import logging
import os.path as op

import pytest

from pbcore.io import AlignmentSet

from kineticsTools import ReferenceUtils

big_data_dir = "/pbi/dept/secondary/siv/testdata/kineticsTools"
ref_dir = "/pbi/dept/secondary/siv/references"

logging.basicConfig()
log = logging.getLogger()


@pytest.mark.internal_data
class TestReferenceUtils:

    def test_bam(self):
        bamFile = op.join(big_data_dir, "ecoli_first_50k.mapped.bam")
        refFile = op.join(ref_dir, "ecoli_k12_MG1655_first50k",
                          "ecoli_k12_MG1655_first50k.referenceset.xml")
        ds = AlignmentSet(bamFile, referenceFastaFname=refFile)
        contigs = ReferenceUtils.loadReferenceContigs(refFile, ds)
        assert len(contigs) == 1
        assert contigs[0].alignmentID == 0
        chemistry = ReferenceUtils.loadAlignmentChemistry(ds)
        assert chemistry == "S/P3-C3/5.0"

    def test_dataset(self):
        pass  # TODO

    def test_parseReferenceWindow(self):
        window = "gi|12057207|gb|AE001439.1|:1-5000"
        bamFile = op.join(big_data_dir, "Hpyl_1_5000.bam")
        refFile = op.join(ref_dir, "Helicobacter_pylori_J99", "sequence",
                          "Helicobacter_pylori_J99.fasta")
        alnFile = AlignmentSet(bamFile, referenceFastaFname=refFile)
        win = ReferenceUtils.parseReferenceWindow(window,
                                                  alnFile.referenceInfo)
        assert [win.refId, win.start, win.end] == [0, 1, 5000]

    def test_createReferenceWindows(self):
        bamFile = op.join(big_data_dir, "Hpyl_1_5000.bam")
        ds = AlignmentSet(bamFile, referenceFastaFname=None)
        refInfoTable = ds.referenceInfoTable
        windows = ReferenceUtils.createReferenceWindows(refInfoTable)
        assert len(windows) == 1
        w = windows[0]
        assert w.refId == 0
        assert w.refName == 'gi|12057207|gb|AE001439.1|'
        assert w.start == 0
        assert w.end == 1643831

    def test_enumerateChunks(self):
        pass  # TODO