import os
import subprocess
import threading
import errno
import unittest

from pysam import AlignmentFile

DATADIR = os.path.abspath(os.path.join(
    os.path.dirname(__file__),
    "pysam_data"))


def alignmentfile_writer_thread(infile, outfile):
    def _writer_thread(infile, outfile):
        """read  from infile and write to outfile"""
        try:
            i = 0
            for record in infile:
                outfile.write(record)
                i += 1
        except IOError as e:
            if e.errno != errno.EPIPE:
                pass
        finally:
            outfile.close()

    writer = threading.Thread(target=_writer_thread, args=(infile, outfile))
    writer.daemon = True
    writer.start()
    return writer


class StreamTest(unittest.TestCase):

    def stream_process(self, proc, in_stream, out_stream, writer):

        with AlignmentFile(proc.stdout) as infile:
            read = 0
            for record in infile:
                read += 1
        return 0, read

    def test_text_processing(self):

        proc = subprocess.Popen('head -n200',
                                stdin=subprocess.PIPE,
                                stdout=subprocess.PIPE,
                                shell=True)

        in_stream = AlignmentFile('pysam_data/ex1.bam')
        out_stream = AlignmentFile(proc.stdin, 'wh', header=in_stream.header)
        writer = alignmentfile_writer_thread(in_stream,
                                             out_stream)

        written, read = self.stream_process(proc,
                                            in_stream,
                                            out_stream,
                                            writer)
        self.assertEqual(read, 198)

    def test_samtools_processing(self):

        proc = subprocess.Popen('samtools view -b -f 4',
                                stdin=subprocess.PIPE,
                                stdout=subprocess.PIPE,
                                shell=True)

        in_stream = AlignmentFile('pysam_data/ex1.bam')
        out_stream = AlignmentFile(proc.stdin, 'wb', header=in_stream.header)
        writer = alignmentfile_writer_thread(in_stream,
                                             out_stream)

        written, read = self.stream_process(proc,
                                            in_stream,
                                            out_stream,
                                            writer)
        self.assertEqual(read, 35)


if __name__ == "__main__":
    unittest.main()