/// <param name="path">The path to the output file to be opened, or null to send to stdout</param>
public void WriteMzqc(string path, JsonClasses.MzQC metrics)
{
using TextWriter file = null == path ? Console.Out : File.CreateText(path);
file.Write("{ \"mzQC\":");
JsonSerializer serializer = new JsonSerializer()
{
NullValueHandling = NullValueHandling.Ignore
};
serializer.Serialize(file, metrics);
file.Write("}");
}
public void BuildMzqcAndWrite(string path, Run run, Dictionary <string, dynamic> qcParams, string inputFileInclPath)
{
List <JsonClasses.QualityParameters> qualityParameters = new List <JsonClasses.QualityParameters>();
foreach (var metric in qcParams)
{
var matchingMetric = QualityParameterLookup.SingleOrDefault(x => x.accession == metric.Key);
if (matchingMetric != null)
{
matchingMetric.value = metric.Value;
qualityParameters.Add(matchingMetric);
}
else
{
Logger.Warn("Term \"{0}\" was not found in the MZQC definition when attempting to write output. This term was ignored.", metric.Key);
}
}
//Now for the other stuff
JsonClasses.FileFormat fileFormat = new JsonClasses.FileFormat()
{
};
List <JsonClasses.FileProperties> fileProperties = new List <JsonClasses.FileProperties>()
{
};
JsonClasses.FileProperties fileProperty = new JsonClasses.FileProperties("MS", run.FilePropertiesAccession, "SHA-1", run.SourceFileChecksums.First());
JsonClasses.FileProperties completionTime = new JsonClasses.FileProperties("MS", "MS:1000747", "completion time", run.CompletionTime);
fileProperties.Add(fileProperty);
List <JsonClasses.InputFiles> inputFiles = new List <JsonClasses.InputFiles>();
JsonClasses.InputFiles inputFile = new JsonClasses.InputFiles("file://" + inputFileInclPath, run.SourceFileNames.First(), fileFormat, fileProperties);
inputFiles.Add(inputFile);
List <JsonClasses.AnalysisSoftware> analysisSoftwarelist = new List <JsonClasses.AnalysisSoftware>();
JsonClasses.AnalysisSoftware analysisSoftware = new JsonClasses.AnalysisSoftware()
{
cvRef = "MS", accession = "XXXXXXXXXXXXXX", name = "SwaMe", uri = "https://github.com/PaulBrack/Yamato/tree/master/Console", version = "1.0"
};
analysisSoftwarelist.Add(analysisSoftware);
JsonClasses.MetaData metadata = new JsonClasses.MetaData()
{
inputFiles = inputFiles, analysisSoftware = analysisSoftwarelist
};
JsonClasses.RunQuality runQualitySingle = new JsonClasses.RunQuality()
{
metadata = metadata, qualityParameters = qualityParameters.ToArray()
};
List <JsonClasses.RunQuality> runQuality = new List <JsonClasses.RunQuality>();
runQuality.Add(runQualitySingle);
JsonClasses.NUV qualityControl = new JsonClasses.NUV()
{
name = "Proteomics Standards Initiative Quality Control Ontology", uri = "https://raw.githubusercontent.com/HUPO-PSI/mzqc/master/cv/v0_0_11/qc-cv.obo", version = "0.1.0"
};
JsonClasses.NUV massSpectrometry = new JsonClasses.NUV()
{
name = "Proteomics Standards Initiative Mass Spectrometry Ontology", uri = "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo", version = "4.1.7"
};
JsonClasses.NUV UnitOntology = new JsonClasses.NUV()
{
name = "Unit Ontology", uri = "https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo", version = "09:04:2014 13:37"
};
JsonClasses.CV cV = new JsonClasses.CV()
{
QC = qualityControl, MS = massSpectrometry, UO = UnitOntology
};
JsonClasses.MzQC metrics = new JsonClasses.MzQC()
{
runQuality = runQuality, cv = cV
};
//Then save:
WriteMzqc(path, metrics);
}
/// <param name="outputFileName">The path to the output file to be opened, or null to send to stdout</param>
public void BuildMzqcAndWrite(string outputFileName, Run <Scan> run, Dictionary <string, dynamic> qcParams, string inputFileInclPath, object analysisSettings)
{
List <JsonClasses.QualityParameters> qualityParameters = new List <JsonClasses.QualityParameters>();
foreach (var metric in qcParams)
{
// Note that this code smashes a value into the given QualityParameters; this will fail if the same one is used more than once, or the initialisation of those parameters is made static.
if (QualityParametersByAccession.TryGetValue(metric.Key, out var matchingMetric))
{
matchingMetric.value = metric.Value;
qualityParameters.Add(matchingMetric);
}
else
{
Logger.Warn("Term \"{0}\" was not found in the MZQC definition when attempting to write output. This term was ignored.", metric.Key);
}
}
//Now for the other stuff
JsonClasses.InputFiles inputFile = new JsonClasses.InputFiles(
"file://" + inputFileInclPath,
run.SourceFileNames.First(),
ToFileFormat(ms, "MS:1000584"),
new List <JsonClasses.FileProperties>()
{
// ToFileProperties("MS", "MS:1000747", run.CompletionTime), // TODO: Include this?
ToFileProperties(ms, run.FilePropertiesAccession, run.SourceFileChecksums.First())
}
);
Term swaMe = ms.GetById("XXXXXXXXXXXXXX");
JsonClasses.AnalysisSoftware analysisSoftware = new JsonClasses.AnalysisSoftware()
{
cvRef = ms.PrimaryNamespace,
accession = swaMe.Id,
name = swaMe.Name,
uri = "https://github.com/PaulBrack/Yamato/tree/master/Console",
version = typeof(MzqcWriter).Assembly.GetName().Version.ToString(),
analysisSettings = analysisSettings
};
JsonClasses.MzQC metrics = new JsonClasses.MzQC()
{
version = "0.0.11",
runQuality = new List <JsonClasses.RunQuality>
{
new JsonClasses.RunQuality()
{
metadata = new JsonClasses.MetaData()
{
inputFiles = new List <JsonClasses.InputFiles>()
{
inputFile
},
analysisSoftware = new List <JsonClasses.AnalysisSoftware>()
{
analysisSoftware
}
},
qualityParameters = qualityParameters.ToArray()
}
},
cv = cvLibrary.ControlledVocabularies.ToDictionary(cv => cv.PrimaryNamespace, ToNUV)
};
//Then save:
WriteMzqc(outputFileName, metrics);
}
