public StrainIndexer(Configuration config, IDbDriver database, NcbiClient ncbiClient,
CountryCodeHelper countryCodeHelper, DoiClient doiClient, Dictionary <string, int> sitList)
{
Config = config;
Database = database;
NcbiClient = ncbiClient;
CountryCodeHelper = countryCodeHelper;
DoiClient = doiClient;
SitList = sitList;
}
static async Task Main(string[] args)
{
IServiceCollection services = new ServiceCollection();
services.AddEasyCaching(option =>
{
option.UseLiteDB(c =>
{
c.DBConfig = new LiteDBDBOptions
{
FileName = "doi.db"
};
}, "doi");
option.UseLiteDB(c =>
{
c.DBConfig = new LiteDBDBOptions
{
FileName = "ncbi.db"
};
}, "ncbi");
});
IServiceProvider serviceProvider = services.BuildServiceProvider();
var factory = serviceProvider.GetService <IEasyCachingProviderFactory>();
var doiClient = new DoiClient(factory.GetCachingProvider("doi"));
var ncbiClient = new NcbiClient(factory.GetCachingProvider("ncbi"));
ncbiClient.AllowQuery = true;
var config = Configuration.FromYaml("/home/gaetan/API/Web/Data/config.yaml");
Directory.Delete("Index", true);
var db = new LiteDatabase("db");
var driver = new LiteDbDriver(db);
// var driver = new RavenDbDriver(@"C:\Users\Gaetan\RiderProjects\API\Web\bin\Debug\net5.0\RavenDB");
var countryHelper = new CountryCodeHelper();
var sit = await LoadSIT(@"/home/gaetan/API/Web/Data/spol/sit.tsv");
// var geneIndexer = new GffGeneIndexer(driver, "/home/gaetan/API/Web/Data/genes/H37Rv.gff3");
// await geneIndexer.Index();
//
// var snpIndexer = new SnpIndexer(config, driver, doiClient);
// await snpIndexer.Index();
var strainIndexer = new StrainIndexer(config, driver, ncbiClient, countryHelper, doiClient, sit);
await strainIndexer.Index();
await driver.ComputeKeywordStat();
Console.WriteLine("gg");
}
private static NcbiClient CreateNcbiClient()
{
IServiceCollection services = new ServiceCollection();
services.AddEasyCaching(option =>
{
option.UseLiteDB(c =>
{
c.DBConfig = new LiteDBDBOptions
{
FileName = "ncbi.db"
};
}, "ncbi");
});
IServiceProvider serviceProvider = services.BuildServiceProvider();
var factory = serviceProvider.GetService <IEasyCachingProviderFactory>();
var ncbiClient = new NcbiClient(factory.GetCachingProvider("ncbi"));
ncbiClient.AllowQuery = true;
return(ncbiClient);
}
public GetNcbiRun(NcbiClient client)
{
Client = client;
}