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zhaoheting-zontalcaetera
zhaoheting-zontal
authored and
caetera
committed
Remove reduncant properties.
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1 parent 84519e8 commit c4df029

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2 files changed

+28
-42
lines changed

2 files changed

+28
-42
lines changed

‎MainClass.cs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -51,10 +51,10 @@ public static void Main(string[] args)
5151
private static void XicParametersParsing(string[] args)
5252
{
5353
XicParameters parameters = new XicParameters();
54-
string singleFile = "D:\\ht\\testdata\\Columbo-PM-22-291-MetIDEFatePhoto-07092022-MA-04B.raw";
54+
string singleFile = null;
5555
string fileDirectory = null;
5656
string outputFile = null;
57-
string outputDirectory = "D:\\ht\\testdata";
57+
string outputDirectory = null;
5858
string logFormatString = null;
5959

6060
var optionSet = new OptionSet

‎Writer/MetadataWriter.cs‎

Lines changed: 26 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -152,9 +152,7 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
152152
var metadata = new Metadata();
153153

154154
// File Properties
155-
string filePath = rawFile.FileName;
156-
metadata.addFileProperty(new CVTerm("NCIT:C47922", "NCIT", "Pathname", filePath));
157-
metadata.addFileProperty(new CVTerm("NCIT:*****************", "NCIT", "File Name", filePath.Substring(0, filePath.LastIndexOf(".")).Remove(0, filePath.LastIndexOf("\\") + 1)));
155+
metadata.addFileProperty(new CVTerm("NCIT:C47922", "NCIT", "Pathname", rawFile.FileName));
158156
metadata.addFileProperty(new CVTerm("NCIT:C25714", "NCIT", "Version",
159157
rawFile.FileHeader.Revision.ToString()));
160158
metadata.addFileProperty(new CVTerm("NCIT:C69199", "NCIT", "Content Creation Date",
@@ -229,20 +227,20 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
229227
// Sample Data
230228
if (!rawFile.SampleInformation.SampleName.IsNullOrEmpty())
231229
{
232-
metadata.addSampleProperty(new CVTerm("MS:1000002", "MS", "sample name",
230+
metadata.addSampleProperty(new CVTerm("MS:1000002", "MS", "Sample Name",
233231
rawFile.SampleInformation.SampleName));
234232
}
235233

236234
if (!rawFile.SampleInformation.SampleId.IsNullOrEmpty())
237235
{
238-
metadata.addSampleProperty(new CVTerm("MS:1000001", "MS", "sample number",
236+
metadata.addSampleProperty(new CVTerm("MS:1000001", "MS", "Sample Number",
239237
rawFile.SampleInformation.SampleId));
240238
}
241239

242240
if (!rawFile.SampleInformation.SampleType.ToString().IsNullOrEmpty() &&
243241
!rawFile.SampleInformation.SampleType.ToString().Equals("Unknown"))
244242
{
245-
metadata.addSampleProperty(new CVTerm("NCIT:C25284", "NCIT", "Type",
243+
metadata.addSampleProperty(new CVTerm("NCIT:C25284", "NCIT", "Sample Type",
246244
rawFile.SampleInformation.SampleType.ToString()));
247245
}
248246

@@ -260,13 +258,13 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
260258

261259
if (rawFile.SampleInformation.SampleVolume != 0)
262260
{
263-
metadata.addSampleProperty(new CVTerm("MS:1000005", "MS", "sample volume",
261+
metadata.addSampleProperty(new CVTerm("MS:1000005", "MS", "Sample Volume",
264262
rawFile.SampleInformation.SampleVolume.ToString(CultureInfo.InvariantCulture)));
265263
}
266264

267265
if (rawFile.SampleInformation.InjectionVolume != 0)
268266
{
269-
metadata.addSampleProperty(new CVTerm("AFR:0001577", "AFO", "injection volume setting",
267+
metadata.addSampleProperty(new CVTerm("AFR:0001577", "AFO", "Injection Volume",
270268
rawFile.SampleInformation.InjectionVolume.ToString(CultureInfo.InvariantCulture)));
271269
}
272270

@@ -278,38 +276,33 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
278276

279277
if (rawFile.SampleInformation.DilutionFactor != 0)
280278
{
281-
metadata.addSampleProperty(new CVTerm("AFQ:0000178", "AFO", "dilution factor",
279+
metadata.addSampleProperty(new CVTerm("AFQ:0000178", "AFO", "Dilution Factor",
282280
rawFile.SampleInformation.DilutionFactor.ToString(CultureInfo.InvariantCulture)));
283281
}
284282

285-
if (!rawFile.SampleInformation.Path.IsNullOrEmpty())
286-
{
287-
metadata.addSampleProperty(new CVTerm("AFQ:**********************", "AFO", "Path", rawFile.SampleInformation.Path));
288-
}
289-
290283
if (!rawFile.SampleInformation.InstrumentMethodFile.IsNullOrEmpty())
291284
{
292-
metadata.addSampleProperty(new CVTerm("AFQ:******************", "AFO", "Instrument Method", rawFile.SampleInformation.InstrumentMethodFile));
285+
metadata.addSampleProperty(new CVTerm("AFR:0002045", "AFO", "Device Acquisition Method", rawFile.SampleInformation.InstrumentMethodFile));
293286
}
294287

295288
if (rawFile.SampleInformation.IstdAmount != 0)
296289
{
297-
metadata.addSampleProperty(new CVTerm("AFQ:****************", "AFO", "Istd Amount", rawFile.SampleInformation.IstdAmount.ToString()));
290+
metadata.addSampleProperty(new CVTerm("", "", "Internal Standard Amount", rawFile.SampleInformation.IstdAmount.ToString()));
298291
}
299292

300293
if (!rawFile.SampleInformation.CalibrationLevel.IsNullOrEmpty())
301294
{
302-
metadata.addSampleProperty(new CVTerm("AFQ:****************", "AFO", "Calibration Level", rawFile.SampleInformation.CalibrationLevel));
295+
metadata.addSampleProperty(new CVTerm("AFR:0001849", "AFO", "Calibration Level", rawFile.SampleInformation.CalibrationLevel));
303296
}
304297

305298
if (!rawFile.SampleInformation.ProcessingMethodFile.IsNullOrEmpty())
306299
{
307-
metadata.addSampleProperty(new CVTerm("AFQ:****************", "AFO", "Processing Method", rawFile.SampleInformation.ProcessingMethodFile));
300+
metadata.addSampleProperty(new CVTerm("AFR:0002175", "AFO", "Data Processing Method", rawFile.SampleInformation.ProcessingMethodFile));
308301
}
309302

310303
if (rawFile.SampleInformation.SampleWeight != 0)
311304
{
312-
metadata.addSampleProperty(new CVTerm("AFQ:****************", "AFO", "Processing Method", rawFile.SampleInformation.SampleWeight.ToString()));
305+
metadata.addSampleProperty(new CVTerm("", "", "Sample Weight", rawFile.SampleInformation.SampleWeight.ToString()));
313306
}
314307

315308
string[] userLabels = rawFile.UserLabel;
@@ -324,7 +317,7 @@ private void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int last
324317
{
325318
if (!userTexts[i].IsNullOrEmpty())
326319
{
327-
metadata.addSampleProperty(new CVTerm("AFQ:****************", "AFO", userLabels[i], userTexts[i]));
320+
metadata.addSampleProperty(new CVTerm("", "", userLabels[i], userTexts[i]));
328321
}
329322
}
330323
}
@@ -348,14 +341,12 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
348341
// Get the start and end time from the RAW file
349342
var startTime = rawFile.RunHeaderEx.StartTime;
350343
var endTime = rawFile.RunHeaderEx.EndTime;
351-
string filePath = rawFile.FileName;
352344

353345
// File Properties
354346
var output = new List<string>
355347
{
356348
"#FileProperties",
357-
"RAW file path=" + filePath,
358-
"RAW file name=" + filePath.Substring(0, filePath.LastIndexOf(".")).Remove(0, filePath.LastIndexOf("\\") + 1),
349+
"RAW File Path=" + rawFile.FileName,
359350
"RAW file version=" + rawFile.FileHeader.Revision,
360351
"Creation date=" + rawFile.FileHeader.CreationDate
361352
};
@@ -422,53 +413,53 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
422413

423414
if (!rawFile.SampleInformation.SampleName.IsNullOrEmpty())
424415
{
425-
output.Add("Sample name=" + rawFile.SampleInformation.SampleName);
416+
output.Add("Sample Name=" + rawFile.SampleInformation.SampleName);
426417
}
427418

428419
if (!rawFile.SampleInformation.SampleId.IsNullOrEmpty())
429420
{
430-
output.Add("Sample id=" + rawFile.SampleInformation.SampleId);
421+
output.Add("Sample Number=" + rawFile.SampleInformation.SampleId);
431422
}
432423

433424
if (!rawFile.SampleInformation.SampleType.ToString().IsNullOrEmpty() &&
434425
!rawFile.SampleInformation.SampleType.ToString().Equals("Unknown"))
435426
{
436-
output.Add("Sample type=" + rawFile.SampleInformation.SampleType);
427+
output.Add("Sample Type=" + rawFile.SampleInformation.SampleType);
437428
}
438429

439430
if (!rawFile.SampleInformation.Comment.IsNullOrEmpty())
440431
{
441-
output.Add("Sample comment=" + rawFile.SampleInformation.Comment);
432+
output.Add("Comment=" + rawFile.SampleInformation.Comment);
442433
}
443434

444435
if (!rawFile.SampleInformation.Vial.IsNullOrEmpty())
445436
{
446-
output.Add("Sample vial=" + rawFile.SampleInformation.Vial);
437+
output.Add("Vial=" + rawFile.SampleInformation.Vial);
447438
}
448439

449440
if (rawFile.SampleInformation.SampleVolume != 0)
450441
{
451-
output.Add("Sample volume=" + rawFile.SampleInformation.SampleVolume);
442+
output.Add("Sample Volume=" + rawFile.SampleInformation.SampleVolume);
452443
}
453444

454445
if (rawFile.SampleInformation.InjectionVolume != 0)
455446
{
456-
output.Add("Sample injection volume=" + rawFile.SampleInformation.InjectionVolume);
447+
output.Add("Injection Volume=" + rawFile.SampleInformation.InjectionVolume);
457448
}
458449

459450
if (rawFile.SampleInformation.RowNumber != 0)
460451
{
461-
output.Add("Sample row number=" + rawFile.SampleInformation.RowNumber);
452+
output.Add("Sample Row Number=" + rawFile.SampleInformation.RowNumber);
462453
}
463454

464455
if (rawFile.SampleInformation.DilutionFactor != 0)
465456
{
466-
output.Add("Sample dilution factor=" + rawFile.SampleInformation.DilutionFactor);
457+
output.Add("Dilution Factor=" + rawFile.SampleInformation.DilutionFactor);
467458
}
468459

469460
if (rawFile.SampleInformation.IstdAmount != 0)
470461
{
471-
output.Add("Istd Amount=" + rawFile.SampleInformation.IstdAmount);
462+
output.Add("Internal Standard Amount=" + rawFile.SampleInformation.IstdAmount);
472463
}
473464

474465
if (!rawFile.SampleInformation.CalibrationLevel.IsNullOrEmpty())
@@ -478,7 +469,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
478469

479470
if (!rawFile.SampleInformation.InstrumentMethodFile.IsNullOrEmpty())
480471
{
481-
output.Add("Instrument Method=" + rawFile.SampleInformation.InstrumentMethodFile);
472+
output.Add("Device Acquisition Method=" + rawFile.SampleInformation.InstrumentMethodFile);
482473
}
483474

484475
if (rawFile.SampleInformation.SampleWeight != 0)
@@ -488,12 +479,7 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
488479

489480
if (!rawFile.SampleInformation.ProcessingMethodFile.IsNullOrEmpty())
490481
{
491-
output.Add("Processing Method=" + rawFile.SampleInformation.ProcessingMethodFile);
492-
}
493-
494-
if (!rawFile.SampleInformation.Path.IsNullOrEmpty())
495-
{
496-
output.Add("Path=" + rawFile.SampleInformation.Path);
482+
output.Add("Data Processing Method=" + rawFile.SampleInformation.ProcessingMethodFile);
497483
}
498484

499485
string[] userLabels = rawFile.UserLabel;

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