X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5126d94fd644a657243e5ec80d5ef1fc250f8b76..7bf8f6c701e28e574c137b0c942522e8f8ee4d8c:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index 7483ba06ff..254a29f313 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -3,15 +3,17 @@ # ARVADOS_API_TOKEN=abc ARVADOS_API_HOST=arvados.local python -m unittest discover import arvados -import bz2 import copy +import hashlib +import mock import os import pprint -import subprocess +import re import tempfile import unittest -from arvados_testutil import ArvadosKeepLocalStoreTestCase +import run_test_server +import arvados_testutil as tutil class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. @@ -20,9 +22,20 @@ class TestResumableWriter(arvados.ResumableCollectionWriter): return self.dump_state(copy.deepcopy) -class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): +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() + 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') @@ -34,26 +47,32 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): cw.start_new_stream('baz') cw.write('baz') cw.set_current_file_name('baz.txt') - return cw.finish() + 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(arvados.Keep.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put') - self.assertEqual(arvados.Keep.get('acbd18db4cc2f85cedef654fccc4a4d8+3'), 'foo', 'wrong data from Keep.get') + 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(), - 'd6c3b8e571f1b81ebb150a45ed06c884+114', - "wrong locator hash for files foo, bar, baz") + '23ca013983d6239e98931cc779e68426+114', + 'wrong locator hash: ' + self.write_foo_bar_baz()) def test_local_collection_reader(self): - self.write_foo_bar_baz() - cr = arvados.CollectionReader('d6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle') + 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, '.', 'bar.txt', 'bar'], - [3, '.', 'foo.txt', 'foo'], + expected = [[3, '.', 'foo.txt', 'foo'], + [3, '.', 'bar.txt', 'bar'], [3, './baz', 'baz.txt', 'baz']] self.assertEqual(got, expected) @@ -69,7 +88,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 'reading zero bytes should have returned empty string') def _test_subset(self, collection, expected): - cr = arvados.CollectionReader(collection) + cr = arvados.CollectionReader(collection, self.api_client) for s in cr.all_streams(): for ex in expected: if ex[0] == s: @@ -80,56 +99,37 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 'all_files|as_manifest did not preserve manifest contents: got %s expected %s' % (got, ex)) def test_collection_manifest_subset(self): - self.write_foo_bar_baz() - self._test_subset('d6c3b8e571f1b81ebb150a45ed06c884+114', + 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" % - (arvados.Keep.put("foo"), - arvados.Keep.put("bar"))), + (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" % - (arvados.Keep.put("foo"), - arvados.Keep.put("bar"))), + (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" % - (arvados.Keep.put("foo"), - arvados.Keep.put("bar"))), + (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() - cw.start_new_file('test.txt') - cw.write(what_in) - test1 = cw.finish() - cr = arvados.CollectionReader(test1) - 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() + 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() + cw = arvados.CollectionWriter(self.api_client) cw.start_new_file('zero.txt') cw.write('') cw.start_new_file('one.txt') @@ -137,108 +137,77 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): cw.start_new_stream('foo') cw.start_new_file('zero.txt') cw.write('') - self.check_manifest_file_sizes(cw.manifest_text(), [1,0,0]) + 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) + 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() - cw.start_new_file('test.bz2') - cw.write(compressed_data_in) - bz2_manifest = cw.manifest_text() - - cr = arvados.CollectionReader(bz2_manifest) - - 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() - cw.start_new_file('test.gz') - cw.write(compressed_data_in) - gzip_manifest = cw.manifest_text() - - cr = arvados.CollectionReader(gzip_manifest) - 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).manifest_text(), +. 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).manifest_text(), m2) + 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).manifest_text(), +. 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).manifest_text(), +./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).manifest_text(), +./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).manifest_text(), m6) + 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).manifest_text(), m7) + 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).manifest_text(), m8) + self.assertEqual(arvados.CollectionReader(m8, self.api_client).manifest_text(normalize=True), m8) def test_locators_and_ranges(self): blocks2 = [['a', 10, 0], @@ -333,83 +302,11 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 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 - - def readfrom(self, start, size): - 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): + def __init__(self, content, num_retries=0): self.content = content - def get(self, locator): + def get(self, locator, num_retries=0): return self.content[locator] def test_stream_reader(self): @@ -441,24 +338,27 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): . 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""" +. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt +""" - m2 = arvados.CollectionReader(m1) + m2 = arvados.CollectionReader(m1, self.api_client).manifest_text(normalize=True) - self.assertEqual(m2.manifest_text(), + 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(arvados.CollectionReader(m1).all_streams()[0].files()['md5sum.txt'].as_manifest(), + self.assertEqual(files['md5sum.txt'].as_manifest(), ". 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt\n") - self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md6sum.txt'].as_manifest(), + self.assertEqual(files['md6sum.txt'].as_manifest(), ". 085c37f02916da1cad16f93c54d899b7+41 0:41:md6sum.txt\n") - self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md7sum.txt'].as_manifest(), + self.assertEqual(files['md7sum.txt'].as_manifest(), ". 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md7sum.txt\n") - self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md9sum.txt'].as_manifest(), + 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() + cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree(self.build_directory_tree( ['basefile', 'subdir/subfile'])) self.assertEqual(cwriter.manifest_text(), @@ -466,7 +366,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): ./subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""") def test_write_named_directory_tree(self): - cwriter = arvados.CollectionWriter() + cwriter = arvados.CollectionWriter(self.api_client) cwriter.write_directory_tree(self.build_directory_tree( ['basefile', 'subdir/subfile']), 'root') self.assertEqual( @@ -475,25 +375,34 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): ./root/subdir 1ca4dec89403084bf282ad31e6cf7972+14 0:14:subfile\n""") def test_write_directory_tree_in_one_stream(self): - cwriter = arvados.CollectionWriter() + 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 -./subdir 4ace875ffdc6824a04950f06858f4465+22 8:14:subfile\n""") + """. 4ace875ffdc6824a04950f06858f4465+22 0:8:basefile 8:14:subdir/subfile\n""") def test_write_directory_tree_with_limited_recursion(self): - cwriter = arvados.CollectionWriter() + 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 8:5:f2 -./d1/d2 50170217e5b04312024aa5cd42934494+13 0:8:f3\n""") +./d1 50170217e5b04312024aa5cd42934494+13 0:8:d2/f3 8:5:f2\n""") + + def test_write_directory_tree_with_zero_recursion(self): + cwriter = arvados.CollectionWriter(self.api_client) + content = 'd1/d2/f3d1/f2f1' + blockhash = hashlib.md5(content).hexdigest() + '+' + str(len(content)) + cwriter.write_directory_tree( + self.build_directory_tree(['f1', 'd1/f2', 'd1/d2/f3']), + max_manifest_depth=0) + self.assertEqual( + cwriter.manifest_text(), + ". {} 0:8:d1/d2/f3 8:5:d1/f2 13:2:f1\n".format(blockhash)) def test_write_one_file(self): - cwriter = arvados.CollectionWriter() + cwriter = arvados.CollectionWriter(self.api_client) with self.make_test_file() as testfile: cwriter.write_file(testfile.name) self.assertEqual( @@ -502,14 +411,14 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): os.path.basename(testfile.name))) def test_write_named_file(self): - cwriter = arvados.CollectionWriter() + 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() + cwriter = arvados.CollectionWriter(self.api_client) for letter in 'ABC': with self.make_test_file(letter) as testfile: cwriter.write_file(testfile.name, letter) @@ -566,7 +475,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): state = cwriter.current_state() # Add an expired locator to the state. state['_current_stream_locators'].append(''.join([ - 'a' * 32, '+A', 'b' * 40, '@', '10000000'])) + 'a' * 32, '+1+A', 'b' * 40, '@', '10000000'])) self.assertRaises(arvados.errors.StaleWriterStateError, TestResumableWriter.from_state, state) @@ -581,6 +490,307 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 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_get_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_get_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_get_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_get_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_get_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()]) + + def test_read_empty_collection(self): + client = self.api_client_mock(200) + self.mock_get_collection(client, 200, 'empty') + reader = arvados.CollectionReader('d41d8cd98f00b204e9800998ecf8427e+0', + api_client=client) + self.assertEqual('', reader.manifest_text()) + + def check_open_file(self, coll_file, stream_name, file_name, file_size): + self.assertFalse(coll_file.closed, "returned file is not open") + self.assertEqual(stream_name, coll_file.stream_name()) + self.assertEqual(file_name, coll_file.name()) + self.assertEqual(file_size, coll_file.size()) + + def test_open_collection_file_one_argument(self): + client = self.api_client_mock(200) + reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) + cfile = reader.open('./foo') + self.check_open_file(cfile, '.', 'foo', 3) + + def test_open_collection_file_two_arguments(self): + client = self.api_client_mock(200) + reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) + cfile = reader.open('.', 'foo') + self.check_open_file(cfile, '.', 'foo', 3) + + def test_open_deep_file(self): + coll_name = 'collection_with_files_in_subdir' + client = self.api_client_mock(200) + self.mock_get_collection(client, 200, coll_name) + reader = arvados.CollectionReader( + self.API_COLLECTIONS[coll_name]['uuid'], api_client=client) + cfile = reader.open('./subdir2/subdir3/file2_in_subdir3.txt') + self.check_open_file(cfile, './subdir2/subdir3', 'file2_in_subdir3.txt', + 32) + + def test_open_nonexistent_stream(self): + client = self.api_client_mock(200) + reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) + self.assertRaises(ValueError, reader.open, './nonexistent', 'foo') + + def test_open_nonexistent_file(self): + client = self.api_client_mock(200) + reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) + self.assertRaises(ValueError, reader.open, '.', 'nonexistent') + + +@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_put_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()) + + def test_one_open(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + with writer.open('out') as out_file: + self.assertEqual('.', writer.current_stream_name()) + self.assertEqual('out', writer.current_file_name()) + out_file.write('test data') + data_loc = hashlib.md5('test data').hexdigest() + '+9' + self.assertTrue(out_file.closed, "writer file not closed after context") + self.assertRaises(ValueError, out_file.write, 'extra text') + with self.mock_keep(data_loc, 200) as keep_mock: + self.assertEqual(". {} 0:9:out\n".format(data_loc), + writer.manifest_text()) + + def test_open_writelines(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + with writer.open('six') as out_file: + out_file.writelines(['12', '34', '56']) + data_loc = hashlib.md5('123456').hexdigest() + '+6' + with self.mock_keep(data_loc, 200) as keep_mock: + self.assertEqual(". {} 0:6:six\n".format(data_loc), + writer.manifest_text()) + + def test_open_flush(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + with writer.open('flush_test') as out_file: + out_file.write('flush1') + data_loc1 = hashlib.md5('flush1').hexdigest() + '+6' + with self.mock_keep(data_loc1, 200) as keep_mock: + out_file.flush() + out_file.write('flush2') + data_loc2 = hashlib.md5('flush2').hexdigest() + '+6' + with self.mock_keep(data_loc2, 200) as keep_mock: + self.assertEqual(". {} {} 0:12:flush_test\n".format(data_loc1, + data_loc2), + writer.manifest_text()) + + def test_two_opens_same_stream(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + with writer.open('.', '1') as out_file: + out_file.write('1st') + with writer.open('.', '2') as out_file: + out_file.write('2nd') + data_loc = hashlib.md5('1st2nd').hexdigest() + '+6' + with self.mock_keep(data_loc, 200) as keep_mock: + self.assertEqual(". {} 0:3:1 3:3:2\n".format(data_loc), + writer.manifest_text()) + + def test_two_opens_two_streams(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + with writer.open('file') as out_file: + out_file.write('file') + data_loc1 = hashlib.md5('file').hexdigest() + '+4' + with self.mock_keep(data_loc1, 200) as keep_mock: + with writer.open('./dir', 'indir') as out_file: + out_file.write('indir') + data_loc2 = hashlib.md5('indir').hexdigest() + '+5' + with self.mock_keep(data_loc2, 200) as keep_mock: + expected = ". {} 0:4:file\n./dir {} 0:5:indir\n".format( + data_loc1, data_loc2) + self.assertEqual(expected, writer.manifest_text()) + + def test_dup_open_fails(self): + client = self.api_client_mock() + writer = arvados.CollectionWriter(client) + file1 = writer.open('one') + self.assertRaises(arvados.errors.AssertionError, writer.open, 'two') + if __name__ == '__main__': unittest.main()