# usage example: # # ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover import arvados import bz2 import copy import mock import os import pprint import re import subprocess import tempfile import unittest import run_test_server import arvados_testutil as tutil class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. def current_state(self): return self.dump_state(copy.deepcopy) class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, tutil.ArvadosBaseTestCase): MAIN_SERVER = {} @classmethod def setUpClass(cls): super(ArvadosCollectionsTest, cls).setUpClass() run_test_server.authorize_with('active') cls.api_client = arvados.api('v1') cls.keep_client = arvados.KeepClient(api_client=cls.api_client, local_store=cls.local_store) def write_foo_bar_baz(self): cw = arvados.CollectionWriter(self.api_client) self.assertEqual(cw.current_stream_name(), '.', 'current_stream_name() should be "." now') cw.set_current_file_name('foo.txt') cw.write('foo') self.assertEqual(cw.current_file_name(), 'foo.txt', 'current_file_name() should be foo.txt now') cw.start_new_file('bar.txt') cw.write('bar') cw.start_new_stream('baz') cw.write('baz') cw.set_current_file_name('baz.txt') self.assertEqual(cw.manifest_text(), ". 3858f62230ac3c915f300c664312c63f+6 0:3:foo.txt 3:3:bar.txt\n" + "./baz 73feffa4b7f6bb68e44cf984c85f6e88+3 0:3:baz.txt\n", "wrong manifest: got {}".format(cw.manifest_text())) cw.finish() return cw.portable_data_hash() def test_keep_local_store(self): self.assertEqual(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put') self.assertEqual(self.keep_client.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get') def test_local_collection_writer(self): self.assertEqual(self.write_foo_bar_baz(), '23ca013983d6239e98931cc779e68426+114', 'wrong locator hash: ' + self.write_foo_bar_baz()) def test_local_collection_reader(self): foobarbaz = self.write_foo_bar_baz() cr = arvados.CollectionReader( foobarbaz + '+Xzizzle', self.api_client) got = [] for s in cr.all_streams(): for f in s.all_files(): got += [[f.size(), f.stream_name(), f.name(), f.read(2**26)]] expected = [[3, '.', 'foo.txt', 'foo'], [3, '.', 'bar.txt', 'bar'], [3, './baz', 'baz.txt', 'baz']] self.assertEqual(got, expected) stream0 = cr.all_streams()[0] self.assertEqual(stream0.readfrom(0, 0), '', 'reading zero bytes should have returned empty string') self.assertEqual(stream0.readfrom(0, 2**26), 'foobar', 'reading entire stream failed') self.assertEqual(stream0.readfrom(2**26, 0), '', 'reading zero bytes should have returned empty string') def _test_subset(self, collection, expected): cr = arvados.CollectionReader(collection, self.api_client) for s in cr.all_streams(): for ex in expected: if ex[0] == s: f = s.files()[ex[2]] got = [f.size(), f.stream_name(), f.name(), "".join(f.readall(2**26))] self.assertEqual(got, ex, 'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex)) def test_collection_manifest_subset(self): foobarbaz = self.write_foo_bar_baz() self._test_subset(foobarbaz, [[3, '.', 'bar.txt', 'bar'], [3, '.', 'foo.txt', 'foo'], [3, './baz', 'baz.txt', 'baz']]) self._test_subset((". %s %s 0:3:foo.txt 3:3:bar.txt\n" % (self.keep_client.put("foo"), self.keep_client.put("bar"))), [[3, '.', 'bar.txt', 'bar'], [3, '.', 'foo.txt', 'foo']]) self._test_subset((". %s %s 0:2:fo.txt 2:4:obar.txt\n" % (self.keep_client.put("foo"), self.keep_client.put("bar"))), [[2, '.', 'fo.txt', 'fo'], [4, '.', 'obar.txt', 'obar']]) self._test_subset((". %s %s 0:2:fo.txt 2:0:zero.txt 2:2:ob.txt 4:2:ar.txt\n" % (self.keep_client.put("foo"), self.keep_client.put("bar"))), [[2, '.', 'ar.txt', 'ar'], [2, '.', 'fo.txt', 'fo'], [2, '.', 'ob.txt', 'ob'], [0, '.', 'zero.txt', '']]) def _test_readline(self, what_in, what_out): cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('test.txt') cw.write(what_in) test1 = cw.finish() cr = arvados.CollectionReader(test1, self.api_client) got = [] for x in list(cr.all_files())[0].readlines(): got += [x] self.assertEqual(got, what_out, "readlines did not split lines correctly: %s" % got) def test_collection_readline(self): self._test_readline("\na\nbcd\n\nefg\nz", ["\n", "a\n", "bcd\n", "\n", "efg\n", "z"]) self._test_readline("ab\ncd\n", ["ab\n", "cd\n"]) def test_collection_empty_file(self): cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('zero.txt') cw.write('') self.assertEqual(cw.manifest_text(), ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:zero.txt\n") self.check_manifest_file_sizes(cw.manifest_text(), [0]) cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('zero.txt') cw.write('') cw.start_new_file('one.txt') cw.write('1') cw.start_new_stream('foo') cw.start_new_file('zero.txt') cw.write('') self.check_manifest_file_sizes(cw.manifest_text(), [0,1,0]) def test_no_implicit_normalize(self): cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('b') cw.write('b') cw.start_new_file('a') cw.write('') self.check_manifest_file_sizes(cw.manifest_text(), [1,0]) self.check_manifest_file_sizes( arvados.CollectionReader( cw.manifest_text()).manifest_text(normalize=True), [0,1]) def check_manifest_file_sizes(self, manifest_text, expect_sizes): cr = arvados.CollectionReader(manifest_text, self.api_client) got_sizes = [] for f in cr.all_files(): got_sizes += [f.size()] self.assertEqual(got_sizes, expect_sizes, "got wrong file sizes %s, expected %s" % (got_sizes, expect_sizes)) def test_collection_bz2_decompression(self): n_lines_in = 2**18 data_in = "abc\n" for x in xrange(0, 18): data_in += data_in compressed_data_in = bz2.compress(data_in) cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('test.bz2') cw.write(compressed_data_in) bz2_manifest = cw.manifest_text() cr = arvados.CollectionReader(bz2_manifest, self.api_client) got = 0 for x in list(cr.all_files())[0].readlines(): self.assertEqual(x, "abc\n", "decompression returned wrong data: %s" % x) got += 1 self.assertEqual(got, n_lines_in, "decompression returned %d lines instead of %d" % (got, n_lines_in)) def test_collection_gzip_decompression(self): n_lines_in = 2**18 data_in = "abc\n" for x in xrange(0, 18): data_in += data_in p = subprocess.Popen(["gzip", "-1cn"], stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE, shell=False, close_fds=True) compressed_data_in, stderrdata = p.communicate(data_in) cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('test.gz') cw.write(compressed_data_in) gzip_manifest = cw.manifest_text() cr = arvados.CollectionReader(gzip_manifest, self.api_client) got = 0 for x in list(cr.all_files())[0].readlines(): self.assertEqual(x, "abc\n", "decompression returned wrong data: %s" % x) got += 1 self.assertEqual(got, n_lines_in, "decompression returned %d lines instead of %d" % (got, n_lines_in)) def test_normalized_collection(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt """ self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True), """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt """) m2 = """. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2 """ self.assertEqual(arvados.CollectionReader(m2, self.api_client).manifest_text(normalize=True), m2) m3 = """. 5348b82a029fd9e971a811ce1f71360b+43 3:40:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt """ self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(normalize=True), """. 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 3:124:md5sum.txt """) m4 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz ./foo 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar """ self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(normalize=True), """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz """) m5 = """. 204e43b8a1185621ca55a94839582e6f+67108864 0:3:foo/bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz ./foo 204e43b8a1185621ca55a94839582e6f+67108864 3:3:bar """ self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(normalize=True), """./foo 204e43b8a1185621ca55a94839582e6f+67108864 0:6:bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz """) with self.data_file('1000G_ref_manifest') as f6: m6 = f6.read() self.assertEqual(arvados.CollectionReader(m6, self.api_client).manifest_text(normalize=True), m6) with self.data_file('jlake_manifest') as f7: m7 = f7.read() self.assertEqual(arvados.CollectionReader(m7, self.api_client).manifest_text(normalize=True), m7) m8 = """./a\\040b\\040c 59ca0efa9f5633cb0371bbc0355478d8+13 0:13:hello\\040world.txt """ self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8) def test_locators_and_ranges(self): blocks2 = [['a', 10, 0], ['b', 10, 10], ['c', 10, 20], ['d', 10, 30], ['e', 10, 40], ['f', 10, 50]] self.assertEqual(arvados.locators_and_ranges(blocks2, 2, 2), [['a', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [['b', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [['c', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [['d', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [['e', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [['f', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 62, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, 0, 2), [['a', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [['b', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [['c', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [['d', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [['e', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [['f', 10, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 60, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, -2, 2), []) self.assertEqual(arvados.locators_and_ranges(blocks2, 9, 2), [['a', 10, 9, 1], ['b', 10, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [['b', 10, 9, 1], ['c', 10, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [['c', 10, 9, 1], ['d', 10, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [['d', 10, 9, 1], ['e', 10, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [['e', 10, 9, 1], ['f', 10, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [['f', 10, 9, 1]]) blocks3 = [['a', 10, 0], ['b', 10, 10], ['c', 10, 20], ['d', 10, 30], ['e', 10, 40], ['f', 10, 50], ['g', 10, 60]] self.assertEqual(arvados.locators_and_ranges(blocks3, 2, 2), [['a', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [['b', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [['c', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [['d', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [['e', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [['f', 10, 2, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [['g', 10, 2, 2]]) blocks = [['a', 10, 0], ['b', 15, 10], ['c', 5, 25]] self.assertEqual(arvados.locators_and_ranges(blocks, 1, 0), []) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [['a', 10, 0, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [['a', 10, 3, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [['a', 10, 0, 10]]) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [['a', 10, 0, 10], ['b', 15, 0, 1]]) self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [['a', 10, 1, 9], ['b', 15, 0, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [['a', 10, 0, 10], ['b', 15, 0, 15]]) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [['a', 10, 0, 10], ['b', 15, 0, 15], ['c', 5, 0, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [['a', 10, 1, 9], ['b', 15, 0, 15], ['c', 5, 0, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [['a', 10, 0, 10], ['b', 15, 0, 15], ['c', 5, 0, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [['b', 15, 5, 5]]) self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [['a', 10, 8, 2], ['b', 15, 0, 15]]) self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [['a', 10, 8, 2], ['b', 15, 0, 15], ['c', 5, 0, 3]]) self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [['c', 5, 1, 2]]) self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [['a', 10, 9, 1], ['b', 15, 0, 14]]) self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [['b', 15, 0, 15]]) self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [['b', 15, 1, 14], ['c', 5, 0, 1]]) class MockStreamReader(object): def __init__(self, content): self.content = content self.num_retries = 0 def readfrom(self, start, size, num_retries=0): return self.content[start:start+size] def test_file_stream(self): content = 'abcdefghijklmnopqrstuvwxyz0123456789' msr = self.MockStreamReader(content) segments = [[0, 10, 0], [10, 15, 10], [25, 5, 25]] sfr = arvados.StreamFileReader(msr, segments, "test") self.assertEqual(sfr.name(), "test") self.assertEqual(sfr.size(), 30) self.assertEqual(sfr.readfrom(0, 30), content[0:30]) self.assertEqual(sfr.readfrom(2, 30), content[2:30]) self.assertEqual(sfr.readfrom(2, 8), content[2:10]) self.assertEqual(sfr.readfrom(0, 10), content[0:10]) self.assertEqual(sfr.tell(), 0) self.assertEqual(sfr.read(5), content[0:5]) self.assertEqual(sfr.tell(), 5) self.assertEqual(sfr.read(5), content[5:10]) self.assertEqual(sfr.tell(), 10) self.assertEqual(sfr.read(5), content[10:15]) self.assertEqual(sfr.tell(), 15) self.assertEqual(sfr.read(5), content[15:20]) self.assertEqual(sfr.tell(), 20) self.assertEqual(sfr.read(5), content[20:25]) self.assertEqual(sfr.tell(), 25) self.assertEqual(sfr.read(5), content[25:30]) self.assertEqual(sfr.tell(), 30) self.assertEqual(sfr.read(5), '') self.assertEqual(sfr.tell(), 30) segments = [[26, 10, 0], [0, 15, 10], [15, 5, 25]] sfr = arvados.StreamFileReader(msr, segments, "test") self.assertEqual(sfr.size(), 30) self.assertEqual(sfr.readfrom(0, 30), content[26:36] + content[0:20]) self.assertEqual(sfr.readfrom(2, 30), content[28:36] + content[0:20]) self.assertEqual(sfr.readfrom(2, 8), content[28:36]) self.assertEqual(sfr.readfrom(0, 10), content[26:36]) self.assertEqual(sfr.tell(), 0) self.assertEqual(sfr.read(5), content[26:31]) self.assertEqual(sfr.tell(), 5) self.assertEqual(sfr.read(5), content[31:36]) self.assertEqual(sfr.tell(), 10) self.assertEqual(sfr.read(5), content[0:5]) self.assertEqual(sfr.tell(), 15) self.assertEqual(sfr.read(5), content[5:10]) self.assertEqual(sfr.tell(), 20) self.assertEqual(sfr.read(5), content[10:15]) self.assertEqual(sfr.tell(), 25) self.assertEqual(sfr.read(5), content[15:20]) self.assertEqual(sfr.tell(), 30) self.assertEqual(sfr.read(5), '') self.assertEqual(sfr.tell(), 30) class MockKeep(object): def __init__(self, content, num_retries=0): self.content = content def get(self, locator, num_retries=0): return self.content[locator] def test_stream_reader(self): keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij', 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy', 'cccccccccccccccccccccccccccccccc+5': 'z0123'} mk = self.MockKeep(keepblocks) sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:30:foo"], mk) content = 'abcdefghijklmnopqrstuvwxyz0123456789' self.assertEqual(sr.readfrom(0, 30), content[0:30]) self.assertEqual(sr.readfrom(2, 30), content[2:30]) self.assertEqual(sr.readfrom(2, 8), content[2:10]) self.assertEqual(sr.readfrom(0, 10), content[0:10]) self.assertEqual(sr.readfrom(0, 5), content[0:5]) self.assertEqual(sr.readfrom(5, 5), content[5:10]) self.assertEqual(sr.readfrom(10, 5), content[10:15]) self.assertEqual(sr.readfrom(15, 5), content[15:20]) self.assertEqual(sr.readfrom(20, 5), content[20:25]) self.assertEqual(sr.readfrom(25, 5), content[25:30]) self.assertEqual(sr.readfrom(30, 5), '') def test_file_reader(self): keepblocks = {'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10': 'abcdefghij', 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15': 'klmnopqrstuvwxy', 'cccccccccccccccccccccccccccccccc+5': 'z0123'} mk = self.MockKeep(keepblocks) sr = arvados.StreamReader([".", "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa+10", "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb+15", "cccccccccccccccccccccccccccccccc+5", "0:10:foo", "15:10:foo"], mk) content = 'abcdefghijpqrstuvwxy' f = sr.files()["foo"] # f.read() calls will be aligned on block boundaries (as a # result of ticket #3663). f.seek(0) self.assertEqual(f.read(20), content[0:10]) f.seek(0) self.assertEqual(f.read(6), content[0:6]) self.assertEqual(f.read(6), content[6:10]) self.assertEqual(f.read(6), content[10:16]) self.assertEqual(f.read(6), content[16:20]) def test_extract_file(self): m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt . 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt . 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt """ m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True) self.assertEqual(m2, ". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt 43:41:md6sum.txt 84:43:md7sum.txt 6:37:md8sum.txt 84:43:md8sum.txt 83:1:md9sum.txt 0:43:md9sum.txt 84:36:md9sum.txt\n") files = arvados.CollectionReader( m2, self.api_client).all_streams()[0].files() self.assertEqual(files['md5sum.txt'].as_manifest(), ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n") self.assertEqual(files['md6sum.txt'].as_manifest(), ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n") self.assertEqual(files['md7sum.txt'].as_manifest(), ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n") self.assertEqual(files['md9sum.txt'].as_manifest(), ". 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt\n") def test_write_directory_tree(self): cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree(self.build_directory_tree( ['basefile', 'subdir/subfile'])) self.assertEqual(cwriter.manifest_text(), """. c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""") def test_write_named_directory_tree(self): cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree(self.build_directory_tree( ['basefile', 'subdir/subfile']), 'root') self.assertEqual( cwriter.manifest_text(), """./root c5110c5ac93202d8e0f9e381f22bac0f+8 0:8:basefile ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""") def test_write_directory_tree_in_one_stream(self): cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree(self.build_directory_tree( ['basefile', 'subdir/subfile']), max_manifest_depth=0) self.assertEqual(cwriter.manifest_text(), """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""") def test_write_directory_tree_with_limited_recursion(self): cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree( self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']), max_manifest_depth=1) self.assertEqual(cwriter.manifest_text(), """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1 ./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""") def test_write_one_file(self): cwriter = arvados.CollectionWriter(self.api_client) with self.make_test_file() as testfile: cwriter.write_file(testfile.name) self.assertEqual( cwriter.manifest_text(), ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:{}\n".format( os.path.basename(testfile.name))) def test_write_named_file(self): cwriter = arvados.CollectionWriter(self.api_client) with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'foo') self.assertEqual(cwriter.manifest_text(), ". 098f6bcd4621d373cade4e832627b4f6+4 0:4:foo\n") def test_write_multiple_files(self): cwriter = arvados.CollectionWriter(self.api_client) for letter in 'ABC': with self.make_test_file(letter) as testfile: cwriter.write_file(testfile.name, letter) self.assertEqual( cwriter.manifest_text(), ". 902fbdd2b1df0c4f70b4a5d23525e932+3 0:1:A 1:1:B 2:1:C\n") def test_basic_resume(self): cwriter = TestResumableWriter() with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') resumed = TestResumableWriter.from_state(cwriter.current_state()) self.assertEquals(cwriter.manifest_text(), resumed.manifest_text(), "resumed CollectionWriter had different manifest") def test_resume_fails_when_missing_dependency(self): cwriter = TestResumableWriter() with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, cwriter.current_state()) def test_resume_fails_when_dependency_mtime_changed(self): cwriter = TestResumableWriter() with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') os.utime(testfile.name, (0, 0)) self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, cwriter.current_state()) def test_resume_fails_when_dependency_is_nonfile(self): cwriter = TestResumableWriter() cwriter.write_file('/dev/null', 'empty') self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, cwriter.current_state()) def test_resume_fails_when_dependency_size_changed(self): cwriter = TestResumableWriter() with self.make_test_file() as testfile: cwriter.write_file(testfile.name, 'test') orig_mtime = os.fstat(testfile.fileno()).st_mtime testfile.write('extra') testfile.flush() os.utime(testfile.name, (orig_mtime, orig_mtime)) self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, cwriter.current_state()) def test_resume_fails_with_expired_locator(self): cwriter = TestResumableWriter() state = cwriter.current_state() # Add an expired locator to the state. state['_current_stream_locators'].append(''.join([ 'a' * 32, '+1+A', 'b' * 40, '@', '10000000'])) self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, state) def test_arbitrary_objects_not_resumable(self): cwriter = TestResumableWriter() with open('/dev/null') as badfile: self.assertRaises(arvados.errors.AssertionError, cwriter.write_file, badfile) def test_arbitrary_writes_not_resumable(self): cwriter = TestResumableWriter() self.assertRaises(arvados.errors.AssertionError, cwriter.write, "badtext") def test_read_arbitrary_data_with_collection_reader(self): # arv-get relies on this to do "arv-get {keep-locator} -". self.write_foo_bar_baz() self.assertEqual( 'foobar', arvados.CollectionReader( '3858f62230ac3c915f300c664312c63f+6' ).manifest_text()) class CollectionTestMixin(object): PROXY_RESPONSE = { 'items_available': 1, 'items': [{ 'uuid': 'zzzzz-bi6l4-mockproxy012345', 'owner_uuid': 'zzzzz-tpzed-mockowner012345', 'service_host': tutil.TEST_HOST, 'service_port': 65535, 'service_ssl_flag': True, 'service_type': 'proxy', }]} API_COLLECTIONS = run_test_server.fixture('collections') DEFAULT_COLLECTION = API_COLLECTIONS['foo_file'] DEFAULT_DATA_HASH = DEFAULT_COLLECTION['portable_data_hash'] DEFAULT_MANIFEST = DEFAULT_COLLECTION['manifest_text'] DEFAULT_UUID = DEFAULT_COLLECTION['uuid'] ALT_COLLECTION = API_COLLECTIONS['bar_file'] ALT_DATA_HASH = ALT_COLLECTION['portable_data_hash'] ALT_MANIFEST = ALT_COLLECTION['manifest_text'] def _mock_api_call(self, mock_method, code, body): mock_method = mock_method().execute if code == 200: mock_method.return_value = body else: mock_method.side_effect = arvados.errors.ApiError( tutil.fake_httplib2_response(code), "{}") def mock_keep_services(self, api_mock, code, body): self._mock_api_call(api_mock.keep_services().accessible, code, body) def api_client_mock(self, code=200): client = mock.MagicMock(name='api_client') self.mock_keep_services(client, code, self.PROXY_RESPONSE) return client @tutil.skip_sleep class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): def mock_get_collection(self, api_mock, code, body): body = self.API_COLLECTIONS.get(body) self._mock_api_call(api_mock.collections().get, code, body) def api_client_mock(self, code=200): client = super(CollectionReaderTestCase, self).api_client_mock(code) self.mock_get_collection(client, code, 'foo_file') return client def test_init_no_default_retries(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) reader.manifest_text() client.collections().get().execute.assert_called_with(num_retries=0) def test_uuid_init_success(self): client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) self.assertEqual(self.DEFAULT_COLLECTION['manifest_text'], reader.manifest_text()) client.collections().get().execute.assert_called_with(num_retries=3) def test_uuid_init_failure_raises_api_error(self): client = self.api_client_mock(500) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) with self.assertRaises(arvados.errors.ApiError): reader.manifest_text() def test_locator_init(self): client = self.api_client_mock(200) # Ensure Keep will not return anything if asked. with tutil.mock_responses(None, 404): reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, api_client=client) self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text()) def test_locator_init_fallback_to_keep(self): # crunch-job needs this to read manifests that have only ever # been written to Keep. client = self.api_client_mock(200) self.mock_get_collection(client, 404, None) with tutil.mock_responses(self.DEFAULT_MANIFEST, 200): reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, api_client=client) self.assertEqual(self.DEFAULT_MANIFEST, reader.manifest_text()) def test_uuid_init_no_fallback_to_keep(self): # Do not look up a collection UUID in Keep. client = self.api_client_mock(404) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) with tutil.mock_responses(self.DEFAULT_MANIFEST, 200): with self.assertRaises(arvados.errors.ApiError): reader.manifest_text() def test_try_keep_first_if_permission_hint(self): # To verify that CollectionReader tries Keep first here, we # mock API server to return the wrong data. client = self.api_client_mock(200) with tutil.mock_responses(self.ALT_MANIFEST, 200): self.assertEqual( self.ALT_MANIFEST, arvados.CollectionReader( self.ALT_DATA_HASH + '+Affffffffffffffffffffffffffffffffffffffff@fedcba98', api_client=client).manifest_text()) def test_init_num_retries_propagated(self): # More of an integration test... client = self.api_client_mock(200) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client, num_retries=3) with tutil.mock_responses('foo', 500, 500, 200): self.assertEqual('foo', ''.join(f.read(9) for f in reader.all_files())) def test_read_nonnormalized_manifest_with_collection_reader(self): # client should be able to use CollectionReader on a manifest without normalizing it client = self.api_client_mock(500) nonnormal = ". acbd18db4cc2f85cedef654fccc4a4d8+3+Aabadbadbee@abeebdee 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n" reader = arvados.CollectionReader( nonnormal, api_client=client, num_retries=0) # Ensure stripped_manifest() doesn't mangle our manifest in # any way other than stripping hints. self.assertEqual( re.sub('\+[^\d\s\+]+', '', nonnormal), reader.stripped_manifest()) # Ensure stripped_manifest() didn't mutate our reader. self.assertEqual(nonnormal, reader.manifest_text()) # Ensure the files appear in the order given in the manifest. self.assertEqual( [[6, '.', 'foo.txt'], [0, '.', 'bar.txt']], [[f.size(), f.stream_name(), f.name()] for f in reader.all_streams()[0].all_files()]) @tutil.skip_sleep class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): def mock_keep(self, body, *codes, **headers): headers.setdefault('x-keep-replicas-stored', 2) return tutil.mock_responses(body, *codes, **headers) def foo_writer(self, **kwargs): api_client = self.api_client_mock() writer = arvados.CollectionWriter(api_client, **kwargs) writer.start_new_file('foo') writer.write('foo') return writer def test_write_whole_collection(self): writer = self.foo_writer() with self.mock_keep(self.DEFAULT_DATA_HASH, 200, 200): self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish()) def test_write_no_default(self): writer = self.foo_writer() with self.mock_keep(None, 500): with self.assertRaises(arvados.errors.KeepWriteError): writer.finish() def test_write_whole_collection_through_retries(self): writer = self.foo_writer(num_retries=2) with self.mock_keep(self.DEFAULT_DATA_HASH, 500, 500, 200, 500, 500, 200): self.assertEqual(self.DEFAULT_DATA_HASH, writer.finish()) def test_flush_data_retries(self): writer = self.foo_writer(num_retries=2) foo_hash = self.DEFAULT_MANIFEST.split()[1] with self.mock_keep(foo_hash, 500, 200): writer.flush_data() self.assertEqual(self.DEFAULT_MANIFEST, writer.manifest_text()) if __name__ == '__main__': unittest.main()