X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5bbd6abc7a32c6912db5f36f0af5a923ac4b7c79..b23bcfdc041fa9459d2beb423eea35e3ad34e64a:/sdk/python/tests/test_collections.py diff --git a/sdk/python/tests/test_collections.py b/sdk/python/tests/test_collections.py index 5354f3a9f7..f6abe2b35a 100644 --- a/sdk/python/tests/test_collections.py +++ b/sdk/python/tests/test_collections.py @@ -11,7 +11,8 @@ import subprocess import tempfile import unittest -from arvados_testutil import ArvadosKeepLocalStoreTestCase +import run_test_server +from arvados_testutil import ArvadosBaseTestCase class TestResumableWriter(arvados.ResumableCollectionWriter): KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K. @@ -20,9 +21,20 @@ class TestResumableWriter(arvados.ResumableCollectionWriter): return self.dump_state(copy.deepcopy) -class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): +class ArvadosCollectionsTest(run_test_server.TestCaseWithServers, + 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') @@ -37,8 +49,8 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): return cw.finish() 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(), @@ -47,7 +59,8 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): def test_local_collection_reader(self): self.write_foo_bar_baz() - cr = arvados.CollectionReader('d6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle') + cr = arvados.CollectionReader( + 'd6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle', self.api_client) got = [] for s in cr.all_streams(): for f in s.all_files(): @@ -69,7 +82,7 @@ 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: @@ -86,29 +99,29 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): [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 = arvados.CollectionWriter(self.api_client) cw.start_new_file('test.txt') cw.write(what_in) test1 = cw.finish() - cr = arvados.CollectionReader(test1) + cr = arvados.CollectionReader(test1, self.api_client) got = [] for x in list(cr.all_files())[0].readlines(): got += [x] @@ -123,13 +136,13 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): ["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') @@ -140,7 +153,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): self.check_manifest_file_sizes(cw.manifest_text(), [1,0,0]) 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()] @@ -152,12 +165,12 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): for x in xrange(0, 18): data_in += data_in compressed_data_in = bz2.compress(data_in) - cw = arvados.CollectionWriter() + 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) + cr = arvados.CollectionReader(bz2_manifest, self.api_client) got = 0 for x in list(cr.all_files())[0].readlines(): @@ -179,12 +192,12 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): shell=False, close_fds=True) compressed_data_in, stderrdata = p.communicate(data_in) - cw = arvados.CollectionWriter() + 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) + 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) @@ -197,25 +210,25 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 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(), + self.assertEqual(arvados.CollectionReader(m1, self.api_client).manifest_text(), """. 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(), 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(), + self.assertEqual(arvados.CollectionReader(m3, self.api_client).manifest_text(), """. 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(), + self.assertEqual(arvados.CollectionReader(m4, self.api_client).manifest_text(), """./foo 204e43b8a1185621ca55a94839582e6f+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:3:bar 67108864:3:bar ./zzz 204e43b8a1185621ca55a94839582e6f+67108864 0:999:zzz """) @@ -223,22 +236,22 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 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(), + self.assertEqual(arvados.CollectionReader(m5, self.api_client).manifest_text(), """./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(), 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(), 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(), m8) def test_locators_and_ranges(self): blocks2 = [['a', 10, 0], @@ -448,13 +461,17 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): 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[0:20]) + 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[6:12]) - self.assertEqual(f.read(6), content[12:18]) + 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 @@ -463,22 +480,22 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 47:80:md8sum.txt . 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt""" - m2 = arvados.CollectionReader(m1) + m2 = arvados.CollectionReader(m1, self.api_client) self.assertEqual(m2.manifest_text(), ". 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") - self.assertEqual(arvados.CollectionReader(m1).all_streams()[0].files()['md5sum.txt'].as_manifest(), + self.assertEqual(arvados.CollectionReader(m1, self.api_client).all_streams()[0].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(arvados.CollectionReader(m1, self.api_client).all_streams()[0].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(arvados.CollectionReader(m1, self.api_client).all_streams()[0].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(arvados.CollectionReader(m1, self.api_client).all_streams()[0].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(), @@ -486,7 +503,7 @@ 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( @@ -495,7 +512,7 @@ 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(), @@ -503,7 +520,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): ./subdir 4ace875ffdc6824a04950f06858f4465+22 8:14: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) @@ -513,7 +530,7 @@ class ArvadosCollectionsTest(ArvadosKeepLocalStoreTestCase): ./d1/d2 50170217e5b04312024aa5cd42934494+13 0:8:f3\n""") 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( @@ -522,14 +539,14 @@ 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) @@ -586,7 +603,7 @@ 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)