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.
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')
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(),
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():
'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:
[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]
["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')
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()]
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():
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)
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
""")
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],
. 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(),
./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(
./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(),
./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)
./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(
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)
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)
projects / arvados.git / blobdiff