individual metadata

Author: molpopgen

python/test_bincode_metadata.py

@@ -8,14 +8,14 @@ def setup_ts_without_schema():
     return ts
 
 
-# def test_individual_metadata():
-#     # NOTE: the assertions here rely on knowing
-#     # what examples/json_metadata.rs put into the
-#     # metadata!
-#     ts = setup_ts_without_schema()
-#     md = ts.individual(0).metadata
-#     assert md["name"] == "Jerome"
-#     assert md["phenotypes"] == [0, 1, 2, 0]
+def test_individual_metadata():
+    # NOTE: the assertions here rely on knowing
+    # what examples/json_metadata.rs put into the
+    # metadata!
+    ts = setup_ts_without_schema()
+    md = tskit_glue.decode_bincode_individual_metadata(ts.individual(0).metadata)
+    assert md.name() == "Jerome"
+    assert md.phenotypes() == [0, 1, 2, 0]
 
 
 def test_mutation_metadata():

python/tskit_glue/src/lib.rs

@@ -1,4 +1,5 @@
 use pyo3::prelude::*;
+use serde::Deserialize;
 
 #[derive(serde::Serialize, serde::Deserialize)]
 #[pyclass]
@@ -24,6 +25,16 @@ struct IndividualMetadata {
     phenotypes: Vec<i32>,
 }
 
+#[pymethods]
+impl IndividualMetadata {
+    fn name(&self) -> String {
+        self.name.clone()
+    }
+    fn phenotypes(&self) -> Vec<i32> {
+        self.phenotypes.clone()
+    }
+}
+
 /// Decode mutation metadata generated in rust via the `bincode` crate.
 #[pyfunction]
 fn decode_bincode_mutation_metadata(md: Vec<u8>) -> MutationMetadata {
@@ -33,9 +44,19 @@ fn decode_bincode_mutation_metadata(md: Vec<u8>) -> MutationMetadata {
     md
 }
 
+/// Decode mutation metadata generated in rust via the `bincode` crate.
+#[pyfunction]
+fn decode_bincode_individual_metadata(md: Vec<u8>) -> IndividualMetadata {
+    // NOTE: the unwrap here is not correct for production code
+    // and a failure will crash the Python interpreter!
+    let md = bincode::deserialize_from(md.as_slice()).unwrap();
+    md
+}
+
 /// A Python module implemented in Rust.
 #[pymodule]
 fn tskit_glue(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(decode_bincode_mutation_metadata, m)?)?;
+    m.add_function(wrap_pyfunction!(decode_bincode_individual_metadata, m)?)?;
     Ok(())
 }