X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f9328bf507490f48e57b196be1de55d946644dea..7bf8f6c701e28e574c137b0c942522e8f8ee4d8c:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index df8ba388d8..254a29f313 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -3,12 +3,12 @@ # 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 @@ -122,25 +122,6 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, [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') @@ -177,53 +158,6 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, 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 @@ -368,79 +302,6 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, 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 @@ -472,30 +333,6 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, 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 @@ -553,6 +390,17 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, """. bd19836ddb62c11c55ab251ccaca5645+2 0:2:f1 ./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(self.api_client) with self.make_test_file() as testfile: @@ -723,7 +571,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): 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): + 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()) @@ -732,7 +580,8 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): # crunch-job needs this to read manifests that have only ever # been written to Keep. client = self.api_client_mock(200) - with tutil.mock_responses(self.DEFAULT_MANIFEST, 404, 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()) @@ -742,7 +591,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): client = self.api_client_mock(404) reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) - with tutil.mock_responses(self.DEFAULT_MANIFEST, 200): + with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200): with self.assertRaises(arvados.errors.ApiError): reader.manifest_text() @@ -750,7 +599,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): # 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): + with tutil.mock_get_responses(self.ALT_MANIFEST, 200): self.assertEqual( self.ALT_MANIFEST, arvados.CollectionReader( @@ -762,7 +611,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): 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): + with tutil.mock_get_responses('foo', 500, 500, 200): self.assertEqual('foo', ''.join(f.read(9) for f in reader.all_files())) @@ -770,26 +619,74 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): # 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( - ". acbd18db4cc2f85cedef654fccc4a4d8+3 0:3:foo.txt 1:0:bar.txt 0:3:foo.txt\n", - arvados.CollectionReader( - nonnormal, - api_client=client, num_retries=0).stripped_manifest()) + 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 - arvados.CollectionReader( - nonnormal, - api_client=client, num_retries=0).all_streams()[0].all_files()]) + 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_responses(body, *codes, **headers) + return tutil.mock_put_responses(body, *codes, **headers) def foo_writer(self, **kwargs): api_client = self.api_client_mock() @@ -822,6 +719,78 @@ class CollectionWriterTestCase(unittest.TestCase, CollectionTestMixin): 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()