mocked hgvs client

src/hgvs/error.rs

@@ -9,6 +9,10 @@ pub enum HGVSError {
         "Variant Validator did not accept submitted HGVS {hgvs}. Validation warnings: {problems:?}"
     )]
     InvalidHgvs { hgvs: String, problems: Vec<String> },
+    #[error(
+        "Could not find corresponding HgvsVariant object in the MockHGVSClient for unvalidated hgvs {unvalidated_hgvs}."
+    )]
+    MockClient { unvalidated_hgvs: String },
     #[error("Hgvs string {hgvs} not accepted due to format problem: {problem}.")]
     HgvsFormatNotAccepted { hgvs: String, problem: String },
     #[error(

src/hgvs/mock_hgvs_client.rs

@@ -0,0 +1,175 @@
+use crate::hgvs::{HGVSData, HGVSError, HgvsVariant};
+use std::collections::HashMap;
+
+/// A Mock client for the HGVS interface.
+///
+/// This struct is intended for use in unit testing. Instead of making live HTTP
+/// requests to the VariantValidator API, it serves data from an internal `HashMap`.
+/// This allows for deterministic testing of components that rely on `HGVSData`.
+#[derive(Debug)]
+pub struct MockHGVSClient {
+    hgvs_variants: HashMap<String, HgvsVariant>,
+}
+
+impl MockHGVSClient {
+    pub fn new(hgvs_variants: HashMap<String, HgvsVariant>) -> MockHGVSClient {
+        MockHGVSClient { hgvs_variants }
+    }
+}
+
+impl HGVSData for MockHGVSClient {
+    fn request_and_validate_hgvs(&self, unvalidated_hgvs: &str) -> Result<HgvsVariant, HGVSError> {
+        self.hgvs_variants
+            .get(unvalidated_hgvs)
+            .cloned()
+            .ok_or(HGVSError::MockClient {
+                unvalidated_hgvs: unvalidated_hgvs.to_string(),
+            })
+    }
+}
+
+impl Default for MockHGVSClient {
+    fn default() -> Self {
+        let mut hgvs_variants = HashMap::new();
+
+        //coding autosomal variant
+        hgvs_variants.insert(
+            "NM_001173464.1:c.2860C>T".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chr12",
+                39332405,
+                "G",
+                "A",
+                "KIF21A",
+                "HGNC:19349",
+                "NM_001173464.1",
+                "c.2860C>T",
+                "NM_001173464.1:c.2860C>T",
+                "NC_000012.12:g.39332405G>A",
+                Some("NP_001166935.1:p.(Arg954Trp)"),
+            ),
+        );
+
+        //another coding autosomal variant
+        hgvs_variants.insert(
+            "NM_001173464.1:c.2861G>A".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chr12",
+                39332404,
+                "C",
+                "T",
+                "KIF21A",
+                "HGNC:19349",
+                "NM_001173464.1",
+                "c.2861G>A",
+                "NM_001173464.1:c.2861G>A",
+                "NC_000012.12:g.39332404C>T",
+                Some("NP_001166935.1:p.(Arg954Gln)"),
+            ),
+        );
+
+        //coding x variant
+        hgvs_variants.insert(
+            "NM_000132.4:c.3637A>T".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chrX",
+                154930153,
+                "T",
+                "A",
+                "F8",
+                "HGNC:3546",
+                "NM_000132.4",
+                "c.3637A>T",
+                "NM_000132.4:c.3637A>T",
+                "NC_000023.11:g.154930153T>A",
+                Some("NP_000123.1:p.(Ile1213Phe)"),
+            ),
+        );
+
+        //non-coding variant
+        hgvs_variants.insert(
+            "NR_002196.1:n.601G>T".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chr11",
+                1997235,
+                "C",
+                "A",
+                "H19",
+                "HGNC:4713",
+                "NR_002196.1",
+                "n.601G>T",
+                "NR_002196.1:n.601G>T",
+                "NC_000011.10:g.1997235C>A",
+                None::<&str>,
+            ),
+        );
+
+        //another non-coding variant
+        hgvs_variants.insert(
+            "NR_002196.1:n.602C>T".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chr11",
+                1997234,
+                "G",
+                "A",
+                "H19",
+                "HGNC:4713",
+                "NR_002196.1",
+                "n.601C>T",
+                "NR_002196.1:n.602C>T",
+                "NC_000011.10:g.1997234G>A",
+                None::<&str>,
+            ),
+        );
+
+        //mitochondrial variant
+        hgvs_variants.insert(
+            "NC_012920.1:m.616T>C".to_string(),
+            HgvsVariant::new(
+                "hg38",
+                "chrM",
+                616,
+                "T",
+                "C",
+                "",
+                "",
+                "NC_012920.1",
+                "m.616T>C",
+                "NC_012920.1:m.616T>C",
+                "NC_012920.1:m.616T>C",
+                None::<&str>,
+            ),
+        );
+
+        MockHGVSClient::new(hgvs_variants)
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use rstest::rstest;
+
+    #[rstest]
+    fn test_validate_hgvs_success() {
+        let mock = MockHGVSClient::default();
+
+        let unvalidated_hgvs = "NM_001173464.1:c.2860C>T";
+
+        let hgvs_variant = mock.request_and_validate_hgvs(unvalidated_hgvs).unwrap();
+        assert_eq!(hgvs_variant.transcript_hgvs(), unvalidated_hgvs);
+    }
+
+    #[rstest]
+    fn test_request_gene_data_not_found() {
+        let mock = MockHGVSClient::default();
+
+        let invalid_hgvs = "INVALID_HGVS";
+        assert!(mock.request_and_validate_hgvs(invalid_hgvs).is_err());
+    }
+}

src/hgvs/mod.rs

@@ -20,6 +20,10 @@
 //!
 //! A cached implementation of the HGVSData trait. The HgvsVariant objects will be cached and can thereafter be accessed without an API call.
 //!
+//! # [`MockHGVSClient`]
+//!
+//! A mocked implementation of the HGVSData trait for tests and CI.
+//!
 //! # [`AlleleCount`]
 //!
 //! An enum with two variants Single and Double. This is used for create a VariantInterpretation from a HgvsVariant object.
@@ -81,6 +85,7 @@ pub use enums::ChromosomalSex;
 pub use error::HGVSError;
 pub use hgvs_client::HGVSClient;
 pub use hgvs_variant::HgvsVariant;
+pub use mock_hgvs_client::MockHGVSClient;
 pub use traits::HGVSData;
 
 mod cached_hgvs_client;
@@ -89,5 +94,6 @@ mod error;
 mod hgvs_client;
 mod hgvs_variant;
 mod json_schema;
+mod mock_hgvs_client;
 mod traits;
 mod utils;