public override ExpandedPath.Action HandlePath(ExpandedPath ep)
{
LoadSpeciesList();
if (ep.Level == 0)
{
throw new ArgumentOutOfRangeException("ExpandedPath.Level cannot be 0 here");
}
var requestedSpecies = species.Where(s => s.Name == ep.Components[ep.Level - 1]).FirstOrDefault();
if (requestedSpecies == null)
{
return(ExpandedPath.Action.NotFound);
}
if (ep.Level == ep.Components.Count)
{
return(ExpandedPath.Action.Handle);
}
else
{
return(ExpandedPath.Action.PassThrough);
}
}
/// <summary>
/// Initializes a new instance of the <see cref="NugetPackageSource"/> class.
/// </summary>
/// <param name="name">The name of the package source.</param>
/// <param name="path">The path to the package source.</param>
public NugetPackageSource(string name, string path)
{
Name = name;
SavedPath = path;
IsLocalPath = !ExpandedPath.StartsWith("http");
IsEnabled = true;
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
var result = base.OnGetPathStatus(path, out entry);
var stat = entry.Stat;
stat.st_size = Content.Length;
entry.Stat = stat;
return(result);
}
public void DispatcherLocatesCorrectSpecificFileHandlingNode()
{
var ep = new ExpandedPath("/homo_sapiens_core_99_38/chromosomes/1/REF");
NodeProvider handlingNode;
var res = dispatcher.LocateNodeByExpandedPath(ep, dispatcher.Root, out handlingNode);
Assert.AreEqual(ExpandedPath.Action.Handle, res);
Assert.AreEqual(typeof(RefSequenceFile), handlingNode.GetType());
}
public override Errno OnReadHandle(ExpandedPath file, PathInfo info, byte[] buf, long offset, out int bytesRead)
{
Trace.WriteLine($"*** StaticStringFile.OnReadHandle({file.FullPath}, offset={offset}, buf_len={buf.Length})");
var start = (int)offset;
var length = Math.Min(buf.Length, Content.Length);
var data = Content.Substring(start, length);
bytesRead = CopyBuf(data, buf, length);
return(0);
}
public override sealed ExpandedPath.Action HandlePath(ExpandedPath ep)
{
if (ep.Components.Last() == Name)
{
return(ExpandedPath.Action.Handle);
}
else
{
return(ExpandedPath.Action.NotFound);
}
}
public override Errno OnReadDirectory(ExpandedPath directory, PathInfo info, out IEnumerable <NamedStat> paths)
{
if (directory.Components.Count < Level)
{
paths = subdirs;
return(0);
}
else
{
return(Children[0].OnReadDirectory(directory, info, out paths));
}
}
public override Errno OnReadDirectory(ExpandedPath directory, PathInfo info, out IEnumerable <NamedStat> paths)
{
LoadSpeciesList();
if (directory.Components.Count < Level)
{
paths = species;
return(0);
}
else
{
return(Children[0].OnReadDirectory(directory.NextLevel(), info, out paths));
}
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
var desiredFile = path.Components.Last();
if (sequenceFiles.TryGetValue(desiredFile, out var ns))
{
entry = ns;
return(0);
}
else
{
entry = new NamedStat();
return(Errno.ENOENT);
}
}
public override ExpandedPath.Action HandlePath(ExpandedPath ep)
{
if (ep.Level > ep.Components.Count)
{
return(ExpandedPath.Action.Unknown);
}
else if (ep.Level == ep.Components.Count)
{
return(ExpandedPath.Action.Handle);
}
else
{
return(ExpandedPath.Action.PassThrough);
}
}
public override Errno OnReadHandle(ExpandedPath file, PathInfo info, byte[] buf, long offset, out int bytesRead)
{
Trace.WriteLine($"*** RefSequenceFile.OnReadHandle({file.FullPath}, offset={offset}, buf_len={buf.Length})");
var species = file.Components[0];
var chromosome = file.Components[2];
var slice = new Slice(species, chromosome);
var start = offset + 1;
var end = start + buf.Length - 1;
var data = slice.GetSequenceString((int)start, (int)end);
int toBeReadCount = buf.Length;
bytesRead = CopyBuf(data, buf, toBeReadCount);
return(0);
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
var desiredDir = path.Components.Last();
var selectedDir = subdirs.Where(s => s.Name == desiredDir).FirstOrDefault();
if (selectedDir != null)
{
entry = selectedDir;
return(0);
}
else
{
entry = new NamedStat();
return(Errno.ENOENT);
}
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
if (!fileCache.ContainsKey(path.FullPath))
{
var species = path.Components[0];
var chromosome = path.Components[2];
var slice = new Slice(species, chromosome);
var stat = Extensions.StandardFile();
stat.st_size = slice.Length;
var ns = new NamedStat(Name, stat);
fileCache[path.FullPath] = ns;
}
entry = fileCache[path.FullPath];
return(0);
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
LoadSpeciesList();
var dirname = path.Components.Last();
if (species.Where(ns => ns.Name == dirname).FirstOrDefault() != null)
{
entry = new NamedStat(dirname, Extensions.StandardDir());
return(0);
}
else
{
entry = new NamedStat();
return(Errno.ENOENT);
}
}
public override ExpandedPath.Action HandlePath(ExpandedPath ep)
{
var desiredFile = ep.Components.Last();
if (ep.Components.Count < Level)
{
return(ExpandedPath.Action.Handle);
}
else
{
// we're asking about files in the dir
foreach (var child in Children)
{
var action = child.HandlePath(ep);
if (action == ExpandedPath.Action.Handle)
{
return(ExpandedPath.Action.PassThrough);
}
}
return(ExpandedPath.Action.NotFound);
}
}
public override Errno OnReadHandle(ExpandedPath file, PathInfo info, byte[] buf, long offset, out int bytesRead)
{
throw new NotImplementedException();
}
public override Errno OnReadDirectory(ExpandedPath directory, PathInfo info, out IEnumerable <NamedStat> paths)
{
paths = sequenceFiles.Values;
return(0);
}
public override Errno OnReadDirectory(ExpandedPath directory, PathInfo info, out IEnumerable <NamedStat> paths)
{
return(Children[0].OnReadDirectory(directory.NextLevel(), info, out paths));
}
public override Errno OnGetPathStatus(ExpandedPath path, out NamedStat entry)
{
entry = rootDirEntry;
return(0);
}
public override ExpandedPath.Action HandlePath(ExpandedPath ep)
{
return(ep.Level == ep.Components.Count ? ExpandedPath.Action.Handle : ExpandedPath.Action.PassThrough);
}
