Merge pull request #13 from sapporo-wes/enhancement/11

Add support for M1 Mac

Cargo.toml

@@ -32,7 +32,7 @@ serde_yaml = "0.9.27"
 serde_json = "1.0.109"
 url = "2.5.0"
 reqwest = { version = "0.12.5", features = ["blocking"] }
-tempfile = "3.9.0"
+tempfile = "3.12.0"
 csv = "1.3.0"
 log = "0.4.20"
 env_logger = "0.11.0"

src/ext_tools.rs

@@ -2,7 +2,9 @@ use anyhow::{anyhow, bail, Context, Result};
 use log::{debug, info};
 use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
+use std::fs;
 use std::io::Write;
+use std::os::unix::fs::PermissionsExt;
 use std::path::{Path, PathBuf};
 use tempfile::{Builder, NamedTempFile, TempDir};
 
@@ -17,16 +19,11 @@ pub fn invoke(
     cwl_file_path: &Path,
     target_file_path: &Path,
     cwl_input_file_path: &NamedTempFile,
+    dummy_docker_path: &NamedTempFile,
     _options: &InvokeOptions,
 ) -> Result<ModuleResult> {
     info!("Invoking ext_tools {}", cwl_file_path.display());
 
-    let docker_path = docker_path()?;
-    debug!(
-        "The path of the docker command in your environment: {:?}.",
-        docker_path
-    );
-
     // make sure that the both paths are canonicalized.
     let target_file_path = target_file_path.canonicalize().with_context(|| {
         format!(
@@ -50,7 +47,7 @@ pub fn invoke(
             "--rm",
             "-i",
             "-v",
-            &format!("{}:/usr/bin/docker:ro", docker_path.to_str().unwrap()),
+            &format!("{}:/usr/bin/docker:ro", dummy_docker_path.path().display()),
             "-v",
             &format!(
                 "{}:/workdir/input_file.yaml:ro",
@@ -141,7 +138,8 @@ pub fn invoke(
     Ok(module_result)
 }
 
-fn docker_path() -> Result<PathBuf> {
+// check whether `which docker` succeeds or not to see the docker binary is in the PATH.
+pub fn ensure_docker_presence() -> Result<PathBuf> {
     let process = std::process::Command::new("which")
         .arg("docker")
         .stdout(std::process::Stdio::piped())
@@ -152,10 +150,24 @@ fn docker_path() -> Result<PathBuf> {
         let path = String::from_utf8(process.stdout)?;
         Ok(PathBuf::from(path.trim()))
     } else {
-        bail!("Please make sure that the docker command is present in your PATH");
+        bail!("Please make sure that the docker command is present in your PATH when invoking CWL modules.");
     }
 }
 
+// create a dummy Docker executable
+// - create a empty file in the temporary directory.
+// - grant execution permission to the file.
+// - return the file as NamedTempFile.
+pub fn create_dummy_docker_executable(temp_dir: &TempDir) -> Result<NamedTempFile> {
+    let read_execution_permission = std::fs::Permissions::from_mode(0o500);
+    let dummy_docker_file = Builder::new()
+        .prefix("dummy_docker_")
+        .permissions(read_execution_permission)
+        .tempfile_in(temp_dir)?;
+
+    Ok(dummy_docker_file)
+}
+
 #[derive(Deserialize, Debug)]
 struct CwlFields {
     #[serde(flatten)]

src/module.rs

@@ -7,6 +7,7 @@ use tempfile::{NamedTempFile, TempDir};
 use url::Url;
 
 use crate::args::{Args, OutputFormat};
+use crate::ext_tools::{create_dummy_docker_executable, ensure_docker_presence};
 use crate::source::{CompressedFormat, Source};
 
 // Struct to store the result of Parser invocation and ExtTools invocation.
@@ -455,6 +456,13 @@ fn run_modules(
         None
     };
 
+    // create a dummy Docker executable just for cwl-inspecter to work properly in Docker container only if there are one or more CWL module in the config file
+    let dummy_docker_path = if cwl_module_exists(config)? {
+        Some(create_dummy_docker_executable(temp_dir)?)
+    } else {
+        None
+    };
+
     let module_result = config
         .order
         .iter()
@@ -474,6 +482,7 @@ fn run_modules(
                         module_path,
                         target_file_path,
                         cwl_input_file_path.as_ref().unwrap(),
+                        dummy_docker_path.as_ref().unwrap(),
                         invoke_options,)
                 },
                 _ => Err(anyhow!(
@@ -552,8 +561,19 @@ fn check_run_condition_cwl_module(
         - tidy needed
      */
 
-    if cwl_module_exists && stdin_exists && !invoke_options.tidy {
-        bail!("The `--tidy` option is required when reading from STDIN and invoking CWL modules.");
+    if cwl_module_exists {
+        if stdin_exists && !invoke_options.tidy {
+            bail!(
+                "The `--tidy` option is required when reading from STDIN and invoking CWL modules."
+            );
+        }
+
+        // check for existence of docker binary if a CWL module is specified
+        let docker_path = ensure_docker_presence()?;
+        debug!(
+            "The path of the docker command in your environment: {:?}.",
+            docker_path
+        );
     }
 
     Ok(())

tests/common.rs

@@ -47,6 +47,7 @@ pub fn check_and_create_cache_dir() -> io::Result<()> {
 }
 
 // whether the current environment is M1 Mac
+#[allow(dead_code)]
 pub fn is_running_on_m1_mac() -> bool {
     let os = std::env::consts::OS;
     let arch = std::env::consts::ARCH;

tests/integration_tests.rs

@@ -240,12 +240,6 @@ fn can_be_verbose() {
 #[test]
 // 9. -c cwl.conf
 fn can_run_cwl() {
-    // TEMPORARY: skip this test on M1 Mac due (issue #9)
-    // This will be removed when tataki supports M1 Mac.
-    if is_running_on_m1_mac() {
-        return;
-    }
-
     check_and_create_cache_dir().expect("Failed to create the cache directory");
 
     let out = tataki(