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electricboogie 2021-04-25 00:20:56 -05:00
parent 25021f31eb
commit 2b8a6e98ee
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2
Cargo.lock generated
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@ -2305,7 +2305,7 @@ dependencies = [
"serde", "serde",
"serde_json", "serde_json",
"smallvec 1.6.1", "smallvec 1.6.1",
"tempfile", "tempdir",
"uucore", "uucore",
"uucore_procs", "uucore_procs",
] ]

2
src/uu/sort/Cargo.toml
View file

@ -26,7 +26,7 @@ semver = "0.9.0"
smallvec = { version = "1.6.1", features = ["serde"] } smallvec = { version = "1.6.1", features = ["serde"] }
uucore = { version=">=0.0.8", package="uucore", path="../../uucore", features=["fs"] } uucore = { version=">=0.0.8", package="uucore", path="../../uucore", features=["fs"] }
uucore_procs = { version=">=0.0.5", package="uucore_procs", path="../../uucore_procs" } uucore_procs = { version=">=0.0.5", package="uucore_procs", path="../../uucore_procs" }
tempfile = "3.1.0" tempdir = "0.3.7"
[[bin]] [[bin]]
name = "sort" name = "sort"

202
src/uu/sort/src/ext_sorter/LICENSE
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@ -1,202 +0,0 @@
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9
src/uu/sort/src/ext_sorter/NOTICE
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@ -1,9 +0,0 @@
ext_sorter
Copyright 2018 Andre-Philippe Paquet
Modifications copyright 2021 Robert Swinford
This ext_sorter module includes software developed by Andre-Philippe Paquet as extsort.
The sorter.rs file was copied and modified for use in the uutils' coreutils subproject, sort.
sort is licensed according to the term of the LICENSE file found in root directory of the uutils' coreutils project.

277
src/uu/sort/src/ext_sorter/mod.rs
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@ -1,277 +0,0 @@
// Copyright 2018 Andre-Philippe Paquet
// Modifications copyright 2021 Robert Swinford
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
// This file has been modified for use in the uutils' coreutils subproject, sort.
use rayon::prelude::*;
use std::{
cmp::Ordering,
collections::VecDeque,
fs::{File, OpenOptions},
io::{BufReader, BufWriter, Error, Read, Seek, SeekFrom, Write},
path::{Path, PathBuf},
};
/// Exposes external sorting (i.e. on disk sorting) capability on arbitrarily
/// sized iterator, even if the generated content of the iterator doesn't fit in
/// memory.
///
/// It uses an in-memory buffer sorted and flushed to disk in segment files when
/// full. Once sorted, it returns a new sorted iterator with all items. In order
/// to remain efficient for all implementations, the crate doesn't handle
/// serialization, but leaves that to the user.
pub struct ExternalSorter {
segment_size: usize,
sort_dir: Option<PathBuf>,
parallel: bool,
}
impl ExternalSorter {
pub fn new() -> ExternalSorter {
ExternalSorter {
// Default is 16G - But we never use it,
// because we always set or ignore
segment_size: 16000000000,
sort_dir: None,
parallel: false,
}
}
/// Sets the maximum size of each segment in number of sorted items.
///
/// This number of items needs to fit in memory. While sorting, a
/// in-memory buffer is used to collect the items to be sorted. Once
/// it reaches the maximum size, it is sorted and then written to disk.
///
/// Using a higher segment size makes sorting faster by leveraging
/// faster in-memory operations.
pub fn with_segment_size(mut self, size: usize) -> Self {
self.segment_size = size;
self
}
/// Sets directory in which sorted segments will be written (if it doesn't
/// fit in memory).
pub fn with_sort_dir(mut self, path: PathBuf) -> Self {
self.sort_dir = Some(path);
self
}
/// Uses Rayon to sort the in-memory buffer.
///
/// This may not be needed if the buffer isn't big enough for parallelism to
/// be gainful over the overhead of multithreading.
pub fn with_parallel_sort(mut self) -> Self {
self.parallel = true;
self
}
/// Sorts a given iterator with a comparator function, returning a new iterator with items
pub fn sort_by<T, I, F>(&self, iterator: I, cmp: F) -> Result<SortedIterator<T, F>, Error>
where
T: Sortable,
I: Iterator<Item = T>,
F: Fn(&T, &T) -> Ordering + Send + Sync,
{
let mut tempdir: Option<tempfile::TempDir> = None;
let mut sort_dir: Option<PathBuf> = None;
let mut count = 0;
let mut segments_file: Vec<File> = Vec::new();
let size_of_items = std::mem::size_of::<T>();
// Get size of iterator
let (_, upper_bound) = iterator.size_hint();
// Buffer size specified + minimum overhead of struct / size of items
let initial_capacity = (self.segment_size + (upper_bound.unwrap() * size_of_items)) / size_of_items;
let mut buffer: Vec<T> = Vec::with_capacity(initial_capacity);
for next_item in iterator {
count += 1;
buffer.push(next_item);
// if after push, number of elements in vector > initial capacity
if buffer.len() > initial_capacity {
let sort_dir = self.lazy_create_dir(&mut tempdir, &mut sort_dir)?;
self.sort_and_write_segment(sort_dir, &mut segments_file, &mut buffer, &cmp)?;
// Truncate buffer back to initial capacity
buffer.truncate(initial_capacity);
}
}
// Write any items left in buffer, but only if we had at least 1 segment
// written. Otherwise we use the buffer itself to iterate from memory
let pass_through_queue = if !buffer.is_empty() && !segments_file.is_empty() {
let sort_dir = self.lazy_create_dir(&mut tempdir, &mut sort_dir)?;
self.sort_and_write_segment(sort_dir, &mut segments_file, &mut buffer, &cmp)?;
None
} else {
buffer.sort_by(&cmp);
Some(VecDeque::from(buffer))
};
SortedIterator::new(tempdir, pass_through_queue, segments_file, count, cmp)
}
/// We only want to create directory if it's needed (i.e. if the dataset
/// doesn't fit in memory) to prevent filesystem latency
fn lazy_create_dir<'a>(
&self,
tempdir: &mut Option<tempfile::TempDir>,
sort_dir: &'a mut Option<PathBuf>,
) -> Result<&'a Path, Error> {
if let Some(sort_dir) = sort_dir {
return Ok(sort_dir);
}
*sort_dir = if let Some(ref sort_dir) = self.sort_dir {
Some(sort_dir.to_path_buf())
} else {
*tempdir = Some(tempfile::TempDir::new()?);
Some(tempdir.as_ref().unwrap().path().to_path_buf())
};
Ok(sort_dir.as_ref().unwrap())
}
fn sort_and_write_segment<T, F>(
&self,
sort_dir: &Path,
segments: &mut Vec<File>,
buffer: &mut Vec<T>,
cmp: F,
) -> Result<(), Error>
where
T: Sortable,
F: Fn(&T, &T) -> Ordering + Send + Sync,
{
if self.parallel {
buffer.par_sort_by(|a, b| cmp(a, b));
} else {
buffer.sort_by(|a, b| cmp(a, b));
}
let segment_path = sort_dir.join(format!("{}", segments.len()));
let segment_file = OpenOptions::new()
.create(true)
.truncate(true)
.read(true)
.write(true)
.open(&segment_path)?;
let mut buf_writer = BufWriter::new(segment_file);
// Possible panic here.
// Why use drain here, if we want to dump the entire buffer?
// Was "buffer.drain(0..)"
for item in buffer {
item.encode(&mut buf_writer);
}
let file = buf_writer.into_inner()?;
segments.push(file);
Ok(())
}
}
impl Default for ExternalSorter {
fn default() -> Self {
ExternalSorter::new()
}
}
pub trait Sortable: Sized + Send {
fn encode<W: Write>(&self, writer: &mut W);
fn decode<R: Read>(reader: &mut R) -> Option<Self>;
}
pub struct SortedIterator<T: Sortable, F> {
_tempdir: Option<tempfile::TempDir>,
pass_through_queue: Option<VecDeque<T>>,
segments_file: Vec<BufReader<File>>,
next_values: Vec<Option<T>>,
count: u64,
cmp: F,
}
impl<T: Sortable, F: Fn(&T, &T) -> Ordering + Send + Sync> SortedIterator<T, F> {
fn new(
tempdir: Option<tempfile::TempDir>,
pass_through_queue: Option<VecDeque<T>>,
mut segments_file: Vec<File>,
count: u64,
cmp: F,
) -> Result<SortedIterator<T, F>, Error> {
for segment in &mut segments_file {
segment.seek(SeekFrom::Start(0))?;
}
let next_values = segments_file
.iter_mut()
.map(|file| T::decode(file))
.collect();
let segments_file_buffered = segments_file.into_iter().map(BufReader::new).collect();
Ok(SortedIterator {
_tempdir: tempdir,
pass_through_queue,
segments_file: segments_file_buffered,
next_values,
count,
cmp,
})
}
pub fn sorted_count(&self) -> u64 {
self.count
}
}
impl<T: Sortable, F: Fn(&T, &T) -> Ordering> Iterator for SortedIterator<T, F> {
type Item = T;
fn next(&mut self) -> Option<T> {
// if we have a pass through, we dequeue from it directly
if let Some(ptb) = self.pass_through_queue.as_mut() {
return ptb.pop_front();
}
// otherwise, we iter from segments on disk
let mut smallest_idx: Option<usize> = None;
{
let mut smallest: Option<&T> = None;
for idx in 0..self.segments_file.len() {
let next_value = self.next_values[idx].as_ref();
if next_value.is_none() {
continue;
}
if smallest.is_none()
|| (self.cmp)(next_value.unwrap(), smallest.unwrap()) == Ordering::Less
{
smallest = Some(next_value.unwrap());
smallest_idx = Some(idx);
}
}
}
smallest_idx.map(|idx| {
let file = &mut self.segments_file[idx];
let value = self.next_values[idx].take().unwrap();
self.next_values[idx] = T::decode(file);
value
})
}
}

108
src/uu/sort/src/sort.rs
View file

@ -15,11 +15,11 @@
#[macro_use] #[macro_use]
extern crate uucore; extern crate uucore;
mod ext_sorter;
mod numeric_str_cmp; mod numeric_str_cmp;
mod external_sort;
use external_sort::{ExternalSorter, ExternallySortable};
use clap::{App, Arg}; use clap::{App, Arg};
use ext_sorter::{ExternalSorter, Sortable};
use fnv::FnvHasher; use fnv::FnvHasher;
use itertools::Itertools; use itertools::Itertools;
use numeric_str_cmp::{numeric_str_cmp, NumInfo, NumInfoParseSettings}; use numeric_str_cmp::{numeric_str_cmp, NumInfo, NumInfoParseSettings};
@ -27,7 +27,7 @@ use rand::distributions::Alphanumeric;
use rand::{thread_rng, Rng}; use rand::{thread_rng, Rng};
use rayon::prelude::*; use rayon::prelude::*;
use semver::Version; use semver::Version;
use serde::{Deserialize, Serialize}; use serde::{Deserializer, Deserialize, Serialize};
use smallvec::SmallVec; use smallvec::SmallVec;
use std::borrow::Cow; use std::borrow::Cow;
use std::cmp::Ordering; use std::cmp::Ordering;
@ -103,7 +103,7 @@ enum SortMode {
Version, Version,
Default, Default,
} }
#[derive(Clone)]
struct GlobalSettings { struct GlobalSettings {
mode: SortMode, mode: SortMode,
ignore_blanks: bool, ignore_blanks: bool,
@ -176,7 +176,7 @@ impl Default for GlobalSettings {
} }
} }
} }
#[derive(Clone)]
struct KeySettings { struct KeySettings {
mode: SortMode, mode: SortMode,
ignore_blanks: bool, ignore_blanks: bool,
@ -201,7 +201,7 @@ impl From<&GlobalSettings> for KeySettings {
} }
} }
#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)] #[derive(Debug, Serialize, Deserialize, Clone)]
/// Represents the string selected by a FieldSelector. /// Represents the string selected by a FieldSelector.
enum SelectionRange { enum SelectionRange {
/// If we had to transform this selection, we have to store a new string. /// If we had to transform this selection, we have to store a new string.
@ -232,13 +232,23 @@ impl SelectionRange {
} }
} }
} }
#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
#[derive(Debug, Serialize, Deserialize, Clone)]
enum NumCache { enum NumCache {
#[serde(deserialize_with="bailout_parse_f64")]
AsF64(f64), AsF64(f64),
WithInfo(NumInfo), WithInfo(NumInfo),
None, None,
} }
// Only used when serde can't parse a null value
fn bailout_parse_f64<'de, D>(d: D) -> Result<f64, D::Error> where D: Deserializer<'de> {
Deserialize::deserialize(d)
.map(|x: Option<_>| {
x.unwrap_or(0f64)
})
}
impl NumCache { impl NumCache {
fn as_f64(&self) -> f64 { fn as_f64(&self) -> f64 {
match self { match self {
@ -253,7 +263,7 @@ impl NumCache {
} }
} }
} }
#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)] #[derive(Debug, Serialize, Deserialize, Clone)]
struct Selection { struct Selection {
range: SelectionRange, range: SelectionRange,
num_cache: NumCache, num_cache: NumCache,
@ -267,56 +277,29 @@ impl Selection {
} }
type Field = Range<usize>; type Field = Range<usize>;
#[derive(Debug, Serialize, Deserialize)]
#[derive(Serialize, Deserialize, Clone)]
struct Line { struct Line {
line: String, line: String,
// The common case is not to specify fields. Let's make this fast. // The common case is not to specify fields. Let's make this fast.
selections: SmallVec<[Selection; 1]>, selections: SmallVec<[Selection; 1]>,
} }
impl Sortable for Line { impl ExternallySortable for Line {
fn encode<W: Write>(&self, write: &mut W) { fn get_size(&self) -> u64 {
let line = Line { // Currently 96 bytes, but that could change, so we get that size here
line: self.line.to_owned(), std::mem::size_of::<Line>() as u64
selections: self.selections.to_owned(),
};
let serialized = serde_json::to_string(&line).unwrap();
// Each instance of valid JSON needs to be seperated by something, so here we use a newline
write
.write_all(format!("{}{}", serialized, "\n").as_bytes())
.unwrap();
}
// This crate asks us to write one Line struct at a time, but then returns multiple Lines to us at once.
// We concatanate them and return them as one big Line here.
fn decode<R: Read>(read: &mut R) -> Option<Line> {
let buf_reader = BufReader::new(read);
let result = {
let mut line_joined = String::new();
// Return an empty vec for selections
let selections_joined = SmallVec::new();
let mut p_iter = buf_reader.lines().peekable();
while let Some(line) = p_iter.next() {
let deserialized_line: Line =
serde_json::from_str(&line.as_ref().unwrap()).unwrap();
if let Some(_next_line) = p_iter.peek() {
line_joined = format!("{}\n{}\n", line_joined, deserialized_line.line)
} else {
line_joined = format!("{}\n{}", line_joined, deserialized_line.line)
}
// I think we've done our sorting already and these selctions are irrelevant?
// @miDeb what's your sense? Could we just return an empty vec?
//selections_joined.append(&mut deserialized_line.selections);
}
Some(Line {
line: line_joined,
selections: selections_joined,
})
};
result
} }
} }
impl PartialEq for Line {
fn eq(&self, other: &Self) -> bool {
self.line == other.line
}
}
impl Eq for Line {}
impl Line { impl Line {
fn new(line: String, settings: &GlobalSettings) -> Self { fn new(line: String, settings: &GlobalSettings) -> Self {
let fields = if settings let fields = if settings
@ -449,6 +432,7 @@ fn tokenize_with_separator(line: &str, separator: char) -> Vec<Field> {
tokens tokens
} }
#[derive(Clone)]
struct KeyPosition { struct KeyPosition {
/// 1-indexed, 0 is invalid. /// 1-indexed, 0 is invalid.
field: usize, field: usize,
@ -516,7 +500,7 @@ impl KeyPosition {
} }
} }
} }
#[derive(Clone)]
struct FieldSelector { struct FieldSelector {
from: KeyPosition, from: KeyPosition,
to: Option<KeyPosition>, to: Option<KeyPosition>,
@ -1014,10 +998,10 @@ pub fn uumain(args: impl uucore::Args) -> i32 {
}); });
} }
exec(files, &settings) exec(files, settings)
} }
fn exec(files: Vec<String>, settings: &GlobalSettings) -> i32 { fn exec(files: Vec<String>, settings: GlobalSettings) -> i32 {
let mut lines = Vec::new(); let mut lines = Vec::new();
let mut file_merger = FileMerger::new(&settings); let mut file_merger = FileMerger::new(&settings);
@ -1059,7 +1043,7 @@ fn exec(files: Vec<String>, settings: &GlobalSettings) -> i32 {
// Probably faster that we don't create // Probably faster that we don't create
// an owned value each run // an owned value each run
if settings.buffer_size != DEFAULT_BUF_SIZE { if settings.buffer_size != DEFAULT_BUF_SIZE {
lines = ext_sort_by(lines, &settings); lines = ext_sort_by(lines, settings.clone());
} else { } else {
sort_by(&mut lines, &settings); sort_by(&mut lines, &settings);
} }
@ -1074,7 +1058,7 @@ fn exec(files: Vec<String>, settings: &GlobalSettings) -> i32 {
print_sorted( print_sorted(
lines lines
.into_iter() .into_iter()
.dedup_by(|a, b| compare_by(a, b, settings) == Ordering::Equal) .dedup_by(|a, b| compare_by(a, b, &settings) == Ordering::Equal)
.map(|line| line.line), .map(|line| line.line),
&settings, &settings,
) )
@ -1117,15 +1101,13 @@ fn exec_check_file(unwrapped_lines: &[Line], settings: &GlobalSettings) -> i32 {
} }
} }
fn ext_sort_by(lines: Vec<Line>, settings: &GlobalSettings) -> Vec<Line> { fn ext_sort_by(unsorted: Vec<Line>, settings: GlobalSettings) -> Vec<Line> {
let sorter = ExternalSorter::new() let external_sorter = ExternalSorter::new(settings.buffer_size as u64, Some(settings.tmp_dir.clone()), settings.clone());
.with_segment_size(settings.buffer_size) let iter = external_sorter.sort_by(unsorted.into_iter(), settings.clone()).unwrap();
.with_sort_dir(settings.tmp_dir.clone()) let vec = iter.filter(|x| x.is_ok() )
.with_parallel_sort(); .map(|x| x.unwrap())
sorter .collect::<Vec<Line>>();
.sort_by(lines.into_iter(), |a, b| compare_by(a, b, &settings)) vec
.unwrap()
.collect()
} }
fn sort_by(lines: &mut Vec<Line>, settings: &GlobalSettings) { fn sort_by(lines: &mut Vec<Line>, settings: &GlobalSettings) {