static void Main(string[] args)
{
var parser = new Parser();
parser.ReadFile();
parser.ParseFile();
using (var context = new SerratusSummaryContext())
{
context.CommentLines.Add(parser.CommentLine);
context.SaveChanges();
}
}
public CommentLinesController(SerratusSummaryContext context, ISerratusSummaryService serratusSummaryService)
{
_context = context;
_serratusSummaryService = serratusSummaryService;
}
public SerratusSummaryService(SerratusSummaryContext serratusSummaryContext)
{
_serratusSummaryContext = serratusSummaryContext;
}
public RunsController(SerratusSummaryContext context)
{
_context = context;
}
public async Task GetDataFromBucketList()
{
ReadFile();
Console.WriteLine($"get data from bucket started");
AmazonS3Config config = new AmazonS3Config();
AmazonS3Client s3Client = new AmazonS3Client(
_accessKey,
_secretKey,
config
);
var oneFile = Stopwatch.StartNew();
var tasks = new List <Task>();
foreach (string fileName in SummaryFiles)
{
var request = new GetObjectRequest
{
BucketName = "lovelywater",
Key = $"{fileName}"
};
string responseBody = "";
var s3Stopwatch = Stopwatch.StartNew();
try
{
Console.WriteLine("test");
var result = await s3Client.GetObjectAsync(request);
using (var stream = result.ResponseStream)
using (var reader = new StreamReader(stream))
{
Console.WriteLine($"file read");
var readerStopwatch = Stopwatch.StartNew();
responseBody = await reader.ReadToEndAsync();
//Console.WriteLine($"{readerStopwatch.ElapsedMilliseconds}");
var task = Task.Run(async() =>
{
using (var context = new SerratusSummaryContext())
{
var parserStopwatch = Stopwatch.StartNew();
var lines = responseBody.Split('\n');
var unparsedFile = ReadFile(lines);
var finishedFile = ParseFile(fileName, unparsedFile);
Console.WriteLine($"file parsed");
//Console.WriteLine($"{parserStopwatch.ElapsedMilliseconds}");
var dbStopwatch = Stopwatch.StartNew();
context.ChangeTracker.QueryTrackingBehavior = QueryTrackingBehavior.NoTracking;
context.Runs.Add(finishedFile.Run);
await context.SaveChangesAsync();
Console.WriteLine($"file saved in db");
//Console.WriteLine($"{dbStopwatch.ElapsedMilliseconds}");
}
});
tasks.Add(task);
}
}
catch
{
continue;
}
if (tasks.Count == 100)
{
await Task.WhenAll(tasks);
Console.WriteLine("tasks done!");
}
//Console.WriteLine($"{s3Stopwatch.ElapsedMilliseconds}");
}
Console.WriteLine("PARSER COMPLETE");
//if (moreKeys == true)
//{
// Console.WriteLine("getting more buckets");
// GetBucketsFromS3();
//}
//else
//{
// return;
//}
}
public AccessionSectionsController(SerratusSummaryContext context, ISerratusSummaryService serratusSummaryService)
{
_context = context;
_serratusSummaryService = serratusSummaryService;
}
public FastaSectionsController(SerratusSummaryContext context)
{
_context = context;
}
