simple-sds-sbwt 0.3.3

A fork of simple-sds used in the sbwt crate.
Documentation
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
416
417
418
419
420
421
422
423
424
425
426
427
428
429
use super::*;

use crate::serialize::MappingMode;
use crate::serialize;

use std::fs;

use rand::Rng;

//-----------------------------------------------------------------------------

fn random_vector(n: usize, width: usize) -> Vec<u64> {
    let mut result: Vec<u64> = Vec::new();
    let mut rng = rand::thread_rng();
    for _ in 0..n {
        let value: u64 = rng.gen();
        result.push(value & bits::low_set(width));
    }
    result
}

fn random_raw_vector(n: usize, width: usize) -> RawVector {
    let values = random_vector(n, width);
    let mut result = RawVector::with_capacity(values.len() * width);
    for value in values.iter() {
        unsafe { result.push_int(*value, width); }
    }
    result
}

//-----------------------------------------------------------------------------

#[test]
fn empty_vector() {
    let empty = RawVector::new();
    assert!(empty.is_empty(), "Created a non-empty empty vector");
    assert_eq!(empty.len(), 0, "Nonzero length for an empty vector");
    assert_eq!(empty.capacity(), 0, "Reserved unnecessary memory for an empty vector");

    let with_capacity = RawVector::with_capacity(137);
    assert!(with_capacity.is_empty(), "Created a non-empty vector by specifying capacity");
    assert!(with_capacity.capacity() >= 137, "Vector capacity is lower than specified");
}

#[test]
fn with_len_and_clear() {
    let mut v = RawVector::with_len(137, true);
    assert_eq!(v.len(), 137, "Vector length is not as specified");
    v.clear();
    assert!(v.is_empty(), "Could not clear the vector");
}

#[test]
fn initialization_vs_push() {
    let ones_set = RawVector::with_len(137, true);
    let mut ones_pushed = RawVector::new();
    for _ in 0..137 {
        ones_pushed.push_bit(true);
    }
    assert_eq!(ones_set, ones_pushed, "Initializing with and pushing ones yield different vectors");

    let zeros_set = RawVector::with_len(137, false);
    let mut zeros_pushed = RawVector::new();
    for _ in 0..137 {
        zeros_pushed.push_bit(false);
    }
    assert_eq!(zeros_set, zeros_pushed, "Initializing with and pushing zeros yield different vectors");
}

#[test]
fn initialization_vs_resize() {
    let initialized = RawVector::with_len(137, true);

    let mut extended = RawVector::with_len(66, true);
    extended.resize(137, true);
    assert_eq!(extended, initialized, "Extended vector is invalid");

    let mut truncated = RawVector::with_len(212, true);
    truncated.resize(137, true);
    assert_eq!(truncated, initialized, "Truncated vector is invalid");

    let mut popped = RawVector::with_len(97, true);
    for _ in 0..82 {
        popped.pop_bit();
    }
    popped.resize(137, true);
    assert_eq!(popped, initialized, "Popped vector is invalid after extension");
}

#[test]
fn reserving_capacity() {
    let mut original = RawVector::with_len(137, true);
    let copy = original.clone();
    original.reserve(31 + original.capacity() - original.len());

    assert!(original.capacity() >= 137 + 31, "Reserving additional capacity failed");
    assert_eq!(original, copy, "Reserving additional capacity changed the vector");
}

#[test]
fn push_bits() {
    let mut source: Vec<bool> = Vec::new();
    for i in 0..137 {
        source.push(i & 1 == 1);
    }

    let mut v = RawVector::new();
    for i in 0..137 {
        v.push_bit(source[i]);
    }
    assert_eq!(v.len(), 137, "Invalid vector length");

    let mut popped: Vec<bool> = Vec::new();
    while let Some(bit) = v.pop_bit() {
        popped.push(bit);
    }
    popped.reverse();
    assert!(v.is_empty(), "Non-empty vector after popping all bits");
    assert_eq!(popped, source, "Invalid sequence of bits popped from RawVector");
}

#[test]
fn set_bits() {
    let mut v = RawVector::with_len(137, false);
    let mut w = RawVector::with_len(137, true);
    assert_eq!(v.count_ones(), 0, "Non-zero bits in a zero-initialized vector");
    assert_eq!(w.count_ones(), 137, "Zero bits in an one-initialized vector");
    for i in 0..137 {
        v.set_bit(i, i & 1 == 1);
        w.set_bit(i, i & 1 == 1);
    }
    assert_eq!(v.len(), 137, "Invalid vector length");
    assert_eq!(v.count_ones(), 68, "Invalid number of ones in the vector");

    for i in 0..137 {
        assert_eq!(v.bit(i), i & 1 == 1, "Invalid bit {}", i);
    }
    assert_eq!(v, w, "Fully overwritten vector still depends on the initialization value");

    let complement = v.complement();
    for i in 0..137 {
        assert_eq!(!(complement.bit(i)), v.bit(i), "Invalid bit {} in the complement", i);
    }
}

#[test]
fn push_ints() {
    let mut correct: Vec<(u64, usize)> = Vec::new();
    for i in 0..64 {
        correct.push((i, 63)); correct.push((i * (i + 1), 64));
    }

    let mut v = RawVector::new();
    for (value, width) in correct.iter() {
        unsafe { v.push_int(*value, *width); }
    }
    assert_eq!(v.len(), 64 * (63 + 64), "Invalid vector length");

    correct.reverse();
    let mut popped: Vec<(u64, usize)> = Vec::new();
    for i in 0..correct.len() {
        let width = correct[i].1;
        if let Some(value) = unsafe { v.pop_int(width) } {
            popped.push((value, width));
        }
    }
    assert_eq!(popped.len(), correct.len(), "Invalid number of popped ints");
    assert!(v.is_empty(), "Non-empty vector after popping all ints");
    assert_eq!(popped, correct, "Invalid popped ints");
}

#[test]
fn set_ints() {
    let mut v = RawVector::with_len(64 * (63 + 64), false);
    let mut w = RawVector::with_len(64 * (63 + 64), true);
    let mut bit_offset = 0;
    for i in 0..64 {
        unsafe {
            v.set_int(bit_offset, i, 63); w.set_int(bit_offset, i, 63); bit_offset += 63;
            v.set_int(bit_offset, i * (i + 1), 64); w.set_int(bit_offset, i * (i + 1), 64); bit_offset += 64;
        }
    }
    assert_eq!(v.len(), 64 * (63 + 64), "Invalid vector length");

    bit_offset = 0;
    for i in 0..64 {
        unsafe {
            assert_eq!(v.int(bit_offset, 63), i, "Invalid integer [{}].0", i); bit_offset += 63;
            assert_eq!(v.int(bit_offset, 64), i * (i + 1), "Invalid integer [{}].1", i); bit_offset += 64;
        }
    }
    assert_eq!(v, w, "Fully overwritten vector still depends on the initialization value");
}

#[test]
fn get_words() {
    let correct: Vec<u64> = vec![0x123456, 0x789ABC, 0xFEDCBA, 0x987654];
    let mut v = RawVector::with_len(correct.len() * 64, false);
    for (index, value) in correct.iter().enumerate() {
        unsafe { v.set_int(index * 64, *value, 64); }
    }
    for (index, value) in correct.iter().enumerate() {
        assert_eq!(v.word(index), *value, "Invalid integer {}", index);
    }

    unsafe {
        for (index, value) in correct.iter().enumerate() {
            assert_eq!(v.word_unchecked(index), *value, "Invalid integer {} (unchecked)", index);
        }
    }
}

#[test]
fn serialize() {
    let mut original = RawVector::new();
    for i in 0..64 {
        unsafe { original.push_int(i * (i + 1) * (i + 2), 16); }
    }
    let _ = serialize::test(&original, "raw-vector", Some(18), true);
}

#[test]
fn invalid_data() {
    let filename = serialize::temp_file_name("raw-vector-invalid-data");
    let mut options = OpenOptions::new();
    let mut file = options.create(true).write(true).truncate(true).open(&filename).unwrap();

    // 123 bits will fit in 2 words, but data length is 3.
    let len: usize = 123;
    let data: Vec<u64> = vec![123, 456, 789];
    len.serialize(&mut file).unwrap();
    data.serialize(&mut file).unwrap();
    drop(file);

    let result: io::Result<RawVector> = serialize::load_from(&filename);
    assert_eq!(result.map_err(|e| e.kind()), Err(ErrorKind::InvalidData), "Expected ErrorKind::InvalidData");

    fs::remove_file(&filename).unwrap();
}

//-----------------------------------------------------------------------------

#[test]
fn empty_writer() {
    let first = serialize::temp_file_name("empty-raw-vector-writer");
    let second = serialize::temp_file_name("empty-raw-vector-writer");

    let mut header: Vec<u64> = Vec::new();
    let mut v = RawVectorWriter::new(&first, &mut header).unwrap();
    assert!(v.is_empty(), "Created a non-empty empty writer");
    assert_eq!(v.len(), 0, "Nonzero length for an empty writer");
    assert!(v.is_open(), "Newly created writer is not open");
    assert_eq!(v.filename(), first, "Invalid file name");
    v.close().unwrap();

    let mut header: Vec<u64> = Vec::new();
    let mut w = RawVectorWriter::with_buf_len(&second, &mut header, 1024).unwrap();
    assert!(w.is_empty(), "Created a non-empty empty writer with custom buffer size");
    assert!(w.is_open(), "Newly created writer is not open with custom buffer size");
    assert_eq!(w.filename(), second, "Invalid file name with custom buffer size");
    w.close().unwrap();

    fs::remove_file(&first).unwrap();
    fs::remove_file(&second).unwrap();
}

#[test]
fn push_bits_to_writer() {
    let filename = serialize::temp_file_name("push-bits-to-raw-vector-writer");

    let mut correct: Vec<bool> = Vec::new();
    let mut rng = rand::thread_rng();
    for _ in 0..3523 {
        correct.push(rng.gen());
    }

    let mut header: Vec<u64> = Vec::new();
    let mut v = RawVectorWriter::with_buf_len(&filename, &mut header, 1024).unwrap();
    for bit in correct.iter() {
        v.push_bit(*bit);
    }
    assert_eq!(v.len(), correct.len(), "Invalid size for the writer after push_bit");
    v.close().unwrap();
    assert!(!v.is_open(), "Could not close the writer");

    let w: RawVector = serialize::load_from(&filename).unwrap();
    assert_eq!(w.len(), correct.len(), "Invalid size for the loaded vector");
    for i in 0..correct.len() {
        assert_eq!(w.bit(i), correct[i], "Invalid bit {}", i);
    }

    fs::remove_file(&filename).unwrap();
}

#[test]
fn push_ints_to_writer() {
    let filename = serialize::temp_file_name("push-ints-to-raw-vector-writer");
    let width: usize = 31;
    let correct = random_vector(71, width);

    let mut header: Vec<u64> = Vec::new();
    let mut v = RawVectorWriter::with_buf_len(&filename, &mut header, 1024).unwrap();
    for value in correct.iter() {
        unsafe { v.push_int(*value, width); }
    }
    assert_eq!(v.len(), correct.len() * width, "Invalid size for the writer");
    v.close().unwrap();
    assert!(!v.is_open(), "Could not close the writer");

    let w: RawVector = serialize::load_from(&filename).unwrap();
    assert_eq!(w.len(), correct.len() * width, "Invalid size for the loaded vector");
    for i in 0..correct.len() {
        unsafe { assert_eq!(w.int(i * width, width), correct[i], "Invalid integer {}", i); }
    }

    fs::remove_file(&filename).unwrap();
}

#[test]
#[ignore]
fn large_writer() {
    let filename = serialize::temp_file_name("large-raw-vector-writer");
    let width: usize = 31;
    let correct = random_vector(620001, width);

    let mut header: Vec<u64> = Vec::new();
    let mut v = RawVectorWriter::new(&filename, &mut header).unwrap();
    for value in correct.iter() {
        unsafe { v.push_int(*value, width); }
    }
    assert_eq!(v.len(), correct.len() * width, "Invalid size for the writer");
    v.close().unwrap();
    assert!(!v.is_open(), "Could not close the writer");

    let w: RawVector = serialize::load_from(&filename).unwrap();
    assert_eq!(w.len(), correct.len() * width, "Invalid size for the loaded vector");
    for i in 0..correct.len() {
        unsafe { assert_eq!(w.int(i * width, width), correct[i], "Invalid integer {}", i); }
    }

    fs::remove_file(&filename).unwrap();
}

//-----------------------------------------------------------------------------

fn check_mapper(mapper: &RawVectorMapper, truth: &RawVector, width: usize) {
    assert!(!mapper.is_mutable(), "Read-only mapper is mutable");
    assert_eq!(mapper.len(), truth.len(), "Invalid mapper length");
    assert_eq!(mapper.is_empty(), truth.is_empty(), "Invalid mapper emptiness");
    assert_eq!(mapper.count_ones(), truth.count_ones(), "Invalid mapper length");

    for i in 0..mapper.len() {
        assert_eq!(mapper.bit(i), truth.bit(i), "Invalid bit {}", i);
    }
    for i in (0..mapper.len()).step_by(width) {
        unsafe { assert_eq!(mapper.int(i, width), truth.int(i, width), "Invalid int at {}", i); }
    }
    for i in 0..bits::bits_to_words(mapper.len()) {
        assert_eq!(mapper.word(i), truth.word(i), "Invalid word {}", i);
        unsafe { assert_eq!(mapper.word_unchecked(i), truth.word_unchecked(i), "Invalid word {} (unchecked)", i); }
    }
}

#[test]
fn empty_mapper() {
    let filename = serialize::temp_file_name("empty-raw-vector-mapper");
    let truth = RawVector::new();
    serialize::serialize_to(&truth, &filename).unwrap();

    let map = MemoryMap::new(&filename, MappingMode::ReadOnly).unwrap();
    let mapper = RawVectorMapper::new(&map, 0).unwrap();
    check_mapper(&mapper, &truth, 31);

    drop(mapper); drop(map);
    fs::remove_file(&filename).unwrap();
}

#[test]
fn non_empty_mapper() {
    let filename = serialize::temp_file_name("non-empty-raw-vector-mapper");
    let width: usize = 31;
    let truth = random_raw_vector(247, width);
    serialize::serialize_to(&truth, &filename).unwrap();

    let map = MemoryMap::new(&filename, MappingMode::ReadOnly).unwrap();
    let mapper = RawVectorMapper::new(&map, 0).unwrap();
    check_mapper(&mapper, &truth, width);

    drop(mapper); drop(map);
    fs::remove_file(&filename).unwrap();
}

#[test]
fn mapper_offset() {
    let filename = serialize::temp_file_name("raw-vector-mapper-offset");
    let width: usize = 31;
    let truth = random_raw_vector(247, width);

    let mut options = OpenOptions::new();
    let mut file = options.create(true).write(true).truncate(true).open(&filename).unwrap();
    width.serialize(&mut file).unwrap(); // One element of padding.
    truth.serialize(&mut file).unwrap();
    drop(file);

    let map = MemoryMap::new(&filename, MappingMode::ReadOnly).unwrap();
    let mapper = RawVectorMapper::new(&map, 1).unwrap();
    check_mapper(&mapper, &truth, width);

    drop(mapper); drop(map);
    fs::remove_file(&filename).unwrap();
}

#[test]
#[ignore]
fn large_mapper() {
    let filename = serialize::temp_file_name("large-raw-vector-mapper");
    let width: usize = 31;
    let truth = random_raw_vector(731175, width);
    serialize::serialize_to(&truth, &filename).unwrap();

    let map = MemoryMap::new(&filename, MappingMode::ReadOnly).unwrap();
    let mapper = RawVectorMapper::new(&map, 0).unwrap();
    check_mapper(&mapper, &truth, width);

    drop(mapper); drop(map);
    fs::remove_file(&filename).unwrap();
}

//-----------------------------------------------------------------------------