cellxgene/server/test/test_cxgtool.py

import random
import shutil
import string
import unittest

import anndata

from server.common.data_locator import DataLocator
from server.converters.cxgtool import write_cxg
from server.data_cxg.cxg_adaptor import CxgAdaptor
from server.test import PROJECT_ROOT, app_config
from server.test.test_datasets.fixtures import pbmc3k_colors


class TestCxgAdaptor(unittest.TestCase):
    def setUp(self) -> None:
        self.fixtures = []

    def tearDown(self) -> None:
        try:
            for data_locator in self.fixtures:
                print("REMOVING ", data_locator)
                shutil.rmtree(data_locator)
        except FileNotFoundError:
            pass

    def test_cxg_category_colors(self):
        data = self.convert_pbmc3k(extract_colors=True)
        self.assertEqual(data.get_colors(), pbmc3k_colors)
        data = self.convert_pbmc3k(extract_colors=False)
        self.assertEqual(data.get_colors(), {})

    def convert_pbmc3k(self, **kwargs):
        random_string = "".join(random.choice(string.ascii_letters) for _ in range(8))
        data_locator = f"/tmp/test_{random_string}.cxg"
        self.fixtures.append(data_locator)
        source_h5ad = anndata.read_h5ad(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
        write_cxg(adata=source_h5ad, container=data_locator, title="pbmc3k", **kwargs)
        config = app_config(data_locator)
        return CxgAdaptor(DataLocator(data_locator), config)