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Removed all fallible casts (except in tests)

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This commit is contained in:
Josh Mitchell
2020-11-11 18:42:21 +11:00
parent b0875b60a5
commit 58719dad5d
4 changed files with 73 additions and 44 deletions
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34
src/errors.rs
View File

@@ -1,6 +1,7 @@
use crate::c_abi;
use crate::FileMode;
use crate::Frame;
use std::convert::TryInto;
use std::error::Error as StdError;
use std::path::{Path, PathBuf};
@@ -27,6 +28,14 @@ pub enum Error {
/// A path could not be converted to &CStr because it had a null byte
NullInStr(std::ffi::NulError),
CouldNotCheckNAtoms(Box<Error>),
/// Step was out of range for usize on this platform
StepSizeOutOfRange(i32),
/// A numeric cast from `value` failed during `task`
NumericCastFailed {
source: std::num::TryFromIntError,
task: ErrorTask,
value: usize,
},
}
impl Error {
@@ -64,6 +73,7 @@ impl std::error::Error for Error {
match &self {
NullInStr(err) => Some(err),
CouldNotCheckNAtoms(err) => Some(err.as_ref()),
NumericCastFailed { source, .. } => Some(source),
_ => None,
}
}
@@ -105,7 +115,7 @@ impl From<(&Frame, usize)> for Error {
impl std::fmt::Display for Error {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
use Error::*;
match &self {
match self {
CApiError { code, task } => write!(
f,
"Error while {task}: C API returned error code {code}",
@@ -122,10 +132,16 @@ impl std::fmt::Display for Error {
}
InvalidOsStr => write!(f, "Paths must be valid unicode on this platform"),
NullInStr(_err) => write!(f, "Paths cannot include null bytes"),
CouldNotCheckNAtoms(_err) => write!(
CouldNotCheckNAtoms(_err) => {
write!(f, "Failed to read number of atoms in trajectory file")
}
StepSizeOutOfRange(n) => write!(f, "Step {} does not fit in usize on this platform", n),
NumericCastFailed { value, task, .. } => write!(
f,
"Failed to read number of atoms in trajectory file"
)
"Numeric cast from {value} failed while {task}",
value = value,
task = task
),
}
}
}
@@ -200,9 +216,13 @@ impl ErrorCode {
}
}
impl From<c_abi::xdrfile::BindgenTy1> for ErrorCode {
fn from(code: c_abi::xdrfile::BindgenTy1) -> Self {
match code {
impl<T> From<T> for ErrorCode
where
T: TryInto<c_abi::xdrfile::BindgenTy1>,
<T as TryInto<c_abi::xdrfile::BindgenTy1>>::Error: std::fmt::Debug,
{
fn from(code: T) -> Self {
match code.try_into().expect("C API return code was out of range") {
c_abi::xdrfile::exdrOK => Self::ExdrOk,
c_abi::xdrfile::exdrHEADER => Self::ExdrHeader,
c_abi::xdrfile::exdrSTRING => Self::ExdrString,

9
src/frame.rs
View File

@@ -28,9 +28,7 @@ impl Default for Frame {
impl Frame {
/// Creates an empty frame with a capacity of 0
pub fn new() -> Frame {
Frame {
..Default::default()
}
Default::default()
}
/// Creates a frame with the given capacity
@@ -55,6 +53,11 @@ impl Frame {
/// Length of the frame (number of atoms)
pub fn len(self: &Frame) -> usize {
self.num_atoms()
}
/// The number of atoms in the frame
pub fn num_atoms(self: &Frame) -> usize {
self.coords.len()
}

70
src/lib.rs
View File

@@ -77,6 +77,7 @@ use c_abi::xdrfile_xtc;
use lazy_init::Lazy;
use std::cell::Cell;
use std::convert::{TryFrom, TryInto};
use std::ffi::CString;
use std::io;
use std::path::{Path, PathBuf};
@@ -108,6 +109,14 @@ fn path_to_cstring(path: impl AsRef<Path>) -> Result<CString> {
Ok(CString::new(s)?)
}
fn to_i32(value: usize, task: ErrorTask) -> Result<i32> {
value.try_into().map_err(|e| Error::NumericCastFailed {
source: e,
value,
task,
})
}
/// Convert an error code from a C call to an Error
///
/// `code` should be an integer return code returned from the C API.
@@ -250,7 +259,7 @@ impl Trajectory for XTCTrajectory {
.map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
if num_atoms != frame.coords.len() {
Err((&*frame, num_atoms))?;
}
};
unsafe {
// C lib requires an i32 to be passed, but step is exposed it as u32
@@ -258,19 +267,18 @@ impl Trajectory for XTCTrajectory {
// variable to pass to read_xtc and cast it afterwards to u32
let code = xdrfile_xtc::read_xtc(
self.handle.xdrfile,
num_atoms as i32,
to_i32(num_atoms, ErrorTask::Read)?,
&mut step,
&mut frame.time,
&mut frame.box_vector,
frame.coords.as_mut_ptr(),
&mut self.precision.get(),
) as u32;
frame.step = step as usize;
);
if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err)
} else {
Ok(())
return Err(err);
}
frame.step = usize::try_from(step).map_err(|_| Error::StepSizeOutOfRange(step))?;
Ok(())
}
}
@@ -278,13 +286,13 @@ impl Trajectory for XTCTrajectory {
unsafe {
let code = xdrfile_xtc::write_xtc(
self.handle.xdrfile,
frame.len() as i32,
frame.step as i32,
to_i32(frame.len(), ErrorTask::Write)?,
to_i32(frame.step, ErrorTask::Write)?,
frame.time,
frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
frame.coords[..].as_ptr() as *mut [f32; 3],
1000.0,
) as u32;
);
if let Some(err) = check_code(code, ErrorTask::Write) {
Err(err)
} else {
@@ -295,7 +303,7 @@ impl Trajectory for XTCTrajectory {
fn flush(&mut self) -> Result<()> {
unsafe {
let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
let code = xdr_seek::xdr_flush(self.handle.xdrfile);
if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err)
} else {
@@ -312,15 +320,15 @@ impl Trajectory for XTCTrajectory {
unsafe {
let path = path_to_cstring(&self.handle.path)?;
let path_p = path.into_raw();
let code =
xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32) as u32;
let code = xdrfile_xtc::read_xtc_natoms(path_p, &mut num_atoms as *const i32);
// Reconstitute the CString so it is deallocated correctly
let _ = CString::from_raw(path_p);
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err)
} else {
Ok(num_atoms as usize)
Ok(usize::try_from(num_atoms)
.expect("Number of atoms in file does not fit in usize"))
}
}
})
@@ -391,7 +399,7 @@ impl Trajectory for TRRTrajectory {
// Similar for lambda.
let code = xdrfile_trr::read_trr(
self.handle.xdrfile,
num_atoms as i32,
to_i32(num_atoms, ErrorTask::Read)?,
&mut step,
&mut frame.time,
&mut lambda,
@@ -399,14 +407,12 @@ impl Trajectory for TRRTrajectory {
frame.coords.as_mut_ptr(),
std::ptr::null_mut(),
std::ptr::null_mut(),
) as u32;
frame.step = step as usize;
);
if let Some(err) = check_code(code, ErrorTask::Read) {
Err(err)
} else {
Ok(())
return Err(err);
}
frame.step = usize::try_from(step).map_err(|_| Error::StepSizeOutOfRange(step))?;
Ok(())
}
}
@@ -414,15 +420,15 @@ impl Trajectory for TRRTrajectory {
unsafe {
let code = xdrfile_trr::write_trr(
self.handle.xdrfile,
frame.len() as i32,
frame.step as i32,
to_i32(frame.len(), ErrorTask::Write)?,
to_i32(frame.step, ErrorTask::Write)?,
frame.time,
0.0,
frame.box_vector.as_ptr() as *mut [[f32; 3]; 3],
frame.coords[..].as_ptr() as *mut [f32; 3],
std::ptr::null_mut(),
std::ptr::null_mut(),
) as u32;
);
if let Some(err) = check_code(code, ErrorTask::Write) {
Err(err)
} else {
@@ -433,7 +439,7 @@ impl Trajectory for TRRTrajectory {
fn flush(&mut self) -> Result<()> {
unsafe {
let code = xdr_seek::xdr_flush(self.handle.xdrfile) as u32;
let code = xdr_seek::xdr_flush(self.handle.xdrfile);
if let Some(err) = check_code(code, ErrorTask::Flush) {
Err(err)
} else {
@@ -449,15 +455,15 @@ impl Trajectory for TRRTrajectory {
unsafe {
let path = path_to_cstring(&self.handle.path)?;
let path_p = path.into_raw();
let code =
xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32) as u32;
let code = xdrfile_trr::read_trr_natoms(path_p, &mut num_atoms as *const i32);
// Reconstitute the CString so it is deallocated correctly
let _ = CString::from_raw(path_p);
if let Some(err) = check_code(code, ErrorTask::ReadNumAtoms) {
Err(err)
} else {
Ok(num_atoms as usize)
Ok(usize::try_from(num_atoms)
.expect("Number of atoms in file does not fit in usize"))
}
}
})
@@ -530,7 +536,7 @@ mod tests {
let tempfile = NamedTempFile::new().expect("Could not create temporary file");
let tmp_path = tempfile.path();
let natoms: u32 = 2;
let natoms = 2;
let frame = Frame {
step: 5,
time: 2.0,
@@ -545,7 +551,7 @@ mod tests {
}
f.flush()?;
let mut new_frame = Frame::with_len(natoms as usize);
let mut new_frame = Frame::with_len(natoms);
let mut f = TRRTrajectory::open_read(tmp_path)?;
// let num_atoms = f.get_num_atoms()?;
// assert_eq!(num_atoms, natoms);
@@ -744,7 +750,7 @@ mod tests {
let tempfile = NamedTempFile::new()?;
let tmp_path = tempfile.path();
let natoms: u32 = 2;
let natoms = 2;
let frame = Frame {
step: 5,
time: 2.0,
@@ -755,7 +761,7 @@ mod tests {
f.write(&frame)?;
f.flush()?;
let mut new_frame = Frame::with_len(natoms as usize);
let mut new_frame = Frame::with_len(natoms);
let mut f = XTCTrajectory::open_read(tmp_path)?;
f.read(&mut new_frame)?;

4
tests/integration.rs
View File

@@ -8,7 +8,7 @@ mod integration {
fn test_use_library() -> Result<()> {
let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
let num_atoms = trj.get_num_atoms()?;
let mut frame = Frame::with_len(num_atoms as usize);
let mut frame = Frame::with_len(num_atoms);
trj.read(&mut frame)?;
trj.read(&mut frame)?;
@@ -21,7 +21,7 @@ mod integration {
let trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
let frames: Result<Vec<Rc<Frame>>> = trj.into_iter().collect();
for (idx, frame) in frames?.iter().enumerate() {
assert_eq!(frame.step as usize, idx + 1);
assert_eq!(frame.step, idx + 1);
}
Ok(())
}