feat!: provide sub command "server run" (#600) (#602)

This moves "run-server" to "server run".

Release-As: 0.30.0

Cargo.toml

@@ -7,7 +7,7 @@ description = "Variant effect prediction all in Rust"
 license = "MIT"
 repository = "https://github.com/varfish-org/mehari"
 readme = "README.md"
-rust-version = "1.70.0"
+rust-version = "1.75.0"
 
 [features]
 default = []
@@ -33,6 +33,7 @@ async-compression = { version = "0.4", features = ["tokio", "gzip"] }
 bgzip = "0.3"
 bio = "2.0.3"
 biocommons-bioutils = "0.1.4"
+built = { version = "0.7", features = ["chrono", "semver"] }
 byteorder = "1.4"
 byte-unit = "5.1"
 chrono = "0.4"
@@ -82,15 +83,19 @@ tracing-subscriber = "0.3"
 tracing = { version = "0.1", features = ["log"] }
 uuid = { version = "1.11", features = ["fast-rng", "serde"] }
 zstd = "0.13"
+utoipa = { version = "4.2.3", features = ["actix_extras", "chrono", "indexmap", "openapi_extensions", "preserve_order", "yaml"] }
+utoipa-swagger-ui = { version = "7.0.1", features = ["actix-web"] }
+utoipa-actix-web = "0.1.1"
 
 [dependencies.noodles]
 version = "0.77.0"
 features = ["async", "bgzf", "core", "vcf", "bcf", "csi", "fasta", "tabix"]
 
 [build-dependencies]
 anyhow = "1.0"
-prost-build = "0.13.3"
+built = { version = "0.7", features = ["cargo-lock", "dependency-tree", "git2", "chrono", "semver"] }
 pbjson-build = "0.7.0"
+prost-build = "0.13.3"
 
 [dev-dependencies]
 async-std = { version = "1.13", features = ["attributes"] }

build.rs

@@ -4,6 +4,7 @@
 use std::{env, path::PathBuf};
 
 fn main() -> Result<(), anyhow::Error> {
+    // Integration of `prost-build` and `pbjson-build`.
     let root = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("protos");
     let proto_files = ["mehari/txs.proto", "mehari/server.proto"]
         .iter()
@@ -32,5 +33,8 @@ fn main() -> Result<(), anyhow::Error> {
         .register_descriptors(&descriptor_set)?
         .build(&[".mehari"])?;
 
+    // Integration of `built`.
+    built::write_built_file().map_err(|e| anyhow::anyhow!("Failed to write built file: {}", e))?;
+
     Ok(())
 }

src/annotate/seqvars/provider.rs

@@ -136,7 +136,9 @@ pub struct Provider {
     picked_gene_to_tx_id: Option<Vec<GeneToTxId>>,
     /// The assembly of the provider.
     assembly: Assembly,
+    /// The data version.
     data_version: String,
+    /// The schema version.
     schema_version: String,
 }
 
@@ -357,6 +359,15 @@ impl Provider {
         }
     }
 
+    /// Return the assembly of the provider.
+    ///
+    /// # Returns
+    ///
+    /// The assembly of the provider.
+    pub fn assembly(&self) -> Assembly {
+        self.assembly
+    }
+
     /// Return whether transcript picking is enabled.
     pub fn transcript_picking(&self) -> bool {
         self.picked_gene_to_tx_id.is_some()

src/common/io/std.rs

@@ -116,7 +116,7 @@ mod test {
         // Note that the 14kb.txt file contains about 14 KB of data so bgz will have multiple 4KB
         // blocks.
 
-        let mut reader = super::open_read_maybe_gz(&format!("tests/common/io/{}", path))?;
+        let mut reader = super::open_read_maybe_gz(format!("tests/common/io/{}", path))?;
         let mut buf = Vec::new();
         reader.read_to_end(&mut buf)?;
 

src/lib.rs

@@ -26,3 +26,8 @@ pub mod pbs;
 pub mod ped;
 pub mod server;
 pub mod verify;
+
+/// Information about the build.
+pub mod built_info {
+    include!(concat!(env!("OUT_DIR"), "/built.rs"));
+}

src/main.rs

@@ -104,10 +104,10 @@ enum Commands {
     Db(Db),
     /// Annotation related commands.
     Annotate(Annotate),
+    /// Server related commands.
+    Server(Server),
     /// Verification related commands.
     Verify(Verify),
-    /// Server related commands.
-    RunServer(server::Args),
 }
 
 /// Parsing of "db *" sub commands.
@@ -145,6 +145,22 @@ enum AnnotateCommands {
     Strucvars(annotate::strucvars::Args),
 }
 
+/// Parsing of "server *" sub commands.
+#[derive(Debug, Args)]
+#[command(args_conflicts_with_subcommands = true)]
+struct Server {
+    /// The sub command to run
+    #[command(subcommand)]
+    command: ServerCommands,
+}
+
+/// Enum supporting the parsing of "server *" sub commands.
+#[derive(Debug, Subcommand)]
+enum ServerCommands {
+    Run(server::run::Args),
+    Schema(server::schema::Args),
+}
+
 /// Parsing of "verify *" sub commands.
 #[derive(Debug, Args)]
 #[command(args_conflicts_with_subcommands = true)]
@@ -202,10 +218,13 @@ async fn main() -> Result<(), anyhow::Error> {
                 annotate::strucvars::run(&cli.common, args).await?
             }
         },
+        Commands::Server(server) => match &server.command {
+            ServerCommands::Run(args) => server::run::run(&cli.common, args).await?,
+            ServerCommands::Schema(args) => server::schema::run(&cli.common, args)?,
+        },
         Commands::Verify(verify) => match &verify.command {
             VerifyCommands::Seqvars(args) => verify::seqvars::run(&cli.common, args)?,
         },
-        Commands::RunServer(args) => server::run(&cli.common, args).await?,
     }
 
     tracing::info!("... the dromedary is back in the stable.");