refactor(main): refactor rsoft function parameters

Cargo.toml

@@ -59,3 +59,4 @@ assert_cmd = "2.0"
 assert_fs = "1.0"
 pretty_assertions = "1"
 sha256 = "1.4"
+tempfile = "3.8"

src/main.rs

@@ -57,8 +57,13 @@ enum Commands {
     /// Create softlinks to files with same suffix in one directory recursively
     Rsoft {
         /// The directory to search
-        target: PathBuf,
-        /// The suffix of the files to link default is all files
+        source: PathBuf,
+
+        /// The directory to create the softlinks. default is current directory
+        #[arg(short = 't')]
+        target: Option<PathBuf>,
+
+        /// The suffix of the files to link. default is all files
         #[arg(short = 's')]
         suffix: Option<String>,
     },
@@ -110,9 +115,13 @@ fn main() {
             fq2fa::fq2fa(input).unwrap();
         }
 
-        Some(Commands::Rsoft { target, suffix }) => {
+        Some(Commands::Rsoft {
+            source,
+            target,
+            suffix,
+        }) => {
             info!("'rsoft'  {target:?} {suffix:?} ");
-            rsoft::rsoft(target, suffix.clone()).unwrap();
+            rsoft::rsoft(source, target.as_ref(), suffix.clone()).unwrap();
         }
 
         // If no subcommand was used, it's a normal top level command

src/rsoft.rs

@@ -11,17 +11,25 @@ use std::os::unix::fs as unix_fs;
 #[cfg(windows)]
 use std::os::windows::fs as windows_fs;
 
-pub fn rsoft<P: AsRef<Path>>(target_directory: P, suffix: Option<String>) -> Result<()> {
+pub fn rsoft<P: AsRef<Path>>(
+    source_directory: P,
+    target_directory: Option<P>,
+    suffix: Option<String>,
+) -> Result<()> {
     let pattern = if suffix.is_some() {
         format!(r".*\.{}", suffix.unwrap())
     } else {
         ".*".to_string()
     };
 
     let re = Regex::new(&pattern).unwrap();
-    let current_directory = env::current_dir().unwrap();
 
-    for entry in WalkDir::new(target_directory)
+    let mut current_directory = env::current_dir().unwrap();
+    if target_directory.is_some() {
+        current_directory = target_directory.unwrap().as_ref().to_path_buf();
+    }
+
+    for entry in WalkDir::new(source_directory)
         .into_iter()
         .filter_map(|e| e.ok())
         .filter(|e| e.path().is_file() && re.is_match(&e.path().to_string_lossy()))

tests/test_rsoft.rs

@@ -0,0 +1,42 @@
+use assert_cmd::cmd::Command;
+use tempfile::tempdir;
+
+#[test]
+fn test_rsoft() {
+    let mut cmd = Command::cargo_bin("rboss").unwrap();
+
+    let temp_dir = tempdir().unwrap();
+
+    cmd.args([
+        "rsoft",
+        "tests",
+        "-t",
+        temp_dir.path().to_str().unwrap(),
+        "-s",
+        "bam",
+    ]);
+
+    cmd.assert().success();
+
+    assert!(temp_dir.path().join("extract_1.bam").is_symlink());
+    assert!(temp_dir.path().join("reads.bam").is_symlink());
+}
+
+#[test]
+fn test_rsoft_all() {
+    let mut cmd = Command::cargo_bin("rboss").unwrap();
+
+    let temp_dir = tempdir().unwrap();
+
+    cmd.args([
+        "rsoft",
+        "tests/data",
+        "-t",
+        temp_dir.path().to_str().unwrap(),
+    ]);
+
+    cmd.assert().success();
+
+    assert!(temp_dir.path().join("extract_1.bam").is_symlink());
+    assert!(temp_dir.path().join("reads.bam").is_symlink());
+}