public void AddCacheFiles_Nominal()
{
var comparer = new RemoteFileComparer();
var genomeAssemblies = new List <GenomeAssembly> {
GenomeAssembly.GRCh37, GenomeAssembly.GRCh38
};
const string remoteCacheDirectory = "remote";
const string cacheDirectory = "local";
const ushort dataVersion = CacheConstants.DataVersion;
var expectedFiles = new List <RemoteFile>
{
new RemoteFile($"remote/{dataVersion}/GRCh37/Both.transcripts.ndb", Path.Combine("local", "GRCh37", "Both.transcripts.ndb"), "Both.transcripts.ndb (GRCh37)"),
new RemoteFile($"remote/{dataVersion}/GRCh37/Both.sift.ndb", Path.Combine("local", "GRCh37", "Both.sift.ndb"), "Both.sift.ndb (GRCh37)"),
new RemoteFile($"remote/{dataVersion}/GRCh37/Both.polyphen.ndb", Path.Combine("local", "GRCh37", "Both.polyphen.ndb"), "Both.polyphen.ndb (GRCh37)"),
new RemoteFile($"remote/{dataVersion}/GRCh38/Both.transcripts.ndb", Path.Combine("local", "GRCh38", "Both.transcripts.ndb"), "Both.transcripts.ndb (GRCh38)"),
new RemoteFile($"remote/{dataVersion}/GRCh38/Both.sift.ndb", Path.Combine("local", "GRCh38", "Both.sift.ndb"), "Both.sift.ndb (GRCh38)"),
new RemoteFile($"remote/{dataVersion}/GRCh38/Both.polyphen.ndb", Path.Combine("local", "GRCh38", "Both.polyphen.ndb"), "Both.polyphen.ndb (GRCh38)")
};
var files = new List <RemoteFile>();
files.AddCacheFiles(genomeAssemblies, remoteCacheDirectory, cacheDirectory);
Assert.Equal(expectedFiles, files, comparer);
}
public void AddSupplementaryAnnotationFiles_Nominal()
{
var comparer = new RemoteFileComparer();
const string saDirectory = "local";
var remotePaths37 = new List <string>
{
"/0bf0cb93e64824b20f0b551a629596fd-TopMed/2/GRCh37/TOPMed_freeze_5.nsa"
};
var remotePaths38 = new List <string>
{
"/43cafec8b0624b77663e2ba1dec32883-gnomAD-exome/2/GRCh38/gnomAD_exome_2.0.2.nsa",
"/2551e067cb59c540a4da905a99ee5ff4-ClinGen/2/GRCh38/ClinGen_20160414.nsi"
};
var remotePathsByGenomeAssembly = new Dictionary <GenomeAssembly, List <string> >
{
[GenomeAssembly.GRCh37] = remotePaths37,
[GenomeAssembly.GRCh38] = remotePaths38
};
var expectedFiles = new List <RemoteFile>
{
new RemoteFile("/0bf0cb93e64824b20f0b551a629596fd-TopMed/2/GRCh37/TOPMed_freeze_5.nsa", Path.Combine("local", "GRCh37", "TOPMed_freeze_5.nsa"), "TOPMed_freeze_5.nsa (GRCh37)"),
new RemoteFile("/0bf0cb93e64824b20f0b551a629596fd-TopMed/2/GRCh37/TOPMed_freeze_5.nsa.idx", Path.Combine("local", "GRCh37", "TOPMed_freeze_5.nsa.idx"), "TOPMed_freeze_5.nsa.idx (GRCh37)"),
new RemoteFile("/43cafec8b0624b77663e2ba1dec32883-gnomAD-exome/2/GRCh38/gnomAD_exome_2.0.2.nsa", Path.Combine("local", "GRCh38", "gnomAD_exome_2.0.2.nsa"), "gnomAD_exome_2.0.2.nsa (GRCh38)"),
new RemoteFile("/43cafec8b0624b77663e2ba1dec32883-gnomAD-exome/2/GRCh38/gnomAD_exome_2.0.2.nsa.idx", Path.Combine("local", "GRCh38", "gnomAD_exome_2.0.2.nsa.idx"), "gnomAD_exome_2.0.2.nsa.idx (GRCh38)"),
new RemoteFile("/2551e067cb59c540a4da905a99ee5ff4-ClinGen/2/GRCh38/ClinGen_20160414.nsi", Path.Combine("local", "GRCh38", "ClinGen_20160414.nsi"), "ClinGen_20160414.nsi (GRCh38)")
};
var files = new List <RemoteFile>();
files.AddSupplementaryAnnotationFiles(remotePathsByGenomeAssembly, saDirectory);
Assert.Equal(expectedFiles, files, comparer);
}
public void AddReferenceFiles_Nominal()
{
var comparer = new RemoteFileComparer();
var genomeAssemblies = new List <GenomeAssembly> {
GenomeAssembly.GRCh37, GenomeAssembly.GRCh38
};
const string remoteReferencesDirectory = "remote";
const string referencesDirectory = "local";
const ushort dataVersion = ReferenceSequenceCommon.HeaderVersion;
var expectedFiles = new List <RemoteFile>
{
new RemoteFile($"remote/{dataVersion}/Homo_sapiens.GRCh37.Nirvana.dat", Path.Combine("local", "Homo_sapiens.GRCh37.Nirvana.dat"), "Homo_sapiens.GRCh37.Nirvana.dat"),
new RemoteFile($"remote/{dataVersion}/Homo_sapiens.GRCh38.Nirvana.dat", Path.Combine("local", "Homo_sapiens.GRCh38.Nirvana.dat"), "Homo_sapiens.GRCh38.Nirvana.dat")
};
var files = new List <RemoteFile>();
files.AddReferenceFiles(genomeAssemblies, remoteReferencesDirectory, referencesDirectory);
Assert.Equal(expectedFiles, files, comparer);
}
