test: metadata without serde (#753)

Author: molpopgen

Cargo.toml

@@ -64,3 +64,6 @@ required-features = ["derive"]
 [[example]]
 name = "bincode_metadata"
 required-features = ["derive"]
+
+[[example]]
+name = "manual_metadata_encoding"

examples/manual_metadata_encoding.rs

@@ -0,0 +1,137 @@
+use core::str;
+
+use tskit::metadata::MetadataRoundtrip;
+
+struct MutationMetadata {
+    effect_size: f64,
+    dominance: f64,
+}
+
+impl MetadataRoundtrip for MutationMetadata {
+    fn encode(&self) -> Result<Vec<u8>, tskit::metadata::MetadataError> {
+        let mut rv = vec![];
+        rv.extend_from_slice(&self.effect_size.to_le_bytes());
+        rv.extend_from_slice(&self.dominance.to_le_bytes());
+        Ok(rv)
+    }
+
+    fn decode(md: &[u8]) -> Result<Self, tskit::metadata::MetadataError>
+    where
+        Self: Sized,
+    {
+        let slice: [u8; 8] = md[0..8].try_into().unwrap();
+        let effect_size = f64::from_le_bytes(slice);
+        let slice: [u8; 8] = md[8..].try_into().unwrap();
+        let dominance = f64::from_le_bytes(slice);
+        Ok(Self {
+            effect_size,
+            dominance,
+        })
+    }
+}
+
+impl tskit::metadata::MutationMetadata for MutationMetadata {}
+
+struct IndividualMetadata {
+    name: String,
+    phenotypes: Vec<i32>,
+}
+
+impl MetadataRoundtrip for IndividualMetadata {
+    fn encode(&self) -> Result<Vec<u8>, tskit::metadata::MetadataError> {
+        let mut rv = vec![];
+        rv.extend_from_slice(self.name.len().to_le_bytes().as_slice());
+        rv.extend_from_slice(self.name.as_bytes());
+        rv.extend_from_slice(self.phenotypes.len().to_le_bytes().as_slice());
+        for i in self.phenotypes.iter() {
+            rv.extend_from_slice(i.to_le_bytes().as_slice());
+        }
+        Ok(rv)
+    }
+    fn decode(md: &[u8]) -> Result<Self, tskit::metadata::MetadataError>
+    where
+        Self: Sized,
+    {
+        let size: [u8; std::mem::size_of::<usize>()] =
+            md[0..std::mem::size_of::<usize>()].try_into().unwrap();
+        let size = usize::from_le_bytes(size);
+        let md = &md[std::mem::size_of::<usize>()..];
+        let name = str::from_utf8(&md[0..size]).unwrap().to_string();
+        let md = &md[size..];
+        let md = &md[std::mem::size_of::<usize>()..];
+        let mut phenotypes = vec![];
+        // NOTE: production code would want to validate that
+        // the remaining number of bytes are correct
+        let chunks = md.chunks_exact(std::mem::size_of::<i32>());
+        for c in chunks {
+            // Unwrap b/c the conversion cannot fail b/c the chunk size is correct!
+            let a: [u8; std::mem::size_of::<i32>()] = c.try_into().unwrap();
+            phenotypes.push(i32::from_le_bytes(a));
+        }
+        Ok(Self { name, phenotypes })
+    }
+}
+
+impl tskit::metadata::IndividualMetadata for IndividualMetadata {}
+
+fn main() {
+    let ts = make_treeseq().unwrap();
+    ts.dump("with_json_metadata.trees", 0).unwrap();
+}
+
+fn make_tables() -> anyhow::Result<tskit::TableCollection> {
+    let mut tables = tskit::TableCollection::new(100.0)?;
+    let pop0 = tables.add_population()?;
+    let ind0 = tables.add_individual_with_metadata(
+        0,
+        None,
+        None,
+        &IndividualMetadata {
+            name: "Jerome".to_string(),
+            phenotypes: vec![0, 1, 2, 0],
+        },
+    )?;
+    let node0 = tables.add_node(tskit::NodeFlags::new_sample(), 0.0, pop0, ind0)?;
+    let site0 = tables.add_site(50.0, Some("A".as_bytes()))?;
+    let _ = tables.add_mutation_with_metadata(
+        site0,
+        node0,
+        tskit::MutationId::NULL,
+        1.0,
+        Some("G".as_bytes()),
+        &MutationMetadata {
+            effect_size: -1e-3,
+            dominance: 0.1,
+        },
+    )?;
+    tables.build_index()?;
+    Ok(tables)
+}
+
+fn make_treeseq() -> anyhow::Result<tskit::TreeSequence> {
+    Ok(make_tables()?.tree_sequence(0)?)
+}
+
+#[test]
+fn test_mutation_metadata_roundtrip() {
+    let md = MutationMetadata {
+        effect_size: 0.1,
+        dominance: 0.25,
+    };
+    let encoded = md.encode().unwrap();
+    let decoded = MutationMetadata::decode(&encoded).unwrap();
+    assert_eq!(md.effect_size, decoded.effect_size);
+    assert_eq!(md.dominance, decoded.dominance);
+}
+
+#[test]
+fn test_individual_metadata_roundtrip() {
+    let md = IndividualMetadata {
+        name: "Jerome".to_string(),
+        phenotypes: vec![10, 9],
+    };
+    let encoded = md.encode().unwrap();
+    let decoded = IndividualMetadata::decode(&encoded).unwrap();
+    assert_eq!(md.name, decoded.name);
+    assert_eq!(md.phenotypes, decoded.phenotypes);
+}