feat: make spec.yaml files optional

src/main.rs

@@ -327,9 +327,9 @@ struct Server {
 #[derive(Debug, Subcommand, Clone)]
 enum ServerCommands {
  /// "run" sub command.
- Run(server::run::Args),
+ Run(Box<server::run::Args>),
  /// Dump the schema.
- Schema(crate::server::schema::Args),
+ Schema(Box<crate::server::schema::Args>),
 }
 
 pub fn main() -> Result<(), anyhow::Error> {

src/server/run/mod.rs

@@ -264,20 +264,23 @@ pub struct WithVersionSpec<T: std::fmt::Debug> {
  /// The actual data.
  pub data: T,
  /// Version specification.
- pub version_spec: pbs::common::versions::VersionSpec,
+ pub version_spec: Option<pbs::common::versions::VersionSpec>,
 }
 
 impl<T> WithVersionSpec<T>
 where
  T: std::fmt::Debug,
 {
  /// Construct with the given data and path to specification YAML file.
- pub fn from_data_and_path<P>(data: T, path: P) -> Result<Self, anyhow::Error>
+ pub fn from_data_and_path<P>(data: T, path: &Option<P>) -> Result<Self, anyhow::Error>
  where
  P: AsRef<Path>,
  {
- let version_spec: pbs::common::versions::VersionSpec =
- versions::schema::VersionSpec::from_path(path)?.into();
+ let version_spec: Option<pbs::common::versions::VersionSpec> = path
+ .as_ref()
+ .map(versions::schema::VersionSpec::from_path)
+ .transpose()?
+ .map(|version_spec| version_spec.into());
  Ok(Self { data, version_spec })
  }
 }
@@ -483,11 +486,16 @@ pub fn run(args_common: &common::cli::Args, args: &Args) -> Result<(), anyhow::E
  .parent()
  .ok_or_else(|| anyhow::anyhow!("cannot get parent directory of path {}", path_genes))?
  .join("spec.yaml");
+ let path_buf = path_buf.exists().then_some(path_buf);
  data.genes = Some(
  WithVersionSpec::from_data_and_path(gene_info_db, &path_buf).map_err(|e| {
  anyhow::anyhow!(
  "problem loading gene info spec from {}: {}",
- path_buf.display(),
+ if let Some(path_buf) = path_buf.as_ref() {
+ format!("{}", path_buf.display())
+ } else {
+ "None".to_string()
+ },
  e
  )
  })?,
@@ -564,13 +572,18 @@ pub fn run(args_common: &common::cli::Args, args: &Args) -> Result<(), anyhow::E
  anyhow::anyhow!("cannot get parent directory of path {}", path_rocksdb)
  })?
  .join("spec.yaml");
+ let spec_path = spec_path.exists().then_some(spec_path);
  let name = db_info.name;
  data.db_infos[genome_release][name] = Some(db_info);
  data.annos[genome_release][name] = Some(
  WithVersionSpec::from_data_and_path(db, &spec_path).map_err(|e| {
  anyhow::anyhow!(
  "problem loading gene info spec from {}: {}",
- spec_path.display(),
+ if let Some(spec_path) = spec_path.as_ref() {
+ format!("{}", spec_path.display())
+ } else {
+ "None".to_string()
+ },
  e
  )
  })?,

src/server/run/versions.rs

@@ -25,9 +25,9 @@ pub mod schema {
  pub version: String,
  }
 
- impl Into<pbs::common::versions::CreatedFrom> for CreatedFrom {
- fn into(self) -> pbs::common::versions::CreatedFrom {
- let Self { name, version } = self;
+ impl From<CreatedFrom> for pbs::common::versions::CreatedFrom {
+ fn from(val: CreatedFrom) -> Self {
+ let CreatedFrom { name, version } = val;
  pbs::common::versions::CreatedFrom { name, version }
  }
  }
@@ -81,16 +81,16 @@ pub mod schema {
  let full_path = p.as_ref().to_str().ok_or_else(|| {
  anyhow::anyhow!("problem converting path to string: {:?}", p.as_ref())
  })?;
- let yaml_str = std::fs::read_to_string(&full_path)
+ let yaml_str = std::fs::read_to_string(full_path)
  .map_err(|e| anyhow::anyhow!("problem reading file {}: {}", &full_path, e))?;
  serde_yaml::from_str(&yaml_str)
  .map_err(|e| anyhow::anyhow!("problem deserializing {}: {}", full_path, e))
  }
  }
 
- impl Into<pbs::common::versions::VersionSpec> for VersionSpec {
- fn into(self) -> pbs::common::versions::VersionSpec {
- let Self {
+ impl From<VersionSpec> for pbs::common::versions::VersionSpec {
+ fn from(val: VersionSpec) -> Self {
+ let VersionSpec {
  identifier,
  title,
  creator,
@@ -102,7 +102,7 @@ pub mod schema {
  description,
  source,
  created_from,
- } = self;
+ } = val;
  pbs::common::versions::VersionSpec {
  identifier,
  title,
@@ -131,7 +131,7 @@ pub struct AnnoVersionInfo {
  /// Database name.
  pub database: AnnoDb,
  /// Version information of the database.
- pub version_spec: VersionSpec,
+ pub version_spec: Option<VersionSpec>,
 }
 
 /// Version information for databases in a given release.
@@ -177,8 +177,8 @@ async fn handle(
  for (anno_db, with_version) in anno_dbs {
  if let Some(with_version) = with_version.as_ref() {
  version_infos.push(AnnoVersionInfo {
- database: anno_db.clone(),
- version_spec: with_version.version_spec.clone().into(),
+ database: anno_db,
+ version_spec: with_version.version_spec.clone(),
  });
  }
  }
@@ -193,7 +193,7 @@ async fn handle(
  .as_ref()
  .genes
  .as_ref()
- .map(|genes| genes.version_spec.clone()),
+ .and_then(|genes| genes.version_spec.clone()),
  annos,
  };
 
@@ -216,7 +216,7 @@ pub mod test {
  crate::common::set_snapshot_suffix!("{}", &name);
 
  let full_path = format!("tests/server/annonars/{}/spec.yaml", &name);
- let spec = super::schema::VersionSpec::from_path(&full_path)?;
+ let spec = super::schema::VersionSpec::from_path(full_path)?;
  insta::assert_yaml_snapshot!(&spec);
 
  let proto_spec: crate::pbs::common::versions::VersionSpec = spec.into();