dont open stdin by default

[maxogden]

this makes a breaking change I think

me and @mafintosh were trying to figure out why this was hanging:

bionode ncbi search genome eukaryota | dat import --json

and it was because of how bionode was always doing process.stdin.pipe(cli.stdin).

the more unixy way to do it would be to require a - as the last argument, which is what this implements, so now if you want bionode to read from stdin you can do:

bionode ncbi search genome eukaryota

otherwise it won't open stdin

[maxogden]

ah, this causes errors like this:

events.js:72
        throw er; // Unhandled 'error' event
              ^
Error: 2014-10-21T08:22:18 fastq-dump.2.3.5 err: param incorrect while reading argument list within application support module - -

    at Socket.<anonymous> (/Users/maxogden/src/js/bionode/node_modules/bionode-sra/lib/bionode-sra.js:105:28)
    at Socket.EventEmitter.emit (events.js:95:17)
    at Socket.<anonymous> (_stream_readable.js:745:14)
    at Socket.EventEmitter.emit (events.js:92:17)
    at emitReadable_ (_stream_readable.js:407:10)
    at emitReadable (_stream_readable.js:403:5)
    at readableAddChunk (_stream_readable.js:165:9)
    at Socket.Readable.push (_stream_readable.js:127:10)
    at Pipe.onread (net.js:528:21)

[maxogden]

maybe another way to do it that is less unixy but more practical would be to have an opt-out flag rather than an opt-in

[wilzbach]

@maxogden sorry. I can't follow you why checking whether there is a tty on stdin is a bad idea?

If you don't pipe anything into your program like

node -p -e "Boolean(process.stdin.isTTY)"

will be true. So what is the matter with this?

if (!process.stdin.isTTY) { 
   process.stdin.pipe(cli.stdin) 
}

[mafintosh]

@greenify the problem is that isTTY is false if you run this inside a script that is not attached to your terminal. So stuff like

var proc = require('child_process')
var child = proc.spawn('bionode')

Will open stdin which IMO is a bit magical.

[wilzbach]

Ah I see. How about using the "node way"?

process.stdin.setEncoding('utf8');

process.stdin.on('readable', function() {
  process.stdin.pipe(cli.stdin) 
});

process.stdin.on('end', function() {
  cli.stdin.end();
});

[mafintosh]

@greenify that could probably work for our node use case but you still have this problem if someone uses bionode inside a bash script or similar that isn't running as a tty.