# 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
import run_test_server
-from arvados_testutil import ArvadosBaseTestCase
+import arvados_testutil as tutil
class TestResumableWriter(arvados.ResumableCollectionWriter):
KEEP_BLOCK_SIZE = 1024 # PUT to Keep every 1K.
class ArvadosCollectionsTest(run_test_server.TestCaseWithServers,
- ArvadosBaseTestCase):
+ tutil.ArvadosBaseTestCase):
MAIN_SERVER = {}
@classmethod
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(self.keep_client.put('foo'), 'acbd18db4cc2f85cedef654fccc4a4d8+3', 'wrong md5 hash from Keep.put')
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()
+ foobarbaz = self.write_foo_bar_baz()
cr = arvados.CollectionReader(
- 'd6c3b8e571f1b81ebb150a45ed06c884+114+Xzizzle', self.api_client)
+ 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)
'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']])
[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.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, self.api_client)
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(),
+. 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(), 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, self.api_client).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, self.api_client).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, self.api_client).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, self.api_client).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, self.api_client).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, self.api_client).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],
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):
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.seek(0)
- self.assertEqual(f.read(20), content[0:20])
-
- 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])
-
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"""
+. 085c37f02916da1cad16f93c54d899b7+41 5348b82a029fd9e971a811ce1f71360b+43 8b22da26f9f433dea0a10e5ec66d73ba+43 40:80:md9sum.txt
+"""
- m2 = arvados.CollectionReader(m1, self.api_client)
+ 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, self.api_client).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, self.api_client).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, self.api_client).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, self.api_client).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.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(self.api_client)
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(self.api_client)
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()
projects / arvados.git / blobdiff