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feat: hdf5::Dir API update. #301

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merged 4 commits into from
Jul 18, 2024
Merged

feat: hdf5::Dir API update. #301

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4687837
update Dir::create_dir API and mechanics, refactor AppPackage and Was…
Mr-Leshiy Jul 18, 2024
c05364a
fix bootstrapping and app packaging
Mr-Leshiy Jul 18, 2024
44143b6
fix lints
Mr-Leshiy Jul 18, 2024
07d22b2
add `Dire::create_file` function
Mr-Leshiy Jul 18, 2024
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85 changes: 48 additions & 37 deletions hermes/bin/src/hdf5/dir.rs
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
//! A Hermes HDF5 directory abstraction over the HDF5 Group object.

use std::io::Read;

use super::{
resources::{Hdf5Resource, ResourceTrait},
File, Path,
Expand Down Expand Up @@ -38,38 +36,41 @@ impl Dir {
Ok(())
}

/// Create a new empty file in the provided path.
pub(crate) fn create_file(&self, mut path: Path) -> anyhow::Result<File> {
let file_name = path.pop_elem()?;
let dir = self.get_dir(&path)?;
let file = File::create(&dir.0, file_name.as_str())?;
Ok(file)
}

/// Copy resource file to the provided path.
pub(crate) fn copy_resource_file(
&self, resource: &impl ResourceTrait, mut path: Path,
&self, resource: &impl ResourceTrait, path: Path,
) -> anyhow::Result<()> {
let file_name = path.pop_elem()?;

let mut file = self.create_file(path)?;
let mut reader = resource.get_reader()?;
let mut resource_data = Vec::new();
reader.read_to_end(&mut resource_data)?;
if resource_data.is_empty() {
anyhow::bail!("Resource {} is empty", resource.to_string());
}

let dir = self.create_dir(&path)?;
File::create(&dir.0, file_name.as_str(), &resource_data)?;
std::io::copy(&mut reader, &mut file)?;
Ok(())
}

/// Copy resource dir recursively to the provided path.
pub(crate) fn copy_resource_dir(
&self, resource: &impl ResourceTrait, path: &Path,
) -> anyhow::Result<()> {
let dir = self.create_dir(path)?;
let dir = self.get_dir(path)?;

let mut errors = Errors::new();
for resource in resource.get_directory_content()? {
let path: Path = resource.name()?.into();
if resource.is_dir() {
dir.copy_resource_dir(&resource, &resource.name()?.into())
dir.create_dir(path.clone())?;
dir.copy_resource_dir(&resource, &path)
.unwrap_or_else(errors.get_add_err_fn());
}
if resource.is_file() {
dir.copy_resource_file(&resource, resource.name()?.into())
dir.copy_resource_file(&resource, path)
.unwrap_or_else(errors.get_add_err_fn());
}
}
Expand All @@ -86,17 +87,14 @@ impl Dir {
/// Create dir recursively from path related to current dir.
/// If some dir already exists it will be skipped, if some dir does not exist it will
/// be created.
/// If path is empty it will return cloned `Dir`.
pub(crate) fn create_dir(&self, path: &Path) -> anyhow::Result<Self> {
let mut dir = self.0.clone();
for path_element in path.iter() {
if let Ok(known_dir) = dir.group(path_element) {
dir = known_dir;
} else {
dir = dir.create_group(path_element)?;
}
}
Ok(Self(dir))
pub(crate) fn create_dir(&self, mut path: Path) -> anyhow::Result<Self> {
let dir_name = path.pop_elem()?;
let dir = self.get_dir(&path)?;
let new_dir = dir
.0
.create_group(&dir_name)
.map_err(|_| anyhow::anyhow!("Dir `{path}/{dir_name}` already exists"))?;
Ok(Self(new_dir))
}

/// Remove file by the provided path.
Expand Down Expand Up @@ -156,7 +154,7 @@ impl Dir {
for path_element in path.iter() {
dir = dir
.group(path_element)
.map_err(|_| anyhow::anyhow!("Dir {path} not found"))?;
.map_err(|_| anyhow::anyhow!("Dir `{path}` not found"))?;
}
Ok(Self(dir))
}
Expand All @@ -171,6 +169,8 @@ impl Dir {

#[cfg(test)]
mod tests {
use std::io::Read;

use temp_dir::TempDir;

use super::*;
Expand All @@ -183,18 +183,27 @@ mod tests {
let package = hdf5::File::create(package_name).expect("Failed to create a new package.");
let dir = Dir::new(package.as_group().expect("Failed to create a root group."));

let path = Path::from_str("dir_1/dir_2/dir_3/dir_4");
dir.create_dir(&path)
let dir_1 = "dir_1";
let dir_2 = "dir_2";
let dir_3 = "dir_3";
let new_dir = dir
.create_dir(dir_1.into())
.expect("Failed to create directories in package.");
let new_dir = new_dir
.create_dir(dir_2.into())
.expect("Failed to create directories in package.");
new_dir
.create_dir(dir_3.into())
.expect("Failed to create directories in package.");

assert!(dir.get_dir(&Path::from_str("dir_1")).is_ok());
assert!(dir.get_dir(&Path::from_str("dir_1/dir_2")).is_ok());
assert!(dir.get_dir(&Path::from_str("dir_1/dir_2/dir_3")).is_ok());
assert!(dir.get_dir(&path).is_ok());
assert!(dir.get_dir(&dir_1.into()).is_ok());
assert!(dir.get_dir(&format!("{dir_1}/{dir_2}").into()).is_ok());
assert!(dir
.get_dir(&format!("{dir_1}/{dir_2}/{dir_3}").into())
.is_ok());
assert!(dir.get_dir(&Path::from_str("not_created_dir")).is_err());

dir.create_dir(&path)
.expect("Failed to create directories in package.");
assert!(dir.create_dir(dir_1.into()).is_err());
}

#[test]
Expand All @@ -212,10 +221,10 @@ mod tests {
let child_dir_path = Path::from_str(child_dir_name);

let child_dir = dir2
.create_dir(&child_dir_path)
.create_dir(child_dir_path.clone())
.expect("Failed to create dir.");
child_dir
.create_dir(&child_dir_path)
.create_dir(child_dir_path)
.expect("Failed to create dir.");

let mounted_dir_name = "mounted_dir";
Expand Down Expand Up @@ -314,6 +323,8 @@ mod tests {
let file_3 = fs_child_dir.join(file_3_name);
std::fs::write(file_3, file_content).expect("Failed to create file_3 file.");

dir.create_dir(base_dir_name.into())
.expect("Failed to create dir.");
dir.copy_resource_dir(&FsResource::new(fs_base_dir), &base_dir_name.into())
.expect("Failed to copy dir to package.");

Expand Down
17 changes: 9 additions & 8 deletions hermes/bin/src/hdf5/file.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -13,16 +13,13 @@ pub(crate) struct File {

impl File {
/// Create a new file.
pub(crate) fn create(
group: &hdf5::Group, file_name: &str, data: &[u8],
) -> anyhow::Result<Self> {
pub(crate) fn create(group: &hdf5::Group, file_name: &str) -> anyhow::Result<Self> {
let builder = group.new_dataset_builder();
let shape = hdf5::SimpleExtents::resizable([data.len()]);
let shape = hdf5::SimpleExtents::resizable([0]);
let hdf5_ds = enable_compression(builder)
.empty::<u8>()
.shape(shape)
.create(file_name)?;
hdf5_ds.write(data)?;
Ok(Self { hdf5_ds, pos: 0 })
}

Expand Down Expand Up @@ -152,13 +149,17 @@ mod tests {
.expect("Failed to get a root group from package.");

let file_name = "test.txt";
let file_content = b"file_content";

assert!(group.dataset(file_name).is_err());
let mut file =
File::create(&group, file_name, file_content).expect("Failed to create a new file.");
let mut file = File::create(&group, file_name).expect("Failed to create a new file.");
assert!(group.dataset(file_name).is_ok());

let file_content = b"file_content";
file.write_all(file_content)
.expect("Failed to write to file.");

file.seek(std::io::SeekFrom::Start(0))
.expect("Failed to seek.");
let mut buffer = Vec::new();
file.read_to_end(&mut buffer)
.expect("Failed to read from file.");
Expand Down
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