how to read a compressed file from c# in R - c#

String fileName = "0001.gff";
using (FileStream zipToOpen = new FileStream(fileName, FileMode.Create))
{
using (ZipArchive archive = new ZipArchive(zipToOpen, ZipArchiveMode.Create))
{
ZipArchiveEntry write_entry = archive.CreateEntry(fileName);
using (BinaryWriter writer = new BinaryWriter(write_entry.Open()))
{
writer.Write((Int32)1);
writer.Write((Int32)2);
writer.Write((Int32)3);
writer.Write((Int32)4);
}
}
}
I have created the file myFile in c#, but i want to read it in R. How can i do that?

There is a function called read.gff from the ape package the documentation says to try using
read.gff(file)

Related

Copy files from one Zip file to another

I am copying files from one zip file to another in certain circumstances. I am wondering if there is a better way to do it than what I came up with:
using FileStream sourceFileStream = new FileStream(source.FileName, FileMode.Open);
using FileStream targetFileStream = new FileStream(target.FileName, FileMode.Open, FileAccess.ReadWrite);
using ZipArchive sourceZip = new ZipArchive(sourceFileStream, ZipArchiveMode.Read);
using ZipArchive targetZip = new ZipArchive(targetFileStream, ZipArchiveMode.Update);
ZipArchiveEntry sourceEntry = sourceZip.GetEntry(filePathInArchive);
if (sourceEntry == null)
return;
ZipArchiveEntry targetEntry = targetZip.GetEntry(filePathInArchive);
if (targetEntry != null)
targetEntry.Delete();
targetZip.CreateEntry(filePathInArchive);
targetEntry = targetZip.GetEntry(filePathInArchive);
if (targetEntry != null)
{
Stream writer = targetEntry.Open();
Stream reader = sourceEntry.Open();
int b;
do
{
b = reader.ReadByte();
writer.WriteByte((byte)b);
} while (b != -1);
writer.Close();
reader.Close();
}
Tips and suggestions would be appreciated.
You can iterate each entry from source archive with opening its streams and using Stream.CopyTo write source entry content to target entry.
From C# 8.0 it looks compact and works fine:
static void CopyZipEntries(string sourceZipFile, string targetZipFile)
{
using FileStream sourceFS = new FileStream(sourceZipFile, FileMode.Open);
using FileStream targetFS = new FileStream(targetZipFile, FileMode.Open);
using ZipArchive sourceZIP = new ZipArchive(sourceFS, ZipArchiveMode.Read, false, Encoding.GetEncoding(1251));
using ZipArchive targetZIP = new ZipArchive(targetFS, ZipArchiveMode.Update, false, Encoding.GetEncoding(1251));
foreach (ZipArchiveEntry sourceEntry in sourceZIP.Entries)
{
// 'is' is replacement for 'null' check
if (targetZIP.GetEntry(sourceEntry.FullName) is ZipArchiveEntry existingTargetEntry)
existingTargetEntry.Delete();
using (Stream targetEntryStream = targetZIP.CreateEntry(sourceEntry.FullName).Open())
{
sourceEntry.Open().CopyTo(targetEntryStream);
}
}
}
With earlier than C# 8.0 versions it works fine too, but more braces needed:
static void CopyZipEntries(string sourceZipFile, string targetZipFile)
{
using (FileStream sourceFS = new FileStream(sourceZipFile, FileMode.Open))
{
using (FileStream targetFS = new FileStream(targetZipFile, FileMode.Open))
{
using (ZipArchive sourceZIP = new ZipArchive(sourceFS, ZipArchiveMode.Read, false, Encoding.GetEncoding(1251)))
{
using (ZipArchive targetZIP = new ZipArchive(targetFS, ZipArchiveMode.Update, false, Encoding.GetEncoding(1251)))
{
foreach (ZipArchiveEntry sourceEntry in sourceZIP.Entries)
{
if (targetZIP.GetEntry(sourceEntry.FullName) is ZipArchiveEntry existingTargetEntry)
{
existingTargetEntry.Delete();
}
using (Stream target = targetZIP.CreateEntry(sourceEntry.FullName).Open())
{
sourceEntry.Open().CopyTo(target);
}
}
}
}
}
}
}
For single specified file copy just replace bottom part from foreach loop to if condition:
static void CopyZipEntry(string fileName, string sourceZipFile, string targetZipFile)
{
// ...
// It means specified file exists in source ZIP-archive
// and we can copy it to target ZIP-archive
if (sourceZIP.GetEntry(fileName) is ZipArchiveEntry sourceEntry)
{
if (targetZIP.GetEntry(sourceEntry.FullName) is ZipArchiveEntry existingTargetEntry)
existingTargetEntry.Delete();
using (Stream targetEntryStream = targetZIP.CreateEntry(sourceEntry.FullName).Open())
{
sourceEntry.Open().CopyTo(targetEntryStream);
}
}
else
MessageBox.Show("Source ZIP-archive doesn't contains file " + fileName);
}
Thanks to the input so far, I cleaned up and improved the code. I think this looks cleaner and more reliable.
//Making sure files exist etc before this part...
string filePathInArchive = source.GetFilePath(fileId);
using FileStream sourceFileStream = new FileStream(source.FileName, FileMode.Open);
using FileStream targetFileStream = new FileStream(target.FileName, FileMode.Open, FileAccess.ReadWrite);
using ZipArchive sourceZip = new ZipArchive(sourceFileStream, ZipArchiveMode.Read, false );
using ZipArchive targetZip = new ZipArchive(targetFileStream, ZipArchiveMode.Update, false);
ZipArchiveEntry sourceEntry = sourceZip.GetEntry(filePathInArchive);
if (sourceEntry != null)
{
if (targetZip.GetEntry(filePathInArchive) is { } existingTargetEntry)
{
existingTargetEntry.Delete();
}
using var targetEntryStream = targetZip.CreateEntry(sourceEntry.FullName).Open();
sourceEntry.Open().CopyTo(targetEntryStream);
}

Passing compressed files from C# to R

I don't know very well C# and compressed files, but i need to create comrpessed files with C# and read them with R. So which format should i use, that it is compatible with both C# and R?
I have tried this:
using (FileStream zipToOpen = new FileStream("myfile.gff", FileMode.Create))
{
using (ZipArchive archive = new ZipArchive(zipToOpen, ZipArchiveMode.Create))
{
ZipArchiveEntry write_entry = archive.CreateEntry(path);
using (BinaryWriter writer = new BinaryWriter(write_entry.Open()))
{
//writing
}
}
}
but i can't open this file with the R function unzip().
EDIT:
zipF<-file.choose()
unzip(zipF)
Warning message: In unzip(zipF) : error 1 in extracting from zip file

C# ZipArchive - How to nest internal .zip files without writing to disk

I need to create a zip file in memory, then send the zip file to the client. However, there are cases where the created zip file will need to contain other zip files that were also generated in memory. For instance, the file structure might look like this:
SendToClient.zip
InnerZip1.zip
File1.xml
File2.xml
InnerZip2.zip
File3.xml
File4.xml
I've been attempting to use the System.IO.Compression.ZipArchive library. I cannot use the System.IO.Compression.ZipFile library because my project's version of .NET is not compatible with it.
Here's an example of what I've tried.
public Stream GetMemoryStream() {
var memoryStream = new MemoryStream();
string fileContents = "Lorem ipsum dolor sit amet";
string entryName = "Lorem.txt";
string innerZipName = "InnerZip.zip";
using (var archive = new ZipArchive(memoryStream, ZipArchiveMode.Create, true)) {
ZipArchiveEntry entry = archive.CreateEntry(Path.Combine(innerZipName, entryName), CompressionLevel.Optimal);
using (var writer = new StreamWriter(entry.Open())) {
writer.Write(fileContents);
}
}
return memoryStream
}
However, this just puts Lorem.txt in a folder called "Inner.zip" (instead of in an actual zip file).
I can create an empty inner zip file if I create an entry called "Inner.zip" without writing to it. I can't add anything to it, though, and writing to an entry called "Inner.zip\Lorem.txt" afterward just creates a folder again (alongside the identically named empty .zip file).
I've also tried creating a separate archive, serializing it with a memory stream, then writing that to the original archive as a .zip.
public Stream CreateOuterZip() {
var memoryStream = new MemoryStream();
using (var archive = new ZipArchive(memoryStream, ZipArchiveMode.Create, true)) {
ZipArchiveEntry entry = archive.CreateEntry("Outer.zip", CompressionLevel.NoCompression);
using (var writer = new BinaryWriter(entry.Open())) {
writer.Write(GetMemoryStream().ToArray());
}
}
return memoryStream;
}
This just creates an invalid .zip file that windows doesn't know how to open, though.
Thanks in advance!
So I created a FileStream instead of a MemoryStream so the code can be tested easier
public static Stream CreateOuterZip()
{
string fileContents = "Lorem ipsum dolor sit amet";
// Final zip file
var fs = new FileStream(
Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "SendToClient.zip"), FileMode.OpenOrCreate);
// Create inner zip 1
var innerZip1 = new MemoryStream();
using (var archive = new ZipArchive(innerZip1, ZipArchiveMode.Create, true))
{
var file1 = archive.CreateEntry("File1.xml");
using (var writer = new BinaryWriter(file1.Open()))
{
writer.Write(fileContents); // Change fileContents to real XML content
}
var file2 = archive.CreateEntry("File2.xml");
using (var writer = new BinaryWriter(file2.Open()))
{
writer.Write(fileContents); // Change fileContents to real XML content
}
}
// Create inner zip 2
var innerZip2 = new MemoryStream();
using (var archive = new ZipArchive(innerZip2, ZipArchiveMode.Create, true))
{
var file3 = archive.CreateEntry("File3.xml");
using (var writer = new BinaryWriter(file3.Open()))
{
writer.Write(fileContents); // Change fileContents to real XML content
}
var file4 = archive.CreateEntry("File4.xml");
using (var writer = new BinaryWriter(file4.Open()))
{
writer.Write(fileContents); // Change fileContents to real XML content
}
}
using (var archive = new ZipArchive(fs, ZipArchiveMode.Create, true))
{
// Create inner zip 1
var innerZipEntry = archive.CreateEntry("InnerZip1.zip");
innerZip1.Position = 0;
using (var s = innerZipEntry.Open())
{
innerZip1.WriteTo(s);
}
// Create inner zip 2
var innerZipEntry2 = archive.CreateEntry("InnerZip2.zip");
innerZip2.Position = 0;
using (var s = innerZipEntry2.Open())
{
innerZip2.WriteTo(s);
}
}
fs.Close();
return fs; // The file is written, can probably just close this
}
You can obviously modify this method to return a MemoryStream, or change the method to Void to just have the zip file written out to disk
You should create ZipArchive for internal zip file also. Write it to stream (memorystream). And after write this stream as general stream into main zip.
static Stream Inner() {
var memoryStream = new MemoryStream();
using (var archive = new ZipArchive(memoryStream, ZipArchiveMode.Create, true)) {
var demoFile = archive.CreateEntry("foo2.txt");
using (var entryStream = demoFile.Open())
using (var streamWriter = new StreamWriter(entryStream)) {
streamWriter.Write("Bar2!");
}
}
return memoryStream;
}
static void Main(string[] args) {
using (var memoryStream = new MemoryStream()) {
using (var archive = new ZipArchive(memoryStream, ZipArchiveMode.Create, true)) {
var demoFile = archive.CreateEntry("foo.txt");
using (var entryStream = demoFile.Open())
using (var streamWriter = new StreamWriter(entryStream)) {
streamWriter.Write("Bar!");
}
var zip = archive.CreateEntry("inner.zip");
using (var entryStream = zip.Open()) {
var inner = Inner();
inner.Seek(0, SeekOrigin.Begin);
inner.CopyTo(entryStream);
}
}
using (var fileStream = new FileStream(#"d:\test.zip", FileMode.Create)) {
memoryStream.Seek(0, SeekOrigin.Begin);
memoryStream.CopyTo(fileStream);
}
}
Thanks to this answer.

C# create zip file using zip archive System.IO.Compression

Here is the functionality I want to achieve
Write a JSON file.
Write a PDF file.
Create an archive for these two files
I am using the System.IO.Compression ZipArchive to achieve this. From the documentation, I have not found a good use case for this. The examples in documentation assume that the zip file exists.
What I want to do
Create zipArchive stream write JSON file and pdf file as entries in the zip file.
using (var stream = new FileStream(path, FileMode.Create))
{
using (var archive = new ZipArchive(stream, ZipArchiveMode.Create, true))
{
ZipArchiveEntry manifest = archive.CreateEntry(filenameManifest);
using (StreamWriter writerManifest = new StreamWriter(manifest.Open()))
{
writerManifest.WriteLine(JSONObject_String);
}
ZipArchiveEntry pdfFile = archive.CreateEntry(filenameManifest);
using (StreamWriter writerPDF = new StreamWriter(pdfFile.Open()))
{
writerPDF.WriteLine(pdf);
}
}
}
You don't close the stream, you open with 'manifest.Open()'. Then it might not have written everything to the zip.
Wrap it in another using, like this:
using (var stream = new FileStream(path, FileMode.Create))
{
using (var archive = new ZipArchive(stream, ZipArchiveMode.Create, true))
{
ZipArchiveEntry manifest = archive.CreateEntry(filenameManifest);
using (Stream st = manifest.Open())
{
using (StreamWriter writerManifest = new StreamWriter(st))
{
writerManifest.WriteLine(JSONObject_String);
}
}
ZipArchiveEntry pdfFile = archive.CreateEntry(filenameManifest);
using (Stream st = manifest.Open())
{
using (StreamWriter writerPDF = new StreamWriter(st))
{
writerPDF.WriteLine(pdf);
}
}
}
}

How can i Rewrite File instead of appending using StreamWriter and file stream

I want to rewrite text file using StreamWriter. but when StreamWriter uses stream (like following code), the text will append to file.
StreamWriter sw = new StreamWriter(fstream);
sw.Write(text);
sw.Close();
i must use Stream in code because of that file share limitation
FileMode.Create ll create a new file. If the file excists, it ll show exception. Use FileMode.Truncate.
string txt="your text";
using (FileStream fs = new FileStream(#"C:\Users\rajesh.kumar\Desktop\test123.txt", FileMode.Truncate))
{
using (StreamWriter writer = new StreamWriter(fs))
{
writer.Write("txt");
}
}
If you use file stream, set FileMode:
using (FileStream fs = new FileStream(fileName, FileMode.CreateNew))
{
using (StreamWriter writer = new StreamWriter(fs))
{
writer.Write(textToAdd);
}
}

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