chore: bootstrapping mehari CLI (#4)

Cargo.toml

@@ -12,3 +12,9 @@ readme = "README.md"
 name = "mehari"
 
 [dependencies]
+anyhow = "1.0.69"
+clap = { version = "4.1.8", features = ["derive"] }
+clap-verbosity-flag = "2.0.0"
+log = "0.4.17"
+tracing = { version = "0.1.37", features = ["log"] }
+tracing-subscriber = "0.3.16"

README.md

@@ -1,4 +1,5 @@
 [![CI](https://github.com/bihealth/mehari/actions/workflows/rust.yml/badge.svg)](https://github.com/bihealth/mehari/actions/workflows/rust.yml)
+[![codecov](https://codecov.io/gh/bihealth/mehari/branch/main/graph/badge.svg?token=B1dfb7N2n8)](https://codecov.io/gh/bihealth/mehari)
 
 # Mehari
 

src/common.rs

@@ -0,0 +1,12 @@
+//! Commonly used code.
+
+use clap::Parser;
+use clap_verbosity_flag::{InfoLevel, Verbosity};
+
+/// Commonly used command line arguments.
+#[derive(Parser, Debug)]
+pub struct Args {
+    /// Verbosity of the program
+    #[clap(flatten)]
+    pub verbose: Verbosity<InfoLevel>,
+}

src/db/create/mod.rs

@@ -0,0 +1,4 @@
+//! Creation of mehari internal databases.
+
+pub mod seqvar_freqs;
+pub mod txs;

src/db/create/seqvar_freqs.rs

@@ -0,0 +1,20 @@
+//! Sequence variant frequency annotation.
+
+use clap::Parser;
+
+/// Command line arguments for `db create seqvar-freqs` sub command.
+#[derive(Parser, Debug)]
+#[command(about = "Construct mehari sequence variant frequencies database", long_about = None)]
+pub struct Args {}
+
+/// Main entry point for `db create seqvar_freqs` sub command.
+pub(crate) fn run(common: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> {
+    tracing::info!(
+        "Building sequence variant frequencies table\ncommon args: {:#?}\nargs: {:#?}",
+        common,
+        args
+    );
+
+    tracing::info!("Done building sequence variant frequency table");
+    Ok(())
+}

src/db/create/txs.rs

@@ -0,0 +1,13 @@
+//! Transcript database.
+
+use clap::Parser;
+
+/// Command line arguments for `db create txs` sub command.
+#[derive(Parser, Debug)]
+#[command(about = "Construct mehari transcripts database", long_about = None)]
+pub struct Args {}
+
+/// Main entry point for `db create txs` sub command.
+pub fn run(_common: &crate::common::Args, _args: &Args) -> Result<(), anyhow::Error> {
+    todo!()
+}

src/db/mod.rs

@@ -0,0 +1,3 @@
+//! Database construction and introspection tools.
+
+pub mod create;

src/main.rs

@@ -1,3 +1,107 @@
-fn main() {
-    println!("Hello, world!");
+//! Main entry point for the Mehari CLI.
+
+pub mod common;
+pub mod db;
+
+use clap::{command, Args, Parser, Subcommand};
+
+#[derive(Debug, Parser)]
+#[command(
+    author,
+    version,
+    about = "VCF variant effect prediction and annotation"
+)]
+struct Cli {
+    /// Commonly used arguments
+    #[command(flatten)]
+    common: common::Args,
+
+    /// The sub command to run
+    #[command(subcommand)]
+    command: Commands,
+}
+
+/// Enum supporting the parsing of top-level commands.
+#[allow(clippy::large_enum_variant)]
+#[derive(Debug, Subcommand)]
+enum Commands {
+    /// Database-related commands.
+    Db(Db),
+    // /// SV related commands.
+    // Sv(Sv),
+    // /// Server related commands.
+    // Server(Server),
+}
+
+/// Parsing of "db *" sub commands.
+#[derive(Debug, Args)]
+#[command(args_conflicts_with_subcommands = true)]
+struct Db {
+    /// The sub command to run
+    #[command(subcommand)]
+    command: DbCommands,
+}
+
+/// Enum supporting the parsing of "db *" sub commands.
+#[derive(Debug, Subcommand)]
+enum DbCommands {
+    Create(DbCreate),
+}
+
+/// Parsing of "db create *" sub commands.
+#[derive(Debug, Args)]
+#[command(args_conflicts_with_subcommands = true)]
+struct DbCreate {
+    /// The sub command to run
+    #[command(subcommand)]
+    command: DbCreateCommands,
+}
+
+/// Enum supporting the parsing of "db create *" sub commands.
+#[derive(Debug, Subcommand)]
+enum DbCreateCommands {
+    Txs(db::create::txs::Args),
+    SeqvarFreqs(db::create::seqvar_freqs::Args),
+}
+
+fn main() -> Result<(), anyhow::Error> {
+    let cli = Cli::parse();
+
+    // Build a tracing subscriber according to the configuration in `cli.common`.
+    let collector = tracing_subscriber::fmt()
+        .with_target(false)
+        .with_max_level(match cli.common.verbose.log_level() {
+            Some(level) => match level {
+                log::Level::Error => tracing::Level::ERROR,
+                log::Level::Warn => tracing::Level::WARN,
+                log::Level::Info => tracing::Level::INFO,
+                log::Level::Debug => tracing::Level::DEBUG,
+                log::Level::Trace => tracing::Level::TRACE,
+            },
+            None => tracing::Level::INFO,
+        })
+        .compact()
+        .finish();
+
+    // Install collector and go into sub commands.
+    tracing::subscriber::with_default(collector, || {
+        tracing::info!("Mehari startup -- letting the camel from the leash...");
+
+        match &cli.command {
+            Commands::Db(db) => match &db.command {
+                DbCommands::Create(db_create) => match &db_create.command {
+                    DbCreateCommands::Txs(args) => db::create::txs::run(&cli.common, args)?,
+                    DbCreateCommands::SeqvarFreqs(args) => {
+                        db::create::seqvar_freqs::run(&cli.common, args)?
+                    }
+                },
+            },
+        }
+
+        tracing::info!("All done. Have a nice day!");
+
+        Ok::<(), anyhow::Error>(())
+    })?;
+
+    Ok(())
 }