gpsea/tests/view/test_viewers.py at a6ff4ee8ef22cf93d63dd79dda4045b40f41d5be · P2GX/gpsea · GitHub

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import io
import os

import hpotk
import pytest

from gpsea.analysis.pcats import HpoTermAnalysisResult
from gpsea.model import Cohort, ProteinMetadata
from gpsea.view import (
    CohortViewer,
    CohortVariantViewer,
    GpseaReport,
    MtcStatsViewer,
)
from gpsea.view._viewers import ProteinVariantViewer


@pytest.mark.skip("Just for manual testing and debugging")
class TestCohortViewer:
    @pytest.fixture
    def cohort_viewer(
        self,
        hpo: hpotk.MinimalOntology,
    ) -> CohortViewer:
        return CohortViewer(
            hpo=hpo,
        )

    def test_process_suox_cohort(
        self,
        cohort_viewer: CohortViewer,
        suox_cohort: Cohort,
        suox_mane_tx_id: str,
    ):
        report = cohort_viewer.process(
            cohort=suox_cohort,
            transcript_id=suox_mane_tx_id,
        )

        with open(os.path.join("dev", "SUOX.cohort.html"), "w") as fh:
            report.write(fh)

    def test_process_cyp21a2_cohort(
        self,
        cohort_viewer: CohortViewer,
        cyp21a2_cohort: Cohort,
        cyp21a2_mane_tx_id: str,
    ):
        report = cohort_viewer.process(
            cohort=cyp21a2_cohort,
            transcript_id=cyp21a2_mane_tx_id,
        )

        with open(os.path.join("dev", "CYP21A2.cohort.html"), "w") as fh:
            report.write(fh)


@pytest.mark.skip("Just for manual testing and debugging")
def test_viewer(
    suox_mane_tx_id: str,
    suox_cohort: Cohort,
):
    viewer = CohortVariantViewer(tx_id=suox_mane_tx_id)
    html = viewer.process(suox_cohort)

    with open("all_variants.html", "w") as fh:
        html.write(fh)


class TestMtcStatsViewer:

    @pytest.fixture
    def stats_viewer(self) -> MtcStatsViewer:
        return MtcStatsViewer()

    @pytest.mark.skip("Just for manual testing and debugging")
    def test_process(
        self,
        stats_viewer: MtcStatsViewer,
        hpo_term_analysis_result: HpoTermAnalysisResult,
    ):
        report = stats_viewer.process(result=hpo_term_analysis_result)
        with open("mtc_stats.html", "w") as fh:
            report.write(fh)


class TestProteinVariantViewer:

    @pytest.fixture(scope="class")
    def protein_variant_viewer(
        self,
        suox_protein_metadata: ProteinMetadata,
    ) -> ProteinVariantViewer:
        return ProteinVariantViewer(
            protein_metadata=suox_protein_metadata,
        )

    def test_process(
        self,
        suox_cohort: Cohort,
        protein_variant_viewer: ProteinVariantViewer,
    ):
        report = protein_variant_viewer.process(suox_cohort)
        assert isinstance(report, GpseaReport)

        buf = io.StringIO()
        report.write(buf)
        val = buf.getvalue()

        assert "gpsea-body" in val