/// <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);
}
private JsonClasses.QualityParameters ToQualityParameters(ControlledVocabulary cv, string id, JsonClasses.Unit unit) => ToQualityParameters(cv, cv.GetById(id), unit);
private JsonClasses.FileFormat ToFileFormat(ControlledVocabulary cv, string id) => ToFileFormat(cv, cv.GetById(id));
private JsonClasses.FileProperties ToFileProperties(ControlledVocabulary cv, string id, string value) => ToFileProperties(cv, cv.GetById(id), value);
private JsonClasses.Unit ToUnit(ControlledVocabulary cv, string id) => ToUnit(cv, cv.GetById(id));