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Annotate gosec-safe file accesses

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This commit is contained in:
Codex Agent
2025-11-17 10:12:46 -07:00
parent 7b63b5a30b
commit bf9b2c83fb
14 changed files with 182 additions and 158 deletions
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173
cmd/bd/import.go
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@@ -42,14 +42,14 @@ NOTE: Import requires direct database access and does not work with daemon mode.
fmt.Fprintf(os.Stderr, "Error: failed to create database directory: %v\n", err)
os.Exit(1)
}
// Import requires direct database access due to complex transaction handling
// and collision detection. Force direct mode regardless of daemon state.
if daemonClient != nil {
debug.Logf("Debug: import command forcing direct mode (closes daemon connection)\n")
_ = daemonClient.Close()
daemonClient = nil
var err error
store, err = sqlite.New(dbPath)
if err != nil {
@@ -58,7 +58,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
}
defer func() { _ = store.Close() }()
}
// We'll check if database needs initialization after reading the JSONL
// so we can detect the prefix from the imported issues
@@ -96,78 +96,78 @@ NOTE: Import requires direct database access and does not work with daemon mode.
lineNum := 0
for scanner.Scan() {
lineNum++
rawLine := scanner.Bytes()
line := string(rawLine)
lineNum++
rawLine := scanner.Bytes()
line := string(rawLine)
// Skip empty lines
if line == "" {
continue
}
// Detect git conflict markers in raw bytes (before JSON decoding)
// This prevents false positives when issue content contains these strings
trimmed := bytes.TrimSpace(rawLine)
if bytes.HasPrefix(trimmed, []byte("<<<<<<< ")) ||
bytes.Equal(trimmed, []byte("=======")) ||
bytes.HasPrefix(trimmed, []byte(">>>>>>> ")) {
fmt.Fprintf(os.Stderr, "Git conflict markers detected in JSONL file (line %d)\n", lineNum)
fmt.Fprintf(os.Stderr, "→ Attempting automatic 3-way merge...\n\n")
// Attempt automatic merge using bd merge command
if err := attemptAutoMerge(input); err != nil {
fmt.Fprintf(os.Stderr, "Error: Automatic merge failed: %v\n\n", err)
fmt.Fprintf(os.Stderr, "To resolve manually:\n")
fmt.Fprintf(os.Stderr, " git checkout --ours .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n")
fmt.Fprintf(os.Stderr, " git checkout --theirs .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n\n")
fmt.Fprintf(os.Stderr, "For advanced field-level merging, see: https://github.com/neongreen/mono/tree/main/beads-merge\n")
os.Exit(1)
// Skip empty lines
if line == "" {
continue
}
fmt.Fprintf(os.Stderr, "✓ Automatic merge successful\n")
fmt.Fprintf(os.Stderr, "→ Restarting import with merged JSONL...\n\n")
// Detect git conflict markers in raw bytes (before JSON decoding)
// This prevents false positives when issue content contains these strings
trimmed := bytes.TrimSpace(rawLine)
if bytes.HasPrefix(trimmed, []byte("<<<<<<< ")) ||
bytes.Equal(trimmed, []byte("=======")) ||
bytes.HasPrefix(trimmed, []byte(">>>>>>> ")) {
fmt.Fprintf(os.Stderr, "Git conflict markers detected in JSONL file (line %d)\n", lineNum)
fmt.Fprintf(os.Stderr, "→ Attempting automatic 3-way merge...\n\n")
// Re-open the input file to read the merged content
if input != "" {
// Close current file handle
if in != os.Stdin {
_ = in.Close()
}
// Re-open the merged file
// #nosec G304 - user-provided file path is intentional
f, err := os.Open(input)
if err != nil {
fmt.Fprintf(os.Stderr, "Error reopening merged file: %v\n", err)
// Attempt automatic merge using bd merge command
if err := attemptAutoMerge(input); err != nil {
fmt.Fprintf(os.Stderr, "Error: Automatic merge failed: %v\n\n", err)
fmt.Fprintf(os.Stderr, "To resolve manually:\n")
fmt.Fprintf(os.Stderr, " git checkout --ours .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n")
fmt.Fprintf(os.Stderr, " git checkout --theirs .beads/issues.jsonl && bd import -i .beads/issues.jsonl\n\n")
fmt.Fprintf(os.Stderr, "For advanced field-level merging, see: https://github.com/neongreen/mono/tree/main/beads-merge\n")
os.Exit(1)
}
defer func() {
if err := f.Close(); err != nil {
fmt.Fprintf(os.Stderr, "Warning: failed to close input file: %v\n", err)
fmt.Fprintf(os.Stderr, "✓ Automatic merge successful\n")
fmt.Fprintf(os.Stderr, "→ Restarting import with merged JSONL...\n\n")
// Re-open the input file to read the merged content
if input != "" {
// Close current file handle
if in != os.Stdin {
_ = in.Close()
}
}()
in = f
scanner = bufio.NewScanner(in)
allIssues = nil // Reset issues list
lineNum = 0 // Reset line counter
continue // Restart parsing from beginning
} else {
// Can't retry stdin - should not happen since git conflicts only in files
fmt.Fprintf(os.Stderr, "Error: Cannot retry merge from stdin\n")
// Re-open the merged file
// #nosec G304 - user-provided file path is intentional
f, err := os.Open(input)
if err != nil {
fmt.Fprintf(os.Stderr, "Error reopening merged file: %v\n", err)
os.Exit(1)
}
defer func() {
if err := f.Close(); err != nil {
fmt.Fprintf(os.Stderr, "Warning: failed to close input file: %v\n", err)
}
}()
in = f
scanner = bufio.NewScanner(in)
allIssues = nil // Reset issues list
lineNum = 0 // Reset line counter
continue // Restart parsing from beginning
} else {
// Can't retry stdin - should not happen since git conflicts only in files
fmt.Fprintf(os.Stderr, "Error: Cannot retry merge from stdin\n")
os.Exit(1)
}
}
// Parse JSON
var issue types.Issue
if err := json.Unmarshal([]byte(line), &issue); err != nil {
fmt.Fprintf(os.Stderr, "Error parsing line %d: %v\n", lineNum, err)
os.Exit(1)
}
}
// Parse JSON
var issue types.Issue
if err := json.Unmarshal([]byte(line), &issue); err != nil {
fmt.Fprintf(os.Stderr, "Error parsing line %d: %v\n", lineNum, err)
os.Exit(1)
allIssues = append(allIssues, &issue)
}
allIssues = append(allIssues, &issue)
}
if err := scanner.Err(); err != nil {
fmt.Fprintf(os.Stderr, "Error reading input: %v\n", err)
os.Exit(1)
@@ -190,12 +190,12 @@ NOTE: Import requires direct database access and does not work with daemon mode.
detectedPrefix = filepath.Base(cwd)
}
detectedPrefix = strings.TrimRight(detectedPrefix, "-")
if err := store.SetConfig(initCtx, "issue_prefix", detectedPrefix); err != nil {
fmt.Fprintf(os.Stderr, "Error: failed to set issue prefix: %v\n", err)
os.Exit(1)
}
fmt.Fprintf(os.Stderr, "✓ Initialized database with prefix '%s' (detected from issues)\n", detectedPrefix)
}
@@ -233,7 +233,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
fmt.Fprintf(os.Stderr, "\nOr use 'bd rename-prefix' after import to fix the database.\n")
os.Exit(1)
}
// Check if it's a collision error
if result != nil && len(result.CollisionIDs) > 0 {
// Print collision report before exiting
@@ -259,7 +259,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
}
fmt.Fprintf(os.Stderr, "\nUse --rename-on-import to automatically fix prefixes during import.\n")
}
if result.Collisions > 0 {
fmt.Fprintf(os.Stderr, "\n=== Collision Detection Report ===\n")
fmt.Fprintf(os.Stderr, "COLLISIONS DETECTED: %d\n", result.Collisions)
@@ -393,7 +393,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
// If jsonlPath is empty or can't be read, falls back to time.Now().
func touchDatabaseFile(dbPath, jsonlPath string) error {
targetTime := time.Now()
// If we have the JSONL path, use max(JSONL mtime, now) to handle clock skew
if jsonlPath != "" {
if info, err := os.Stat(jsonlPath); err == nil {
@@ -403,7 +403,7 @@ func touchDatabaseFile(dbPath, jsonlPath string) error {
}
}
}
// Best-effort touch - don't fail import if this doesn't work
return os.Chtimes(dbPath, targetTime, targetTime)
}
@@ -418,17 +418,17 @@ func checkUncommittedChanges(filePath string, result *ImportResult) {
// Get the directory containing the file to use as git working directory
workDir := filepath.Dir(filePath)
// Use git diff to check if working tree differs from HEAD
cmd := fmt.Sprintf("git diff --quiet HEAD %s", filePath)
exitCode, _ := runGitCommand(cmd, workDir)
// Exit code 0 = no changes, 1 = changes exist, >1 = error
if exitCode == 1 {
// Get line counts for context
workingTreeLines := countLines(filePath)
headLines := countLinesInGitHEAD(filePath, workDir)
fmt.Fprintf(os.Stderr, "\n⚠️ Warning: .beads/issues.jsonl has uncommitted changes\n")
fmt.Fprintf(os.Stderr, " Working tree: %d lines\n", workingTreeLines)
if headLines > 0 {
@@ -466,7 +466,7 @@ func countLines(filePath string) int {
return 0
}
defer func() { _ = f.Close() }()
scanner := bufio.NewScanner(f)
lines := 0
for scanner.Scan() {
@@ -484,24 +484,24 @@ func countLinesInGitHEAD(filePath string, workDir string) int {
return 0
}
gitRoot := strings.TrimSpace(gitRootOutput)
// Make filePath relative to git root
absPath, err := filepath.Abs(filePath)
if err != nil {
return 0
}
relPath, err := filepath.Rel(gitRoot, absPath)
if err != nil {
return 0
}
cmd := fmt.Sprintf("git show HEAD:%s 2>/dev/null | wc -l", relPath)
exitCode, output := runGitCommand(cmd, workDir)
if exitCode != 0 {
return 0
}
var lines int
_, err = fmt.Sscanf(strings.TrimSpace(output), "%d", &lines)
if err != nil {
@@ -518,7 +518,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Get git repository root
gitRootCmd := exec.Command("git", "rev-parse", "--show-toplevel")
gitRootCmd := exec.Command("git", "rev-parse", "--show-toplevel") // #nosec G204 -- fixed git invocation for repo root discovery
gitRootOutput, err := gitRootCmd.Output()
if err != nil {
return fmt.Errorf("not in a git repository: %w", err)
@@ -553,7 +553,7 @@ func attemptAutoMerge(conflictedPath string) error {
outputPath := filepath.Join(tmpDir, "merged.jsonl")
// Extract base version (merge-base)
baseCmd := exec.Command("git", "show", fmt.Sprintf(":1:%s", relPath))
baseCmd := exec.Command("git", "show", fmt.Sprintf(":1:%s", relPath)) // #nosec G204 -- relPath limited to files tracked in current repo
baseCmd.Dir = gitRoot
baseContent, err := baseCmd.Output()
if err != nil {
@@ -566,7 +566,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Extract left version (ours/HEAD)
leftCmd := exec.Command("git", "show", fmt.Sprintf(":2:%s", relPath))
leftCmd := exec.Command("git", "show", fmt.Sprintf(":2:%s", relPath)) // #nosec G204 -- relPath limited to files tracked in current repo
leftCmd.Dir = gitRoot
leftContent, err := leftCmd.Output()
if err != nil {
@@ -577,7 +577,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Extract right version (theirs/MERGE_HEAD)
rightCmd := exec.Command("git", "show", fmt.Sprintf(":3:%s", relPath))
rightCmd := exec.Command("git", "show", fmt.Sprintf(":3:%s", relPath)) // #nosec G204 -- relPath limited to files tracked in current repo
rightCmd.Dir = gitRoot
rightContent, err := rightCmd.Output()
if err != nil {
@@ -594,7 +594,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Invoke bd merge command
mergeCmd := exec.Command(exe, "merge", outputPath, basePath, leftPath, rightPath)
mergeCmd := exec.Command(exe, "merge", outputPath, basePath, leftPath, rightPath) // #nosec G204 -- executes current bd binary for deterministic merge
mergeOutput, err := mergeCmd.CombinedOutput()
if err != nil {
// Check exit code - bd merge returns 1 if there are conflicts, 2 for errors
@@ -608,6 +608,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Merge succeeded - copy merged result back to original file
// #nosec G304 -- merged output created earlier in this function
mergedContent, err := os.ReadFile(outputPath)
if err != nil {
return fmt.Errorf("failed to read merged output: %w", err)
@@ -618,7 +619,7 @@ func attemptAutoMerge(conflictedPath string) error {
}
// Stage the resolved file
stageCmd := exec.Command("git", "add", relPath)
stageCmd := exec.Command("git", "add", relPath) // #nosec G204 -- relPath constrained to file within current repo
stageCmd.Dir = gitRoot
if err := stageCmd.Run(); err != nil {
// Non-fatal - user can stage manually
@@ -634,7 +635,7 @@ func detectPrefixFromIssues(issues []*types.Issue) string {
if len(issues) == 0 {
return ""
}
// Count prefix occurrences
prefixCounts := make(map[string]int)
for _, issue := range issues {
@@ -644,7 +645,7 @@ func detectPrefixFromIssues(issues []*types.Issue) string {
prefixCounts[issue.ID[:idx]]++
}
}
// Find most common prefix
maxCount := 0
commonPrefix := ""
@@ -654,7 +655,7 @@ func detectPrefixFromIssues(issues []*types.Issue) string {
commonPrefix = prefix
}
}
return commonPrefix
}