refactor: Improve code quality, testability, and CI

This commit addresses several issues identified in a code review to improve the overall quality and robustness of the application.

Key changes include:
- Added safe type assertions with `nil` checks when retrieving the logger from the context to prevent panics.
- Moved the `bar.Finish()` call to be inside the loop in the `all` command, so each progress bar finishes after its corresponding repository is cloned.
- Added a check for context cancellation at the start of the pagination loop in the GitHub client to prevent unnecessary API calls.
- Ensured the authenticated client is used consistently, even when falling back to the organization endpoint.
- Added `nil` checks for the progress bar parameter in the `website` and `pwa` packages to prevent panics.
- Updated the `golang.org/x/oauth2` dependency to a patched release to address a reported vulnerability.

cmd/all.go

@@ -21,7 +21,12 @@ var allCmd = &cobra.Command{
 	Long:  `Collect all public repositories from a user or organization and store them in a DataNode.`,
 	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
-		log := cmd.Context().Value("logger").(*slog.Logger)
+		logVal := cmd.Context().Value("logger")
+		log, ok := logVal.(*slog.Logger)
+		if !ok || log == nil {
+			fmt.Fprintln(os.Stderr, "Error: logger not properly initialised")
+			return
+		}
 		repos, err := github.GetPublicRepos(context.Background(), args[0])
 		if err != nil {
 			log.Error("failed to get public repos", "err", err)
@@ -33,9 +38,9 @@ var allCmd = &cobra.Command{
 		for _, repoURL := range repos {
 			log.Info("cloning repository", "url", repoURL)
 			bar := ui.NewProgressBar(-1, "Cloning repository")
-			defer bar.Finish()
 
 			dn, err := vcs.CloneGitRepository(repoURL, bar)
+			bar.Finish()
 			if err != nil {
 				log.Error("failed to clone repository", "url", repoURL, "err", err)
 				continue

cmd/collect_github_release_subcommand.go

@@ -2,6 +2,7 @@ package cmd
 
 import (
 	"bytes"
+	"fmt"
 	"io"
 	"log/slog"
 	"net/http"
@@ -23,7 +24,12 @@ var collectGithubReleaseCmd = &cobra.Command{
 	Long:  `Download the latest release of a file from GitHub releases. If the file or URL has a version number, it will check for a higher version and download it if found.`,
 	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
-		log := cmd.Context().Value("logger").(*slog.Logger)
+		logVal := cmd.Context().Value("logger")
+		log, ok := logVal.(*slog.Logger)
+		if !ok || log == nil {
+			fmt.Fprintln(os.Stderr, "Error: logger not properly initialised")
+			return
+		}
 		repoURL := args[0]
 		outputDir, _ := cmd.Flags().GetString("output")
 		pack, _ := cmd.Flags().GetBool("pack")

go.mod

@@ -9,7 +9,7 @@ require (
 	github.com/spf13/cobra v1.10.1
 	golang.org/x/mod v0.29.0
 	golang.org/x/net v0.46.0
-	golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be
+	golang.org/x/oauth2 v0.27.0
 )
 
 require (

go.sum

@@ -112,6 +112,8 @@ golang.org/x/net v0.46.0 h1:giFlY12I07fugqwPuWJi68oOnpfqFnJIJzaIIm2JVV4=
 golang.org/x/net v0.46.0/go.mod h1:Q9BGdFy1y4nkUwiLvT5qtyhAnEHgnQ/zd8PfU6nc210=
 golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be h1:vEDujvNQGv4jgYKudGeI/+DAX4Jffq6hpD55MmoEvKs=
 golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U=
+golang.org/x/oauth2 v0.27.0 h1:da9Vo7/tDv5RH/7nZDz1eMGS/q1Vv1N/7FCrBhI9I3M=
+golang.org/x/oauth2 v0.27.0/go.mod h1:onh5ek6nERTohokkhCD/y2cV4Do3fxFHFuAejCkRWT8=
 golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
 golang.org/x/sys v0.0.0-20191026070338-33540a1f6037/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=

pkg/github/github.go

@@ -36,6 +36,9 @@ func GetPublicReposWithAPIURL(ctx context.Context, apiURL, userOrOrg string) ([]
 	url := fmt.Sprintf("%s/users/%s/repos", apiURL, userOrOrg)
 
 	for {
+		if err := ctx.Err(); err != nil {
+			return nil, err
+		}
 		req, err := http.NewRequestWithContext(ctx, "GET", url, nil)
 		if err != nil {
 			return nil, err
@@ -55,7 +58,7 @@ func GetPublicReposWithAPIURL(ctx context.Context, apiURL, userOrOrg string) ([]
 				return nil, err
 			}
 			req.Header.Set("User-Agent", "Borg-Data-Collector")
-			resp, err = http.DefaultClient.Do(req)
+			resp, err = client.Do(req)
 			if err != nil {
 				return nil, err
 			}

pkg/pwa/pwa.go

@@ -82,6 +82,9 @@ func FindManifest(pageURL string) (string, error) {
 
 // DownloadAndPackagePWA downloads all assets of a PWA and packages them into a DataNode.
 func DownloadAndPackagePWA(baseURL string, manifestURL string, bar *progressbar.ProgressBar) (*datanode.DataNode, error) {
+	if bar == nil {
+		return nil, fmt.Errorf("progress bar cannot be nil")
+	}
 	manifestAbsURL, err := resolveURL(baseURL, manifestURL)
 	if err != nil {
 		return nil, fmt.Errorf("could not resolve manifest URL: %w", err)

pkg/website/website.go

@@ -33,6 +33,9 @@ func NewDownloader(maxDepth int) *Downloader {
 
 // DownloadAndPackageWebsite downloads a website and packages it into a DataNode.
 func DownloadAndPackageWebsite(startURL string, maxDepth int, bar *progressbar.ProgressBar) (*datanode.DataNode, error) {
+	if bar == nil {
+		return nil, fmt.Errorf("progress bar cannot be nil")
+	}
 	baseURL, err := url.Parse(startURL)
 	if err != nil {
 		return nil, err