Refactor module imports and fix module paths

src/ext_tools.rs

@@ -7,7 +7,7 @@ use std::path::{Path, PathBuf};
 use tempfile::{Builder, NamedTempFile, TempDir};
 
 use crate::edam;
-use crate::run::ModuleResult;
+use crate::module::ModuleResult;
 
 const CWL_INSPECTOR_DOCKER_IMAGE: &str = "ghcr.io/tom-tan/cwl-inspector:v0.1.1";
 const LABEL_KEY: &str = "label";
@@ -29,10 +29,10 @@ pub fn invoke(
     // make sure that the both paths are canonicalized.
     let target_file_path = target_file_path
         .canonicalize()
-        .with_context(|| format!("Failed to canonicalize {}", target_file_path.display()))?;
+        .with_context(|| format!("The specified path of CWL document '{}' does not exist. Please check the path for typos and try again.", target_file_path.display()))?;
     let cwl_file_path = cwl_file_path
         .canonicalize()
-        .with_context(|| format!("Failed to canonicalize {}", cwl_file_path.display()))?;
+        .with_context(|| format!("The specified path of CWL document '{}' does not exist. Please check the path for typos and try again.", cwl_file_path.display()))?;
 
     // get the EDAM_ID and LABEL from the comment lines in the CWL file.
     let mut cwl_metadatas = get_metadata_fields_from_cwl_file(&cwl_file_path)?;
@@ -77,7 +77,7 @@ pub fn invoke(
 
     // remove the "-v" options and split the docker command on the "-v" option.
     let mut parts_iter = tmp_cwl_docker_command_split.into_iter().peekable();
-    let cwl_docker_commandname = parts_iter.next().unwrap();
+    let cwl_docker_command_name = parts_iter.next().unwrap();
     let mut cwl_docker_args_before_v: Vec<String> = Vec::new();
     let mut cwl_docker_args_after_v: Vec<String> = Vec::new();
     let mut encountered_v = false;
@@ -110,12 +110,12 @@ pub fn invoke(
     // run the docker command created by cwl-inspector.
     debug!(
         "Running the docker command: '{} {} {}'",
-        cwl_docker_commandname,
+        cwl_docker_command_name,
         cwl_docker_args_before_v.join(" "),
         cwl_docker_args_after_v.join(" ")
     );
 
-    let cwl_docker_process = std::process::Command::new(cwl_docker_commandname)
+    let cwl_docker_process = std::process::Command::new(cwl_docker_command_name)
         .args(cwl_docker_args_before_v)
         .args(cwl_docker_args_after_v)
         .stdout(std::process::Stdio::piped())

src/lib.rs

@@ -0,0 +1,7 @@
+pub mod args;
+mod edam;
+mod ext_tools;
+mod fetch;
+mod logger;
+pub mod module;
+mod parser;

src/logger.rs

@@ -1,5 +1,3 @@
-use std::io::Write;
-
 pub fn init_logger(verbose: bool, quiet: bool) {
     let env = env_logger::Env::default().filter_or(
         env_logger::DEFAULT_FILTER_ENV,
@@ -12,8 +10,5 @@ pub fn init_logger(verbose: bool, quiet: bool) {
         },
     );
     let mut builder = env_logger::Builder::from_env(env);
-    if !verbose {
-        builder.format(|buf, record| writeln!(buf, "{}", record.args()));
-    }
     builder.init();
 }

src/main.rs

@@ -1,26 +1,13 @@
-mod args;
-mod edam;
-mod ext_tools;
-mod fetch;
-mod logger;
-mod parser;
-mod run;
-
 use anyhow::{Context, Result};
 use clap::Parser;
-use log::{debug, info};
 use std::fs::File;
 use std::io::BufReader;
 
-use crate::args::OutputFormat;
-use crate::run::Config;
-
 fn main() -> Result<()> {
     // parse arguments and options with clap
-    let args = args::Args::parse();
-    logger::init_logger(args.verbose, args.quiet);
+    let args = tataki::args::Args::parse();
 
-    let config: Config = match &args.conf {
+    let config: tataki::module::Config = match &args.conf {
         None => {
             let config_str = include_str!("./tataki.conf");
             serde_yaml::from_str(config_str)?
@@ -38,12 +25,9 @@ fn main() -> Result<()> {
     };
 
     if args.dry_run {
-        run::dry_run(config)?;
+        tataki::module::dry_run(config)?;
     } else {
-        info!("tataki started");
-        debug!("Args: {:?}", args);
-        debug!("Output format: {:?}", args.get_output_format());
-        run::run(config, args)?;
+        tataki::module::run(config, args)?;
     }
 
     Ok(())

src/run.rs → src/module.rs

@@ -6,11 +6,7 @@ use std::path::{Path, PathBuf};
 use tempfile::{NamedTempFile, TempDir};
 use url::Url;
 
-use crate::args::Args;
-use crate::ext_tools;
-use crate::fetch;
-use crate::parser;
-use crate::OutputFormat;
+use crate::args::{Args, OutputFormat};
 
 // Struct to store the result of Parser invocation and ExtTools invocation.
 #[derive(Debug)]
@@ -117,7 +113,12 @@ pub struct Config {
 }
 
 pub fn run(config: Config, args: Args) -> Result<()> {
-    let temp_dir = fetch::create_temporary_dir(&args.cache_dir)?;
+    crate::logger::init_logger(args.verbose, args.quiet);
+    info!("tataki started");
+    debug!("Args: {:?}", args);
+    debug!("Output format: {:?}", args.get_output_format());
+
+    let temp_dir = crate::fetch::create_temporary_dir(&args.cache_dir)?;
     info!("Created temporary directory: {}", temp_dir.path().display());
 
     let mut module_results: Vec<ModuleResult> = Vec::new();
@@ -193,7 +194,7 @@ fn run_modules(
 ) -> Result<ModuleResult> {
     // create an input file for CWL modules if there is any CWL module in the config file.
     let cwl_input_file_path: Option<NamedTempFile> = if cwl_module_exists(config)? {
-        Some(ext_tools::make_cwl_input_file(
+        Some(crate::ext_tools::make_cwl_input_file(
             target_file_path.clone(),
             temp_dir,
         )?)
@@ -212,8 +213,8 @@ fn run_modules(
                 .unwrap_or("");
 
             let result = match module_extension {
-                "" => parser::invoke(module, &target_file_path),
-                "cwl" => ext_tools::invoke(
+                "" => crate::parser::invoke(module, &target_file_path),
+                "cwl" => crate::ext_tools::invoke(
                     module_path,
                     &target_file_path,
                     cwl_input_file_path.as_ref().unwrap(),

src/parser.rs

@@ -14,7 +14,7 @@ use anyhow::{bail, Result};
 use log::info;
 use std::path::Path;
 
-use crate::run::ModuleResult;
+use crate::module::ModuleResult;
 
 pub trait Parser {
     /// Determine if the provided file is in a format that this parser can interpret.

src/parser/bam.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Bam;
 

src/parser/bcf.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Bcf;
 

src/parser/bed.rs

@@ -2,8 +2,8 @@ use std::fs::File;
 use std::io::BufReader;
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Bed;
 

src/parser/cram.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Cram;
 

src/parser/empty.rs

@@ -1,8 +1,8 @@
 use std::fs;
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Empty;
 

src/parser/fasta.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Fasta;
 

src/parser/fastq.rs

@@ -2,8 +2,8 @@ use std::fs::File;
 use std::io::BufReader;
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Fastq;
 

src/parser/gff3.rs

@@ -2,8 +2,8 @@ use std::fs::File;
 use std::io::BufReader;
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Gff3;
 

src/parser/gtf.rs

@@ -2,8 +2,8 @@ use std::fs::File;
 use std::io::BufReader;
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Gtf;
 

src/parser/sam.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Sam;
 

src/parser/vcf.rs

@@ -1,7 +1,7 @@
 use std::path::Path;
 
+use crate::module::ModuleResult;
 use crate::parser::Parser;
-use crate::run::ModuleResult;
 
 pub struct Vcf;