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Removed unwrap()s, refactored iterator, removed memleak

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This commit is contained in:
Josh Mitchell
2020-11-08 17:23:08 +11:00
parent 05b309e4bd
commit f9cf479baf
8 changed files with 223 additions and 197 deletions
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158
src/lib.rs
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@@ -9,29 +9,27 @@
//! ```rust
//! use xdrfile::*;
//!
//! // get a handle to the file
//! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
//! fn main() -> Result<()> {
//! // get a handle to the file
//! let mut trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
//!
//! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms().unwrap();
//! // find number of atoms in the file
//! let num_atoms = trj.get_num_atoms()?;
//!
//! // a frame object is used to get to read or write from a trajectory
//! // without instantiating data arrays for every step
//! let mut frame = Frame::with_capacity(num_atoms);
//! // a frame object is used to get to read or write from a trajectory
//! // without instantiating data arrays for every step
//! let mut frame = Frame::with_capacity(num_atoms);
//!
//! // read the first frame of the trajectory
//! let result = trj.read(&mut frame);
//! match result {
//! Ok(_) => {
//! assert_eq!(frame.step, 1);
//! assert_eq!(frame.num_atoms, num_atoms);
//! // read the first frame of the trajectory
//! trj.read(&mut frame)?;
//!
//! let first_atom_coords = frame.coords[0];
//! assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
//! }
//! Err(msg) => {
//! panic!("Something went wrong: {}", msg);
//! }
//! assert_eq!(frame.step, 1);
//! assert_eq!(frame.num_atoms, num_atoms);
//!
//! let first_atom_coords = frame.coords[0];
//! assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
//!
//! Ok(())
//! }
//! ```
//!
@@ -44,13 +42,17 @@
//! ```rust
//! use xdrfile::*;
//!
//! // get a handle to the file
//! let trj = XTCTrajectory::open_read("tests/1l2y.xtc").unwrap();
//! fn main() -> Result<()> {
//! // get a handle to the file
//! let trj = XTCTrajectory::open_read("tests/1l2y.xtc")?;
//!
//! // iterate over all frames
//! for (idx, frame) in trj.into_iter().filter_map(Result::ok).enumerate() {
//! println!("{}", frame.time);
//! assert_eq!(idx+1, frame.step as usize);
//! // iterate over all frames
//! for (idx, result) in trj.into_iter().enumerate() {
//! let frame = result?;
//! println!("{}", frame.time);
//! assert_eq!(idx+1, frame.step as usize);
//! }
//! Ok(())
//! }
//! ```
@@ -74,7 +76,7 @@ use c_abi::xdrfile_xtc;
use lazy_init::Lazy;
use std::cell::Cell;
use std::ffi::CString;
use std::path::Path;
use std::path::{Path, PathBuf};
#[derive(Debug, Clone)]
pub enum Error {
@@ -83,6 +85,7 @@ pub enum Error {
CouldNotRead(u32),
CouldNotWrite(u32),
CouldNotFlush(u32),
PathInvalidCstring,
}
impl std::fmt::Display for Error {
@@ -115,13 +118,34 @@ impl std::fmt::Display for Error {
"Failed to flush trajectory: C API returned error code {}",
code
),
PathInvalidCstring => write!(
f,
"Path cannot be converted to a C string because it has a 0 byte"
),
}
}
}
impl Error {
pub fn is_eof(&self) -> bool {
use Error::*;
match self {
&CouldNotReadAtomNumber(code)
| &CouldNotRead(code)
| &CouldNotWrite(code)
| &CouldNotFlush(code)
if code == xdrfile::exdrENDOFFILE =>
{
true
}
_ => false,
}
}
}
impl std::error::Error for Error {}
type Result<T> = std::result::Result<T, Error>;
pub type Result<T> = std::result::Result<T, Error>;
#[derive(Debug, Clone, PartialEq)]
pub enum FileMode {
@@ -131,17 +155,21 @@ pub enum FileMode {
}
impl FileMode {
pub fn value(&self) -> &str {
match *self {
FileMode::Write => "w",
FileMode::Append => "a",
FileMode::Read => "r",
}
/// Get a CStr slice corresponding to the file mode
fn to_cstr(&self) -> &'static std::ffi::CStr {
let bytes: &[u8; 2] = match *self {
FileMode::Write => b"w\0",
FileMode::Append => b"a\0",
FileMode::Read => b"r\0",
};
std::ffi::CStr::from_bytes_with_nul(bytes).expect("CStr::from_bytes_with_nul failed")
}
}
fn path_to_cstring(path: &Path) -> CString {
CString::new(path.to_str().unwrap()).unwrap()
fn path_to_cstring(path: impl AsRef<Path>) -> Result<CString> {
let s = path.as_ref().to_str().ok_or(Error::PathInvalidCstring)?;
CString::new(s).map_err(|_| Error::PathInvalidCstring)
}
/// A safe wrapper around the c implementation of an XDRFile
@@ -149,20 +177,24 @@ struct XDRFile {
xdrfile: *mut XDRFILE,
#[allow(dead_code)]
filemode: FileMode,
path: String,
path: PathBuf,
}
impl XDRFile {
pub fn open(path: impl AsRef<Path>, filemode: FileMode) -> Result<XDRFile> {
let path = path.as_ref();
let path_p = path_to_cstring(path).into_raw();
let mode_p = CString::new(filemode.value()).unwrap().into_raw();
unsafe {
let path_p = path_to_cstring(path)?.into_raw();
// SAFETY: mode_p must not be mutated by the C code
let mode_p = filemode.to_cstr().as_ptr();
let xdrfile = xdrfile::xdrfile_open(path_p, mode_p);
// Reconstitute the CString so it is deallocated correctly
let _ = CString::from_raw(path_p);
if !xdrfile.is_null() {
let path = String::from(path.to_str().unwrap());
let path = path.to_owned();
Ok(XDRFile {
xdrfile,
filemode,
@@ -290,10 +322,12 @@ impl Trajectory for XTCTrajectory {
.get_or_create(|| {
let mut num_atoms: i32 = 0;
unsafe {
let path = CString::new(self.handle.path.as_str()).unwrap();
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;
// Reconstitute the CString so it is deallocated correctly
let _ = CString::from_raw(path_p);
match code {
xdrfile::exdrOK => Ok(num_atoms as u32),
_ => Err(Error::CouldNotReadAtomNumber(code)),
@@ -398,10 +432,12 @@ impl Trajectory for TRRTrajectory {
.get_or_create(|| {
let mut num_atoms: i32 = 0;
unsafe {
let path = CString::new(self.handle.path.as_str()).unwrap();
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;
// Reconstitute the CString so it is deallocated correctly
let _ = CString::from_raw(path_p);
match code {
xdrfile::exdrOK => Ok(num_atoms as u32),
_ => Err(Error::CouldNotReadAtomNumber(code)),
@@ -419,8 +455,8 @@ mod tests {
use tempfile::NamedTempFile;
#[test]
fn test_read_write_xtc() {
let tempfile = NamedTempFile::new().unwrap();
fn test_read_write_xtc() -> Result<()> {
let tempfile = NamedTempFile::new().expect("Could not create temporary file");
let tmp_path = tempfile.path();
let natoms: u32 = 2;
@@ -431,17 +467,17 @@ mod tests {
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
};
let mut f = XTCTrajectory::open_write(&tmp_path).unwrap();
let mut f = XTCTrajectory::open_write(&tmp_path)?;
let write_status = f.write(&frame);
match write_status {
Err(_) => panic!("Failed"),
Ok(()) => {}
}
f.flush().unwrap();
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut f = XTCTrajectory::open_read(tmp_path).unwrap();
let num_atoms = f.get_num_atoms().unwrap();
let mut f = XTCTrajectory::open_read(tmp_path)?;
let num_atoms = f.get_num_atoms()?;
assert_eq!(num_atoms, natoms);
let read_status = f.read(&mut new_frame);
@@ -455,11 +491,12 @@ mod tests {
assert_approx_eq!(new_frame.time, frame.time);
assert_eq!(new_frame.box_vector, frame.box_vector);
assert_eq!(new_frame.coords, frame.coords);
Ok(())
}
#[test]
fn test_read_write_trr() {
let tempfile = NamedTempFile::new().unwrap();
fn test_read_write_trr() -> Result<()> {
let tempfile = NamedTempFile::new().expect("Could not create temporary file");
let tmp_path = tempfile.path();
let natoms: u32 = 2;
@@ -470,17 +507,17 @@ mod tests {
box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
};
let mut f = TRRTrajectory::open_write(tmp_path).unwrap();
let mut f = TRRTrajectory::open_write(tmp_path)?;
let write_status = f.write(&frame);
match write_status {
Err(_) => panic!("Failed"),
Ok(()) => {}
}
f.flush().unwrap();
f.flush()?;
let mut new_frame = Frame::with_capacity(natoms);
let mut f = TRRTrajectory::open_read(tmp_path).unwrap();
// let num_atoms = f.get_num_atoms().unwrap();
let mut f = TRRTrajectory::open_read(tmp_path)?;
// let num_atoms = f.get_num_atoms()?;
// assert_eq!(num_atoms, natoms);
let read_status = f.read(&mut new_frame);
@@ -494,6 +531,7 @@ mod tests {
assert_eq!(new_frame.time, frame.time);
assert_eq!(new_frame.box_vector, frame.box_vector);
assert_eq!(new_frame.coords, frame.coords);
Ok(())
}
#[test]
@@ -512,9 +550,9 @@ mod tests {
}
#[test]
fn test_err_could_not_read_atom_nr() {
fn test_err_could_not_read_atom_nr() -> Result<()> {
let file_name = "README.md"; // not a trajectory
let mut trr = TRRTrajectory::open_read(file_name).unwrap();
let mut trr = TRRTrajectory::open_read(file_name)?;
if let Err(e) = trr.get_num_atoms() {
match e {
Error::CouldNotReadAtomNumber(code) => {
@@ -522,14 +560,15 @@ mod tests {
}
_ => panic!("Wrong Error type"),
}
}
};
Ok(())
}
#[test]
fn test_err_could_not_read() {
fn test_err_could_not_read() -> Result<()> {
let file_name = "README.md"; // not a trajectory
let mut frame = Frame::with_capacity(1);
let mut trr = TRRTrajectory::open_read(file_name).unwrap();
let mut trr = TRRTrajectory::open_read(file_name)?;
if let Err(e) = trr.read(&mut frame) {
match e {
Error::CouldNotRead(code) => {
@@ -538,5 +577,6 @@ mod tests {
_ => panic!("Wrong Error type"),
}
}
Ok(())
}
}