public ICheckpointRunner GetCheckpointManager(IDirectoryLocation analysisFolder,
string startingCheckpointName, string stopCheckpointName)
{
// Checkpoint Manager
var parentDirectories = new Dictionary<string, IDirectoryLocation>
{
{"AnalysisFolder", analysisFolder},
{"GenomesRoot", _genomesRoot}
};
JsonConverter[] converters =
{
new FileSystemLocationConverter(parentDirectories),
new EnumerableConverter()
};
var settings = new JsonSerializerSettings
{
TypeNameHandling = TypeNameHandling.Auto,
MissingMemberHandling = MissingMemberHandling.Error,
Converters = converters,
ContractResolver = new WritablePropertiesOnlyResolver(),
ConstructorHandling = ConstructorHandling.AllowNonPublicDefaultConstructor,
};
ICheckpointSerializer serializer = new CheckpointJsonSerializer(settings, IsasFilePaths.GetCheckpointFolder(analysisFolder), _logger);
//todo: remove this increment logic once the legacy checkpointer is no longer used
int tempStartCheckpoint;
if (int.TryParse(startingCheckpointName, out tempStartCheckpoint))
{
tempStartCheckpoint++;
startingCheckpointName = tempStartCheckpoint.ToString();
}
ICheckpointManager manager = new CheckpointManager(_logger, startingCheckpointName, stopCheckpointName);
return new CheckpointRunner(_logger, analysisFolder, manager, serializer, _retainTemps);
}
private ICheckpointRunner GetCheckpointRunner(ILogger logger, IDirectoryLocation outputDirectory, string startCheckpoint, string stopCheckpoint, IDirectoryLocation wholeGenomeFastaFolder)
{
var parentDirectories = new Dictionary<string, IDirectoryLocation>
{
{"Output", outputDirectory},
};
// Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta
IDirectoryLocation genomeRoot = wholeGenomeFastaFolder?.Parent?.Parent?.Parent?.Parent?.Parent;
if (genomeRoot != null) parentDirectories.Add("Genome", genomeRoot);
JsonConverter[] converters = { new FileSystemLocationConverter(parentDirectories) };
var settings = new JsonSerializerSettings
{
TypeNameHandling = TypeNameHandling.Auto,
MissingMemberHandling = MissingMemberHandling.Error,
Converters = converters,
ContractResolver = new WritablePropertiesOnlyResolver(),
ConstructorHandling = ConstructorHandling.AllowNonPublicDefaultConstructor,
};
ICheckpointSerializer serializer = new CheckpointJsonSerializer(settings, IsasFilePaths.GetCheckpointFolder(outputDirectory), logger);
ICheckpointManager manager = new CheckpointManager(logger, startCheckpoint, stopCheckpoint);
return new CheckpointRunner(logger, outputDirectory, manager, serializer, true);
}
