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Merged
merged 1 commit into from
Dec 4, 2022
Merged

Generic fn for ragged column access #423

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127 changes: 4 additions & 123 deletions src/_macros.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -27,130 +27,12 @@ macro_rules! panic_on_tskit_error {
};
}

macro_rules! unsafe_tsk_ragged_column_access {
($i: expr, $lo: expr, $hi: expr, $owner: expr, $array: ident, $offset_array: ident, $offset_array_len: ident, $output_id_type: ty) => {{
let i = $crate::SizeType::try_from($i).ok()?;
if $i < $lo || i >= $hi {
None
} else if $owner.$offset_array_len == 0 {
None
} else {
debug_assert!(!$owner.$array.is_null());
if $owner.$array.is_null() {
return None;
}
let offset = i.as_usize() as isize;
// SAFETY: we have checked bounds and ensured not null
let start = unsafe { *$owner.$offset_array.offset(offset) };
let stop = if i < $hi {
unsafe { *$owner.$offset_array.offset((offset + 1) as isize) }
} else {
$owner.$offset_array_len as tsk_size_t
};
if start == stop {
None
} else {
Some(unsafe {
std::slice::from_raw_parts(
$owner.$array.offset(start as isize) as *const $output_id_type,
stop as usize - start as usize,
)
})
}
}
}};
}

// Allow this to be unused for default features
// to pass clippy checks
#[allow(unused_macros)]
macro_rules! unsafe_tsk_ragged_char_column_access {
($i: expr, $lo: expr, $hi: expr, $owner: expr, $array: ident, $offset_array: ident, $offset_array_len: ident) => {{
let i = $crate::SizeType::try_from($i).ok()?;
if $i < $lo || i >= $hi {
None
} else if $owner.$offset_array_len == 0 {
None
} else {
assert!(!$owner.$array.is_null());
assert!(!$owner.$offset_array.is_null());
let start = unsafe { *$owner.$offset_array.offset($i as isize) };
let stop = if i < $hi {
unsafe { *$owner.$offset_array.offset(($i + 1) as isize) }
} else {
$owner.$offset_array_len as tsk_size_t
};
if start == stop {
None
} else {
let mut buffer = String::new();
for i in start..stop {
buffer.push(unsafe { *$owner.$array.offset(i as isize) as u8 as char });
}
Some(buffer)
}
}
}};
}

#[cfg(feature = "provenance")]
macro_rules! unsafe_tsk_ragged_char_column_access_to_slice_u8 {
($i: expr, $lo: expr, $hi: expr, $owner: expr, $array: ident, $offset_array: ident, $offset_array_len: ident) => {{
let i = match $crate::SizeType::try_from($i).ok() {
Some(j) => j,
None => $crate::SizeType::from(u64::MAX),
};
if $i < $lo || i >= $hi {
None
} else if $owner.$offset_array_len == 0 {
None
} else {
assert!(!$owner.$array.is_null());
assert!(!$owner.$offset_array.is_null());
let offset = i.as_usize() as isize;
let start = unsafe { *$owner.$offset_array.offset(offset) };
let stop = if i < $hi {
unsafe { *$owner.$offset_array.offset((offset + 1) as isize) }
} else {
$owner.$offset_array_len as tsk_size_t
};
if start == stop {
None
} else {
let ptr = unsafe { $owner.$array.offset(start as isize) as *const u8 };
let len = (stop - start) as usize;
let slice = unsafe { std::slice::from_raw_parts(ptr, len) };
Some(slice)
}
}
}};
}

macro_rules! metadata_to_vector {
($outer: ident, $table: expr, $row: expr) => {
$crate::metadata::char_column_to_slice(
$outer,
$table.metadata,
$table.metadata_offset,
$row,
$table.num_rows,
$table.metadata_length,
)
};
}

macro_rules! decode_metadata_row {
($T: ty, $buffer: expr) => {
<$T as $crate::metadata::MetadataRoundtrip>::decode($buffer)
};
}

macro_rules! table_row_decode_metadata {
($owner: ident, $table: ident, $pos: ident) => {
metadata_to_vector!($owner, $table, $pos)
};
}

macro_rules! process_state_input {
($state: expr) => {
match $state {
Expand Down Expand Up @@ -1093,14 +975,13 @@ macro_rules! build_owned_table_type {
}

macro_rules! raw_metadata_getter_for_tables {
($idtype: ident) => {
($idtype: ty) => {
fn raw_metadata(&self, row: $idtype) -> Option<&[u8]> {
$crate::metadata::char_column_to_slice(
self,
$crate::sys::tsk_ragged_column_access::<'_, u8, $idtype, _, _>(
row.into(),
self.as_ref().metadata,
self.num_rows(),
self.as_ref().metadata_offset,
row.into(),
self.num_rows().into(),
self.as_ref().metadata_length,
)
}
Expand Down
6 changes: 2 additions & 4 deletions src/edge_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,13 @@ impl PartialEq for EdgeTableRow {
}

fn make_edge_table_row(table: &EdgeTable, pos: tsk_id_t) -> Option<EdgeTableRow> {
let table_ref = table.as_ref();
Some(EdgeTableRow {
id: pos.into(),
left: table.left(pos)?,
right: table.right(pos)?,
parent: table.parent(pos)?,
child: table.child(pos)?,
metadata: table_row_decode_metadata!(table, table_ref, pos).map(|m| m.to_vec()),
metadata: table.raw_metadata(pos.into()).map(|m| m.to_vec()),
})
}

Expand Down Expand Up @@ -238,8 +237,7 @@ impl EdgeTable {
&self,
row: EdgeId,
) -> Option<Result<T, TskitError>> {
let table_ref = self.as_ref();
let buffer = metadata_to_vector!(self, table_ref, row.into())?;
let buffer = self.raw_metadata(row)?;
Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
}

Expand Down
30 changes: 11 additions & 19 deletions src/individual_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use crate::sys;
use crate::IndividualFlags;
use crate::IndividualId;
use crate::Location;
use crate::{tsk_id_t, tsk_size_t, TskitError};
use crate::{tsk_id_t, TskitError};
use ll_bindings::{tsk_individual_table_free, tsk_individual_table_init};

/// Row of a [`IndividualTable`]
Expand Down Expand Up @@ -109,13 +109,12 @@ pub struct IndividualTable {
}

fn make_individual_table_row(table: &IndividualTable, pos: tsk_id_t) -> Option<IndividualTableRow> {
let table_ref = table.as_ref();
Some(IndividualTableRow {
id: pos.into(),
flags: table.flags(pos)?,
location: table.location(pos).map(|s| s.to_vec()),
parents: table.parents(pos).map(|s| s.to_vec()),
metadata: table_row_decode_metadata!(table, table_ref, pos).map(|m| m.to_vec()),
metadata: table.raw_metadata(pos.into()).map(|m| m.to_vec()),
})
}

Expand Down Expand Up @@ -186,15 +185,12 @@ impl IndividualTable {
/// * `Some(location)` if `row` is valid.
/// * `None` otherwise.
pub fn location<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<&[Location]> {
unsafe_tsk_ragged_column_access!(
sys::tsk_ragged_column_access(
row.into(),
0,
self.as_ref().location,
self.num_rows(),
self.as_ref(),
location,
location_offset,
location_length,
Location
self.as_ref().location_offset,
self.as_ref().location_length,
)
}

Expand All @@ -205,15 +201,12 @@ impl IndividualTable {
/// * `Some(parents)` if `row` is valid.
/// * `None` otherwise.
pub fn parents<I: Into<IndividualId> + Copy>(&self, row: I) -> Option<&[IndividualId]> {
unsafe_tsk_ragged_column_access!(
sys::tsk_ragged_column_access(
row.into(),
0,
self.as_ref().parents,
self.num_rows(),
self.as_ref(),
parents,
parents_offset,
parents_length,
IndividualId
self.as_ref().parents_offset,
self.as_ref().parents_length,
)
}

Expand Down Expand Up @@ -391,8 +384,7 @@ match tables.individuals().metadata::<MutationMetadata>(0.into())
&self,
row: IndividualId,
) -> Option<Result<T, TskitError>> {
let table_ref = self.as_ref();
let buffer = metadata_to_vector!(self, table_ref, row.into())?;
let buffer = self.raw_metadata(row)?;
Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
}

Expand Down
54 changes: 0 additions & 54 deletions src/metadata.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,6 @@
//! * We have not yet tested importing metadata encoded using `rust`
//! into `Python` via the `tskit` `Python API`.

use crate::bindings::{tsk_id_t, tsk_size_t};
use crate::SizeType;
use thiserror::Error;

Expand Down Expand Up @@ -250,59 +249,6 @@ pub enum MetadataError {
},
}

pub(crate) fn char_column_to_slice<T: Sized>(
_lifetime: &T,
column: *const libc::c_char,
column_offset: *const tsk_size_t,
row: tsk_id_t,
num_rows: tsk_size_t,
column_length: tsk_size_t,
) -> Option<&[u8]> {
let row = match tsk_size_t::try_from(row).ok() {
Some(r) if r < num_rows => r,
_ => return None,
};
if column_length == 0 {
return None;
}
let row_isize = match isize::try_from(row).ok() {
Some(x) => x,
None => return None,
};
debug_assert!(!column.is_null());
debug_assert!(!column_offset.is_null());
if column.is_null() {
return None;
}
if column_offset.is_null() {
return None;
}
// SAFETY: not null and best effort bounds check
let start = unsafe { *column_offset.offset(row_isize) };
let stop = if (row as tsk_size_t) < num_rows {
unsafe { *column_offset.offset(row_isize + 1) }
} else {
column_length
};
if start >= stop {
return None;
}
if column_length == 0 {
return None;
}
let istart = match isize::try_from(start).ok() {
Some(v) => v,
None => return None,
};
let ustop = match usize::try_from(stop).ok() {
Some(v) => v,
None => return None,
};
Some(unsafe {
std::slice::from_raw_parts(column.offset(istart) as *const u8, ustop - istart as usize)
})
}

#[cfg(test)]
mod tests {
use super::*;
Expand Down
6 changes: 2 additions & 4 deletions src/migration_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@ impl PartialEq for MigrationTableRow {
}

fn make_migration_table_row(table: &MigrationTable, pos: tsk_id_t) -> Option<MigrationTableRow> {
let table_ref = table.as_ref();
Some(MigrationTableRow {
id: pos.into(),
left: table.left(pos)?,
Expand All @@ -46,7 +45,7 @@ fn make_migration_table_row(table: &MigrationTable, pos: tsk_id_t) -> Option<Mig
source: table.source(pos)?,
dest: table.dest(pos)?,
time: table.time(pos)?,
metadata: table_row_decode_metadata!(table, table_ref, pos).map(|m| m.to_vec()),
metadata: table.raw_metadata(pos.into()).map(|m| m.to_vec()),
})
}

Expand Down Expand Up @@ -285,8 +284,7 @@ impl MigrationTable {
&self,
row: MigrationId,
) -> Option<Result<T, TskitError>> {
let table_ref = self.as_ref();
let buffer = metadata_to_vector!(self, table_ref, row.into())?;
let buffer = self.raw_metadata(row)?;
Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
}

Expand Down
13 changes: 5 additions & 8 deletions src/mutation_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,6 @@ fn make_mutation_table_row(table: &MutationTable, pos: tsk_id_t) -> Option<Mutat
let index = ll_bindings::tsk_size_t::try_from(pos).ok()?;
match index {
i if i < table.num_rows() => {
let table_ref = table.as_ref();
let derived_state = table.derived_state(pos).map(|s| s.to_vec());
Some(MutationTableRow {
id: pos.into(),
Expand All @@ -46,7 +45,7 @@ fn make_mutation_table_row(table: &MutationTable, pos: tsk_id_t) -> Option<Mutat
parent: table.parent(pos)?,
time: table.time(pos)?,
derived_state,
metadata: table_row_decode_metadata!(table, table_ref, pos).map(|m| m.to_vec()),
metadata: table.raw_metadata(pos.into()).map(|m| m.to_vec()),
})
}
_ => None,
Expand Down Expand Up @@ -245,12 +244,11 @@ 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]> {
metadata::char_column_to_slice(
self,
sys::tsk_ragged_column_access(
row.into(),
self.as_ref().derived_state,
self.num_rows(),
self.as_ref().derived_state_offset,
row.into().into(),
self.as_ref().num_rows,
self.as_ref().derived_state_length,
)
}
Expand All @@ -275,8 +273,7 @@ impl MutationTable {
&self,
row: MutationId,
) -> Option<Result<T, TskitError>> {
let table_ref = self.as_ref();
let buffer = metadata_to_vector!(self, table_ref, row.into())?;
let buffer = self.raw_metadata(row)?;
Some(decode_metadata_row!(T, buffer).map_err(|e| e.into()))
}

Expand Down
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