feat: make spec.yaml files optional (#503)

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();