\n")
fmt.Fprintf(os.Stderr, "Use: bd --no-daemon repair-deps\n")
os.Exit(1)
}
Long: `Scans all issues for dependencies pointing to non-existent issues.
Reports orphaned dependencies and optionally removes them with --fix.
Interactive mode with --interactive prompts for each orphan.`,
Run: func(cmd *cobra.Command, args []string) {
fix, _ := cmd.Flags().GetBool("fix")
interactive, _ := cmd.Flags().GetBool("interactive")
// If daemon is running but doesn't support this command, use direct storage
if daemonClient != nil && store == nil {
var err error
store, err = sqlite.New(dbPath)
if err != nil {
fmt.Fprintf(os.Stderr, "Error: failed to open database: %v\n", err)
os.Exit(1)
}
defer func() { _ = store.Close() }()
}
ctx := context.Background()
// Get all issues
allIssues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
// Get all dependency records
allDeps, err := store.GetAllDependencyRecords(ctx)
if err != nil {
fmt.Fprintf(os.Stderr, "Error fetching issues: %v\n", err)
fmt.Fprintf(os.Stderr, "Error: failed to get dependencies: %v\n", err)
os.Exit(1)
}
// Build ID existence map
existingIDs := make(map[string]bool)
for _, issue := range allIssues {
existingIDs[issue.ID] = true
// Get all issues to check existence
issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
if err != nil {
fmt.Fprintf(os.Stderr, "Error: failed to list issues: %v\n", err)
os.Exit(1)
}
// Build set of valid issue IDs
validIDs := make(map[string]bool)
for _, issue := range issues {
validIDs[issue.ID] = true
}
// Find orphaned dependencies
type orphanedDep struct {
IssueID string
OrphanedID string
DepType string
type orphan struct {
issueID string
dependsOnID string
depType types.DependencyType
}
var orphaned []orphanedDep
var orphans []orphan
for _, issue := range allIssues {
// Check dependencies
for _, dep := range issue.Dependencies {
if !existingIDs[dep.DependsOnID] {
orphaned = append(orphaned, orphanedDep{
IssueID: issue.ID,
OrphanedID: dep.DependsOnID,
DepType: string(dep.Type),
for issueID, deps := range allDeps {
if !validIDs[issueID] {
// The issue itself doesn't exist, skip (will be cleaned up separately)
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
orphans = append(orphans, orphan{
issueID: dep.IssueID,
dependsOnID: dep.DependsOnID,
depType: dep.Type,
})
}
}
}
// Output results
if jsonOutput {
result := map[string]interface{}{
"orphaned_count": len(orphaned),
"fixed": fix,
"orphaned_deps": []map[string]interface{}{},
"orphans_found": len(orphans),
"orphans": []map[string]string{},
}
for _, o := range orphaned {
result["orphaned_deps"] = append(result["orphaned_deps"].([]map[string]interface{}), map[string]interface{}{
"issue_id": o.IssueID,
"orphaned_id": o.OrphanedID,
"dep_type": o.DepType,
})
if len(orphans) > 0 {
orphanList := make([]map[string]string, len(orphans))
for i, o := range orphans {
orphanList[i] = map[string]string{
"issue_id": o.issueID,
"depends_on_id": o.dependsOnID,
"type": string(o.depType),
}
}
result["orphans"] = orphanList
}
if fix || interactive {
result["fixed"] = len(orphans)
}
outputJSON(result)
return
}
// Human-readable output
if len(orphaned) == 0 {
fmt.Println("No orphaned dependencies found!")
// Report results
if len(orphans) == 0 {
green := color.New(color.FgGreen).SprintFunc()
fmt.Printf("\n%s No orphaned dependencies found\n\n", green("✓"))
return
}
fmt.Printf("Found %d orphaned dependencies:\n\n", len(orphaned))
for _, o := range orphaned {
fmt.Printf(" %s: depends on %s (%s) - DELETED\n", o.IssueID, o.OrphanedID, o.DepType)
yellow := color.New(color.FgYellow).SprintFunc()
fmt.Printf("\n%s Found %d orphaned dependencies:\n\n", yellow("⚠"), len(orphans))
for i, o := range orphans {
fmt.Printf("%d. %s → %s (%s) [%s does not exist]\n",
i+1, o.issueID, o.dependsOnID, o.depType, o.dependsOnID)
}
fmt.Println()
if !fix {
fmt.Printf("\nRun 'bd repair-deps --fix' to remove these references.\n")
return
}
// Fix orphaned dependencies
fmt.Printf("\nRemoving orphaned dependencies...\n")
// Group by issue for efficient updates
orphansByIssue := make(map[string][]string)
for _, o := range orphaned {
orphansByIssue[o.IssueID] = append(orphansByIssue[o.IssueID], o.OrphanedID)
}
fixed := 0
for issueID, orphanedIDs := range orphansByIssue {
// Get current issue to verify
issue, err := store.GetIssue(ctx, issueID)
if err != nil {
fmt.Fprintf(os.Stderr, "Error fetching %s: %v\n", issueID, err)
continue
}
// Collect orphaned dependency IDs to remove
orphanedSet := make(map[string]bool)
for _, orphanedID := range orphanedIDs {
orphanedSet[orphanedID] = true
}
// Build list of dependencies to keep
validDeps := []*types.Dependency{}
for _, dep := range issue.Dependencies {
if !orphanedSet[dep.DependsOnID] {
validDeps = append(validDeps, dep)
// Fix if requested
if interactive {
fixed := 0
for _, o := range orphans {
fmt.Printf("Remove dependency %s → %s (%s)? [y/N]: ", o.issueID, o.dependsOnID, o.depType)
var response string
fmt.Scanln(&response)
if response == "y" || response == "Y" {
// Use direct SQL to remove orphaned dependencies
// RemoveDependency tries to mark the depends_on issue as dirty, which fails for orphans
db := store.UnderlyingDB()
_, err := db.ExecContext(ctx, "DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
o.issueID, o.dependsOnID)
if err != nil {
fmt.Fprintf(os.Stderr, "Error removing dependency: %v\n", err)
} else {
// Mark the issue as dirty
_, _ = db.ExecContext(ctx, "INSERT OR IGNORE INTO dirty_issues (issue_id) VALUES (?)", o.issueID)
fixed++
}
}
}
// Update via storage layer
// We need to remove each orphaned dependency individually
for _, orphanedID := range orphanedIDs {
if err := store.RemoveDependency(ctx, issueID, orphanedID, actor); err != nil {
fmt.Fprintf(os.Stderr, "Error removing %s from %s: %v\n", orphanedID, issueID, err)
continue
markDirtyAndScheduleFlush()
green := color.New(color.FgGreen).SprintFunc()
fmt.Printf("\n%s Fixed %d orphaned dependencies\n\n", green("✓"), fixed)
} else if fix {
db := store.UnderlyingDB()
for _, o := range orphans {
// Use direct SQL to remove orphaned dependencies
_, err := db.ExecContext(ctx, "DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
o.issueID, o.dependsOnID)
if err != nil {
fmt.Fprintf(os.Stderr, "Error removing dependency %s → %s: %v\n",
o.issueID, o.dependsOnID, err)
} else {
// Mark the issue as dirty
_, _ = db.ExecContext(ctx, "INSERT OR IGNORE INTO dirty_issues (issue_id) VALUES (?)", o.issueID)
}
fmt.Printf("✓ Removed %s from %s dependencies\n", orphanedID, issueID)
fixed++
}
markDirtyAndScheduleFlush()
green := color.New(color.FgGreen).SprintFunc()
fmt.Printf("%s Fixed %d orphaned dependencies\n\n", green("✓"), len(orphans))
} else {
fmt.Printf("Run with --fix to automatically remove orphaned dependencies\n")
fmt.Printf("Run with --interactive to review each dependency\n\n")
}
// Schedule auto-flush
markDirtyAndScheduleFlush()
fmt.Printf("\nRepaired %d orphaned dependencies.\n", fixed)
},
}
func init() {
repairDepsCmd.Flags().Bool("fix", false, "Remove orphaned dependency references")
repairDepsCmd.Flags().Bool("fix", false, "Automatically remove orphaned dependencies")
repairDepsCmd.Flags().Bool("interactive", false, "Interactively review each orphaned dependency")
rootCmd.AddCommand(repairDepsCmd)
}

393
cmd/bd/repair_deps_test.go Normal file
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@@ -0,0 +1,393 @@
package main
import (
"context"
"os"
"path/filepath"
"testing"
"github.com/steveyegge/beads/internal/storage/sqlite"
"github.com/steveyegge/beads/internal/types"
)
func TestRepairDeps_NoOrphans(t *testing.T) {
dir := t.TempDir()
dbPath := filepath.Join(dir, ".beads", "beads.db")
if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
t.Fatal(err)
}
store, err := sqlite.New(dbPath)
if err != nil {
t.Fatal(err)
}
defer store.Close()
ctx := context.Background()
// Initialize database
store.SetConfig(ctx, "issue_prefix", "test-")
// Create two issues with valid dependency
i1 := &types.Issue{Title: "Issue 1", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i1, "test")
i2 := &types.Issue{Title: "Issue 2", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i2, "test")
store.AddDependency(ctx, &types.Dependency{
IssueID: i2.ID,
DependsOnID: i1.ID,
Type: types.DepBlocks,
}, "test")
// Get all dependency records
allDeps, err := store.GetAllDependencyRecords(ctx)
if err != nil {
t.Fatal(err)
}
// Get all issues
issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
if err != nil {
t.Fatal(err)
}
// Build valid ID set
validIDs := make(map[string]bool)
for _, issue := range issues {
validIDs[issue.ID] = true
}
// Find orphans
orphanCount := 0
for issueID, deps := range allDeps {
if !validIDs[issueID] {
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
orphanCount++
}
}
}
if orphanCount != 0 {
t.Errorf("Expected 0 orphans, got %d", orphanCount)
}
}
func TestRepairDeps_FindOrphans(t *testing.T) {
dir := t.TempDir()
dbPath := filepath.Join(dir, ".beads", "beads.db")
if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
t.Fatal(err)
}
store, err := sqlite.New(dbPath)
if err != nil {
t.Fatal(err)
}
defer store.Close()
ctx := context.Background()
// Initialize database
store.SetConfig(ctx, "issue_prefix", "test-")
// Create two issues
i1 := &types.Issue{Title: "Issue 1", Priority: 1, Status: "open", IssueType: "task"}
if err := store.CreateIssue(ctx, i1, "test"); err != nil {
t.Fatalf("CreateIssue failed: %v", err)
}
t.Logf("Created i1: %s", i1.ID)
i2 := &types.Issue{Title: "Issue 2", Priority: 1, Status: "open", IssueType: "task"}
if err := store.CreateIssue(ctx, i2, "test"); err != nil {
t.Fatalf("CreateIssue failed: %v", err)
}
t.Logf("Created i2: %s", i2.ID)
// Add dependency
err = store.AddDependency(ctx, &types.Dependency{
IssueID: i2.ID,
DependsOnID: i1.ID,
Type: types.DepBlocks,
}, "test")
if err != nil {
t.Fatalf("AddDependency failed: %v", err)
}
// Manually create orphaned dependency by directly inserting invalid reference
// This simulates corruption or import errors
db := store.UnderlyingDB()
_, err = db.ExecContext(ctx, "PRAGMA foreign_keys = OFF")
if err != nil {
t.Fatal(err)
}
// Insert a dependency pointing to a non-existent issue
_, err = db.ExecContext(ctx, `INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
VALUES (?, 'nonexistent-123', 'blocks', datetime('now'), 'test')`, i2.ID)
if err != nil {
t.Fatalf("Failed to insert orphaned dependency: %v", err)
}
_, err = db.ExecContext(ctx, "PRAGMA foreign_keys = ON")
if err != nil {
t.Fatal(err)
}
// Verify the orphan was actually inserted
var count int
err = db.QueryRowContext(ctx, "SELECT COUNT(*) FROM dependencies WHERE depends_on_id = 'nonexistent-123'").Scan(&count)
if err != nil {
t.Fatal(err)
}
if count != 1 {
t.Fatalf("Orphan dependency not inserted, count=%d", count)
}
// Get all dependency records
allDeps, err := store.GetAllDependencyRecords(ctx)
if err != nil {
t.Fatal(err)
}
t.Logf("Got %d issues with dependencies", len(allDeps))
for issueID, deps := range allDeps {
t.Logf("Issue %s has %d dependencies", issueID, len(deps))
for _, dep := range deps {
t.Logf(" -> %s (%s)", dep.DependsOnID, dep.Type)
}
}
// Get all issues
issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
if err != nil {
t.Fatal(err)
}
// Build valid ID set
validIDs := make(map[string]bool)
for _, issue := range issues {
validIDs[issue.ID] = true
}
t.Logf("Valid issue IDs: %v", validIDs)
// Find orphans
orphanCount := 0
for issueID, deps := range allDeps {
if !validIDs[issueID] {
t.Logf("Skipping %s - issue itself doesn't exist", issueID)
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
t.Logf("Found orphan: %s -> %s", dep.IssueID, dep.DependsOnID)
orphanCount++
}
}
}
if orphanCount != 1 {
t.Errorf("Expected 1 orphan, got %d", orphanCount)
}
}
func TestRepairDeps_FixOrphans(t *testing.T) {
dir := t.TempDir()
dbPath := filepath.Join(dir, ".beads", "beads.db")
if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
t.Fatal(err)
}
store, err := sqlite.New(dbPath)
if err != nil {
t.Fatal(err)
}
defer store.Close()
ctx := context.Background()
// Initialize database
store.SetConfig(ctx, "issue_prefix", "test-")
// Create three issues
i1 := &types.Issue{Title: "Issue 1", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i1, "test")
i2 := &types.Issue{Title: "Issue 2", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i2, "test")
i3 := &types.Issue{Title: "Issue 3", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i3, "test")
// Add dependencies
store.AddDependency(ctx, &types.Dependency{
IssueID: i2.ID,
DependsOnID: i1.ID,
Type: types.DepBlocks,
}, "test")
store.AddDependency(ctx, &types.Dependency{
IssueID: i3.ID,
DependsOnID: i1.ID,
Type: types.DepBlocks,
}, "test")
// Manually create orphaned dependencies by inserting invalid references
db := store.UnderlyingDB()
db.Exec("PRAGMA foreign_keys = OFF")
_, err = db.ExecContext(ctx, `INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
VALUES (?, 'nonexistent-123', 'blocks', datetime('now'), 'test')`, i2.ID)
if err != nil {
t.Fatal(err)
}
_, err = db.ExecContext(ctx, `INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
VALUES (?, 'nonexistent-456', 'blocks', datetime('now'), 'test')`, i3.ID)
if err != nil {
t.Fatal(err)
}
db.Exec("PRAGMA foreign_keys = ON")
// Find and fix orphans
allDeps, _ := store.GetAllDependencyRecords(ctx)
issues, _ := store.SearchIssues(ctx, "", types.IssueFilter{})
validIDs := make(map[string]bool)
for _, issue := range issues {
validIDs[issue.ID] = true
}
type orphan struct {
issueID string
dependsOnID string
}
var orphans []orphan
for issueID, deps := range allDeps {
if !validIDs[issueID] {
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
orphans = append(orphans, orphan{
issueID: dep.IssueID,
dependsOnID: dep.DependsOnID,
})
}
}
}
if len(orphans) != 2 {
t.Fatalf("Expected 2 orphans before fix, got %d", len(orphans))
}
// Fix orphans using direct SQL (like the command does)
for _, o := range orphans {
_, delErr := db.ExecContext(ctx, "DELETE FROM dependencies WHERE issue_id = ? AND depends_on_id = ?",
o.issueID, o.dependsOnID)
if delErr != nil {
t.Errorf("Failed to remove orphan: %v", delErr)
}
}
// Verify orphans removed
allDeps, _ = store.GetAllDependencyRecords(ctx)
orphanCount := 0
for issueID, deps := range allDeps {
if !validIDs[issueID] {
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
orphanCount++
}
}
}
if orphanCount != 0 {
t.Errorf("Expected 0 orphans after fix, got %d", orphanCount)
}
}
func TestRepairDeps_MultipleTypes(t *testing.T) {
dir := t.TempDir()
dbPath := filepath.Join(dir, ".beads", "beads.db")
if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
t.Fatal(err)
}
store, err := sqlite.New(dbPath)
if err != nil {
t.Fatal(err)
}
defer store.Close()
ctx := context.Background()
// Initialize database
store.SetConfig(ctx, "issue_prefix", "test-")
// Create issues
i1 := &types.Issue{Title: "Issue 1", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i1, "test")
i2 := &types.Issue{Title: "Issue 2", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i2, "test")
i3 := &types.Issue{Title: "Issue 3", Priority: 1, Status: "open", IssueType: "task"}
store.CreateIssue(ctx, i3, "test")
// Add different dependency types
store.AddDependency(ctx, &types.Dependency{
IssueID: i2.ID,
DependsOnID: i1.ID,
Type: types.DepBlocks,
}, "test")
store.AddDependency(ctx, &types.Dependency{
IssueID: i3.ID,
DependsOnID: i1.ID,
Type: types.DepRelated,
}, "test")
// Manually create orphaned dependencies with different types
db := store.UnderlyingDB()
db.Exec("PRAGMA foreign_keys = OFF")
_, err = db.ExecContext(ctx, `INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
VALUES (?, 'nonexistent-blocks', 'blocks', datetime('now'), 'test')`, i2.ID)
if err != nil {
t.Fatal(err)
}
_, err = db.ExecContext(ctx, `INSERT INTO dependencies (issue_id, depends_on_id, type, created_at, created_by)
VALUES (?, 'nonexistent-related', 'related', datetime('now'), 'test')`, i3.ID)
if err != nil {
t.Fatal(err)
}
db.Exec("PRAGMA foreign_keys = ON")
// Find orphans
allDeps, _ := store.GetAllDependencyRecords(ctx)
issues, _ := store.SearchIssues(ctx, "", types.IssueFilter{})
validIDs := make(map[string]bool)
for _, issue := range issues {
validIDs[issue.ID] = true
}
orphanCount := 0
depTypes := make(map[types.DependencyType]int)
for issueID, deps := range allDeps {
if !validIDs[issueID] {
continue
}
for _, dep := range deps {
if !validIDs[dep.DependsOnID] {
orphanCount++
depTypes[dep.Type]++
}
}
}
if orphanCount != 2 {
t.Errorf("Expected 2 orphans, got %d", orphanCount)
}
if depTypes[types.DepBlocks] != 1 {
t.Errorf("Expected 1 blocks orphan, got %d", depTypes[types.DepBlocks])
}
if depTypes[types.DepRelated] != 1 {
t.Errorf("Expected 1 related orphan, got %d", depTypes[types.DepRelated])
}
}