X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8192c879caaca60902ca362b4967cf4492d08e0c..62d56bce0d714cc2df2ab5e7f1005dc3d76f783b:/sdk/python/tests/test_arvfile.py diff --git a/sdk/python/tests/test_arvfile.py b/sdk/python/tests/test_arvfile.py index 4bc9c2ef96..6b3562602a 100644 --- a/sdk/python/tests/test_arvfile.py +++ b/sdk/python/tests/test_arvfile.py @@ -6,11 +6,13 @@ import io import mock import os import unittest -import hashlib +import time import arvados -from arvados import ArvadosFile, ArvadosFileReader, Range, import_manifest, export_manifest, KeepLocator -from arvados.arvfile import SYNC_READONLY, SYNC_EXPLICIT +from arvados._ranges import Range +from arvados.keep import KeepLocator +from arvados.collection import Collection, CollectionReader +from arvados.arvfile import ArvadosFile, ArvadosFileReader import arvados_testutil as tutil from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin @@ -20,207 +22,311 @@ class ArvadosFileWriterTestCase(unittest.TestCase): def __init__(self, blocks): self.blocks = blocks self.requests = [] - def get(self, locator, num_retries=0, cache_only=False): + def get(self, locator, num_retries=0): self.requests.append(locator) return self.blocks.get(locator) - def put(self, data): - pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data)) + def get_from_cache(self, locator): + self.requests.append(locator) + return self.blocks.get(locator) + def put(self, data, num_retries=None, copies=None): + pdh = tutil.str_keep_locator(data) self.blocks[pdh] = str(data) return pdh class MockApi(object): def __init__(self, b, r): - self.b = b - self.r = r + self.body = b + self.response = r + self._schema = ArvadosFileWriterTestCase.MockApi.MockSchema() + self._rootDesc = {} + class MockSchema(object): + def __init__(self): + self.schemas = {'Collection': {'properties': {'replication_desired': {'type':'integer'}}}} class MockCollections(object): def __init__(self, b, r): - self.b = b - self.r = r + self.body = b + self.response = r class Execute(object): def __init__(self, r): - self.r = r + self.response = r def execute(self, num_retries=None): - return self.r + return self.response def create(self, ensure_unique_name=False, body=None): - if body != self.b: - raise Exception("Body %s does not match expectation %s" % (body, self.b)) - return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r) + if body != self.body: + raise Exception("Body %s does not match expectation %s" % (body, self.body)) + return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response) def update(self, uuid=None, body=None): - return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r) + return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.response) def collections(self): - return ArvadosFileWriterTestCase.MockApi.MockCollections(self.b, self.r) + return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response) def test_truncate(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate", - "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"}) + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual(writer.size(), 10) - writer.seek(5) - self.assertEqual("56789", writer.read(8)) + self.assertEqual("0123456789", writer.read(12)) + writer.truncate(8) - writer.seek(5, os.SEEK_SET) - self.assertEqual("567", writer.read(8)) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - c.save_as("test_truncate") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + # Make sure reading off the end doesn't break + self.assertEqual("", writer.read(12)) - def test_append(self): + self.assertEqual(writer.size(), 8) + writer.seek(0, os.SEEK_SET) + self.assertEqual("01234567", writer.read(12)) + + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_truncate") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) + + def test_write_to_end(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_append", - "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"}) + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "r+") + self.assertEqual(writer.size(), 10) + writer.seek(5, os.SEEK_SET) self.assertEqual("56789", writer.read(8)) + writer.seek(10, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 13) + writer.seek(5, os.SEEK_SET) self.assertEqual("56789foo", writer.read(8)) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) - c.save_as("test_append") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + self.assertIsNone(keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) + + c.save_new("test_append") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) - def test_write0(self): + + def test_append(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + c = Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', keep_client=keep) + writer = c.open("count.txt", "a+") + self.assertEqual(writer.read(20), "0123456789") + writer.seek(0, os.SEEK_SET) + + writer.write("hello") + self.assertEqual(writer.read(20), "0123456789hello") + writer.seek(0, os.SEEK_SET) + + writer.write("world") + self.assertEqual(writer.read(20), "0123456789helloworld") + + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n", c.portable_manifest_text()) + + def test_write_at_beginning(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual("0123456789", writer.readfrom(0, 13)) writer.seek(0, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) self.assertEqual("foo3456789", writer.readfrom(0, 13)) - self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", export_manifest(c)) + self.assertEqual(". acbd18db4cc2f85cedef654fccc4a4d8+3 781e5e245d69b566979b86e28d23f2c7+10 0:3:count.txt 6:7:count.txt\n", c.portable_manifest_text()) + + def test_write_empty(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + with Collection(keep_client=keep) as c: + writer = c.open("count.txt", "w") + self.assertEqual(writer.size(), 0) + self.assertEqual(". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n", c.portable_manifest_text()) - def test_write1(self): + def test_save_manifest_text(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + with Collection(keep_client=keep) as c: + writer = c.open("count.txt", "w") + writer.write("0123456789") + self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text()) + self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) + + self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False)) + self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) + + def test_get_manifest_text_commits(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + with Collection(keep_client=keep) as c: + writer = c.open("count.txt", "w") + writer.write("0123456789") + self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text()) + self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) + self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text()) + self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks) + + + def test_write_in_middle(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual("0123456789", writer.readfrom(0, 13)) writer.seek(3, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) self.assertEqual("012foo6789", writer.readfrom(0, 13)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:count.txt 10:3:count.txt 6:4:count.txt\n", c.portable_manifest_text()) - def test_write2(self): + def test_write_at_end(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual("0123456789", writer.readfrom(0, 13)) writer.seek(7, os.SEEK_SET) writer.write("foo") self.assertEqual(writer.size(), 10) self.assertEqual("0123456foo", writer.readfrom(0, 13)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text()) - def test_write3(self): + def test_write_across_segment_boundary(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n', + keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual("012345678901234", writer.readfrom(0, 15)) writer.seek(7, os.SEEK_SET) writer.write("foobar") self.assertEqual(writer.size(), 20) self.assertEqual("0123456foobar34", writer.readfrom(0, 15)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text()) - def test_write4(self): + def test_write_across_several_segments(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt', + keep_client=keep) as c: writer = c.open("count.txt", "r+") self.assertEqual("012301230123", writer.readfrom(0, 15)) writer.seek(2, os.SEEK_SET) writer.write("abcdefg") self.assertEqual(writer.size(), 12) self.assertEqual("01abcdefg123", writer.readfrom(0, 15)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text()) def test_write_large(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large", - "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', - api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text": ". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"}) + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "r+") - text = ''.join(["0123456789" for a in xrange(0, 100)]) + text = "0123456789" * 100 for b in xrange(0, 100000): writer.write(text) self.assertEqual(writer.size(), 100000000) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - c.save_as("test_write_large") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_write_large") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) + + + def test_large_write(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + api = ArvadosFileWriterTestCase.MockApi({}, {}) + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + api_client=api, keep_client=keep) as c: + writer = c.open("count.txt", "r+") + self.assertEqual(writer.size(), 0) + + text = "0123456789" + writer.write(text) + text = "0123456789" * 9999999 + writer.write(text) + self.assertEqual(writer.size(), 100000000) + + self.assertEqual(c.manifest_text(), ". 781e5e245d69b566979b86e28d23f2c7+10 48dd23ea1645fd47d789804d71b5bb8e+67108864 77c57dc6ac5a10bb2205caaa73187994+32891126 0:100000000:count.txt\n") - def test_write_rewrite0(self): + def test_rewrite_on_empty_file(self): keep = ArvadosFileWriterTestCase.MockKeep({}) - with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + keep_client=keep) as c: writer = c.open("count.txt", "r+") for b in xrange(0, 10): writer.seek(0, os.SEEK_SET) writer.write("0123456789") - writer.arvadosfile._repack_writes() + + self.assertEqual(writer.size(), 10) + self.assertEqual("0123456789", writer.readfrom(0, 20)) + self.assertEqual(". 7a08b07e84641703e5f2c836aa59a170+100 90:10:count.txt\n", c.portable_manifest_text()) + writer.flush() self.assertEqual(writer.size(), 10) self.assertEqual("0123456789", writer.readfrom(0, 20)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.portable_manifest_text()) - def test_write_rewrite1(self): + def test_rewrite_append_existing_file(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', + keep_client=keep) as c: writer = c.open("count.txt", "r+") for b in xrange(0, 10): writer.seek(10, os.SEEK_SET) writer.write("abcdefghij") - writer.arvadosfile._repack_writes() + + self.assertEqual(writer.size(), 20) + self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:10:count.txt 100:10:count.txt\n", c.portable_manifest_text()) + + writer.arvadosfile.flush() self.assertEqual(writer.size(), 20) self.assertEqual("0123456789abcdefghij", writer.readfrom(0, 20)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.portable_manifest_text()) - def test_write_rewrite2(self): + def test_rewrite_over_existing_file(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', - keep=keep, sync=SYNC_EXPLICIT) as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', + keep_client=keep) as c: writer = c.open("count.txt", "r+") for b in xrange(0, 10): writer.seek(5, os.SEEK_SET) writer.write("abcdefghij") - writer.arvadosfile._repack_writes() + + self.assertEqual(writer.size(), 15) + self.assertEqual("01234abcdefghij", writer.readfrom(0, 20)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n", c.portable_manifest_text()) + + writer.arvadosfile.flush() + self.assertEqual(writer.size(), 15) self.assertEqual("01234abcdefghij", writer.readfrom(0, 20)) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", export_manifest(c)) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.portable_manifest_text()) - def test_write_large_rewrite0(self): + def test_write_large_rewrite(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_write_large", - "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', - api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text": ". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"}) + with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', + api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "r+") text = ''.join(["0123456789" for a in xrange(0, 100)]) for b in xrange(0, 100000): @@ -229,76 +335,88 @@ class ArvadosFileWriterTestCase(unittest.TestCase): writer.write("foo") self.assertEqual(writer.size(), 100000000) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - c.save_as("test_write_large") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_write_large") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) def test_create(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_create", - "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}) + with Collection(api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "w+") self.assertEqual(writer.size(), 0) writer.write("01234567") self.assertEqual(writer.size(), 8) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8")) - c.save_as("test_create") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8")) + c.save_new("test_create") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) def test_create_subdir(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_create", - "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":"./foo/bar 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}) + with Collection(api_client=api, keep_client=keep) as c: + self.assertIsNone(c.api_response()) writer = c.open("foo/bar/count.txt", "w+") writer.write("01234567") - c.save_as("test_create") + self.assertFalse(c.committed()) + c.save_new("test_create") + self.assertTrue(c.committed()) + self.assertEqual(c.api_response(), api.response) def test_overwrite(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_overwrite", - "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - api_client=api, keep=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"}) + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', + api_client=api, keep_client=keep) as c: writer = c.open("count.txt", "w+") self.assertEqual(writer.size(), 0) writer.write("01234567") self.assertEqual(writer.size(), 8) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - c.save_as("test_overwrite") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + c.save_new("test_overwrite") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) def test_file_not_found(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: with self.assertRaises(IOError): writer = c.open("nocount.txt", "r") def test_cannot_open_directory(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n') as c: with self.assertRaises(IOError): writer = c.open(".", "r") def test_create_multiple(self): keep = ArvadosFileWriterTestCase.MockKeep({}) api = ArvadosFileWriterTestCase.MockApi({"name":"test_create_multiple", - "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"}, - {"uuid":"zzzzz-4zz18-mockcollection0"}) - with arvados.Collection(api_client=api, keep_client=keep, sync=SYNC_EXPLICIT) as c: + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n", + "replication_desired":None}, + {"uuid":"zzzzz-4zz18-mockcollection0", + "manifest_text":". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"}) + with Collection(api_client=api, keep_client=keep) as c: w1 = c.open("count1.txt", "w") w2 = c.open("count2.txt", "w") w1.write("01234567") @@ -306,47 +424,14 @@ class ArvadosFileWriterTestCase(unittest.TestCase): self.assertEqual(w1.size(), 8) self.assertEqual(w2.size(), 8) - self.assertEqual(None, c._manifest_locator) - self.assertEqual(True, c.modified()) - self.assertEqual(None, keep.get("2e9ec317e197819358fbc43afca7d837+8")) - c.save_as("test_create_multiple") - self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) - self.assertEqual(False, c.modified()) + self.assertIsNone(c.manifest_locator()) + self.assertTrue(c.modified()) + self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8")) + c.save_new("test_create_multiple") + self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator()) + self.assertFalse(c.modified()) self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) - def test_remove(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", export_manifest(c)) - self.assertTrue("count1.txt" in c) - c.remove("count1.txt") - self.assertFalse("count1.txt" in c) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", export_manifest(c)) - - def test_remove_in_subdir(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: - c.remove("foo/count2.txt") - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) - - def test_remove_empty_subdir(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: - c.remove("foo/count2.txt") - c.remove("foo") - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) - - def test_remove_empty_subdir(self): - with import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: - with self.assertRaises(IOError): - c.remove("foo") - c.remove("foo", rm_r=True) - self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) - - def test_prefetch(self): - keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"}) - with import_manifest(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep=keep) as c: - r = c.open("count.txt", "r") - self.assertEqual("0123", r.read(4)) - self.assertTrue("2e9ec317e197819358fbc43afca7d837+8" in keep.requests) - self.assertTrue("e8dc4081b13434b45189a720b77b6818+8" in keep.requests) class ArvadosFileReaderTestCase(StreamFileReaderTestCase): class MockParent(object): @@ -358,7 +443,7 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): def block_prefetch(self, loc): pass - def get_block(self, loc, num_retries=0, cache_only=False): + def get_block_contents(self, loc, num_retries=0, cache_only=False): if self.nocache and cache_only: return None return self.blocks[loc] @@ -366,39 +451,78 @@ class ArvadosFileReaderTestCase(StreamFileReaderTestCase): def __init__(self, blocks, nocache): self.blocks = blocks self.nocache = nocache + self.lock = arvados.arvfile.NoopLock() + + def root_collection(self): + return self def _my_block_manager(self): return ArvadosFileReaderTestCase.MockParent.MockBlockMgr(self.blocks, self.nocache) - def sync_mode(self): - return SYNC_READONLY def make_count_reader(self, nocache=False): stream = [] n = 0 blocks = {} for d in ['01234', '34567', '67890']: - loc = '{}+{}'.format(hashlib.md5(d).hexdigest(), len(d)) + loc = tutil.str_keep_locator(d) blocks[loc] = d stream.append(Range(loc, n, len(d))) n += len(d) - af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)]) - return ArvadosFileReader(af, "count.txt") + af = ArvadosFile(ArvadosFileReaderTestCase.MockParent(blocks, nocache), "count.txt", stream=stream, segments=[Range(1, 0, 3), Range(6, 3, 3), Range(11, 6, 3)]) + return ArvadosFileReader(af) - def test_read_returns_first_block(self): - # read() calls will be aligned on block boundaries - see #3663. + def test_read_block_crossing_behavior(self): + # read() needs to return all the data requested if possible, even if it + # crosses uncached blocks: https://arvados.org/issues/5856 sfile = self.make_count_reader(nocache=True) - self.assertEqual('123', sfile.read(10)) + self.assertEqual('12345678', sfile.read(8)) def test_successive_reads(self): + # Override StreamFileReaderTestCase.test_successive_reads sfile = self.make_count_reader(nocache=True) - for expect in ['123', '456', '789', '']: - self.assertEqual(expect, sfile.read(10)) + self.assertEqual('1234', sfile.read(4)) + self.assertEqual('5678', sfile.read(4)) + self.assertEqual('9', sfile.read(4)) + self.assertEqual('', sfile.read(4)) def test_tell_after_block_read(self): + # Override StreamFileReaderTestCase.test_tell_after_block_read sfile = self.make_count_reader(nocache=True) - sfile.read(5) - self.assertEqual(3, sfile.tell()) + self.assertEqual('12345678', sfile.read(8)) + self.assertEqual(8, sfile.tell()) + + def test_prefetch(self): + keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"}) + with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c: + r = c.open("count.txt", "r") + self.assertEqual("0123", r.read(4)) + self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests) + self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests) + + def test__eq__from_manifest(self): + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2: + self.assertTrue(c1["count1.txt"] == c2["count1.txt"]) + self.assertFalse(c1["count1.txt"] != c2["count1.txt"]) + + def test__eq__from_writes(self): + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: + with Collection() as c2: + f = c2.open("count1.txt", "w") + f.write("0123456789") + + self.assertTrue(c1["count1.txt"] == c2["count1.txt"]) + self.assertFalse(c1["count1.txt"] != c2["count1.txt"]) + + def test__ne__(self): + with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: + with Collection() as c2: + f = c2.open("count1.txt", "w") + f.write("1234567890") + + self.assertTrue(c1["count1.txt"] != c2["count1.txt"]) + self.assertFalse(c1["count1.txt"] == c2["count1.txt"]) class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin): @@ -414,12 +538,14 @@ class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin): n += k.size except ValueError: pass - col = arvados.Collection(keep_client=self.keep_client()) - col._my_block_manager().prefetch_enabled = False - af = ArvadosFile(col, + + blockmanager = arvados.arvfile._BlockManager(self.keep_client()) + blockmanager.prefetch_enabled = False + col = Collection(keep_client=self.keep_client(), block_manager=blockmanager) + af = ArvadosFile(col, "test", stream=stream, segments=segments) - return ArvadosFileReader(af, "test", **kwargs) + return ArvadosFileReader(af, **kwargs) def read_for_test(self, reader, byte_count, **kwargs): return reader.read(byte_count, **kwargs) @@ -443,3 +569,103 @@ class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase): class ArvadosFileReadlinesTestCase(ArvadosFileReadTestCase): def read_for_test(self, reader, byte_count, **kwargs): return ''.join(reader.readlines(**kwargs)) + +class BlockManagerTest(unittest.TestCase): + def test_bufferblock_append(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + with arvados.arvfile._BlockManager(keep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + + self.assertEqual(bufferblock.size(), 3) + self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") + + bufferblock.append("bar") + + self.assertEqual(bufferblock.size(), 6) + self.assertEqual(bufferblock.buffer_view[0:6], "foobar") + self.assertEqual(bufferblock.locator(), "3858f62230ac3c915f300c664312c63f+6") + + bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING) + with self.assertRaises(arvados.errors.AssertionError): + bufferblock.append("bar") + + def test_bufferblock_dup(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + with arvados.arvfile._BlockManager(keep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + + self.assertEqual(bufferblock.size(), 3) + self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") + bufferblock.set_state(arvados.arvfile._BufferBlock.PENDING) + + bufferblock2 = blockmanager.dup_block(bufferblock, None) + self.assertNotEqual(bufferblock.blockid, bufferblock2.blockid) + + bufferblock2.append("bar") + + self.assertEqual(bufferblock2.size(), 6) + self.assertEqual(bufferblock2.buffer_view[0:6], "foobar") + self.assertEqual(bufferblock2.locator(), "3858f62230ac3c915f300c664312c63f+6") + + self.assertEqual(bufferblock.size(), 3) + self.assertEqual(bufferblock.buffer_view[0:3], "foo") + self.assertEqual(bufferblock.locator(), "acbd18db4cc2f85cedef654fccc4a4d8+3") + + def test_bufferblock_get(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + with arvados.arvfile._BlockManager(keep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + + self.assertEqual(blockmanager.get_block_contents("781e5e245d69b566979b86e28d23f2c7+10", 1), "0123456789") + self.assertEqual(blockmanager.get_block_contents(bufferblock.blockid, 1), "foo") + + def test_bufferblock_commit(self): + mockkeep = mock.MagicMock() + with arvados.arvfile._BlockManager(mockkeep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.owner = mock.MagicMock() + def flush(sync=None): + blockmanager.commit_bufferblock(bufferblock, sync) + bufferblock.owner.flush.side_effect = flush + bufferblock.append("foo") + blockmanager.commit_all() + self.assertTrue(bufferblock.owner.flush.called) + self.assertTrue(mockkeep.put.called) + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED) + self.assertIsNone(bufferblock.buffer_view) + + def test_bufferblock_commit_pending(self): + # Test for bug #7225 + mockkeep = mock.MagicMock() + mockkeep.put.side_effect = lambda x: time.sleep(1) + with arvados.arvfile._BlockManager(mockkeep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + + blockmanager.commit_bufferblock(bufferblock, False) + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING) + + blockmanager.commit_bufferblock(bufferblock, True) + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED) + + + def test_bufferblock_commit_with_error(self): + mockkeep = mock.MagicMock() + mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail") + with arvados.arvfile._BlockManager(mockkeep) as blockmanager: + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.owner = mock.MagicMock() + def flush(sync=None): + blockmanager.commit_bufferblock(bufferblock, sync) + bufferblock.owner.flush.side_effect = flush + bufferblock.append("foo") + with self.assertRaises(arvados.errors.KeepWriteError) as err: + blockmanager.commit_all() + self.assertTrue(bufferblock.owner.flush.called) + self.assertEqual(str(err.exception), "Error writing some blocks: block acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)") + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.ERROR)