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#[cfg(feature = "derive")]
#[test]
fn book_mutation_metadata() {
use tskit::metadata::MetadataRoundtrip;
use tskit::StreamingIterator;
// ANCHOR: metadata_derive
#[derive(serde::Serialize, serde::Deserialize, tskit::metadata::MutationMetadata)]
#[serializer("serde_json")]
struct MutationMetadata {
effect_size: f64,
dominance: f64,
}
// ANCHOR_END: metadata_derive
// ANCHOR: add_mutation_table_row_with_metadata
let mut tables = tskit::TableCollection::new(50.0).unwrap();
let md = MutationMetadata {
effect_size: 1e-3,
dominance: 1.0,
};
let mut_id_0 = tables
.add_mutation_with_metadata(
0, // site id
0, // node id
-1, // mutation parent id
0.0, // time
None, // derived state is Option<&[u8]>
&md, // metadata for this row
)
.unwrap();
// ANCHOR_END: add_mutation_table_row_with_metadata
// ANCHOR: add_mutation_table_row_without_metadata
let mut_id_1 = tables
.add_mutation(
0, // site id
0, // node id
-1, // mutation parent id
0.0, // time
None, // derived state is Option<&[u8]>
)
.unwrap();
// ANCHOR_END: add_mutation_table_row_without_metadata
// ANCHOR: validate_metadata_row_contents
assert_eq!(
tables
.mutations_iter()
.filter(|m| m.metadata.is_some())
.count(),
1
);
assert_eq!(
tables
.mutations_iter()
.filter(|m| m.metadata.is_none())
.count(),
1
);
// ANCHOR_END: validate_metadata_row_contents
// ANCHOR: metadata_retrieval
let fetched_md = match tables.mutations().metadata::<MutationMetadata>(mut_id_0) {
Some(Ok(m)) => m,
Some(Err(e)) => panic!("metadata decoding failed: {:?}", e),
None => panic!(
"hmmm...row {} should have been a valid row with metadata...",
mut_id_0
),
};
assert_eq!(md.effect_size, fetched_md.effect_size);
assert_eq!(md.dominance, fetched_md.dominance);
// ANCHOR_END: metadata_retrieval
// ANCHOR: metadata_retrieval_none
// There is no metadata at row 1, so
// you get None back
assert!(tables
.mutations()
.metadata::<MutationMetadata>(mut_id_1)
.is_none());
// There is also no metadata at row 2,
// because that row does not exist, so
// you get None back
assert!(tables.mutations().metadata::<MutationMetadata>(2).is_none());
// ANCHOR_END: metadata_retrieval_none
// ANCHOR: metadata_bulk_decode_lending_iter
let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
let mut decoded_md = vec![];
while let Some(row_view) = mutation_row_lending_iterator.next() {
match row_view.metadata {
Some(slice) => decoded_md.push(Some(MutationMetadata::decode(slice).unwrap())),
None => decoded_md.push(None),
}
}
// ANCHOR_END: metadata_bulk_decode_lending_iter
// ANCHOR: metadata_bulk_decode_lending_iter_with_filter
let mut mutation_row_lending_iterator = tables.mutations().lending_iter();
let mut decoded_md = vec![];
while let Some(row_view) = mutation_row_lending_iterator
.next()
.filter(|rv| rv.metadata.is_some())
{
decoded_md.push((
row_view.id,
// The unwrap will never panic because of our filter
MutationMetadata::decode(row_view.metadata.unwrap()).unwrap(),
));
}
// ANCHOR_END: metadata_bulk_decode_lending_iter_with_filter
}