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https://github.com/chanzuckerberg/cellxgene.git
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f69d141336
This will give us the ability to specify different config options for different dataroots. the key of the dataroot dictionary is no longer the same as the dataroot_url. Previously key==dataroot_url, and now those are separated. Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi. Simplified the rest.py interface by no longer passing in the user annotations object, since that can be retrieved from the dataset.
127 lines
4.8 KiB
Python
127 lines
4.8 KiB
Python
import unittest
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from server.data_common.matrix_loader import MatrixDataCacheManager
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from server.common.app_config import AppConfig
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from server.common.errors import DatasetAccessError
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import tempfile
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import shutil
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import os
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import time
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from server.test import PROJECT_ROOT
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class MatrixCacheTest(unittest.TestCase):
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def setup(self):
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pass
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def make_temporay_datasets(self, dirname, num):
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source = f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg"
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for i in range(num):
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target = os.path.join(dirname, str(i) + ".cxg")
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shutil.copytree(source, target)
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def use_dataset(self, matrix_cache, dirname, app_config, dataset_index):
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with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
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pass
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return adaptor
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def use_dataset_with_error(self, matrix_cache, dirname, app_config, dataset_index):
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try:
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with matrix_cache.data_adaptor(None, os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
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raise DatasetAccessError("something bad happened")
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except DatasetAccessError:
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# the MatrixDataCacheManager rethrows the exception, so catch and ignore
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pass
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def get_datasets(self, matrix_cache, dirname):
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datasets = matrix_cache.datasets
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result = {}
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for k, v in datasets.items():
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# filter out the dirname and the .cxg from the name
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newk = int(k[1][len(dirname) + 1 : -4])
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result[newk] = v
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return result
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def check_datasets(self, matrix_cache, dirname, expected):
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res = self.get_datasets(matrix_cache, dirname)
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actual = res.keys()
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self.assertSetEqual(set(actual), set(expected))
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def test_basic(self):
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with tempfile.TemporaryDirectory() as dirname:
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self.make_temporay_datasets(dirname, 5)
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app_config = AppConfig()
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m = MatrixDataCacheManager(max_cached=3, timelimit_s=None)
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# should have only dataset 0
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self.use_dataset(m, dirname, app_config, 0)
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self.check_datasets(m, dirname, [0])
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# should have datasets 0, 1
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self.use_dataset(m, dirname, app_config, 1)
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self.check_datasets(m, dirname, [0, 1])
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# should have datasets 0, 1, 2
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self.use_dataset(m, dirname, app_config, 2)
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self.check_datasets(m, dirname, [0, 1, 2])
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# should have datasets 1, 2, 3
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self.use_dataset(m, dirname, app_config, 3)
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self.check_datasets(m, dirname, [1, 2, 3])
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# use dataset 1, making is more recent than dataset 2
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self.use_dataset(m, dirname, app_config, 1)
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self.check_datasets(m, dirname, [1, 2, 3])
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# use dataset 4, should have 1,3,4
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self.use_dataset(m, dirname, app_config, 4)
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self.check_datasets(m, dirname, [1, 3, 4])
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# use dataset 4 a few more times, get the count to 3
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self.use_dataset(m, dirname, app_config, 4)
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self.use_dataset(m, dirname, app_config, 4)
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datasets = self.get_datasets(m, dirname)
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self.assertEqual(datasets[1].num_access, 2)
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self.assertEqual(datasets[3].num_access, 1)
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self.assertEqual(datasets[4].num_access, 3)
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def test_timelimit(self):
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with tempfile.TemporaryDirectory() as dirname:
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self.make_temporay_datasets(dirname, 2)
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app_config = AppConfig()
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m = MatrixDataCacheManager(max_cached=3, timelimit_s=1)
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adaptor = self.use_dataset(m, dirname, app_config, 0)
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adaptor1 = self.use_dataset(m, dirname, app_config, 0)
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self.assertTrue(adaptor is adaptor1)
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# wait until the timelimit expires and check that there is a new adaptor
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time.sleep(1.1)
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adaptor2 = self.use_dataset(m, dirname, app_config, 0)
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self.assertTrue(adaptor is not adaptor2)
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self.check_datasets(m, dirname, [0])
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# now load a different dataset and see if dataset 0 gets evicted
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time.sleep(1.1)
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self.use_dataset(m, dirname, app_config, 1)
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self.check_datasets(m, dirname, [1])
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def test_access_error(self):
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with tempfile.TemporaryDirectory() as dirname:
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self.make_temporay_datasets(dirname, 1)
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app_config = AppConfig()
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m = MatrixDataCacheManager(max_cached=3, timelimit_s=1)
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# use the 0 datasets
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self.use_dataset(m, dirname, app_config, 0)
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self.check_datasets(m, dirname, [0])
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# use the 0 datasets, but this time a DatasetAccessError is raised.
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# verify that dataset is removed from the cache.
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self.use_dataset_with_error(m, dirname, app_config, 0)
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self.check_datasets(m, dirname, [])
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