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Merged
merged 1 commit into from
Jan 26, 2023
Merged

Add type for managing pointers to tskit-c types. #448

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69 changes: 0 additions & 69 deletions src/_macros.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -380,56 +380,6 @@ macro_rules! handle_metadata_return {
};
}

macro_rules! build_owned_tables {
($name: ty, $deref: ident, $lltype: ty, $tsktable: ty) => {
impl $name {
fn new() -> Self {
let table = <$lltype>::new();
Self { table }
}

/// Clear the table.
pub fn clear(&mut self) -> $crate::TskReturnValue {
self.table.clear().map_err(|e| e.into())
}
}

impl Default for $name {
fn default() -> Self {
Self::new()
}
}

impl std::ops::Deref for $name {
type Target = $deref;

fn deref(&self) -> &Self::Target {
// SAFETY: that T* and &T have same layout,
// and Target is repr(transparent).
unsafe { std::mem::transmute(&self.table) }
}
}

impl std::ops::DerefMut for $name {
fn deref_mut(&mut self) -> &mut Self::Target {
// SAFETY: that T* and &T have same layout,
// and Target is repr(transparent).
unsafe { std::mem::transmute(&mut self.table) }
}
}

impl $name {
pub fn as_ptr(&self) -> *const $tsktable {
self.table.as_ptr()
}

pub fn as_mut_ptr(&mut self) -> *mut $tsktable {
self.table.as_mut_ptr()
}
}
};
}

macro_rules! node_table_add_row_details {
($flags: ident,
$time: ident,
Expand Down Expand Up @@ -929,25 +879,6 @@ macro_rules! provenance_table_add_row {
};
}

macro_rules! build_owned_table_type {
($(#[$attr:meta])* => $name: ident,
$deref_type: ident,
$lltype: ty,
$tsktable: ty) => {
$(#[$attr])*
pub struct $name {
table: $lltype
}

build_owned_tables!(
$name,
$deref_type,
$lltype,
$tsktable
);
};
}

macro_rules! raw_metadata_getter_for_tables {
($idtype: ty) => {
fn raw_metadata<I: Into<$idtype>>(&self, row: I) -> Option<&[u8]> {
Expand Down
139 changes: 76 additions & 63 deletions src/edge_table.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -137,29 +137,86 @@ impl<'a> streaming_iterator::StreamingIterator for EdgeTableRowView<'a> {
}
}

/// An immutable view of an edge table.
/// An edge table.
///
/// These are not created directly but are accessed
/// by types implementing [`std::ops::Deref`] to
/// [`crate::table_views::TableViews`]
/// # Examples
///
/// ## Standalone tables
///
/// ```
/// use tskit::EdgeTable;
///
/// let mut edges = EdgeTable::default();
/// let rowid = edges.add_row(1., 2., 0, 1).unwrap();
/// assert_eq!(rowid, 0);
/// assert_eq!(edges.num_rows(), 1);
///
/// edges.clear().unwrap();
/// assert_eq!(edges.num_rows(), 0);
/// ```
///
/// An example with metadata.
/// This requires the cargo feature `"derive"` for `tskit`.
///
/// ```
/// # #[cfg(any(feature="doc", feature="derive"))] {
/// use tskit::EdgeTable;
///
/// #[derive(serde::Serialize,
/// serde::Deserialize,
/// tskit::metadata::EdgeMetadata)]
/// #[serializer("serde_json")]
/// struct EdgeMetadata {
/// value: i32,
/// }
///
/// let metadata = EdgeMetadata{value: 42};
///
/// let mut edges = EdgeTable::default();
///
/// let rowid = edges.add_row_with_metadata(0., 1., 5, 10, &metadata).unwrap();
/// assert_eq!(rowid, 0);
///
/// match edges.metadata::<EdgeMetadata>(rowid) {
/// // rowid is in range, decoding succeeded
/// Some(Ok(decoded)) => assert_eq!(decoded.value, 42),
/// // rowid is in range, decoding failed
/// Some(Err(e)) => panic!("error decoding metadata: {:?}", e),
/// None => panic!("row id out of range")
/// }
/// # }
/// ```
#[repr(transparent)]
#[derive(Debug)]
pub struct EdgeTable {
table_: sys::LLEdgeTableRef,
table_: sys::LLEdgeTable,
}

impl EdgeTable {
pub(crate) fn as_ptr(&self) -> *const ll_bindings::tsk_edge_table_t {
self.table_.as_ptr()
}

pub(crate) fn as_mut_ptr(&mut self) -> *mut ll_bindings::tsk_edge_table_t {
self.table_.as_mut_ptr()
}

pub(crate) fn new_from_table(
edges: *mut ll_bindings::tsk_edge_table_t,
) -> Result<Self, TskitError> {
let table_ = sys::LLEdgeTableRef::new_from_table(edges)?;
let table_ = sys::LLEdgeTable::new_non_owning(edges)?;
Ok(EdgeTable { table_ })
}

pub(crate) fn as_ref(&self) -> &ll_bindings::tsk_edge_table_t {
self.table_.as_ref()
}

pub fn new() -> Result<Self, TskitError> {
let table_ = sys::LLEdgeTable::new_owning(0)?;
Ok(Self { table_ })
}

/// Return the number of rows
pub fn num_rows(&self) -> crate::SizeType {
self.as_ref().num_rows.into()
Expand Down Expand Up @@ -283,6 +340,13 @@ impl EdgeTable {
Some(view)
}

pub fn clear(&mut self) -> Result<(), TskitError> {
self.table_.clear().map_err(|e| e.into())
}

edge_table_add_row!(=> add_row, self, self.as_mut_ptr());
edge_table_add_row_with_metadata!(=> add_row_with_metadata, self, self.as_mut_ptr());

build_table_column_slice_getter!(
/// Get the left column as a slice
=> left, left_slice, Position);
Expand All @@ -309,61 +373,10 @@ impl EdgeTable {
=> child, child_slice_raw, ll_bindings::tsk_id_t);
}

build_owned_table_type!(
/// A standalone edge table that owns its data.
///
/// # Examples
///
/// ```
/// use tskit::OwningEdgeTable;
///
/// let mut edges = OwningEdgeTable::default();
/// let rowid = edges.add_row(1., 2., 0, 1).unwrap();
/// assert_eq!(rowid, 0);
/// assert_eq!(edges.num_rows(), 1);
///
/// edges.clear().unwrap();
/// assert_eq!(edges.num_rows(), 0);
/// ```
///
/// An example with metadata.
/// This requires the cargo feature `"derive"` for `tskit`.
///
/// ```
/// # #[cfg(any(feature="doc", feature="derive"))] {
/// use tskit::OwningEdgeTable;
///
/// #[derive(serde::Serialize,
/// serde::Deserialize,
/// tskit::metadata::EdgeMetadata)]
/// #[serializer("serde_json")]
/// struct EdgeMetadata {
/// value: i32,
/// }
///
/// let metadata = EdgeMetadata{value: 42};
///
/// let mut edges = OwningEdgeTable::default();
///
/// let rowid = edges.add_row_with_metadata(0., 1., 5, 10, &metadata).unwrap();
/// assert_eq!(rowid, 0);
///
/// match edges.metadata::<EdgeMetadata>(rowid) {
/// // rowid is in range, decoding succeeded
/// Some(Ok(decoded)) => assert_eq!(decoded.value, 42),
/// // rowid is in range, decoding failed
/// Some(Err(e)) => panic!("error decoding metadata: {:?}", e),
/// None => panic!("row id out of range")
/// }
/// # }
/// ```
=> OwningEdgeTable,
EdgeTable,
crate::sys::LLOwningEdgeTable,
crate::bindings::tsk_edge_table_t
);

impl OwningEdgeTable {
edge_table_add_row!(=> add_row, self, self.as_mut_ptr());
edge_table_add_row_with_metadata!(=> add_row_with_metadata, self, self.as_mut_ptr());
impl Default for EdgeTable {
fn default() -> Self {
Self::new().unwrap()
}
}

pub type OwningEdgeTable = EdgeTable;
5 changes: 4 additions & 1 deletion src/error.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,11 @@ pub enum TskitError {
impl From<crate::sys::Error> for TskitError {
fn from(error: sys::Error) -> Self {
match error {
sys::Error::Message(msg) => TskitError::LibraryError(msg),
sys::Error::Code(code) => TskitError::ErrorCode { code },
sys::Error::Message(msg) => TskitError::LibraryError(msg),
sys::Error::NullPointer => {
TskitError::LibraryError("null pointer encountered".to_owned())
}
}
}
}
Expand Down
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