annonars 0.42.2

//! Implementation of endpoint `/api/v1/genes/transcripts`.

use actix_web::{
    get,
    web::{self, Data, Json, Path},
    Responder,
};

use crate::common::cli::GenomeRelease;

use super::{error::CustomError, AnnoDb, WebServerData};

/// Code for deserializing the version `spec.yaml` files.
pub mod schema {
    use std::path::Path;

    /// Information about input data.
    #[derive(serde::Deserialize, serde::Serialize, Debug, Clone)]
    pub struct CreatedFrom {
        /// Data source name.
        pub name: String,
        /// Version of the data source.
        pub version: String,
    }

    impl From<CreatedFrom> for super::VersionsCreatedFrom {
        fn from(val: CreatedFrom) -> Self {
            let CreatedFrom { name, version } = val;
            super::VersionsCreatedFrom { name, version }
        }
    }

    /// Version specification.
    #[serde_with::skip_serializing_none]
    #[serde_with::serde_as]
    #[derive(serde::Deserialize, serde::Serialize, Debug, Clone)]
    pub struct VersionSpec {
        /// Identifier of the data.
        #[serde(rename = "dc.identifier")]
        pub identifier: String,
        /// Title of the data.
        #[serde(rename = "dc.title")]
        pub title: String,
        /// Creator of the data.
        #[serde(rename = "dc.creator")]
        pub creator: String,
        /// Contributors of the data.
        #[serde(rename = "dc.contributor")]
        pub contributor: Option<Vec<String>>,
        /// Format of the data.
        #[serde(rename = "dc.format")]
        pub format: String,
        /// Date of the data.
        #[serde(rename = "dc.date")]
        pub date: String,
        /// Version of the data.
        #[serde(rename = "x-version")]
        pub version: String,
        /// Optional genome release.
        #[serde(rename = "x-genome-release")]
        pub genome_release: Option<String>,
        /// Data description.
        #[serde(rename = "dc.description")]
        pub description: String,
        /// Data source.
        #[serde(rename = "dc.source")]
        pub source: Vec<String>,
        /// Created from information.
        #[serde(rename = "x-created-from")]
        pub created_from: Vec<CreatedFrom>,
    }

    impl VersionSpec {
        /// Read a `VersionSpec` from a YAML file.
        pub fn from_path<P>(p: P) -> Result<Self, anyhow::Error>
        where
            P: AsRef<Path>,
        {
            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)
                .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 From<VersionSpec> for super::VersionsVersionSpec {
        fn from(val: VersionSpec) -> Self {
            let VersionSpec {
                identifier,
                title,
                creator,
                contributor,
                format,
                date,
                version,
                genome_release,
                description,
                source,
                created_from,
            } = val;
            super::VersionsVersionSpec {
                identifier,
                title,
                creator,
                contributor: contributor.unwrap_or_default(),
                format,
                date,
                version,
                genome_release,
                description,
                source,
                created_from: created_from.into_iter().map(Into::into).collect(),
            }
        }
    }
}

/// Query parameters for `handle()`.
#[derive(
    Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::IntoParams, utoipa::ToSchema,
)]
pub struct VersionsInfoQuery {}

/// Source name and version.
#[derive(Debug, Clone, PartialEq, Eq, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
pub struct VersionsCreatedFrom {
    /// The name of the data source.
    pub name: String,
    /// The version of the data source.
    pub version: String,
}

/// Version specification.
#[derive(Debug, Clone, PartialEq, Eq, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
pub struct VersionsVersionSpec {
    /// Identifier of the data.
    pub identifier: String,
    /// Title of the data.
    pub title: String,
    /// Creator of the data.
    pub creator: String,
    /// Contributors of the data.
    pub contributor: Vec<String>,
    /// Format of the data.
    pub format: String,
    /// Date of the data.
    pub date: String,
    /// Version of the data.
    pub version: String,
    /// Optional genome release.
    pub genome_release: Option<String>,
    /// Data description.
    pub description: String,
    /// Data source.
    pub source: Vec<String>,
    /// Created from information.
    pub created_from: Vec<VersionsCreatedFrom>,
}

/// Version information for one database.
#[derive(Debug, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
#[serde(rename_all = "snake_case")]
pub struct VersionsAnnotationInfo {
    /// Database name.
    pub database: AnnoDb,
    /// Version information of the database.
    pub version_spec: Option<VersionsVersionSpec>,
}

/// Version information for databases in a given release.
#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
pub struct VersionsPerRelease {
    /// The genome release.
    pub release: GenomeRelease,
    /// Version information of annotation databases.
    #[serde(skip_serializing_if = "Vec::is_empty")]
    pub version_infos: Vec<VersionsAnnotationInfo>,
}

/// Response for `handle()`.
#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, utoipa::ToSchema)]
pub struct VersionsInfoResponse {
    /// Version information of the genes.
    #[serde(skip_serializing_if = "Option::is_none")]
    pub genes: Option<VersionsVersionSpec>,
    /// Version information of annotation databases per release.
    #[serde(skip_serializing_if = "Vec::is_empty")]
    pub seqvars: Vec<VersionsPerRelease>,
}

/// Query for annotations for one variant.
#[utoipa::path(
    get,
    operation_id = "versionsInfo",
    params(VersionsInfoQuery),
    responses(
        (status = 200, description = "Version information.", body = VersionsInfoResponse),
        (status = 500, description = "Internal server error.", body = CustomError)
    )
)]
#[get("/api/v1/versionsInfo")]
async fn handle(
    data: Data<WebServerData>,
    _path: Path<()>,
    _query: web::Query<VersionsInfoQuery>,
) -> actix_web::Result<impl Responder, CustomError> {
    let mut seqvars = Vec::new();
    for (release, anno_dbs) in data.as_ref().annos.iter() {
        let mut version_infos = Vec::new();
        for (anno_db, with_version) in anno_dbs {
            if let Some(with_version) = with_version.as_ref() {
                version_infos.push(VersionsAnnotationInfo {
                    database: anno_db,
                    version_spec: with_version.version_spec.clone().map(Into::into),
                });
            }
        }
        seqvars.push(VersionsPerRelease {
            release,
            version_infos,
        });
    }

    let response = VersionsInfoResponse {
        genes: data
            .as_ref()
            .genes
            .as_ref()
            .and_then(|genes| genes.version_spec.clone().map(Into::into)),
        seqvars,
    };

    Ok(Json(response))
}

#[cfg(test)]
pub mod test {
    #[rstest::rstest]
    #[case("alphamissense-grch37-1+0.33.0")]
    #[case("alphamissense-grch38-1+0.33.0")]
    #[case("functional-grch37-105.20201022+0.33.0")]
    #[case("functional-grch38-110+0.33.0")]
    #[case("genes-3.1+4.0+4.5+20230606+10.1+20240105+0.33.0")]
    #[case("gnomad-mtdna-grch37-3.1+0.33.0")]
    #[case("gnomad-mtdna-grch38-3.1+0.33.0")]
    #[case("helixmtdb-grch37-20200327+0.33.0")]
    #[case("helixmtdb-grch38-20200327+0.33.0")]
    fn test_deserialize_spec_yaml(#[case] name: &str) -> Result<(), anyhow::Error> {
        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)?;
        insta::assert_yaml_snapshot!(&spec);

        let proto_spec: super::VersionsVersionSpec = spec.into();
        insta::assert_yaml_snapshot!(&proto_spec);

        Ok(())
    }
}