import subprocess
import tempfile
import unittest
import os.path
import sys

import pbcommand.testkit
from pbcommand.models import DataStore
from pbcore.io import AlignmentSet, ConsensusAlignmentSet, openDataSet

import pbtestdata

DATA_DIR = "/pbi/dept/secondary/siv/testdata/SA3-DS"
DATA2 = "/pbi/dept/secondary/siv/testdata/pbalign-unittest2/data"
REF_DIR = "/pbi/dept/secondary/siv/references"


class TestPbalign(pbcommand.testkit.PbTestApp):
    DRIVER_BASE = "pbalign "
    REQUIRES_PBCORE = True
    INPUT_FILES = [
        pbtestdata.get_file("subreads-xml"),
        pbtestdata.get_file("lambdaNEB")
    ]
    TASK_OPTIONS = {
        "pbalign.task_options.algorithm_options": "--holeNumbers 1-1000,30000-30500,60000-60600,100000-100500",
    }

    def run_after(self, rtc, output_dir):
        ds_out = openDataSet(rtc.task.output_files[0])
        self.assertTrue(isinstance(ds_out, AlignmentSet),
                        type(ds_out).__name__)


class TestPbalignCCS(pbcommand.testkit.PbTestApp):
    DRIVER_BASE = "python -m pbalign.ccs"
    INPUT_FILES = [
        pbtestdata.get_file("rsii-ccs"),
        pbtestdata.get_file("lambdaNEB")
    ]

    def run_after(self, rtc, output_dir):
        ds_out = openDataSet(rtc.task.output_files[0])
        self.assertTrue(isinstance(ds_out, ConsensusAlignmentSet),
                        type(ds_out).__name__)


class TestPbalignMinorVariants(pbcommand.testkit.PbTestApp):
    DRIVER_BASE = "python -m pbalign.tasks.align_minorvariants"
    INPUT_FILES = [
        pbtestdata.get_file("rsii-ccs"),
        pbtestdata.get_file("lambdaNEB")
    ]

    def run_after(self, rtc, output_dir):
        ds_out = openDataSet(rtc.task.output_files[0])
        self.assertTrue(isinstance(ds_out, ConsensusAlignmentSet),
                        type(ds_out).__name__)


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