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)
+ writer.seek(5)
+ self.assertEqual("56789", writer.read(8))
+ 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_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)
projects / arvados.git / blobdiff