X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a117d9790fc566653aead700f8cb207858c8fca9..ad69b48e324c3ce29a4d2c84732dfd3d0288ebb3:/sdk/python/tests/test_arvfile.py diff --git a/sdk/python/tests/test_arvfile.py b/sdk/python/tests/test_arvfile.py index 9edb2c5a79..9c67fbd53f 100644 --- a/sdk/python/tests/test_arvfile.py +++ b/sdk/python/tests/test_arvfile.py @@ -9,142 +9,559 @@ import unittest import hashlib import arvados -from arvados import StreamReader, StreamFileReader, Range, import_manifest, export_manifest +from arvados._ranges import Range +from arvados.keep import KeepLocator +from arvados.collection import Collection, CollectionReader +from arvados.arvfile import ArvadosFile, ArvadosFileReader, SYNC_READONLY, SYNC_EXPLICIT import arvados_testutil as tutil - +from test_stream import StreamFileReaderTestCase, StreamRetryTestMixin class ArvadosFileWriterTestCase(unittest.TestCase): class MockKeep(object): def __init__(self, blocks): self.blocks = blocks + self.requests = [] def get(self, locator, num_retries=0): - return self.blocks[locator] - def put(self, data): + self.requests.append(locator) + return self.blocks.get(locator) + def get_from_cache(self, locator): + self.requests.append(locator) + return self.blocks.get(locator) + def put(self, data, num_retries=None): pdh = "%s+%i" % (hashlib.md5(data).hexdigest(), len(data)) self.blocks[pdh] = str(data) return pdh + class MockApi(object): + def __init__(self, b, r): + self.body = b + self.response = r + class MockCollections(object): + def __init__(self, b, r): + self.body = b + self.response = r + class Execute(object): + def __init__(self, r): + self.response = r + def execute(self, num_retries=None): + return self.response + def create(self, ensure_unique_name=False, body=None): + 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.response) + def collections(self): + return ArvadosFileWriterTestCase.MockApi.MockCollections(self.body, self.response) + + def test_truncate(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - writer = c.open("count.txt", "r+") - self.assertEqual(writer.size(), 10) - writer.seek(5) - self.assertEqual("56789", writer.read(8)) - writer.truncate(8) - writer.seek(5, os.SEEK_SET) - self.assertEqual("567", writer.read(8)) + 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", + "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) + self.assertEqual("0123456789", writer.read(12)) + + writer.truncate(8) + + # Make sure reading off the end doesn't break + self.assertEqual("", writer.read(12)) + + self.assertEqual(writer.size(), 8) + writer.seek(0, os.SEEK_SET) + self.assertEqual("01234567", writer.read(12)) + + self.assertEqual(None, c._manifest_locator) + self.assertEqual(True, c.modified()) + c.save_new("test_truncate") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, 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", + "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_new("test_append") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, c.modified()) + self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3")) + def test_append(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - writer = c.open("count.txt", "r+") - 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)) - - def test_write0(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - writer = c.open("count.txt", "r+") - self.assertEqual("0123456789", writer.readfrom(0, 13)) + 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("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)) - - def test_write1(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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)) - - def test_write2(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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)) - - def test_write3(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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)) - - def test_write4(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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)) + + 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.manifest_text()) + + def test_write_at_beginning(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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", c.manifest_text()) + + def test_write_in_middle(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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", c.manifest_text()) + + def test_write_at_end(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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", c.manifest_text()) + + def test_write_across_segment_boundary(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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", c.manifest_text()) + + def test_write_across_several_segments(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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", c.manifest_text()) def test_write_large(self): - c = import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', - keep=ArvadosFileWriterTestCase.MockKeep({})) - writer = c.open("count.txt", "r+") - text = ''.join(["0123456789" for a in xrange(0, 100)]) - for b in xrange(0, 100000): - writer.write(text) - self.assertEqual(writer.size(), 100000000) - self.assertEqual(". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n", export_manifest(c)) - - def test_write_rewrite0(self): - c = import_manifest('. ' + arvados.config.EMPTY_BLOCK_LOCATOR + ' 0:0:count.txt', - keep=ArvadosFileWriterTestCase.MockKeep({})) - writer = c.open("count.txt", "r+") - for b in xrange(0, 10): + 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", + "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)]) + 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_new("test_write_large") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, c.modified()) + + def test_rewrite_on_empty_file(self): + keep = ArvadosFileWriterTestCase.MockKeep({}) + 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(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", c.manifest_text()) + + def test_rewrite_append_existing_file(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", c.manifest_text()) + + def test_rewrite_over_existing_file(self): + keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) + 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 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", c.manifest_text()) + + 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", + "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): + writer.write(text) 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(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n", export_manifest(c)) - - def test_write_rewrite1(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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 a925576942e94b2ef57a066101b48876+10 0:20:count.txt\n", export_manifest(c)) - - def test_write_rewrite2(self): - c = import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt', - keep=ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})) - 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 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n", export_manifest(c)) + writer.write("foo") + self.assertEqual(writer.size(), 100000000) + + self.assertEqual(None, c._manifest_locator) + self.assertEqual(True, c.modified()) + c.save_new("test_write_large") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, 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", + "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_new("test_create") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, 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", + "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_new("test_create") + 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", + "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_new("test_overwrite") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, c.modified()) + + def test_file_not_found(self): + 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 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", + "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") + w2.write("abcdefgh") + 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_new("test_create_multiple") + self.assertEqual("zzzzz-4zz18-mockcollection0", c._manifest_locator) + self.assertEqual(False, c.modified()) + self.assertEqual("01234567", keep.get("2e9ec317e197819358fbc43afca7d837+8")) + + +class ArvadosFileReaderTestCase(StreamFileReaderTestCase): + class MockParent(object): + class MockBlockMgr(object): + def __init__(self, blocks, nocache): + self.blocks = blocks + self.nocache = nocache + + def block_prefetch(self, loc): + pass + + def get_block_contents(self, loc, num_retries=0, cache_only=False): + if self.nocache and cache_only: + return None + return self.blocks[loc] + + 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)) + 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") + + def test_read_returns_first_block(self): + # read() calls will be aligned on block boundaries - see #3663. + sfile = self.make_count_reader(nocache=True) + self.assertEqual('123', sfile.read(10)) + + def test_successive_reads(self): + sfile = self.make_count_reader(nocache=True) + for expect in ['123', '456', '789', '']: + self.assertEqual(expect, sfile.read(10)) + + def test_tell_after_block_read(self): + sfile = self.make_count_reader(nocache=True) + sfile.read(5) + self.assertEqual(3, 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: + with c2.open("count1.txt", "w") as f: + 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: + with c2.open("count1.txt", "w") as f: + f.write("1234567890") + + self.assertTrue(c1["count1.txt"] != c2["count1.txt"]) + self.assertFalse(c1["count1.txt"] == c2["count1.txt"]) + + +class ArvadosFileReadTestCase(unittest.TestCase, StreamRetryTestMixin): + def reader_for(self, coll_name, **kwargs): + stream = [] + segments = [] + n = 0 + for d in self.manifest_for(coll_name).split(): + try: + k = KeepLocator(d) + segments.append(Range(n, n, k.size)) + stream.append(Range(d, n, k.size)) + n += k.size + except ValueError: + pass + col = Collection(keep_client=self.keep_client()) + col._my_block_manager().prefetch_enabled = False + af = ArvadosFile(col, + stream=stream, + segments=segments) + return ArvadosFileReader(af, "test", **kwargs) + + def read_for_test(self, reader, byte_count, **kwargs): + return reader.read(byte_count, **kwargs) + + +class ArvadosFileReadFromTestCase(ArvadosFileReadTestCase): + def read_for_test(self, reader, byte_count, **kwargs): + return reader.readfrom(0, byte_count, **kwargs) + + +class ArvadosFileReadAllTestCase(ArvadosFileReadTestCase): + def read_for_test(self, reader, byte_count, **kwargs): + return ''.join(reader.readall(**kwargs)) + + +class ArvadosFileReadAllDecompressedTestCase(ArvadosFileReadTestCase): + def read_for_test(self, reader, byte_count, **kwargs): + return ''.join(reader.readall_decompressed(**kwargs)) + + +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({}) + blockmanager = arvados.arvfile._BlockManager(keep) + 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({}) + blockmanager = arvados.arvfile._BlockManager(keep) + 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"}) + blockmanager = arvados.arvfile._BlockManager(keep) + 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() + blockmanager = arvados.arvfile._BlockManager(mockkeep) + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + blockmanager.commit_all() + self.assertTrue(mockkeep.put.called) + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.COMMITTED) + self.assertIsNone(bufferblock.buffer_view) + + + def test_bufferblock_commit_with_error(self): + mockkeep = mock.MagicMock() + mockkeep.put.side_effect = arvados.errors.KeepWriteError("fail") + blockmanager = arvados.arvfile._BlockManager(mockkeep) + bufferblock = blockmanager.alloc_bufferblock() + bufferblock.append("foo") + with self.assertRaises(arvados.errors.KeepWriteError) as err: + blockmanager.commit_all() + self.assertEquals(str(err.exception), "Error writing some blocks: acbd18db4cc2f85cedef654fccc4a4d8+3 raised KeepWriteError (fail)") + self.assertEqual(bufferblock.state(), arvados.arvfile._BufferBlock.PENDING)