import unittest

from inmoose.deseq2 import DESeq, makeExampleDESeqDataSet, nbinomLRT

from inmoose.utils import Factor

class Test(unittest.TestCase):

    def test_LRT(self):

        """test that test='LRT' gives correct errors"""

        dds = makeExampleDESeqDataSet(n=100, m=4)

        dds.obs["group"] = Factor([1, 2, 1, 2])

        dds.design = "~condition"

        with self.assertRaisesRegex(

            ValueError,

            expected_regex="the following variables in the reduced formula not in the full formula: group",

        ):

            DESeq(dds, test="LRT", reduced="~group")

        with self.assertRaisesRegex(

            ValueError,

            expected_regex="test='LRT' does not support use of expanded model matrix",

        ):

            DESeq(dds, test="LRT", reduced="~1", modelMatrixType="expanded")

        with self.assertRaisesRegex(

            ValueError,

            expected_regex="test='LRT' does not support use of LFC shrinkage, use betaPrior=False",

        ):

            DESeq(dds, test="LRT", reduced="~group", betaPrior=True)

        dds = dds.estimateSizeFactors()

        dds = dds.estimateDispersions()

        with self.assertRaisesRegex(

            ValueError, expected_regex="provide a reduced formula for the LRT"

        ):

            nbinomLRT(dds)

    @unittest.skip("unimplemented")

    def test_glmGamPoi(self):

        raise NotImplementedError()

    def test_LRT2(self):

        """test that test='LRT' with quasi-likelihood estimates gives correct errors"""

        dds = makeExampleDESeqDataSet(n=100, m=4)

        dds.obs["group"] = Factor([1, 2, 1, 2])

        dds.design = "~condition + group"

        with self.assertRaises(NotImplementedError):

            DESeq(dds, test="Wald", fitType="glmGamPoi")

        dds = dds.estimateSizeFactors()

        dds_gp = dds.estimateDispersions()

        with self.assertRaises(NotImplementedError):

            nbinomLRT(dds_gp, reduced="~condition", type_="glmGamPoi")