#!/usr/bin/env python import bz2 import gzip import io import mock import os import unittest import hashlib import arvados from arvados import ArvadosFile, ArvadosFileReader, Range, import_manifest, export_manifest, KeepLocator from arvados.arvfile import 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): 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.b = b self.r = r class MockCollections(object): def __init__(self, b, r): self.b = b self.r = r class Execute(object): def __init__(self, r): self.r = r def execute(self, num_retries=None): return self.r 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) def update(self, uuid=None, body=None): return ArvadosFileWriterTestCase.MockApi.MockCollections.Execute(self.r) def collections(self): return ArvadosFileWriterTestCase.MockApi.MockCollections(self.b, self.r) 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 arvados.WritableCollection('. 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_append(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 arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', api_client=api, keep_client=keep) as c: 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)) 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_write0(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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)) def test_write1(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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)) def test_write2(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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)) def test_write3(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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)) def test_write4(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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)) 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 arvados.WritableCollection('. ' + 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_write_rewrite0(self): keep = ArvadosFileWriterTestCase.MockKeep({}) with arvados.WritableCollection('. ' + 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", export_manifest(c)) def test_write_rewrite1(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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", export_manifest(c)) def test_write_rewrite2(self): keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"}) with arvados.WritableCollection('. 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", export_manifest(c)) def test_write_large_rewrite0(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 arvados.WritableCollection('. ' + 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("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"}) with arvados.WritableCollection(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"}) with arvados.WritableCollection(api_client=api, keep_client=keep) as c: writer = c.open("foo/bar/count.txt", "w+") writer.write("01234567") c.save_new("test_create") 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 arvados.WritableCollection('. 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 arvados.WritableCollection('. 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 arvados.WritableCollection('. 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.WritableCollection(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(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 arvados.WritableCollection(". 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__(self): with arvados.arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1: with arvados.arvados.WritableCollection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c2: 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 = arvados.ReadOnlyCollection(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))