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Merged
ypriverol merged 3 commits into from
Aug 29, 2018
Merged

All the json format for the metadata is now in CVterms #14

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860e557
minro changes - has bugs still
ypriverol Aug 29, 2018
577d4db
minro changes - has bugs still
ypriverol Aug 29, 2018
d12ef02
minor changes
ypriverol Aug 29, 2018
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61 changes: 28 additions & 33 deletions Writer/Metadata.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,79 +7,74 @@ namespace ThermoRawFileParser.Writer
public class Metadata
{
/** The general Path properties contains: RAW path , RAW file version **/
private List<Dictionary<string, string>> fileProperties = new List<Dictionary<string, string>>();
private List<CVTerm> fileProperties = new List<CVTerm>();

/** The Instruments properties contains the information of the instrument **/
private List<Dictionary<string, CVTerm>> instrumentProperties = new List<Dictionary<string, CVTerm>>();
private List<CVTerm> instrumentProperties = new List<CVTerm>();

/** Scan Settings **/
private List<Dictionary<String, Object>> scanSettings = new List<Dictionary<string, Object>>();
private List<CVTerm> scanSettings = new List<CVTerm>();

/** MS and MS data including number of MS and MS/MS **/
private List<Dictionary<String, Object>> msData = new List<Dictionary<string, Object>>();
private List<CVTerm> msData = new List<CVTerm>();

private List<Dictionary<string, string>> sampleData = new List<Dictionary<string, string>>();
private List<CVTerm> sampleData = new List<CVTerm>();

/**
* Default constructor
*/
public Metadata(){}

public Metadata(List<Dictionary<string, string>> fileProperties,
List<Dictionary<string, CVTerm>> instrumentProperties,
List<Dictionary<string, Object>> msData)
public Metadata(List<CVTerm> fileProperties,
List<CVTerm> instrumentProperties,
List<CVTerm> msData)
{
this.fileProperties = fileProperties;
this.instrumentProperties = instrumentProperties;
this.msData = msData;
}

public List<Dictionary<string, string>> FileProperties => fileProperties;
public List<CVTerm> FileProperties => fileProperties;

public List<Dictionary<string, CVTerm>> InstrumentProperties => instrumentProperties;
public List<CVTerm> InstrumentProperties => instrumentProperties;

public List<Dictionary<string, Object>> MsData => msData;
public List<CVTerm> MsData => msData;

public List<Dictionary<string, string>> SampleData => sampleData;
public List<CVTerm> SampleData => sampleData;

public List<Dictionary<string, Object>> ScanSettings => scanSettings;
public List<CVTerm> ScanSettings => scanSettings;

/**
* Add a File property to the fileProperties
*/
public void addFileProperty(String key, String value)
public void addFileProperty(CVTerm value)
{
var dic = new Dictionary<string, string>();
dic.Add(key, value);
fileProperties.Add(dic);
fileProperties.Add(value);
}

public void addInstrumentProperty(string key, CVTerm value)
public void addInstrumentProperty( CVTerm value)
{
var dic = new Dictionary<string, CVTerm>();
dic.Add(key, value);
instrumentProperties.Add(dic);
instrumentProperties.Add(value);
}

public void addScanSetting(string key, Object value)
public void addScanSetting(CVTerm value)
{
var dic = new Dictionary<string, Object>();
dic.Add(key, value);
scanSettings.Add(dic);
scanSettings.Add(value);
}

public void addMSData(string key, Object value)
public void addMSData(CVTerm value)
{
var dic = new Dictionary<string, Object>();
dic.Add(key, value);
msData.Add(dic);
msData.Add(value);
}

public void addMSData(HashSet<CVTerm> value)
{
msData.AddRange(value);
}

public void addSampleProperty(string key, string value)
public void addSampleProperty(CVTerm value)
{
var dic = new Dictionary<string, string>();
dic.Add(key, value);
sampleData.Add(dic);
sampleData.Add(value);
}
}

Expand Down
74 changes: 42 additions & 32 deletions Writer/MetadataWriter.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -96,34 +96,33 @@ public void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int lastS
var metadata = new Metadata();

/** File Properties **/
metadata.addFileProperty("path", rawFile.FileName);
metadata.addFileProperty("version", rawFile.FileHeader.Revision.ToString());
metadata.addFileProperty("creation-date", rawFile.FileHeader.CreationDate.ToString());
metadata.addFileProperty("number-instruments", rawFile.InstrumentCount.ToString());
metadata.addFileProperty("description", rawFile.FileHeader.FileDescription);
metadata.addFileProperty(new CVTerm("NCIT:C47922", "NCIT", "Pathname", rawFile.FileName));
metadata.addFileProperty(new CVTerm("NCIT:C25714", "NCIT", "Version", rawFile.FileHeader.Revision.ToString()));
metadata.addFileProperty(new CVTerm("NCIT:C69199", "NCIT", "Content Creation Date", rawFile.FileHeader.CreationDate.ToString()));
metadata.addFileProperty(new CVTerm("NCIT:C25365", "NCIT", "Description", rawFile.FileHeader.FileDescription));

/** Sample Properties **/
metadata.addSampleProperty("name", rawFile.SampleInformation.SampleName);
metadata.addSampleProperty("id", rawFile.SampleInformation.SampleId);
metadata.addSampleProperty("type", rawFile.SampleInformation.SampleType.ToString());
metadata.addSampleProperty("comment", rawFile.SampleInformation.Comment);
metadata.addSampleProperty("vial", rawFile.SampleInformation.Vial);
metadata.addSampleProperty("volume", rawFile.SampleInformation.SampleVolume.ToString());
metadata.addSampleProperty("injection-volume", rawFile.SampleInformation.InjectionVolume.ToString());
metadata.addSampleProperty("row-number", rawFile.SampleInformation.RowNumber.ToString());
metadata.addSampleProperty("dilution-factor", rawFile.SampleInformation.DilutionFactor.ToString());
// metadata.addSampleProperty("name", rawFile.SampleInformation.SampleName);
// metadata.addSampleProperty("id", rawFile.SampleInformation.SampleId);
// metadata.addSampleProperty("type", rawFile.SampleInformation.SampleType.ToString());
// metadata.addSampleProperty("comment", rawFile.SampleInformation.Comment);
// metadata.addSampleProperty("vial", rawFile.SampleInformation.Vial);
// metadata.addSampleProperty("volume", rawFile.SampleInformation.SampleVolume.ToString());
// metadata.addSampleProperty("injection-volume", rawFile.SampleInformation.InjectionVolume.ToString());
// metadata.addSampleProperty("row-number", rawFile.SampleInformation.RowNumber.ToString());
// metadata.addSampleProperty("dilution-factor", rawFile.SampleInformation.DilutionFactor.ToString());

metadata.addScanSetting("start-time", new CVTerm("MS:1000016", "MS", "scan start time",startTime.ToString()));
metadata.addScanSetting("resolution", new CVTerm("MS:1000011", "MS", "mass resolution", rawFile.RunHeaderEx.MassResolution.ToString()));
metadata.addScanSetting("tolerance-unit", new CVTerm("UO:0000002", "MS", "mass unit", rawFile.GetInstrumentData().Units.ToString()));
metadata.addScanSetting("number-scans", rawFile.RunHeaderEx.SpectraCount.ToString());
metadata.addScanSetting("scan-range", firstScanNumber + ":" + lastScanNumber);
metadata.addScanSetting("time-range", startTime + ":" + endTime);
metadata.addScanSetting("mass-range", rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass);
metadata.addScanSetting(new CVTerm("MS:1000016", "MS", "scan start time",startTime.ToString()));
metadata.addScanSetting(new CVTerm("MS:1000011", "MS", "mass resolution", rawFile.RunHeaderEx.MassResolution.ToString()));
metadata.addScanSetting(new CVTerm("UO:0000002", "MS", "mass unit", rawFile.GetInstrumentData().Units.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000478", "PRIDE","Number of scans", rawFile.RunHeaderEx.SpectraCount.ToString()));
metadata.addScanSetting(new CVTerm("PRIDE:0000479", "PRIDE", "MS scan range", firstScanNumber + ":" + lastScanNumber));
metadata.addScanSetting(new CVTerm("PRIDE:0000484", "PRIDE", "Retention time range", startTime + ":" + endTime));
metadata.addScanSetting(new CVTerm("PRIDE:0000485", "PRIDE", "Mz range", rawFile.RunHeaderEx.LowMass + ":" + rawFile.RunHeaderEx.HighMass));

metadata.addInstrumentProperty("model", new CVTerm("MS:1000494", "MS","Thermo Scientific instrument model", rawFile.GetInstrumentData().Model));
metadata.addInstrumentProperty("name", new CVTerm("MS:1000496", "MS","instrument attribute", rawFile.GetInstrumentData().Name));
metadata.addInstrumentProperty("serial", new CVTerm("MS:1000529", "MS", "instrument serial number", rawFile.GetInstrumentData().SerialNumber));
metadata.addInstrumentProperty(new CVTerm("MS:1000494", "MS","Thermo Scientific instrument model", rawFile.GetInstrumentData().Model));
metadata.addInstrumentProperty(new CVTerm("MS:1000496", "MS","instrument attribute", rawFile.GetInstrumentData().Name));
metadata.addInstrumentProperty(new CVTerm("MS:1000529", "MS", "instrument serial number", rawFile.GetInstrumentData().SerialNumber));

var msTypes = new Dictionary<string, int>();
double minTime = 1000000000000000;
Expand Down Expand Up @@ -202,17 +201,28 @@ public void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int lastS
minCharge = 0;
}

metadata.addMSData("ms-number", msTypes);
metadata.addMSData("activation-ypes", fragmentationType);

metadata.addMSData("min-charge", minCharge);
metadata.addMSData("max-charge", maxCharge);
foreach(KeyValuePair<string, int> entry in msTypes)
{
if(entry.Key.Equals(MSOrderType.Ms.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000481", "PRIDE", "Number of MS1 spectra", entry.Value.ToString()));
if(entry.Key.Equals(MSOrderType.Ms2.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000482", "PRIDE", "Number of MS2 spectra", entry.Value.ToString()));
if(entry.Key.Equals(MSOrderType.Ms3.ToString()))
metadata.addMSData(new CVTerm("PRIDE:0000483", "PRIDE", "Number of MS3 spectra", entry.Value.ToString()));

}

metadata.addMSData(fragmentationType);

metadata.addMSData(new CVTerm("PRIDE:0000472", "PRIDE", "MS min charge", minCharge.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000473", "PRIDE", "MS max charge", maxCharge.ToString()));

metadata.addMSData("min-Time", minTime);
metadata.addMSData("max-Time", maxTime);
metadata.addMSData(new CVTerm("PRIDE:0000474", "PRIDE", "MS min RT", minTime.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000475", "PRIDE", "MS max RT", maxTime.ToString()));

metadata.addMSData("min-Mz", minMz);
metadata.addMSData("max-Mz", maxMz);
metadata.addMSData(new CVTerm("PRIDE:0000476", "PRIDE", "MS min MZ", minMz.ToString()));
metadata.addMSData(new CVTerm("PRIDE:0000477", "PRIDE", "MS min MZ", maxMz.ToString()));


// Write the meta data to file
Expand Down