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zhaoheting-zontalcaetera
zhaoheting-zontal
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caetera
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Solve code review issues.
Squash 2 Solve code review issues.
1 parent c4df029 commit 7e64b28

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1 file changed

+28
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‎Writer/MetadataWriter.cs‎

Lines changed: 28 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -227,20 +227,20 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
227227
// Sample Data
228228
if (!rawFile.SampleInformation.SampleName.IsNullOrEmpty())
229229
{
230-
metadata.addSampleProperty(new CVTerm("MS:1000002", "MS", "Sample Name",
230+
metadata.addSampleProperty(new CVTerm("MS:1000002", "MS", "sample name",
231231
rawFile.SampleInformation.SampleName));
232232
}
233233

234234
if (!rawFile.SampleInformation.SampleId.IsNullOrEmpty())
235235
{
236-
metadata.addSampleProperty(new CVTerm("MS:1000001", "MS", "Sample Number",
236+
metadata.addSampleProperty(new CVTerm("MS:1000001", "MS", "sample number",
237237
rawFile.SampleInformation.SampleId));
238238
}
239239

240240
if (!rawFile.SampleInformation.SampleType.ToString().IsNullOrEmpty() &&
241241
!rawFile.SampleInformation.SampleType.ToString().Equals("Unknown"))
242242
{
243-
metadata.addSampleProperty(new CVTerm("NCIT:C25284", "NCIT", "Sample Type",
243+
metadata.addSampleProperty(new CVTerm("NCIT:C25284", "NCIT", "Type",
244244
rawFile.SampleInformation.SampleType.ToString()));
245245
}
246246

@@ -258,13 +258,13 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
258258

259259
if (rawFile.SampleInformation.SampleVolume != 0)
260260
{
261-
metadata.addSampleProperty(new CVTerm("MS:1000005", "MS", "Sample Volume",
261+
metadata.addSampleProperty(new CVTerm("MS:1000005", "MS", "sample volume",
262262
rawFile.SampleInformation.SampleVolume.ToString(CultureInfo.InvariantCulture)));
263263
}
264264

265265
if (rawFile.SampleInformation.InjectionVolume != 0)
266266
{
267-
metadata.addSampleProperty(new CVTerm("AFR:0001577", "AFO", "Injection Volume",
267+
metadata.addSampleProperty(new CVTerm("AFR:0001577", "AFO", "injection volume setting",
268268
rawFile.SampleInformation.InjectionVolume.ToString(CultureInfo.InvariantCulture)));
269269
}
270270

@@ -276,53 +276,48 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
276276

277277
if (rawFile.SampleInformation.DilutionFactor != 0)
278278
{
279-
metadata.addSampleProperty(new CVTerm("AFQ:0000178", "AFO", "Dilution Factor",
279+
metadata.addSampleProperty(new CVTerm("AFQ:0000178", "AFO", "dilution factor",
280280
rawFile.SampleInformation.DilutionFactor.ToString(CultureInfo.InvariantCulture)));
281281
}
282282

283283
if (!rawFile.SampleInformation.InstrumentMethodFile.IsNullOrEmpty())
284284
{
285-
metadata.addSampleProperty(new CVTerm("AFR:0002045", "AFO", "Device Acquisition Method", rawFile.SampleInformation.InstrumentMethodFile));
285+
metadata.addSampleProperty(new CVTerm("AFR:0002045", "AFO", "device acquisition method", rawFile.SampleInformation.InstrumentMethodFile));
286286
}
287287

288288
if (rawFile.SampleInformation.IstdAmount != 0)
289289
{
290-
metadata.addSampleProperty(new CVTerm("", "", "Internal Standard Amount", rawFile.SampleInformation.IstdAmount.ToString()));
290+
metadata.addSampleProperty(new CVTerm("", "", "internal standard amount", rawFile.SampleInformation.IstdAmount.ToString()));
291291
}
292292

293293
if (!rawFile.SampleInformation.CalibrationLevel.IsNullOrEmpty())
294294
{
295-
metadata.addSampleProperty(new CVTerm("AFR:0001849", "AFO", "Calibration Level", rawFile.SampleInformation.CalibrationLevel));
295+
metadata.addSampleProperty(new CVTerm("AFR:0001849", "AFO", "calibration level", rawFile.SampleInformation.CalibrationLevel));
296296
}
297297

298298
if (!rawFile.SampleInformation.ProcessingMethodFile.IsNullOrEmpty())
299299
{
300-
metadata.addSampleProperty(new CVTerm("AFR:0002175", "AFO", "Data Processing Method", rawFile.SampleInformation.ProcessingMethodFile));
300+
metadata.addSampleProperty(new CVTerm("AFR:0002175", "AFO", "data processing method", rawFile.SampleInformation.ProcessingMethodFile));
301301
}
302302

303303
if (rawFile.SampleInformation.SampleWeight != 0)
304304
{
305-
metadata.addSampleProperty(new CVTerm("", "", "Sample Weight", rawFile.SampleInformation.SampleWeight.ToString()));
305+
metadata.addSampleProperty(new CVTerm("AFR:0001982", "AFO", "sample weight", rawFile.SampleInformation.SampleWeight.ToString()));
306306
}
307307

308308
string[] userLabels = rawFile.UserLabel;
309309
string[] userTexts = rawFile.SampleInformation.UserText;
310310
if (!userLabels.IsNullOrEmpty() && !userTexts.IsNullOrEmpty())
311311
{
312-
if (userLabels.Length > userTexts.Length)
313-
{
314-
throw new RawFileParserException();
315-
}
316312
for (int i = 0; i < userLabels.Length; i++)
317313
{
318-
if (!userTexts[i].IsNullOrEmpty())
314+
if (i < userTexts.Length && !userTexts[i].IsNullOrEmpty())
319315
{
320316
metadata.addSampleProperty(new CVTerm("", "", userLabels[i], userTexts[i]));
321317
}
322318
}
323319
}
324320

325-
326321
// Write the meta data to file
327322
var json = JsonConvert.SerializeObject(metadata);
328323
json.Replace("\r\n", "\n");
@@ -346,7 +341,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
346341
var output = new List<string>
347342
{
348343
"#FileProperties",
349-
"RAW File Path=" + rawFile.FileName,
344+
"RAW file path=" + rawFile.FileName,
350345
"RAW file version=" + rawFile.FileHeader.Revision,
351346
"Creation date=" + rawFile.FileHeader.CreationDate
352347
};
@@ -413,86 +408,82 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
413408

414409
if (!rawFile.SampleInformation.SampleName.IsNullOrEmpty())
415410
{
416-
output.Add("Sample Name=" + rawFile.SampleInformation.SampleName);
411+
output.Add("Sample name=" + rawFile.SampleInformation.SampleName);
417412
}
418413

419414
if (!rawFile.SampleInformation.SampleId.IsNullOrEmpty())
420415
{
421-
output.Add("Sample Number=" + rawFile.SampleInformation.SampleId);
416+
output.Add("Sample id=" + rawFile.SampleInformation.SampleId);
422417
}
423418

424419
if (!rawFile.SampleInformation.SampleType.ToString().IsNullOrEmpty() &&
425420
!rawFile.SampleInformation.SampleType.ToString().Equals("Unknown"))
426421
{
427-
output.Add("Sample Type=" + rawFile.SampleInformation.SampleType);
422+
output.Add("Sample type=" + rawFile.SampleInformation.SampleType);
428423
}
429424

430425
if (!rawFile.SampleInformation.Comment.IsNullOrEmpty())
431426
{
432-
output.Add("Comment=" + rawFile.SampleInformation.Comment);
427+
output.Add("Sample comment=" + rawFile.SampleInformation.Comment);
433428
}
434429

435430
if (!rawFile.SampleInformation.Vial.IsNullOrEmpty())
436431
{
437-
output.Add("Vial=" + rawFile.SampleInformation.Vial);
432+
output.Add("Sample vial=" + rawFile.SampleInformation.Vial);
438433
}
439434

440435
if (rawFile.SampleInformation.SampleVolume != 0)
441436
{
442-
output.Add("Sample Volume=" + rawFile.SampleInformation.SampleVolume);
437+
output.Add("Sample volume=" + rawFile.SampleInformation.SampleVolume);
443438
}
444439

445440
if (rawFile.SampleInformation.InjectionVolume != 0)
446441
{
447-
output.Add("Injection Volume=" + rawFile.SampleInformation.InjectionVolume);
442+
output.Add("Sample injection volume=" + rawFile.SampleInformation.InjectionVolume);
448443
}
449444

450445
if (rawFile.SampleInformation.RowNumber != 0)
451446
{
452-
output.Add("Sample Row Number=" + rawFile.SampleInformation.RowNumber);
447+
output.Add("Sample row number=" + rawFile.SampleInformation.RowNumber);
453448
}
454449

455450
if (rawFile.SampleInformation.DilutionFactor != 0)
456451
{
457-
output.Add("Dilution Factor=" + rawFile.SampleInformation.DilutionFactor);
452+
output.Add("Sample dilution factor=" + rawFile.SampleInformation.DilutionFactor);
458453
}
459454

460455
if (rawFile.SampleInformation.IstdAmount != 0)
461456
{
462-
output.Add("Internal Standard Amount=" + rawFile.SampleInformation.IstdAmount);
457+
output.Add("Internal standard amount=" + rawFile.SampleInformation.IstdAmount);
463458
}
464459

465460
if (!rawFile.SampleInformation.CalibrationLevel.IsNullOrEmpty())
466461
{
467-
output.Add("Calibration Level=" + rawFile.SampleInformation.CalibrationLevel);
462+
output.Add("Calibration level=" + rawFile.SampleInformation.CalibrationLevel);
468463
}
469464

470465
if (!rawFile.SampleInformation.InstrumentMethodFile.IsNullOrEmpty())
471466
{
472-
output.Add("Device Acquisition Method=" + rawFile.SampleInformation.InstrumentMethodFile);
467+
output.Add("Device acquisition method=" + rawFile.SampleInformation.InstrumentMethodFile);
473468
}
474469

475470
if (rawFile.SampleInformation.SampleWeight != 0)
476471
{
477-
output.Add("Sample Weight=" + rawFile.SampleInformation.SampleWeight);
472+
output.Add("Sample weight=" + rawFile.SampleInformation.SampleWeight);
478473
}
479474

480475
if (!rawFile.SampleInformation.ProcessingMethodFile.IsNullOrEmpty())
481476
{
482-
output.Add("Data Processing Method=" + rawFile.SampleInformation.ProcessingMethodFile);
477+
output.Add("Data processing method=" + rawFile.SampleInformation.ProcessingMethodFile);
483478
}
484479

485480
string[] userLabels = rawFile.UserLabel;
486481
string[] userTexts = rawFile.SampleInformation.UserText;
487482
if (!userLabels.IsNullOrEmpty() && !userTexts.IsNullOrEmpty())
488483
{
489-
if (userLabels.Length > userTexts.Length)
490-
{
491-
throw new RawFileParserException();
492-
}
493484
for (int i = 0; i < userLabels.Length; i++)
494485
{
495-
if (!userTexts[i].IsNullOrEmpty())
486+
if (i < userTexts.Length && !userTexts[i].IsNullOrEmpty())
496487
{
497488
output.Add(userLabels[i] + "=" + userTexts[i]);
498489
}

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