Path with spaces does not work when controlling IGV through a port

[Philipp]

I'm trying to control IGV through port with VB.NET and the following code:

Using client As New TcpClient()
    client.Connect("127.0.0.1", 60151)

    Using stream = client.GetStream()
        Using writer As New StreamWriter(stream)
            writer.AutoFlush = True
            writer.WriteLine("new")
            writer.WriteLine("genome ""C:\Folder with spaces\test.fasta""")
            writer.WriteLine("load ""C:\Folder with spaces\test.bam""")

            stream.Close()
            client.Close()        
        End Using
    End Using
End Using

When I execute this, nothing happens.

This is the line that causes the problem:

writer.WriteLine("genome ""C:\Folder with spaces\test.fasta""")

If I do any of the following, it works:

• No quotes and only file name (if the file would be in the IGV viewer directory) -> writer.WriteLine("genome test.fasta")
  
• No quotes and full file path. That works of course only if I don't have any spaces in the path. -> writer.WriteLine("genome C:\Folder_without_spaces\test.fasta")
  
• Load the fasta file via the GUI and omit the loading genome step in the code

Unfortunately I cannot use any of those solutions.

The files will not be in the same folder as the IGV viewer and I will have file paths with spaces inside.

Interestingly this is only a problem when loading the genome. Loading the bam file works fine, even with the quotes.

IGV Version: 2.3.93 (151)

OS: Windows 7 SP1

In the log file you can see first the failed loading.

Afterwards a loading that succeeded, although there seems to be an error when closing the connection.

Is this a bug or am I doing something wrong here?

Thanks

Philipp

[James Robinson]

I'm not familiar with visual basic,  but in most languages the quotes would need to be escaped.    If you change writer.WriteLine and print to the console what do you see?

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[Philipp]

When I print to the console, I get this:

new

genome "C:\Folder with spaces\test.fasta"

load "C:\Folder with spaces\test.bam"

[James Robinson]

Thanks for checking.

I've confirmed this is an IGV bug.  I opened a git issue for it here:  https://github.com/igvteam/igv/issues/423.

In the meantime,  the following might help as a workaround.

up vote8down vote

If double quotes do not solve the issue then try e.g. dir /X ~1 c:\ to get a list of alternative file or directory names. Example output: 11/09/2014 12:54 AM 8,065 DEFAUL~1.XML Default Desktop Policy.xml 06/12/2014 03:49 PM <DIR> PROGRA~1 Program Files 10/12/2014 12:46 AM <DIR> PROGRA~2 Program Files (x86) 07/11/2014 03:10 PM <DIR> servers Now us the short 8 character file or folder name in the 5th column, e.g. PROGRA~1 or DEFAUL~1.XML, in your commands. For instance: set JAVA_HOME=c:\PROGRA~1\Java\jdk1.6.0_45

[Philipp]

Thanks a lot for the quick answer.

Using short names works for me as workaround.

Just to be sure:

Do I have to worry about that java.net.SocketException that shows up in my log when closing the client connection?