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mark internal fns for column access unsafe #712

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Merged
molpopgen merged 1 commit into from
Feb 24, 2025
Merged

mark internal fns for column access unsafe #712

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21 changes: 14 additions & 7 deletions src/_macros.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -68,13 +68,20 @@ macro_rules! handle_metadata_return {
macro_rules! raw_metadata_getter_for_tables {
($idtype: ty) => {
fn raw_metadata<I: Into<$idtype>>(&self, row: I) -> Option<&[u8]> {
$crate::sys::tsk_ragged_column_access::<'_, u8, $idtype, _, _>(
row.into(),
self.as_ref().metadata,
self.num_rows(),
self.as_ref().metadata_offset,
self.as_ref().metadata_length,
)
assert!(
(self.num_rows() == 0 && self.as_ref().metadata_length == 0)
|| (!self.as_ref().metadata.is_null()
&& !self.as_ref().metadata_offset.is_null())
);
unsafe {
$crate::sys::tsk_ragged_column_access::<'_, u8, $idtype, _, _>(
row.into(),
self.as_ref().metadata,
self.num_rows(),
self.as_ref().metadata_offset,
self.as_ref().metadata_length,
)
}
}
};
}
Expand Down
44 changes: 36 additions & 8 deletions src/edge_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,15 @@ impl EdgeTable {
/// * `Some(parent)` if `u` is valid.
/// * `None` otherwise.
pub fn parent<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<NodeId> {
sys::tsk_column_access::<NodeId, _, _, _>(row.into(), self.as_ref().parent, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().parent.is_null());
// SAFETY: either the column is empty or the point is not NULL
unsafe {
sys::tsk_column_access::<NodeId, _, _, _>(
row.into(),
self.as_ref().parent,
self.num_rows(),
)
}
}

/// Return the ``child`` value from row ``row`` of the table.
Expand All @@ -233,7 +241,15 @@ impl EdgeTable {
/// * `Some(child)` if `u` is valid.
/// * `None` otherwise.
pub fn child<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<NodeId> {
sys::tsk_column_access::<NodeId, _, _, _>(row.into(), self.as_ref().child, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().child.is_null());
// SAFETY: either the column is empty or the point is not NULL
unsafe {
sys::tsk_column_access::<NodeId, _, _, _>(
row.into(),
self.as_ref().child,
self.num_rows(),
)
}
}

/// Return the ``left`` value from row ``row`` of the table.
Expand All @@ -243,7 +259,15 @@ impl EdgeTable {
/// * `Some(position)` if `u` is valid.
/// * `None` otherwise.
pub fn left<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<Position> {
sys::tsk_column_access::<Position, _, _, _>(row.into(), self.as_ref().left, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().left.is_null());
// SAFETY: either the column is empty or the point is not NULL
unsafe {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().left,
self.num_rows(),
)
}
}

/// Return the ``right`` value from row ``row`` of the table.
Expand All @@ -253,11 +277,15 @@ impl EdgeTable {
/// * `Some(position)` if `u` is valid.
/// * `None` otherwise.
pub fn right<E: Into<EdgeId> + Copy>(&self, row: E) -> Option<Position> {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().right,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().right.is_null());
// SAFETY: either the column is empty or the point is not NULL
unsafe {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().right,
self.num_rows(),
)
}
}

/// Retrieve decoded metadata for a `row`.
Expand Down
54 changes: 35 additions & 19 deletions src/individual_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -209,11 +209,15 @@ impl IndividualTable {
/// * `Some(flags)` if `row` is valid.
/// * `None` otherwise.
pub fn flags<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<IndividualFlags> {
sys::tsk_column_access::<IndividualFlags, _, _, _>(
row.into(),
self.as_ref().flags,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().flags.is_null());
// SAFETY: either the column is empty or the point is not NULL
unsafe {
sys::tsk_column_access::<IndividualFlags, _, _, _>(
row.into(),
self.as_ref().flags,
self.num_rows(),
)
}
}

/// Return the locations for a given row.
Expand All @@ -223,13 +227,19 @@ impl IndividualTable {
/// * `Some(location)` if `row` is valid.
/// * `None` otherwise.
pub fn location<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<&[Location]> {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().location,
self.num_rows(),
self.as_ref().location_offset,
self.as_ref().location_length,
)
assert!(
(self.num_rows() == 0 && self.as_ref().location_length == 0)
|| (!self.as_ref().location.is_null() && !self.as_ref().location_offset.is_null())
);
unsafe {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().location,
self.num_rows(),
self.as_ref().location_offset,
self.as_ref().location_length,
)
}
}

/// Return the parents for a given row.
Expand All @@ -239,13 +249,19 @@ impl IndividualTable {
/// * `Some(parents)` if `row` is valid.
/// * `None` otherwise.
pub fn parents<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<&[IndividualId]> {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().parents,
self.num_rows(),
self.as_ref().parents_offset,
self.as_ref().parents_length,
)
assert!(
(self.num_rows() == 0 && self.as_ref().parents_length == 0)
|| (!self.as_ref().parents.is_null() && !self.as_ref().location_offset.is_null())
);
unsafe {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().parents,
self.num_rows(),
self.as_ref().parents_offset,
self.as_ref().parents_length,
)
}
}

/// Return the metadata for a given row.
Expand Down
74 changes: 56 additions & 18 deletions src/migration_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -237,7 +237,16 @@ impl MigrationTable {
/// * `Some(position)` if `row` is valid.
/// * `None` otherwise.
pub fn left<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<Position> {
sys::tsk_column_access::<Position, _, _, _>(row.into(), self.as_ref().left, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().time.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().left,
self.num_rows(),
)
}
}

/// Return the right coordinate for a given row.
Expand All @@ -247,11 +256,16 @@ impl MigrationTable {
/// * `Some(positions)` if `row` is valid.
/// * `None` otherwise.
pub fn right<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<Position> {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().right,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().right.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<Position, _, _, _>(
row.into(),
self.as_ref().right,
self.num_rows(),
)
}
}

/// Return the node for a given row.
Expand All @@ -261,7 +275,16 @@ impl MigrationTable {
/// * `Some(node)` if `row` is valid.
/// * `None` otherwise.
pub fn node<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<NodeId> {
sys::tsk_column_access::<NodeId, _, _, _>(row.into(), self.as_ref().node, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().node.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<NodeId, _, _, _>(
row.into(),
self.as_ref().node,
self.num_rows(),
)
}
}

/// Return the source population for a given row.
Expand All @@ -271,11 +294,16 @@ impl MigrationTable {
/// * `Some(population)` if `row` is valid.
/// * `None` otherwise.
pub fn source<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<PopulationId> {
sys::tsk_column_access::<PopulationId, _, _, _>(
row.into(),
self.as_ref().source,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().time.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<PopulationId, _, _, _>(
row.into(),
self.as_ref().source,
self.num_rows(),
)
}
}

/// Return the destination population for a given row.
Expand All @@ -285,11 +313,16 @@ impl MigrationTable {
/// * `Some(population)` if `row` is valid.
/// * `None` otherwise.
pub fn dest<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<PopulationId> {
sys::tsk_column_access::<PopulationId, _, _, _>(
row.into(),
self.as_ref().dest,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().dest.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<PopulationId, _, _, _>(
row.into(),
self.as_ref().dest,
self.num_rows(),
)
}
}

/// Return the time of the migration event for a given row.
Expand All @@ -299,7 +332,12 @@ impl MigrationTable {
/// * `Some(time)` if `row` is valid.
/// * `None` otherwise.
pub fn time<M: Into<MigrationId> + Copy>(&self, row: M) -> Option<Time> {
sys::tsk_column_access::<Time, _, _, _>(row.into(), self.as_ref().time, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().time.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<Time, _, _, _>(row.into(), self.as_ref().time, self.num_rows())
}
}

/// Retrieve decoded metadata for a `row`.
Expand Down
67 changes: 52 additions & 15 deletions src/mutation_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,16 @@ impl MutationTable {
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn site<M: Into<MutationId> + Copy>(&self, row: M) -> Option<SiteId> {
sys::tsk_column_access::<SiteId, _, _, _>(row.into(), self.as_ref().site, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().site.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<SiteId, _, _, _>(
row.into(),
self.as_ref().site,
self.num_rows(),
)
}
}

/// Return the ``node`` value from row ``row`` of the table.
Expand All @@ -243,7 +252,16 @@ impl MutationTable {
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn node<M: Into<MutationId> + Copy>(&self, row: M) -> Option<NodeId> {
sys::tsk_column_access::<NodeId, _, _, _>(row.into(), self.as_ref().node, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().node.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<NodeId, _, _, _>(
row.into(),
self.as_ref().node,
self.num_rows(),
)
}
}

/// Return the ``parent`` value from row ``row`` of the table.
Expand All @@ -253,11 +271,16 @@ impl MutationTable {
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn parent<M: Into<MutationId> + Copy>(&self, row: M) -> Option<MutationId> {
sys::tsk_column_access::<MutationId, _, _, _>(
row.into(),
self.as_ref().parent,
self.num_rows(),
)
assert!(self.num_rows() == 0 || !self.as_ref().parent.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<MutationId, _, _, _>(
row.into(),
self.as_ref().parent,
self.num_rows(),
)
}
}

/// Return the ``time`` value from row ``row`` of the table.
Expand All @@ -267,7 +290,12 @@ impl MutationTable {
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn time<M: Into<MutationId> + Copy>(&self, row: M) -> Option<Time> {
sys::tsk_column_access::<Time, _, _, _>(row.into(), self.as_ref().time, self.num_rows())
assert!(self.num_rows() == 0 || !self.as_ref().time.is_null());
// SAFETY: either the column is empty or the pointer is not null,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_column_access::<Time, _, _, _>(row.into(), self.as_ref().time, self.num_rows())
}
}

/// Get the ``derived_state`` value from row ``row`` of the table.
Expand All @@ -281,13 +309,22 @@ impl MutationTable {
/// Will return [``IndexError``](crate::TskitError::IndexError)
/// if ``row`` is out of range.
pub fn derived_state<M: Into<MutationId>>(&self, row: M) -> Option<&[u8]> {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().derived_state,
self.num_rows(),
self.as_ref().derived_state_offset,
self.as_ref().derived_state_length,
)
assert!(
(self.num_rows() == 0 && self.as_ref().derived_state_length == 0)
|| (!self.as_ref().derived_state.is_null()
&& !self.as_ref().derived_state_offset.is_null())
);
// SAFETY: either both columns are empty or both pointers at not NULL,
// in which case the correct lengths are from the low-level objects
unsafe {
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().derived_state,
self.num_rows(),
self.as_ref().derived_state_offset,
self.as_ref().derived_state_length,
)
}
}

/// Retrieve decoded metadata for a `row`.
Expand Down
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