X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/95d1231a25637c5ba0fd07b116876b17711ec201..a7b16675337995c65b909a7519178efed98a3089:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index c4c7ca238a..892f146e90 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -3,19 +3,20 @@ # 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 re -import subprocess import tempfile import unittest import run_test_server import arvados_testutil as tutil +from arvados.ranges import Range, LocatorAndRange +from arvados import import_manifest, export_manifest +from arvados.arvfile import SYNC_EXPLICIT class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. @@ -124,25 +125,6 @@ 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') @@ -179,53 +161,6 @@ 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 @@ -278,170 +213,97 @@ class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, 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]]) + blocks2 = [Range('a', 0, 10), + Range('b', 10, 10), + Range('c', 20, 10), + Range('d', 30, 10), + Range('e', 40, 10), + Range('f', 50, 10)] + + self.assertEqual(arvados.locators_and_ranges(blocks2, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 52, 2), [LocatorAndRange('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, 0, 2), [LocatorAndRange('a', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 10, 2), [LocatorAndRange('b', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 20, 2), [LocatorAndRange('c', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 30, 2), [LocatorAndRange('d', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 40, 2), [LocatorAndRange('e', 10, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 50, 2), [LocatorAndRange('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(blocks2, 9, 2), [LocatorAndRange('a', 10, 9, 1), LocatorAndRange('b', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 19, 2), [LocatorAndRange('b', 10, 9, 1), LocatorAndRange('c', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 29, 2), [LocatorAndRange('c', 10, 9, 1), LocatorAndRange('d', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 39, 2), [LocatorAndRange('d', 10, 9, 1), LocatorAndRange('e', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 49, 2), [LocatorAndRange('e', 10, 9, 1), LocatorAndRange('f', 10, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks2, 59, 2), [LocatorAndRange('f', 10, 9, 1)]) + + + blocks3 = [Range('a', 0, 10), + Range('b', 10, 10), + Range('c', 20, 10), + Range('d', 30, 10), + Range('e', 40, 10), + Range('f', 50, 10), + Range('g', 60, 10)] + + self.assertEqual(arvados.locators_and_ranges(blocks3, 2, 2), [LocatorAndRange('a', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 12, 2), [LocatorAndRange('b', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 22, 2), [LocatorAndRange('c', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 32, 2), [LocatorAndRange('d', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 42, 2), [LocatorAndRange('e', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 52, 2), [LocatorAndRange('f', 10, 2, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks3, 62, 2), [LocatorAndRange('g', 10, 2, 2)]) + + + blocks = [Range('a', 0, 10), + Range('b', 10, 15), + Range('c', 25, 5)] 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) - + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 5), [LocatorAndRange('a', 10, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 3, 5), [LocatorAndRange('a', 10, 3, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 10), [LocatorAndRange('a', 10, 0, 10)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 11), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 1)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 1, 11), [LocatorAndRange('a', 10, 1, 9), + LocatorAndRange('b', 15, 0, 2)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 25), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 30), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 1, 30), [LocatorAndRange('a', 10, 1, 9), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 0, 31), [LocatorAndRange('a', 10, 0, 10), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 5)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 15, 5), [LocatorAndRange('b', 15, 5, 5)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 8, 17), [LocatorAndRange('a', 10, 8, 2), + LocatorAndRange('b', 15, 0, 15)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 8, 20), [LocatorAndRange('a', 10, 8, 2), + LocatorAndRange('b', 15, 0, 15), + LocatorAndRange('c', 5, 0, 3)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 26, 2), [LocatorAndRange('c', 5, 1, 2)]) + + self.assertEqual(arvados.locators_and_ranges(blocks, 9, 15), [LocatorAndRange('a', 10, 9, 1), + LocatorAndRange('b', 15, 0, 14)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 10, 15), [LocatorAndRange('b', 15, 0, 15)]) + self.assertEqual(arvados.locators_and_ranges(blocks, 11, 15), [LocatorAndRange('b', 15, 1, 14), + LocatorAndRange('c', 5, 0, 1)]) class MockKeep(object): def __init__(self, content, num_retries=0): @@ -474,30 +336,6 @@ 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 @@ -736,7 +574,7 @@ 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()) @@ -746,7 +584,7 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): # 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): + 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()) @@ -756,7 +594,7 @@ 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() @@ -764,7 +602,7 @@ 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( @@ -776,7 +614,7 @@ 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())) @@ -801,12 +639,71 @@ class CollectionReaderTestCase(unittest.TestCase, CollectionTestMixin): [[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 test_api_response(self): + client = self.api_client_mock() + reader = arvados.CollectionReader(self.DEFAULT_UUID, api_client=client) + self.assertEqual(self.DEFAULT_COLLECTION, reader.api_response()) + + def test_api_response_with_collection_from_keep(self): + client = self.api_client_mock() + self.mock_get_collection(client, 404, 'foo') + with tutil.mock_get_responses(self.DEFAULT_MANIFEST, 200): + reader = arvados.CollectionReader(self.DEFAULT_DATA_HASH, + api_client=client) + api_response = reader.api_response() + self.assertIsNone(api_response) + + 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() @@ -839,6 +736,139 @@ 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() + data_loc1 = hashlib.md5('flush1').hexdigest() + '+6' + data_loc2 = hashlib.md5('flush2').hexdigest() + '+6' + with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock: + writer = arvados.CollectionWriter(client) + with writer.open('flush_test') as out_file: + out_file.write('flush1') + out_file.flush() + out_file.write('flush2') + 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() + data_loc1 = hashlib.md5('file').hexdigest() + '+4' + data_loc2 = hashlib.md5('indir').hexdigest() + '+5' + with self.mock_keep((data_loc1, 200), (data_loc2, 200)) as keep_mock: + writer = arvados.CollectionWriter(client) + with writer.open('file') as out_file: + out_file.write('file') + with writer.open('./dir', 'indir') as out_file: + out_file.write('indir') + 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') + + +class NewCollectionTestCase(unittest.TestCase, CollectionTestMixin): + def test_import_manifest(self): + m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt +. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt +. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt +""" + self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.import_manifest(m1))) + + def test_init_manifest(self): + m1 = """. 5348b82a029fd9e971a811ce1f71360b+43 0:43:md5sum.txt +. 085c37f02916da1cad16f93c54d899b7+41 0:41:md5sum.txt +. 8b22da26f9f433dea0a10e5ec66d73ba+43 0:43:md5sum.txt +""" + self.assertEqual(". 5348b82a029fd9e971a811ce1f71360b+43 085c37f02916da1cad16f93c54d899b7+41 8b22da26f9f433dea0a10e5ec66d73ba+43 0:127:md5sum.txt\n", arvados.export_manifest(arvados.Collection(m1))) + + + def test_remove(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", export_manifest(c)) + self.assertTrue("count1.txt" in c) + c.remove("count1.txt") + self.assertFalse("count1.txt" in c) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", export_manifest(c)) + + def test_remove_in_subdir(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: + c.remove("foo/count2.txt") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) + + def test_remove_empty_subdir(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: + c.remove("foo/count2.txt") + c.remove("foo") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) + + def test_remove_nonempty_subdir(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n', sync=SYNC_EXPLICIT) as c: + with self.assertRaises(IOError): + c.remove("foo") + c.remove("foo", rm_r=True) + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) + + def test_copy_to_dir1(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c: + c.copy("count1.txt", "foo/count2.txt") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count2.txt\n", export_manifest(c)) + + def test_copy_to_dir2(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c: + c.copy("count1.txt", "foo") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) + + def test_copy_to_dir2(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c: + c.copy("count1.txt", "foo/") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n./foo 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n", export_manifest(c)) + + def test_copy_file(self): + with arvados.import_manifest('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt\n', sync=SYNC_EXPLICIT) as c: + c.copy("count1.txt", "count2.txt") + self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt 0:10:count2.txt\n", export_manifest(c)) + if __name__ == '__main__': unittest.main()