refactor: make versions infos endoint consistent with mehari

.github/workflows/rust.yml

@@ -105,3 +105,38 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: lcov.info
+
+  Schema:
+    needs: Formatting
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y librocksdb-dev libsnappy-dev libsqlite3-dev
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+
+      - name: Setup protoc
+        uses: arduino/[email protected]
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Write schema
+        run: cargo run -- server schema --output-file /tmp/openapi.schema.yaml-gen
+
+      - name: Copy repo schema and strip versions
+        run: |
+          cp openapi.schema.yaml /tmp/openapi.schema.yaml-repo
+          perl -p -i -e 's/^  version: .*/  version: 0.0.0/' /tmp/*.yaml-*
+
+      - name: Compare YAML in git to the one just generated
+        run: diff /tmp/openapi.schema.yaml-repo /tmp/openapi.schema.yaml-gen

Cargo.toml

@@ -3,7 +3,7 @@ name = "annonars"
 version = "0.41.3"
 edition = "2021"
 authors = ["Manuel Holtgrewe <[email protected]>"]
-description = "Rust template repository"
+description = "Genome annotation based on Rust and RocksDB"
 license = "Apache-2.0"
 repository = "https://github.com/varfish-org/annonars"
 readme = "README.md"

build.rs

@@ -14,7 +14,6 @@ fn main() -> Result<(), anyhow::Error> {
         "annonars/clinvar/minimal.proto",
         "annonars/clinvar/per_gene.proto",
         "annonars/clinvar/sv.proto",
-        "annonars/common/versions.proto",
         "annonars/cons/base.proto",
         "annonars/dbsnp/base.proto",
         "annonars/functional/refseq.proto",

openapi.schema.yaml

@@ -0,0 +1,171 @@
+openapi: 3.0.3
+info:
+  title: annonars
+  description: Genome annotation based on Rust and RocksDB
+  contact:
+    name: Manuel Holtgrewe
+    email: [email protected]
+  license:
+    name: Apache-2.0
+  version: 0.41.3
+paths:
+  /api/v1/versionsInfo:
+    get:
+      tags:
+      - versions
+      summary: Query for annotations for one variant.
+      operationId: versionsInfo
+      parameters: []
+      responses:
+        '200':
+          description: Version information.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/VersionsResponse'
+        '500':
+          description: Internal server error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/CustomError'
+components:
+  schemas:
+    AnnoDb:
+      type: string
+      description: Encode annotation database.
+      enum:
+      - other
+      - cadd
+      - dbsnp
+      - dbnsfp
+      - dbscsnv
+      - gnomad_mtdna
+      - gnomad_exomes
+      - gnomad_genomes
+      - helixmtdb
+      - ucsc_conservation
+      - clinvar
+    CustomError:
+      type: object
+      description: Custom error type for the Actix server.
+      required:
+      - err
+      properties:
+        err:
+          type: string
+    GenomeRelease:
+      type: string
+      description: Local genome release for command line arguments.
+      enum:
+      - Grch37
+      - Grch38
+    VersionsAnnotationInfo:
+      type: object
+      description: Version information for one database.
+      required:
+      - database
+      properties:
+        database:
+          $ref: '#/components/schemas/AnnoDb'
+        version_spec:
+          allOf:
+          - $ref: '#/components/schemas/VersionsVersionSpec'
+          nullable: true
+    VersionsCreatedFrom:
+      type: object
+      description: Source name and version.
+      required:
+      - name
+      - version
+      properties:
+        name:
+          type: string
+          description: The name of the data source.
+        version:
+          type: string
+          description: The version of the data source.
+    VersionsInfoQuery:
+      type: object
+      description: Query parameters for `handle()`.
+    VersionsInfoResponse:
+      type: object
+      description: Response for `handle()`.
+      properties:
+        genes:
+          allOf:
+          - $ref: '#/components/schemas/VersionsVersionSpec'
+          nullable: true
+        seqvars:
+          type: array
+          items:
+            $ref: '#/components/schemas/VersionsPerRelease'
+          description: Version information of annotation databases per release.
+    VersionsPerRelease:
+      type: object
+      description: Version information for databases in a given release.
+      required:
+      - release
+      properties:
+        release:
+          $ref: '#/components/schemas/GenomeRelease'
+        version_infos:
+          type: array
+          items:
+            $ref: '#/components/schemas/VersionsAnnotationInfo'
+          description: Version information of annotation databases.
+    VersionsVersionSpec:
+      type: object
+      description: Version specification.
+      required:
+      - identifier
+      - title
+      - creator
+      - contributor
+      - format
+      - date
+      - version
+      - description
+      - source
+      - created_from
+      properties:
+        identifier:
+          type: string
+          description: Identifier of the data.
+        title:
+          type: string
+          description: Title of the data.
+        creator:
+          type: string
+          description: Creator of the data.
+        contributor:
+          type: array
+          items:
+            type: string
+          description: Contributors of the data.
+        format:
+          type: string
+          description: Format of the data.
+        date:
+          type: string
+          description: Date of the data.
+        version:
+          type: string
+          description: Version of the data.
+        genome_release:
+          type: string
+          description: Optional genome release.
+          nullable: true
+        description:
+          type: string
+          description: Data description.
+        source:
+          type: array
+          items:
+            type: string
+          description: Data source.
+        created_from:
+          type: array
+          items:
+            $ref: '#/components/schemas/VersionsCreatedFrom'
+          description: Created from information.

src/common/cli.rs

@@ -34,16 +34,15 @@ pub enum OutputFormat {
     strum::EnumString,
     enum_map::Enum,
     serde::Serialize,
+    serde::Deserialize,
     utoipa::ToSchema,
 )]
 #[strum(serialize_all = "lowercase")]
 pub enum GenomeRelease {
     /// GRCh37 genome release.
-    #[strum(serialize = "grch37")]
     #[default]
     Grch37,
     /// GRCh38 genome release.
-    #[strum(serialize = "grch38")]
     Grch38,
 }
 

src/genes/cli/data.rs

@@ -2796,9 +2796,8 @@ mod tests {
             .lines()
             .map(|s| {
                 serde_json::from_str::<panelapp::Record>(s)
-                    .map_err(|e| {
-                        println!("{}", &s);
-                        e
+                    .inspect_err(|e| {
+                        println!("{} -- {:?}", &s, e);
                     })
                     .unwrap()
             })

src/genes/cli/import.rs

@@ -1156,7 +1156,7 @@ fn write_rocksdb(
             conditions: conditions_by_hgnc_id.get(&hgnc_id).cloned(),
         });
         tracing::debug!("writing {:?} -> {:?}", &hgnc, &record);
-        db.put_cf(&cf_genes, hgnc_id, &record.encode_to_vec())?;
+        db.put_cf(&cf_genes, hgnc_id, record.encode_to_vec())?;
     }
 
     // Finally, compact manually.

src/gnomad_nuclear/cli/import.rs

@@ -418,7 +418,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error>
     for (header_field, val) in more_header_values {
         db.put_cf(
             &cf_meta,
-            &format!("gnomad-{}", header_field.replace('_', "-")),
+            format!("gnomad-{}", header_field.replace('_', "-")),
             &val,
         )?;
     }

src/pbs/mod.rs

@@ -2,7 +2,6 @@
 
 pub mod clinvar;
 pub mod clinvar_data;
-pub mod common;
 pub mod cons;
 pub mod dbsnp;
 pub mod functional;

src/server/run/error.rs

@@ -3,9 +3,9 @@
 use actix_web::ResponseError;
 
 /// Custom error type for the Actix server.
-#[derive(Debug)]
+#[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
 pub struct CustomError {
-    err: anyhow::Error,
+    err: String,
 }
 
 impl std::fmt::Display for CustomError {
@@ -17,7 +17,9 @@ impl std::fmt::Display for CustomError {
 impl CustomError {
     /// Create from `anyhow::Error`.
     pub fn new(err: anyhow::Error) -> Self {
-        CustomError { err }
+        CustomError {
+            err: err.to_string(),
+        }
     }
 }