1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
// [[file:../parser.note::*docs][docs:1]]
//! Split large text stream into multiple parts.
//!
//! # Example
//!
//! ```
//! use gchemol_parser::TextReader;
//! use gchemol_parser::partition::*;
//! 
//! let txt = "part1> line 1
//! part1> line 2 tail
//! part2> line 3
//! part2> line 5 tail
//! part3> line 8 tail ";
//! 
//! // instruct TextReader how to split the text stream into multiple parts.
//! struct PartX;
//! impl ReadPart for PartX {
//!     fn read_next(&self, context: ReadContext) -> ReadAction {
//!         let n = context.number_of_lines();
//!         // check the last line
//!         if context.line(n).ends_with("tail\n") {
//!             // make a new part terminated with this line
//!             ReadAction::Done(n)
//!         } else {
//!             // continue to read next line until find another tail line
//!             ReadAction::Need(1)
//!         }
//!     }
//! }
//! 
//! let reader = TextReader::from_str(txt);
//! let parts = reader.partitions(PartX);
//! assert_eq!(parts.count(), 3);
//! ```
// docs:1 ends here

// [[file:../parser.note::fa39dec3][fa39dec3]]
// #![deprecated(note = "deprecated for bad performance")]

use std::io::prelude::*;

use crate::reader::TextReader;
use gut::prelude::*;
// fa39dec3 ends here

// [[file:../parser.note::de2a5565][de2a5565]]
/// A helper struct for handling buffered text.
pub struct ReadContext<'a> {
    /// Buffered text.
    chunk: &'a str,
    /// byte size for each line of text.
    nlist: &'a [usize],
}

impl<'a> ReadContext<'a> {
    pub(crate) fn new(buf: &'a str, nlist: &'a [usize]) -> Self {
        Self { chunk: buf, nlist }
    }

    /// Return the number of lines that already read in.
    #[inline]
    pub fn number_of_lines(&self) -> usize {
        self.nlist.len()
    }

    /// Return the line numbered as `n` (1-based)
    ///
    /// # Panic
    ///
    /// * Panics if index `n` out of bounds.
    pub fn line(&self, n: usize) -> &str {
        assert_ne!(n, 0, "invalid line number");
        let n = n - 1;
        let ns = self.nlist[0..n].iter().sum();
        let nb = self.nlist[n];
        &self.chunk[ns..ns + nb]
    }

    /// Return buffered text.
    pub fn text(&self) -> &str {
        &self.chunk
    }
}

#[test]
fn test_read_context() {
    let txt = "line1\nLine2\nline 3\n";
    let nlist: Vec<_> = txt.lines().map(|l| l.len() + 1).collect();
    let context = ReadContext::new(txt, &nlist);

    assert_eq!(context.number_of_lines(), 3);
    assert_eq!(context.line(1), "line1\n");
    assert_eq!(context.line(2), "Line2\n");
    assert_eq!(context.line(3), "line 3\n");
}

/// Read text stream at line basis
pub enum ReadAction {
    /// Need next n lines to decide
    Need(usize),
    /// Read part done, return the first n lines as a part
    Done(usize),
    /// Error description
    Error(String),
}

/// Instruct the reader how to read a part of text by inspecting `ReadContext`
pub trait ReadPart {
    /// How to read next lines?
    fn read_next<'a>(&self, context: ReadContext<'a>) -> ReadAction {
        ReadAction::Need(1)
    }

    /// Read `n` lines at each time.
    fn n_stride(&self) -> usize {
        1
    }
}
// de2a5565 ends here

// [[file:../parser.note::11167470][11167470]]
/// An iterator over part of text stream.
pub struct Partitions<R, P>
where
    R: BufRead,
{
    reader: TextReader<R>,
    part: P,
    buf: String,
    nlist: Vec<usize>,
}

impl<R: BufRead, P> Partitions<R, P> {
    fn new(reader: TextReader<R>, part: P) -> Self {
        Self {
            reader,
            part,
            buf: String::new(),
            nlist: vec![],
        }
    }

    /// Read in `n` lines into `buf`. Return the number of bytes read in total.
    ///
    /// # NOTE
    /// - The new line is forced to use unix style line ending.
    fn read_n_lines(&mut self, n: usize) -> Option<usize> {
        assert_ne!(n, 0);
        for _ in 0..n {
            let mut m = self.reader.read_line(&mut self.buf)?;
            // force to use Unix line ending
            if self.buf.ends_with("\r\n") {
                let i = self.buf.len() - 2;
                self.buf.remove(i);
                // we removed one byte
                m -= 1;
            }

            self.nlist.push(m);
        }
        return Some(self.nlist.iter().sum());
    }

    /// build ReadContext for client.
    fn context(&self) -> ReadContext {
        ReadContext::new(&self.buf, &self.nlist)
    }
}

impl<R: BufRead, P: ReadPart> Iterator for Partitions<R, P> {
    type Item = String;

    fn next(&mut self) -> Option<Self::Item> {
        // read next n lines
        let mut m = self.part.n_stride();
        loop {
            // let _ = self.read_n_lines(m)?;
            // process the last part when reaching EOF
            if self.read_n_lines(m).is_none() {
                if self.buf.is_empty() {
                    break None;
                } else {
                    break Some(self.buf.drain(..).collect());
                }
            }
            // read in enough number of lines?
            match self.part.read_next(self.context()) {
                ReadAction::Need(n) => m = n,
                ReadAction::Done(n) => {
                    // take the first `n` lines as a part
                    let ns = self.nlist.drain(0..n).sum();
                    break Some(self.buf.drain(0..ns).collect());
                }
                ReadAction::Error(s) => {
                    error!("partition failure: {}", s);
                    break None;
                }
                _ => unreachable!(),
            }
        }
    }
}

impl<R: BufRead> TextReader<R> {
    /// Returns an iterator over part of text, using a generic text partioner
    /// `p`.
    pub fn partitions<P>(self, p: P) -> Partitions<R, P>
    where
        P: ReadPart,
    {
        Partitions::new(self, p)
    }
}
// 11167470 ends here

// [[file:../parser.note::9f67096e][9f67096e]]
impl<R: BufRead> TextReader<R> {
    /// Returns an iterator over each part of text in `n` lines.
    pub fn chunks(mut self, n: usize) -> impl Iterator<Item = String> {
        std::iter::from_fn(move || {
            let mut s = String::new();
            for i in 0..n {
                // special treatment for the last line
                match (i, self.read_line(&mut s)) {
                    (_, Some(_)) => {}
                    (0, None) => return None,
                    (_, None) => return Some(s),
                }
            }
            Some(s)
        })
    }
}
// 9f67096e ends here

// [[file:../parser.note::f96ed947][f96ed947]]
/// Terminated with a tail line
pub struct Terminated<F>(pub F);

impl<F> ReadPart for Terminated<F>
where
    F: Fn(&str) -> bool,
{
    #[inline]
    fn read_next(&self, context: ReadContext) -> ReadAction {
        let n = context.number_of_lines();
        let last_line = context.line(n);
        if (self.0)(last_line) {
            ReadAction::Done(n)
        } else {
            ReadAction::Need(1)
        }
    }
}

impl<R: BufRead> TextReader<R> {
    /// Returns an iterator over a part of text terminated with a tail line.
    pub fn partitions_terminated<F>(self, f: F) -> Partitions<R, Terminated<F>>
    where
        F: Fn(&str) -> bool,
    {
        Partitions::new(self, Terminated(f))
    }
}

#[test]
fn test_terminated() -> Result<()> {
    let txt = ": part1> line 1
: part1> line 2 tail
: part2> line 3
: part2> line 4
: part2> line 5 tail
: part3> line 6
: part3> line 7
: part3> line 8 tail ";

    let reader = TextReader::from_str(txt);
    let parts: Vec<_> = reader.partitions_terminated(|line| line.ends_with("tail\n")).collect();
    assert_eq!(parts.len(), 3);
    assert_eq!(parts[0].lines().count(), 2);
    assert_eq!(parts[1].lines().count(), 3);
    assert_eq!(parts[2].lines().count(), 3);

    Ok(())
}
// f96ed947 ends here

// [[file:../parser.note::2b9d1c8d][2b9d1c8d]]
/// Preceded with a head line
pub struct Preceded<F>(pub F)
where
    F: Fn(&str) -> bool;

impl<F> ReadPart for Preceded<F>
where
    F: Fn(&str) -> bool,
{
    #[inline]
    fn read_next(&self, context: ReadContext) -> ReadAction {
        let n = context.number_of_lines();
        // n > 1: need at least two lines to decide
        if n > 1 && (self.0)(context.line(n)) {
            ReadAction::Done(n - 1)
        } else {
            ReadAction::Need(1)
        }
    }
}

impl<R: BufRead> TextReader<R> {
    /// Returns an iterator over a part of text preceded with a head line.
    // #[deprecated(note = "please use GrepReader instead")]
    pub fn partitions_preceded<F>(self, f: F) -> Partitions<R, Preceded<F>>
    where
        F: Fn(&str) -> bool,
    {
        Partitions::new(self, Preceded(f))
    }
}

#[test]
fn test_preceded() -> Result<()> {
    let txt = ": part1> line 1 head
: part1> line 2
: part2> line 3 head
: part2> line 4
: part2> line 5
: part3> line 6 head
: part3> line 7
: part3> line 8 ";

    let reader = TextReader::from_str(txt);
    let parts: Vec<_> = reader.partitions_preceded(|line| line.ends_with("head\n")).collect();
    assert_eq!(parts.len(), 3);
    assert_eq!(parts[0].lines().count(), 2);
    assert_eq!(parts[1].lines().count(), 3);
    assert_eq!(parts[2].lines().count(), 3);

    Ok(())
}
// 2b9d1c8d ends here

// [[file:../parser.note::1970f69f][1970f69f]]
#[cfg(test)]
mod test {
    use super::*;

    struct XyzFile;
    impl ReadPart for XyzFile {
        fn read_next(&self, context: ReadContext) -> ReadAction {
            let n = context.number_of_lines();
            // the first line contains the number of atoms in this part
            if let Ok(natoms) = context.line(1).trim().parse::<usize>() {
                if n >= natoms + 2 {
                    ReadAction::Done(n)
                } else {
                    ReadAction::Need(natoms + 2 - n)
                }
            } else {
                ReadAction::Error("invalid xyz format".into())
            }
        }
    }

    #[test]
    fn test_adhoc() -> Result<()> {
        let f = "./tests/files/lammps-test.dump";
        let reader = TextReader::try_from_path(f.as_ref())?;

        // preceded parts
        let parts = reader.partitions_preceded(|line| line.starts_with("ITEM: TIMESTEP"));
        assert_eq!(parts.count(), 3, "preceded");

        // terminated parts
        let f = "./tests/files/multi.xyz";
        let reader = TextReader::try_from_path(f.as_ref())?;
        let parts: Vec<_> = reader.partitions(XyzFile).collect();
        assert_eq!(parts.len(), 6);
        assert_eq!(parts[0].lines().count(), 18);
        assert_eq!(parts[1].lines().count(), 12);
        assert_eq!(parts[2].lines().count(), 18);
        assert_eq!(parts[3].lines().count(), 18);
        assert_eq!(parts[4].lines().count(), 18);
        assert_eq!(parts[5].lines().count(), 15);

        // read chunks in constant number of lines
        let f = "./tests/files/multi.xyz";
        let reader = TextReader::try_from_path(f.as_ref())?;
        assert_eq!(reader.chunks(1).count(), 99, "chunks");
        let reader = TextReader::try_from_path(f.as_ref())?;
        let chunks = reader.chunks(5);
        let nn: Vec<_> = chunks.map(|x| x.lines().count()).collect();
        assert_eq!(nn.len(), 20, "chunks");
        assert_eq!(nn[0], 5, "chunks");
        assert_eq!(nn[19], 4, "chunks");

        Ok(())
    }

    // test default impl
    #[test]
    fn test_read_part_default() -> Result<()> {
        struct OnePart;
        impl ReadPart for OnePart {}

        let f = "./tests/files/multi.xyz";
        let reader = TextReader::try_from_path(f.as_ref())?;
        let parts = reader.partitions(OnePart);
        assert_eq!(parts.count(), 1);

        Ok(())
    }
}
// 1970f69f ends here