public void IndexCreation_multiChromosome()
{
var jsonStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var writeStream = new MemoryStream();
using (var indexCreator = new IndexCreator(jsonStream, writeStream))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
var readStream = new MemoryStream(writeStream.ToArray());
readStream.Seek(0, SeekOrigin.Begin);
using (readStream)
{
readBackIndex = new JasixIndex(readStream);
}
Assert.Equal(2268, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(14035925971, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(433156622693, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(439602269527, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
}
private void btnCreateIndex_Click(object sender, EventArgs e)
{
string sql = "SELECT VerseID, VerseText FROM Verse";
using (SqlCeConnection conn = new SqlCeConnection(ConfigurationManager.ConnectionStrings["ConnectionString"].ConnectionString))
{
conn.Open();
var rdr = new SqlCeCommand(sql, conn).ExecuteReader();
var context = new TextFileAccessContext("Bible", IndexDir, new CultureInfo("en-US"));
var textIndexSaver = new TextIndexSaver <int>(context);
var wordBreaker = new DefaultWordBreaker(new WordBreakingInformationRetriever(context.Directory, context.Culture))
{
DatabasePath = context.Directory
};
var textIndexFiller = new TextIndexFiller <int>(wordBreaker);
var indexCreator = new IndexCreator <int>(textIndexFiller);
var index = indexCreator.CreateIndex(new BibleVersuses(rdr));
textIndexSaver.SaveIndex(index);
rdr.Close();
}
}
public static IIndex Provide(string name, DateTime startDate, DateTime endDate, string frequency)
{
var historicalData = ReadDataFromFile.ReadDataSeriesFromFile(
DownloadedFile.ProvideHistoridalDataFile(name, startDate, endDate, frequency));
var currentPrice = new DataPoint(); //currently not available
var listOfStocks = new List <IStock>(); //currently not available
var index = IndexCreator.CreateIndex(name, currentPrice, listOfStocks, historicalData);
return(index);
}
public void WhenIIndexThePeople()
{
var people = ScenarioContext.Current.Get<IEnumerable<Person>>();
var mock = new Mock<IWordBreakingInformationRetriever>();
mock.Setup(x => x.GetWordBreakingInformation())
.Returns(new WordBreakingInformation{NoiseWords = new Dictionary<string, string>(),
Substitutions = new Dictionary<string, string>(),
Whitespace = new List<char>()});
var indexCreator = new IndexCreator<int>(new TextIndexFiller<int>(new DefaultWordBreaker(mock.Object)));
var phrases = people.Select(x => new Phrase<int> {Key = x.Key, Text = x.FirstName + " " + x.LastName});
var index = indexCreator.CreateIndex(phrases);
ScenarioContext.Current.Set(index);
}
public void WhenIIndexThePeople()
{
var people = ScenarioContext.Current.Get <IEnumerable <Person> >();
var mock = new Mock <IWordBreakingInformationRetriever>();
mock.Setup(x => x.GetWordBreakingInformation())
.Returns(new WordBreakingInformation {
NoiseWords = new Dictionary <string, string>(),
Substitutions = new Dictionary <string, string>(),
Whitespace = new List <char>()
});
var indexCreator = new IndexCreator <int>(new TextIndexFiller <int>(new DefaultWordBreaker(mock.Object)));
var phrases = people.Select(x => new Phrase <int> {
Key = x.Key, Text = x.FirstName + " " + x.LastName
});
var index = indexCreator.CreateIndex(phrases);
ScenarioContext.Current.Set(index);
}
public void TestIndexCreation()
{
var readStream = new BlockGZipStream(ResourceUtilities.GetReadStream(Resources.TopPath("cosmicv72.indels.json.gz")), CompressionMode.Decompress);
var tempFile = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
using (var indexCreator = new IndexCreator(readStream, FileUtilities.GetCreateStream(tempFile)))
{
indexCreator.CreateIndex();
}
JasixIndex readBackIndex;
using (var stream = FileUtilities.GetReadStream(tempFile))
{
readBackIndex = new JasixIndex(stream);
}
Assert.Equal(1591, readBackIndex.GetFirstVariantPosition("chr1", 9775924, 9775924));
Assert.Equal(11500956299, readBackIndex.GetFirstVariantPosition("chr2", 16081096, 16081096));
Assert.Equal(372100991296, readBackIndex.GetFirstVariantPosition("chr20", 36026164, 36026164));
Assert.Equal(377682846863, readBackIndex.GetFirstVariantPosition("chrX", 66765044, 66765044));
File.Delete(tempFile);
}
private static void Main(string[] args)
{
IConfiguration config = new ConfigurationBuilder().AddJsonFile("appsettings.json").Build();
var directoryPath = config.GetValue <string>("DirectoryPath");
var client = new ElasticClientFactory(config).CreateElasticClient();
var queryCreator = new QueryCreator();
var searcher = new Searcher(client, queryCreator, Index);
var consoleView = new ConsoleView();
var controller = new Controller(consoleView, searcher);
if (!IsIndexExisting(Index, client))
{
var indexCreator = new IndexCreator(client);
indexCreator.CreateIndex(Index);
var fileReader = new DocFileReader();
var docCreator = new DocFactory(fileReader);
var importer = new Importer <Doc>(client);
importer.Import(docCreator.GetAllDocuments(directoryPath), Index);
}
controller.Run();
}