Improvements to the matrix cache (#1340)

* Improvements to the matrix cache

- Add a timelimit for the matrix in the cache.
Once the timelimit is reached, the matrix can be removed.

- If a DatasetAccessError occurs, then remove the dataset
from the matrix cache.

Fixes #1322

server/test/test_matrixcache.py

@@ -0,0 +1,124 @@
+import unittest
+from server.data_common.matrix_loader import MatrixDataCacheManager
+from server.common.app_config import AppConfig
+from server.common.errors import DatasetAccessError
+import tempfile
+import shutil
+import os
+import time
+
+
+class MatrixCacheTest(unittest.TestCase):
+    def setup(self):
+        pass
+
+    def make_temporay_datasets(self, dirname, num):
+        source = "test/test_datasets/pbmc3k.cxg"
+        for i in range(num):
+            target = os.path.join(dirname, str(i) + ".cxg")
+            shutil.copytree(source, target)
+
+    def use_dataset(self, matrix_cache, dirname, app_config, dataset_index):
+        with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config) as adaptor:
+            pass
+        return adaptor
+
+    def use_dataset_with_error(self, matrix_cache, dirname, app_config, dataset_index):
+        try:
+            with matrix_cache.data_adaptor(os.path.join(dirname, str(dataset_index) + ".cxg"), app_config):
+                raise DatasetAccessError("something bad happened")
+        except DatasetAccessError:
+            # the MatrixDataCacheManager rethrows the exception, so catch and ignore
+            pass
+
+    def get_datasets(self, matrix_cache, dirname):
+        datasets = matrix_cache.datasets
+        result = {}
+        for k, v in datasets.items():
+            # filter out the dirname and the .cxg from the name
+            newk = int(k[len(dirname) + 1 : -4])
+            result[newk] = v
+
+        return result
+
+    def check_datasets(self, matrix_cache, dirname, expected):
+        res = self.get_datasets(matrix_cache, dirname)
+        actual = res.keys()
+        self.assertSetEqual(set(actual), set(expected))
+
+    def test_basic(self):
+        with tempfile.TemporaryDirectory() as dirname:
+            self.make_temporay_datasets(dirname, 5)
+            app_config = AppConfig()
+            m = MatrixDataCacheManager(max_cached=3, timelimit_s=None)
+
+            # should have only dataset 0
+            self.use_dataset(m, dirname, app_config, 0)
+            self.check_datasets(m, dirname, [0])
+
+            # should have datasets 0, 1
+            self.use_dataset(m, dirname, app_config, 1)
+            self.check_datasets(m, dirname, [0, 1])
+
+            # should have datasets 0, 1, 2
+            self.use_dataset(m, dirname, app_config, 2)
+            self.check_datasets(m, dirname, [0, 1, 2])
+
+            # should have datasets 1, 2, 3
+            self.use_dataset(m, dirname, app_config, 3)
+            self.check_datasets(m, dirname, [1, 2, 3])
+
+            # use dataset 1, making is more recent than dataset 2
+            self.use_dataset(m, dirname, app_config, 1)
+            self.check_datasets(m, dirname, [1, 2, 3])
+
+            # use dataset 4, should have 1,3,4
+            self.use_dataset(m, dirname, app_config, 4)
+            self.check_datasets(m, dirname, [1, 3, 4])
+
+            # use dataset 4 a few more times, get the count to 3
+            self.use_dataset(m, dirname, app_config, 4)
+            self.use_dataset(m, dirname, app_config, 4)
+
+            datasets = self.get_datasets(m, dirname)
+            self.assertEqual(datasets[1].num_access, 2)
+            self.assertEqual(datasets[3].num_access, 1)
+            self.assertEqual(datasets[4].num_access, 3)
+
+    def test_timelimit(self):
+        with tempfile.TemporaryDirectory() as dirname:
+            self.make_temporay_datasets(dirname, 2)
+
+            app_config = AppConfig()
+            m = MatrixDataCacheManager(max_cached=3, timelimit_s=1)
+
+            adaptor = self.use_dataset(m, dirname, app_config, 0)
+            adaptor1 = self.use_dataset(m, dirname, app_config, 0)
+            self.assertTrue(adaptor is adaptor1)
+
+            # wait until the timelimit expires and check that there is a new adaptor
+            time.sleep(1.1)
+            adaptor2 = self.use_dataset(m, dirname, app_config, 0)
+            self.assertTrue(adaptor is not adaptor2)
+            self.check_datasets(m, dirname, [0])
+
+            # now load a different dataset and see if dataset 0 gets evicted
+            time.sleep(1.1)
+            self.use_dataset(m, dirname, app_config, 1)
+            self.check_datasets(m, dirname, [1])
+
+    def test_access_error(self):
+        with tempfile.TemporaryDirectory() as dirname:
+            self.make_temporay_datasets(dirname, 1)
+
+            app_config = AppConfig()
+            m = MatrixDataCacheManager(max_cached=3, timelimit_s=1)
+
+            # use the 0 datasets
+            self.use_dataset(m, dirname, app_config, 0)
+            self.check_datasets(m, dirname, [0])
+
+            # use the 0 datasets, but this time a DatasetAccessError is raised.
+            # verify that dataset is removed from the cache.
+            self.use_dataset_with_error(m, dirname, app_config, 0)
+            self.check_datasets(m, dirname, [])