[download] Delete partial file at the beginning

The partial file should be deleted at the beginning
before checking the ingoreExist flag because if the user
make use of this flag and a partial file is present would
not be deleted as it was before.

Modified the unit test as well because it was checking if
the file is deleted by calling the downloadFile function
and this action is talking place before that now.

Author: kostas-kou

download/download.go

@@ -252,6 +252,14 @@ func fileCase(args []string, token string, fileList bool) error {
 
 	for _, filePath := range files {
 		outputPath := filepath.Join(outDir, filePath)
+		// Cleanup .part if it exists since we are skipping
+		partPath := outputPath + ".part"
+		if _, err := os.Stat(partPath); err == nil {
+			if err := os.Remove(partPath); err != nil {
+				fmt.Printf("Warning: could not remove old partial file %s: %v\n", partPath, err)
+			}
+		}
+
 		if ignoreExisting {
 			if _, err := os.Stat(outputPath); err == nil {
 				fmt.Printf("Skipping download to %s, file already exists\n", outputPath)
@@ -351,15 +359,6 @@ func handleExistingFile(filePath string) (bool, error) {
 		return false, nil
 	}
 
-	partPath := filePath + ".part"
-
-	// If a full file exists, any partial file is definitely garbage and should be removed
-	if _, err := os.Stat(partPath); err == nil {
-		if err := os.Remove(partPath); err != nil {
-			fmt.Printf("Warning: could not remove old partial file %s: %v\n", partPath, err)
-		}
-	}
-
 	if ignoreExisting {
 		fmt.Printf("Skipping download to %s, file already exists\n", filePath)
 

download/download_test.go

@@ -514,11 +514,16 @@ func (s *DownloadTestSuite) TestDownloadCleanupOnFailure() {
 }
 
 func (s *DownloadTestSuite) TestDownloadCleanupPartialFileWhenFullExists() {
-	targetFile := "cleanup-part-test.c4gh"
+	// We need to use a file that exists in our mock server to test through fileCase/Download
+	targetFile := "files/dummy-file.txt.c4gh"
 	fullPath := filepath.Join(s.tempDir, targetFile)
 	partPath := fullPath + ".part"
 
-	err := os.WriteFile(fullPath, []byte("old content"), 0600)
+	// Create the subdirectory first
+	err := os.MkdirAll(filepath.Dir(fullPath), 0750)
+	s.Require().NoError(err)
+
+	err = os.WriteFile(fullPath, []byte("old content"), 0600)
 	s.Require().NoError(err)
 	err = os.WriteFile(partPath, []byte("partial content"), 0600)
 	s.Require().NoError(err)
@@ -533,9 +538,13 @@ func (s *DownloadTestSuite) TestDownloadCleanupPartialFileWhenFullExists() {
 		_ = w.Close()
 	}()
 
-	outDir = s.tempDir
+	os.Args = []string{"", "download", targetFile}
+	downloadCmd.Flag("url").Value.Set(s.httpTestServer.URL)
+	downloadCmd.Flag("outdir").Value.Set(s.tempDir)
+	downloadCmd.Flag("dataset-id").Value.Set("TES01")
+
 	sessionOverwrite = helpers.OverwriteNone
-	err = downloadFile(s.httpTestServer.URL, s.accessToken, "", targetFile)
+	err = downloadCmd.Execute()
 	s.NoError(err)
 
 	// Verify full content is NOT overwritten