opentfraw 1.3.5

Rust parser for Thermo Fisher RAW mass spectrometry files.
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
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
use crate::error::Result;
use crate::reader::BinaryReader;
use crate::types::GenericType;
use std::io::{Cursor, Read, Seek};

/// A field descriptor within a GenericDataHeader.
#[derive(Debug, Clone)]
pub struct GenericDataDescriptor {
    pub field_type: GenericType,
    pub length: u32,
    pub label: String,
}

/// Self-describing header for GenericRecord streams.
#[derive(Debug)]
pub struct GenericDataHeader {
    pub fields: Vec<GenericDataDescriptor>,
}

/// A typed value from a generic record.
#[derive(Debug, Clone)]
pub enum GenericValue {
    Gap,
    Int8(i8),
    Bool(bool),
    UInt8(u8),
    Int16(i16),
    UInt16(u16),
    Int32(i32),
    UInt32(u32),
    Float32(f32),
    Float64(f64),
    String(String),
}

/// A single record decoded using a GenericDataHeader.
#[derive(Debug)]
pub struct GenericRecord {
    pub values: Vec<(String, GenericValue)>,
}

impl GenericDataHeader {
    /// Try to read a GenericDataHeader. Returns `None` if the data at the
    /// current position does not look like a valid header (e.g. unreasonable
    /// field count or invalid type codes). The reader position is restored
    /// on failure.
    pub(crate) fn try_read<R: Read + Seek>(r: &mut BinaryReader<R>) -> Result<Option<Self>> {
        let saved_pos = r.position();
        let n = r.read_u32()?;
        // A genuine schema has at least a couple of fields and fewer than ~500.
        // The error-log "gap" region that precedes the schema in v64+ can
        // otherwise mislead us by looking like a 0- or 1-field header.
        if !(2..=500).contains(&n) {
            r.seek_to(saved_pos)?;
            return Ok(None);
        }
        let mut fields = Vec::with_capacity(n as usize);
        for _ in 0..n {
            let type_code = r.read_u32()?;
            match GenericType::from_u32(type_code) {
                Some(field_type) => {
                    let length = r.read_u32()?;
                    // Character count of the label. Real Thermo labels are
                    // short and printable; require it to look sane or the
                    // whole header is bogus.
                    let label_start = r.position();
                    let char_count = r.read_u32()?;
                    if char_count > 200 {
                        r.seek_to(saved_pos)?;
                        return Ok(None);
                    }
                    r.seek_to(label_start)?;
                    let label = match r.read_pascal_string() {
                        Ok(s) => s,
                        Err(crate::error::Error::InvalidUtf16(_)) => {
                            r.seek_to(saved_pos)?;
                            return Ok(None);
                        }
                        Err(e) => return Err(e),
                    };
                    if !label_is_plausible(&label) {
                        r.seek_to(saved_pos)?;
                        return Ok(None);
                    }
                    fields.push(GenericDataDescriptor {
                        field_type,
                        length,
                        label,
                    });
                }
                None => {
                    r.seek_to(saved_pos)?;
                    return Ok(None);
                }
            }
        }
        let hdr = Self { fields };
        if !hdr.looks_meaningful() {
            r.seek_to(saved_pos)?;
            return Ok(None);
        }
        Ok(Some(hdr))
    }

    /// A schema is "meaningful" if it contains at least a few fields with
    /// real labels and has a non-trivial fixed record size. Used to reject
    /// false positives picked up by the forward scan.
    fn looks_meaningful(&self) -> bool {
        let named = self.fields.iter().filter(|f| !f.label.is_empty()).count();
        named >= 2 && self.fixed_record_size() > 0
    }

    /// Sum of fixed byte sizes contributed by each descriptor. For variable
    /// types (String/WideString) the descriptor's `length` field is used as
    /// the storage allocation - which is the fixed on-disk size per record.
    pub(crate) fn fixed_record_size(&self) -> usize {
        self.fields
            .iter()
            .map(|f| match f.field_type {
                GenericType::Gap => 0,
                GenericType::Int8
                | GenericType::Bool
                | GenericType::BoolYesNo
                | GenericType::BoolOnOff
                | GenericType::UInt8 => 1,
                GenericType::Int16 | GenericType::UInt16 => 2,
                GenericType::Int32 | GenericType::UInt32 | GenericType::Float32 => 4,
                GenericType::Float64 => 8,
                GenericType::AsciiString => f.length as usize,
                GenericType::WideString => f.length as usize * 2,
            })
            .sum()
    }

    /// Scan forward from the current position for a plausible GenericDataHeader
    /// in a bounded window. The v64+ error-log region contains padding bytes
    /// before the scan-parameters schema whose size isn't easily computed, so
    /// we locate the schema by scanning for a valid signature.
    pub(crate) fn find_forward<R: Read + Seek>(
        r: &mut BinaryReader<R>,
        max_scan: u64,
        expected_record_size: Option<usize>,
    ) -> Result<Option<Self>> {
        let start = r.position();
        let cap = max_scan.min(4 * 1024 * 1024) as usize;
        r.seek_to(start)?;
        let buf = r.read_bytes(cap)?;
        // Two passes: first require the schema's fixed record size to match
        // the tail; second accept any meaningful schema.
        //
        // Parse candidates entirely from the in-memory buffer using a Cursor so
        // that we never seek the underlying file reader for each false positive.
        // This avoids O(n) file seeks when the error-log gap is large (>1 MB).
        for pass in 0..2 {
            let mut offset = 0usize;
            while offset + 4 <= buf.len() {
                let n = crate::bytes::read_u32_le(&buf, offset)?;
                if (2..=500).contains(&n) {
                    let mut cursor = BinaryReader::new(Cursor::new(&buf[offset..]));
                    if let Some(hdr) = Self::try_read(&mut cursor)? {
                        let size_ok = match (pass, expected_record_size) {
                            (0, Some(want)) => hdr.fixed_record_size() == want,
                            _ => true,
                        };
                        if size_ok {
                            return Ok(Some(hdr));
                        }
                    }
                }
                offset += 2;
            }
            if expected_record_size.is_none() {
                break;
            }
        }
        r.seek_to(start)?;
        Ok(None)
    }
}

/// Heuristic: a GDH field label must either be empty or have reasonable
/// length. Labels are sometimes short single-character sentinels so we
/// don't require printability.
fn label_is_plausible(s: &str) -> bool {
    s.len() <= 200
}

impl GenericRecord {
    pub(crate) fn read<R: Read + Seek>(
        r: &mut BinaryReader<R>,
        header: &GenericDataHeader,
    ) -> Result<Self> {
        let mut values = Vec::with_capacity(header.fields.len());
        for desc in &header.fields {
            let label = desc.label.clone();
            let value = match desc.field_type {
                GenericType::Gap => GenericValue::Gap,
                GenericType::Int8 => GenericValue::Int8(r.read_i8()?),
                GenericType::Bool | GenericType::BoolYesNo | GenericType::BoolOnOff => {
                    GenericValue::Bool(r.read_u8()? != 0)
                }
                GenericType::UInt8 => GenericValue::UInt8(r.read_u8()?),
                GenericType::Int16 => GenericValue::Int16(r.read_i16()?),
                GenericType::UInt16 => GenericValue::UInt16(r.read_u16()?),
                GenericType::Int32 => GenericValue::Int32(r.read_i32()?),
                GenericType::UInt32 => GenericValue::UInt32(r.read_u32()?),
                GenericType::Float32 => GenericValue::Float32(r.read_f32()?),
                GenericType::Float64 => GenericValue::Float64(r.read_f64()?),
                GenericType::AsciiString => {
                    let s = if desc.length > 0 {
                        let bytes = r.read_bytes(desc.length as usize)?;
                        let end = bytes.iter().position(|&b| b == 0).unwrap_or(bytes.len());
                        String::from_utf8_lossy(&bytes[..end]).into_owned()
                    } else {
                        String::new()
                    };
                    GenericValue::String(s)
                }
                GenericType::WideString => {
                    let s = if desc.length > 0 {
                        r.read_utf16_fixed(desc.length as usize * 2)?
                    } else {
                        String::new()
                    };
                    GenericValue::String(s)
                }
            };
            values.push((label, value));
        }
        Ok(Self { values })
    }

    /// Look up a field by label and return a reference to its value.
    pub fn get(&self, label: &str) -> Option<&GenericValue> {
        self.values.iter().find(|(l, _)| l == label).map(|(_, v)| v)
    }

    /// Get a float64 field by label.
    pub fn get_f64(&self, label: &str) -> Option<f64> {
        match self.get(label)? {
            GenericValue::Float64(v) => Some(*v),
            GenericValue::Float32(v) => Some(*v as f64),
            _ => None,
        }
    }

    /// Get a float32 field by label.
    pub fn get_f32(&self, label: &str) -> Option<f32> {
        match self.get(label)? {
            GenericValue::Float32(v) => Some(*v),
            GenericValue::Float64(v) => Some(*v as f32),
            _ => None,
        }
    }

    /// Get an i32 field by label.
    pub fn get_i32(&self, label: &str) -> Option<i32> {
        match self.get(label)? {
            GenericValue::Int32(v) => Some(*v),
            GenericValue::Int16(v) => Some(*v as i32),
            GenericValue::Int8(v) => Some(*v as i32),
            _ => None,
        }
    }

    /// Get a string field by label.
    pub fn get_string(&self, label: &str) -> Option<&str> {
        match self.get(label)? {
            GenericValue::String(v) => Some(v.as_str()),
            _ => None,
        }
    }
}

impl GenericValue {
    /// Get as f64, converting numeric types.
    pub fn as_f64(&self) -> Option<f64> {
        match self {
            Self::Float64(v) => Some(*v),
            Self::Float32(v) => Some(*v as f64),
            Self::Int32(v) => Some(*v as f64),
            Self::UInt32(v) => Some(*v as f64),
            Self::Int16(v) => Some(*v as f64),
            Self::UInt16(v) => Some(*v as f64),
            Self::Int8(v) => Some(*v as f64),
            Self::UInt8(v) => Some(*v as f64),
            _ => None,
        }
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::test_util::pascal_string;
    use std::io::Cursor;

    /// One field descriptor: type_code(u32) + length(u32) + label (pascal string).
    fn field_bytes(type_code: u32, length: u32, label: &str) -> Vec<u8> {
        let mut out = type_code.to_le_bytes().to_vec();
        out.extend_from_slice(&length.to_le_bytes());
        out.extend_from_slice(&pascal_string(label));
        out
    }

    /// A full GDH blob: field count(u32) + that many field descriptors.
    fn gdh_bytes(fields: &[(u32, u32, &str)]) -> Vec<u8> {
        let mut out = (fields.len() as u32).to_le_bytes().to_vec();
        for &(t, l, label) in fields {
            out.extend_from_slice(&field_bytes(t, l, label));
        }
        out
    }

    fn try_read(bytes: Vec<u8>) -> Result<Option<GenericDataHeader>> {
        let mut r = BinaryReader::new(Cursor::new(bytes));
        GenericDataHeader::try_read(&mut r)
    }

    #[test]
    fn valid_two_field_header_parses() {
        let bytes = gdh_bytes(&[
            (GenericType::Float64 as u32, 0, "RT:"),
            (GenericType::Int32 as u32, 0, "Scan:"),
        ]);
        let hdr = try_read(bytes).unwrap().expect("should parse");
        assert_eq!(hdr.fields.len(), 2);
        assert_eq!(hdr.fields[0].label, "RT:");
        assert_eq!(hdr.fields[1].label, "Scan:");
        assert_eq!(hdr.fixed_record_size(), 8 + 4);
    }

    #[test]
    fn field_count_zero_is_rejected() {
        let bytes = gdh_bytes(&[]);
        assert!(try_read(bytes).unwrap().is_none());
    }

    #[test]
    fn field_count_one_is_rejected() {
        let bytes = gdh_bytes(&[(GenericType::Int32 as u32, 0, "Only:")]);
        assert!(try_read(bytes).unwrap().is_none());
    }

    #[test]
    fn field_count_above_500_is_rejected() {
        let mut bytes = 501u32.to_le_bytes().to_vec();
        bytes.extend_from_slice(&field_bytes(GenericType::Int32 as u32, 0, "A:"));
        assert!(try_read(bytes).unwrap().is_none());
    }

    #[test]
    fn invalid_type_code_is_rejected() {
        let bytes = gdh_bytes(&[(0xDEAD_BEEF, 0, "A:"), (GenericType::Int32 as u32, 0, "B:")]);
        assert!(try_read(bytes).unwrap().is_none());
    }

    #[test]
    fn label_char_count_above_200_is_rejected() {
        let mut out = 2u32.to_le_bytes().to_vec();
        out.extend_from_slice(&(GenericType::Int32 as u32).to_le_bytes());
        out.extend_from_slice(&0u32.to_le_bytes()); // length
        out.extend_from_slice(&300u32.to_le_bytes()); // implausible char count
        out.extend_from_slice(&[0u8; 20]); // some filler bytes (not enough for 300 chars)
        assert!(try_read(out).unwrap().is_none());
    }

    #[test]
    fn all_empty_labels_are_not_meaningful() {
        // named() requires at least 2 non-empty labels; both empty here.
        let bytes = gdh_bytes(&[
            (GenericType::Int32 as u32, 0, ""),
            (GenericType::Int32 as u32, 0, ""),
        ]);
        assert!(try_read(bytes).unwrap().is_none());
    }

    #[test]
    fn position_restored_on_rejection() {
        let mut bytes = vec![0xAAu8; 8]; // leading junk before the candidate
        let candidate_start = bytes.len();
        bytes.extend_from_slice(&gdh_bytes(&[])); // n=0, rejected
        let mut r = BinaryReader::new(Cursor::new(bytes));
        r.seek_to(candidate_start as u64).unwrap();
        let saved = r.position();
        assert!(GenericDataHeader::try_read(&mut r).unwrap().is_none());
        assert_eq!(r.position(), saved);
    }

    #[test]
    fn truncated_header_is_eof_not_panic() {
        let mut bytes = gdh_bytes(&[
            (GenericType::Float64 as u32, 0, "RT:"),
            (GenericType::Int32 as u32, 0, "Scan:"),
        ]);
        bytes.truncate(bytes.len() - 2);
        // Either a clean error or a `None` (truncated pascal string content
        // fails UTF-16 decoding / hits EOF) is acceptable; a panic is not.
        let _ = try_read(bytes);
    }

    #[test]
    fn fixed_record_size_sums_all_field_kinds() {
        let bytes = gdh_bytes(&[
            (GenericType::Int8 as u32, 0, "a:"),
            (GenericType::Int32 as u32, 0, "b:"),
            (GenericType::Float64 as u32, 0, "c:"),
            (GenericType::AsciiString as u32, 10, "d:"),
            (GenericType::WideString as u32, 5, "e:"),
        ]);
        let hdr = try_read(bytes).unwrap().unwrap();
        // 1 (Int8) + 4 (Int32) + 8 (Float64) + 10 (Ascii len) + 5*2 (Wide len*2)
        assert_eq!(hdr.fixed_record_size(), 1 + 4 + 8 + 10 + 10);
    }

    #[test]
    fn find_forward_locates_header_after_garbage_prefix() {
        let mut bytes = vec![0x11u8; 64]; // garbage that doesn't look like a valid GDH
        bytes.extend_from_slice(&gdh_bytes(&[
            (GenericType::Float64 as u32, 0, "RT:"),
            (GenericType::Int32 as u32, 0, "Scan:"),
        ]));
        let max_scan = bytes.len() as u64;
        let mut r = BinaryReader::new(Cursor::new(bytes));
        let hdr = GenericDataHeader::find_forward(&mut r, max_scan, None)
            .unwrap()
            .expect("should find the embedded header");
        assert_eq!(hdr.fields.len(), 2);
    }

    #[test]
    fn find_forward_returns_none_when_absent() {
        let bytes = vec![0x11u8; 128];
        let max_scan = bytes.len() as u64;
        let mut r = BinaryReader::new(Cursor::new(bytes));
        assert!(GenericDataHeader::find_forward(&mut r, max_scan, None)
            .unwrap()
            .is_none());
    }

    #[test]
    fn generic_record_reads_typed_fields() {
        let hdr = GenericDataHeader {
            fields: vec![
                GenericDataDescriptor {
                    field_type: GenericType::Int32,
                    length: 0,
                    label: "Scan:".to_string(),
                },
                GenericDataDescriptor {
                    field_type: GenericType::Float64,
                    length: 0,
                    label: "RT:".to_string(),
                },
                GenericDataDescriptor {
                    field_type: GenericType::AsciiString,
                    length: 8,
                    label: "Note:".to_string(),
                },
            ],
        };
        let mut bytes = 42i32.to_le_bytes().to_vec();
        bytes.extend_from_slice(&1.5f64.to_le_bytes());
        let mut note = b"hi".to_vec();
        note.resize(8, 0); // null-padded fixed-width ASCII field
        bytes.extend_from_slice(&note);

        let mut r = BinaryReader::new(Cursor::new(bytes));
        let record = GenericRecord::read(&mut r, &hdr).unwrap();
        assert_eq!(record.get_i32("Scan:"), Some(42));
        assert_eq!(record.get_f64("RT:"), Some(1.5));
        assert_eq!(record.get_string("Note:"), Some("hi"));
    }

    #[test]
    fn generic_record_truncated_is_eof() {
        let hdr = GenericDataHeader {
            fields: vec![GenericDataDescriptor {
                field_type: GenericType::Float64,
                length: 0,
                label: "RT:".to_string(),
            }],
        };
        let bytes = vec![0u8; 4]; // Float64 needs 8 bytes
        let mut r = BinaryReader::new(Cursor::new(bytes));
        assert!(GenericRecord::read(&mut r, &hdr).is_err());
    }

    #[test]
    fn generic_value_as_f64_converts_numeric_variants() {
        assert_eq!(GenericValue::Float64(2.5).as_f64(), Some(2.5));
        assert_eq!(GenericValue::Int32(7).as_f64(), Some(7.0));
        assert_eq!(GenericValue::UInt8(3).as_f64(), Some(3.0));
        assert_eq!(GenericValue::Gap.as_f64(), None);
        assert_eq!(GenericValue::String("x".into()).as_f64(), None);
    }
}