Fix GitHub enumeration & rate-limiting logic (#2625)

This is a follow-up to #2379.

It fixes the following issues:

GitHub API calls missing rate-limit handling
The fix for Refactor GitHub source #2379 (comment) inadvertently resulting in duplicate API calls

pkg/sources/github/github.go

@@ -404,31 +404,59 @@ func (s *Source) enumerate(ctx context.Context, apiEndpoint string) (*github.Cli
 	}
 
 	s.repos = make([]string, 0, s.filteredRepoCache.Count())
+
+RepoLoop:
 	for _, repo := range s.filteredRepoCache.Values() {
+		repoCtx := context.WithValue(ctx, "repo", repo)
+
 		r, ok := repo.(string)
 		if !ok {
-			ctx.Logger().Error(fmt.Errorf("type assertion failed"), "unexpected value in cache", "repo", repo)
+			repoCtx.Logger().Error(fmt.Errorf("type assertion failed"), "Unexpected value in cache")
 			continue
 		}
 
-		_, urlParts, err := getRepoURLParts(r)
-		if err != nil {
-			ctx.Logger().Error(err, "failed to parse repository URL")
-			continue
-		}
+		// Ensure that |s.repoInfoCache| contains an entry for |repo|.
+		// This compensates for differences in enumeration logic between `--org` and `--repo`.
+		// See: https://github.com/trufflesecurity/trufflehog/pull/2379#discussion_r1487454788
+		if _, ok := s.repoInfoCache.get(r); !ok {
+			repoCtx.Logger().V(2).Info("Caching repository info")
 
-		// Ignore any gists in |s.filteredRepoCache|.
-		// Repos have three parts (github.com, owner, name), gists have two.
-		if len(urlParts) == 3 {
-			// Ensure that individual repos specified in --repo are cached.
-			// Gists should be cached elsewhere.
-			// https://github.com/trufflesecurity/trufflehog/pull/2379#discussion_r1487454788
-			ghRepo, _, err := s.apiClient.Repositories.Get(ctx, urlParts[1], urlParts[2])
+			_, urlParts, err := getRepoURLParts(r)
 			if err != nil {
-				ctx.Logger().Error(err, "failed to fetch repository")
+				repoCtx.Logger().Error(err, "Failed to parse repository URL")
 				continue
 			}
-			s.cacheRepoInfo(ghRepo)
+
+			if strings.EqualFold(urlParts[0], "gist.github.com") {
+				// Cache gist info.
+				for {
+					gistID := extractGistID(urlParts)
+					gist, _, err := s.apiClient.Gists.Get(repoCtx, gistID)
+					if s.handleRateLimit(err) {
+						continue
+					}
+					if err != nil {
+						repoCtx.Logger().Error(err, "Failed to fetch gist")
+						continue RepoLoop
+					}
+					s.cacheGistInfo(gist)
+					break
+				}
+			} else {
+				// Cache repository info.
+				for {
+					ghRepo, _, err := s.apiClient.Repositories.Get(repoCtx, urlParts[1], urlParts[2])
+					if s.handleRateLimit(err) {
+						continue
+					}
+					if err != nil {
+						repoCtx.Logger().Error(err, "Failed to fetch repository")
+						continue RepoLoop
+					}
+					s.cacheRepoInfo(ghRepo)
+					break
+				}
+			}
 		}
 		s.repos = append(s.repos, r)
 	}
@@ -902,16 +930,7 @@ func (s *Source) addUserGistsToCache(ctx context.Context, user string) error {
 
 		for _, gist := range gists {
 			s.filteredRepoCache.Set(gist.GetID(), gist.GetGitPullURL())
-
-			info := repoInfo{
-				owner: gist.GetOwner().GetLogin(),
-			}
-			if gist.GetPublic() {
-				info.visibility = source_metadatapb.Visibility_public
-			} else {
-				info.visibility = source_metadatapb.Visibility_private
-			}
-			s.repoInfoCache.put(gist.GetGitPullURL(), info)
+			s.cacheGistInfo(gist)
 		}
 
 		if res == nil || res.NextPage == 0 {
@@ -998,7 +1017,7 @@ func (s *Source) addOrgsByUser(ctx context.Context, user string) {
 	logger := s.log.WithValues("user", user)
 	for {
 		orgs, resp, err := s.apiClient.Organizations.List(ctx, "", orgOpts)
-		if handled := s.handleRateLimit(err); handled {
+		if s.handleRateLimit(err) {
 			continue
 		}
 		if err != nil {

pkg/sources/github/github_test.go

@@ -451,20 +451,17 @@ func BenchmarkEnumerateWithToken(b *testing.B) {
 func TestEnumerate(t *testing.T) {
 	defer gock.Off()
 
+	// Arrange
 	gock.New("https://api.github.com").
 		Get("/user").
 		Reply(200).
 		JSON(map[string]string{"login": "super-secret-user"})
 
+	//
 	gock.New("https://api.github.com").
 		Get("/users/super-secret-user/repos").
 		Reply(200).
-		JSON([]map[string]string{{"clone_url": "https://github.com/super-secret-user/super-secret-repo.git", "full_name": "super-secret-user/super-secret-repo"}})
-
-	gock.New("https://api.github.com").
-		Get("/repos/super-secret-user/super-secret-repo").
-		Reply(200).
-		JSON(`{"owner": {"login": "super-secret-user"}, "name": "super-secret-repo", "full_name": "super-secret-user/super-secret-repo", "has_wiki": false, "size": 1}`)
+		JSON(`[{"name": "super-secret-repo", "full_name": "super-secret-user/super-secret-repo", "owner": {"login": "super-secret-user"}, "clone_url": "https://github.com/super-secret-user/super-secret-repo.git", "has_wiki": false, "size": 1}]`)
 
 	gock.New("https://api.github.com").
 		Get("/user/orgs").
@@ -483,12 +480,50 @@ func TestEnumerate(t *testing.T) {
 		},
 	})
 
+	// Manually cache a repository to ensure that enumerate
+	// doesn't make duplicate API calls.
+	// See https://github.com/trufflesecurity/trufflehog/pull/2625
+	repo := func() *github.Repository {
+		var (
+			name     = "cached-repo"
+			fullName = "cached-user/cached-repo"
+			login    = "cached-user"
+			cloneUrl = "https://github.com/cached-user/cached-repo.git"
+			owner    = &github.User{
+				Login: &login,
+			}
+			hasWiki = false
+			size    = 1234
+		)
+		return &github.Repository{
+			Name:     &name,
+			FullName: &fullName,
+			Owner:    owner,
+			HasWiki:  &hasWiki,
+			Size:     &size,
+			CloneURL: &cloneUrl,
+		}
+	}()
+	s.cacheRepoInfo(repo)
+	s.filteredRepoCache.Set(repo.GetFullName(), repo.GetCloneURL())
+
+	// Act
 	_, err := s.enumerate(context.Background(), "https://api.github.com")
+
+	// Assert
 	assert.Nil(t, err)
-	assert.Equal(t, 2, s.filteredRepoCache.Count())
-	ok := s.filteredRepoCache.Exists("super-secret-user/super-secret-repo")
+	// Enumeration found all repos.
+	assert.Equal(t, 3, s.filteredRepoCache.Count())
+	assert.True(t, s.filteredRepoCache.Exists("super-secret-user/super-secret-repo"))
+	assert.True(t, s.filteredRepoCache.Exists("cached-user/cached-repo"))
+	assert.True(t, s.filteredRepoCache.Exists("2801a2b0523099d0614a951579d99ba9"))
+	// Enumeration cached all repos.
+	assert.Equal(t, 3, len(s.repoInfoCache.cache))
+	_, ok := s.repoInfoCache.get("https://github.com/super-secret-user/super-secret-repo.git")
 	assert.True(t, ok)
-	ok = s.filteredRepoCache.Exists("2801a2b0523099d0614a951579d99ba9")
+	_, ok = s.repoInfoCache.get("https://github.com/cached-user/cached-repo.git")
+	assert.True(t, ok)
+	_, ok = s.repoInfoCache.get("https://gist.github.com/2801a2b0523099d0614a951579d99ba9.git")
 	assert.True(t, ok)
 	assert.True(t, gock.IsDone())
 }

pkg/sources/github/repo.go

@@ -297,6 +297,18 @@ func (s *Source) cacheRepoInfo(r *github.Repository) {
 	s.repoInfoCache.put(r.GetCloneURL(), info)
 }
 
+func (s *Source) cacheGistInfo(g *github.Gist) {
+	info := repoInfo{
+		owner: g.GetOwner().GetLogin(),
+	}
+	if g.GetPublic() {
+		info.visibility = source_metadatapb.Visibility_public
+	} else {
+		info.visibility = source_metadatapb.Visibility_private
+	}
+	s.repoInfoCache.put(g.GetGitPullURL(), info)
+}
+
 // wikiIsReachable returns true if https://github.com/$org/$repo/wiki is not redirected.
 // Unfortunately, this isn't 100% accurate. Some repositories have `has_wiki: true` and don't redirect their wiki page,
 // but still don't have a cloneable wiki.
@@ -329,12 +341,19 @@ type commitQuery struct {
 // getDiffForFileInCommit retrieves the diff for a specified file in a commit.
 // If the file or its diff is not found, it returns an error.
 func (s *Source) getDiffForFileInCommit(ctx context.Context, query commitQuery) (string, error) {
-	commit, _, err := s.apiClient.Repositories.GetCommit(ctx, query.owner, query.repo, query.sha, nil)
-	if s.handleRateLimit(err) {
-		return "", fmt.Errorf("error fetching commit %s due to rate limit: %w", query.sha, err)
-	}
-	if err != nil {
-		return "", fmt.Errorf("error fetching commit %s: %w", query.sha, err)
+	var (
+		commit *github.RepositoryCommit
+		err    error
+	)
+	for {
+		commit, _, err = s.apiClient.Repositories.GetCommit(ctx, query.owner, query.repo, query.sha, nil)
+		if s.handleRateLimit(err) {
+			continue
+		}
+		if err != nil {
+			return "", fmt.Errorf("error fetching commit %s: %w", query.sha, err)
+		}
+		break
 	}
 
 	if len(commit.Files) == 0 {