def pipeline_instance(uuid, patterns, local):
pi_uuid = uuid
job_patterns = patterns
cluster_uuid = pi_uuid.split('-')[0]
resp = arvados.api().pipeline_instances().list(filters=[["uuid","=", pi_uuid]]).execute()
if not local:
for job in resp.items()[1][1][0]['components']['cwl-runner']['job']['components']:
for pattern in job_patterns:
if re.match(pattern, job):
job_uuid = resp.items()[1][1][0]['components']['cwl-runner']['job']['components'][job]
jobresp = arvados.api().jobs().list(filters=[["uuid", "=", job_uuid]]).execute()
output_pdh = jobresp.items()[1][1][0]['output']
for file in Collection(output_pdh):
print os.path.join(output_pdh,file)
else:
for job in resp.items()[1][1][0]['components']:
for pattern in job_patterns:
if re.match(pattern, job):
job_uuid = resp.items()[1][1][0]['components'][job]['job']['uuid']
jobresp = arvados.api().jobs().list(filters=[["uuid", "=", job_uuid]]).execute()
output_pdh = jobresp.items()[1][1][0]['output']
print job
for file in Collection(output_pdh):
print os.path.join(output_pdh,file)
def test__eq__from_manifest(self):
with Collection(
'. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
with Collection(
'. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt'
) as c2:
self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
def test__ne__(self):
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
with Collection() as c2:
with c2.open("count1.txt", "w") as f:
f.write("1234567890")
self.assertTrue(c1["count1.txt"] != c2["count1.txt"])
self.assertFalse(c1["count1.txt"] == c2["count1.txt"])
def test__eq__from_writes(self):
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count1.txt') as c1:
with Collection() as c2:
f = c2.open("count1.txt", "w")
f.write("0123456789")
self.assertTrue(c1["count1.txt"] == c2["count1.txt"])
self.assertFalse(c1["count1.txt"] != c2["count1.txt"])
def test_permission_expired(self):
base_manifest = ". 781e5e245d69b566979b86e28d23f2c7+10+A715fd31f8111894f717eb1003c1b0216799dd9ec@{} 0:10:count.txt\n"
now = datetime.datetime.now()
a_week_ago = now - datetime.timedelta(days=7)
a_month_ago = now - datetime.timedelta(days=30)
a_week_from_now = now + datetime.timedelta(days=7)
with Collection(base_manifest.format(self.datetime_to_hex(a_week_from_now))) as c:
self.assertFalse(c.find('count.txt').permission_expired())
with Collection(base_manifest.format(self.datetime_to_hex(a_week_ago))) as c:
f = c.find('count.txt')
self.assertTrue(f.permission_expired())
self.assertTrue(f.permission_expired(a_week_from_now))
self.assertFalse(f.permission_expired(a_month_ago))
def test_prefetch(self):
keep = ArvadosFileWriterTestCase.MockKeep({"2e9ec317e197819358fbc43afca7d837+8": "01234567", "e8dc4081b13434b45189a720b77b6818+8": "abcdefgh"})
with Collection(". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:16:count.txt\n", keep_client=keep) as c:
r = c.open("count.txt", "r")
self.assertEqual("0123", r.read(4))
self.assertIn("2e9ec317e197819358fbc43afca7d837+8", keep.requests)
self.assertIn("e8dc4081b13434b45189a720b77b6818+8", keep.requests)
def test_truncate2(self):
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
})
api = ArvadosFileWriterTestCase.MockApi({
"name": "test_truncate2",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
"replication_desired": None,
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 7f614da9329cd3aebf59b91aadc30bf0+67108864 0:12:count.txt\n",
"portable_data_hash": "272da898abdf86ddc71994835e3155f8+95",
})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "rb+")
self.assertEqual(writer.size(), 10)
self.assertEqual(b"0123456789", writer.read(12))
# extend file size
writer.truncate(12)
self.assertEqual(writer.size(), 12)
writer.seek(0, os.SEEK_SET)
self.assertEqual(b"0123456789\x00\x00", writer.read(12))
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
c.save_new("test_truncate2")
self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
self.assertFalse(c.modified())
def test_overwrite(self):
keep = ArvadosFileWriterTestCase.MockKeep(
{"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi(
{
"name": "test_overwrite",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
"replication_desired": None
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n",
"portable_data_hash": "7a461a8c58601798f690f8b368ac4423+51"
})
with Collection(
'. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "wb+")
self.assertEqual(writer.size(), 0)
writer.write("01234567")
self.assertEqual(writer.size(), 8)
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
c.save_new("test_overwrite")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertFalse(c.modified())
def test_create_multiple(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name": "test_create_multiple",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
"replication_desired": None
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n",
"portable_data_hash": "71e7bb6c00d31fc2b4364199fd97be08+102"
})
with Collection(api_client=api, keep_client=keep) as c:
w1 = c.open("count1.txt", "wb")
w2 = c.open("count2.txt", "wb")
w1.write("01234567")
w2.write("abcdefgh")
self.assertEqual(w1.size(), 8)
self.assertEqual(w2.size(), 8)
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
self.assertIsNone(keep.get("2e9ec317e197819358fbc43afca7d837+8"))
c.save_new("test_create_multiple")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertFalse(c.modified())
self.assertEqual(b"01234567",
keep.get("2e9ec317e197819358fbc43afca7d837+8"))
def test_write_large_rewrite(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name": "test_write_large",
"manifest_text":
". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
"replication_desired": None
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text":
". 3dc0d4bc21f48060bedcb2c91af4f906+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 0:3:count.txt 32892006:67107997:count.txt 3:32892000:count.txt\n",
"portable_data_hash": "217665c6b713e1b78dfba7ebd42344db+156"
})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR +
' 0:0:count.txt',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "rb+")
text = b''.join([b"0123456789" for a in range(0, 100)])
for b in range(0, 100000):
writer.write(text)
writer.seek(0, os.SEEK_SET)
writer.write("foo")
self.assertEqual(writer.size(), 100000000)
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
c.save_new("test_write_large")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertFalse(c.modified())
def test_truncate(self):
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10": b"0123456789",
})
api = ArvadosFileWriterTestCase.MockApi({
"name": "test_truncate",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
"replication_desired": None,
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n",
"portable_data_hash":"7fcd0eaac3aad4c31a6a0e756475da92+52",
})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "rb+")
self.assertEqual(writer.size(), 10)
self.assertEqual(b"0123456789", writer.read(12))
writer.truncate(8)
# Make sure reading off the end doesn't break
self.assertEqual(b"", writer.read(12))
self.assertEqual(writer.size(), 8)
writer.seek(0, os.SEEK_SET)
self.assertEqual(b"01234567", writer.read(12))
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
c.save_new("test_truncate")
self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
self.assertFalse(c.modified())
def test_append(self):
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10":
b"0123456789",
})
c = Collection(
'. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
keep_client=keep)
writer = c.open("count.txt", "ab+")
self.assertEqual(writer.read(20), b"0123456789")
writer.seek(0, os.SEEK_SET)
writer.write("hello")
self.assertEqual(writer.read(), b"")
writer.seek(-5, os.SEEK_CUR)
self.assertEqual(writer.read(3), b"hel")
self.assertEqual(writer.read(), b"lo")
writer.seek(0, os.SEEK_SET)
self.assertEqual(writer.read(), b"0123456789hello")
writer.seek(0)
writer.write("world")
self.assertEqual(writer.read(), b"")
writer.seek(0)
self.assertEqual(writer.read(), b"0123456789helloworld")
self.assertEqual(
". 781e5e245d69b566979b86e28d23f2c7+10 fc5e038d38a57032085441e7fe7010b0+10 0:20:count.txt\n",
c.portable_manifest_text())
def test_create_multiple(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name":
"test_create_multiple",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"
}, {
"uuid":
"zzzzz-4zz18-mockcollection0",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 e8dc4081b13434b45189a720b77b6818+8 0:8:count1.txt 8:8:count2.txt\n"
})
with Collection(api_client=api, keep_client=keep) as c:
w1 = c.open("count1.txt", "w")
w2 = c.open("count2.txt", "w")
w1.write("01234567")
w2.write("abcdefgh")
self.assertEqual(w1.size(), 8)
self.assertEqual(w2.size(), 8)
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
self.assertEqual(None,
keep.get("2e9ec317e197819358fbc43afca7d837+8"))
c.save_new("test_create_multiple")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertEqual(False, c.modified())
self.assertEqual("01234567",
keep.get("2e9ec317e197819358fbc43afca7d837+8"))
def test_overwrite(self):
keep = ArvadosFileWriterTestCase.MockKeep(
{"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi(
{
"name":
"test_overwrite",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"
}, {
"uuid":
"zzzzz-4zz18-mockcollection0",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"
})
with Collection(
'. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "w+")
self.assertEqual(writer.size(), 0)
writer.write("01234567")
self.assertEqual(writer.size(), 8)
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
c.save_new("test_overwrite")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertEqual(False, c.modified())
def test_create(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name":
"test_create",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"
}, {
"uuid":
"zzzzz-4zz18-mockcollection0",
"manifest_text":
". 2e9ec317e197819358fbc43afca7d837+8 0:8:count.txt\n"
})
with Collection(api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "w+")
self.assertEqual(writer.size(), 0)
writer.write("01234567")
self.assertEqual(writer.size(), 8)
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
self.assertEqual(None,
keep.get("2e9ec317e197819358fbc43afca7d837+8"))
c.save_new("test_create")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertEqual(False, c.modified())
self.assertEqual("01234567",
keep.get("2e9ec317e197819358fbc43afca7d837+8"))
def test_write_large_rewrite(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name":
"test_write_large",
"manifest_text":
". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"
}, {
"uuid":
"zzzzz-4zz18-mockcollection0",
"manifest_text":
". 37400a68af9abdd76ca5bf13e819e42a+32892003 a5de24f4417cfba9d5825eadc2f4ca49+67108000 32892000:3:count.txt 32892006:67107997:count.txt 0:32892000:count.txt\n"
})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR +
' 0:0:count.txt',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
text = ''.join(["0123456789" for a in xrange(0, 100)])
for b in xrange(0, 100000):
writer.write(text)
writer.seek(0, os.SEEK_SET)
writer.write("foo")
self.assertEqual(writer.size(), 100000000)
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
c.save_new("test_write_large")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertEqual(False, c.modified())
def test_write_large(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name":
"test_write_large",
"manifest_text":
". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"
}, {
"uuid":
"zzzzz-4zz18-mockcollection0",
"manifest_text":
". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n"
})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR +
' 0:0:count.txt',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
text = ''.join(["0123456789" for a in xrange(0, 100)])
for b in xrange(0, 100000):
writer.write(text)
self.assertEqual(writer.size(), 100000000)
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
c.save_new("test_write_large")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertEqual(False, c.modified())
def test_truncate(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_truncate",
"manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text":". 781e5e245d69b566979b86e28d23f2c7+10 0:8:count.txt\n"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual(writer.size(), 10)
self.assertEqual("0123456789", writer.read(12))
writer.truncate(8)
# Make sure reading off the end doesn't break
self.assertEqual("", writer.read(12))
self.assertEqual(writer.size(), 8)
writer.seek(0, os.SEEK_SET)
self.assertEqual("01234567", writer.read(12))
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
c.save_new("test_truncate")
self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
self.assertEqual(False, c.modified())
def test_write_to_end(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
api = ArvadosFileWriterTestCase.MockApi({"name":"test_append",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"},
{"uuid":"zzzzz-4zz18-mockcollection0",
"manifest_text": ". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:13:count.txt\n"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
api_client=api, keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual(writer.size(), 10)
writer.seek(5, os.SEEK_SET)
self.assertEqual("56789", writer.read(8))
writer.seek(10, os.SEEK_SET)
writer.write("foo")
self.assertEqual(writer.size(), 13)
writer.seek(5, os.SEEK_SET)
self.assertEqual("56789foo", writer.read(8))
self.assertEqual(None, c.manifest_locator())
self.assertEqual(True, c.modified())
self.assertEqual(None, keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
c.save_new("test_append")
self.assertEqual("zzzzz-4zz18-mockcollection0", c.manifest_locator())
self.assertEqual(False, c.modified())
self.assertEqual("foo", keep.get("acbd18db4cc2f85cedef654fccc4a4d8+3"))
def spawn_new_task_per_file(script_parameter, regex, if_sequence=0, and_end_task=True):
"""
Generalized form of one_task_per_pair_input_file from
https://github.com/curoverse/arvados/blob/master/crunch_scripts/arvados_bwa.py
Creates a new task if the file in the collection matches the regex
"""
if if_sequence != arvados.current_task()['sequence']:
return
job_input = arvados.current_job()['script_parameters'][script_parameter]
input_collection = Collection(job_input)
for name in input_collection:
if not re.search(regex,name):
continue
new_task_attrs = {
'job_uuid': arvados.current_job()['uuid'],
'created_by_job_task_uuid': arvados.current_task()['uuid'],
'sequence': if_sequence + 1,
'parameters': {
'input_1': name,
}
}
arvados.api().job_tasks().create(body=new_task_attrs).execute()
if and_end_task:
arvados.api().job_tasks().update(uuid=arvados.current_task()['uuid'],
body={'success':True}
).execute()
def test_rewrite_over_existing_file(self):
keep = ArvadosFileWriterTestCase.MockKeep({
"781e5e245d69b566979b86e28d23f2c7+10":
b"0123456789",
})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "rb+")
for b in range(0, 10):
writer.seek(5, os.SEEK_SET)
writer.write("abcdefghij")
self.assertEqual(writer.size(), 15)
self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
self.assertEqual(
". 781e5e245d69b566979b86e28d23f2c7+10 ae5f43bab79cf0be33f025fa97ae7398+100 0:5:count.txt 100:10:count.txt\n",
c.portable_manifest_text())
writer.arvadosfile.flush()
self.assertEqual(writer.size(), 15)
self.assertEqual(b"01234abcdefghij", writer.readfrom(0, 20))
self.assertEqual(
". 781e5e245d69b566979b86e28d23f2c7+10 a925576942e94b2ef57a066101b48876+10 0:5:count.txt 10:10:count.txt\n",
c.portable_manifest_text())
def test_write_large(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
api = ArvadosFileWriterTestCase.MockApi(
{
"name": "test_write_large",
"manifest_text":
". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
"replication_desired": None
}, {
"uuid": "zzzzz-4zz18-mockcollection0",
"manifest_text":
". a5de24f4417cfba9d5825eadc2f4ca49+67108000 598cc1a4ccaef8ab6e4724d87e675d78+32892000 0:100000000:count.txt\n",
"portable_data_hash": "9132ca8e3f671c76103a38f5bc24328c+108"
})
with Collection('. ' + arvados.config.EMPTY_BLOCK_LOCATOR +
' 0:0:count.txt',
api_client=api,
keep_client=keep) as c:
writer = c.open("count.txt", "rb+")
text = "0123456789" * 100
for b in range(0, 100000):
writer.write(text)
self.assertEqual(writer.size(), 100000000)
self.assertIsNone(c.manifest_locator())
self.assertTrue(c.modified())
c.save_new("test_write_large")
self.assertEqual("zzzzz-4zz18-mockcollection0",
c.manifest_locator())
self.assertFalse(c.modified())
def test_write_empty(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
with Collection(keep_client=keep) as c:
writer = c.open("count.txt", "wb")
self.assertEqual(writer.size(), 0)
self.assertEqual(
". d41d8cd98f00b204e9800998ecf8427e+0 0:0:count.txt\n",
c.portable_manifest_text())
def test_get_manifest_text_commits(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
with Collection(keep_client=keep) as c:
writer = c.open("count.txt", "w")
writer.write("0123456789")
self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.manifest_text())
self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--project-uuid',
metavar='UUID',
help='Project to output to')
parser.add_argument('collection_uuid',
metavar='UUID',
help='Collection UUID')
args = parser.parse_args()
collection_uuid = args.collection_uuid
project_uuid = args.project_uuid
c = Collection(collection_uuid)
dest = Collection()
for i in c:
if isinstance(c[i], Subcollection):
dest.copy('./' + i, target_path='./' + i, source_collection=c)
dest.save_new(owner_uuid=project_uuid)
print(dest.manifest_locator())
def test_save_manifest_text(self):
keep = ArvadosFileWriterTestCase.MockKeep({})
with Collection(keep_client=keep) as c:
writer = c.open("count.txt", "wb")
writer.write(b"0123456789")
self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.portable_manifest_text())
self.assertNotIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
self.assertEqual('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n', c.save_new(create_collection_record=False))
self.assertIn('781e5e245d69b566979b86e28d23f2c7+10', keep.blocks)
def get_sample_variantcaller(job):
from arvados.collection import Collection
for k, v in job["mounts"].items():
if k.endswith("cwl.inputs.json"):
c = Collection(v["portable_data_hash"])
with c.open("cwl.inputs.json", "r") as in_handle:
inputs = json.load(in_handle)
return [get_in_inputs("description", inputs),
get_in_inputs("config__algorithm__variantcaller", inputs)]
return None, None
def test_write_across_several_segments(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:4:count.txt 0:4:count.txt 0:4:count.txt',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("012301230123", writer.readfrom(0, 15))
writer.seek(2, os.SEEK_SET)
writer.write("abcdefg")
self.assertEqual(writer.size(), 12)
self.assertEqual("01abcdefg123", writer.readfrom(0, 15))
self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 7ac66c0f148de9519b8bd264312c4d64+7 0:2:count.txt 10:7:count.txt 1:3:count.txt\n", c.portable_manifest_text())
def test_write_at_end(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("0123456789", writer.readfrom(0, 13))
writer.seek(7, os.SEEK_SET)
writer.write("foo")
self.assertEqual(writer.size(), 10)
self.assertEqual("0123456foo", writer.readfrom(0, 13))
self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 acbd18db4cc2f85cedef654fccc4a4d8+3 0:7:count.txt 10:3:count.txt\n", c.portable_manifest_text())
def test_write_across_segment_boundary(self):
keep = ArvadosFileWriterTestCase.MockKeep({"781e5e245d69b566979b86e28d23f2c7+10": "0123456789"})
with Collection('. 781e5e245d69b566979b86e28d23f2c7+10 0:10:count.txt 0:10:count.txt\n',
keep_client=keep) as c:
writer = c.open("count.txt", "r+")
self.assertEqual("012345678901234", writer.readfrom(0, 15))
writer.seek(7, os.SEEK_SET)
writer.write("foobar")
self.assertEqual(writer.size(), 20)
self.assertEqual("0123456foobar34", writer.readfrom(0, 15))
self.assertEqual(". 781e5e245d69b566979b86e28d23f2c7+10 3858f62230ac3c915f300c664312c63f+6 0:7:count.txt 10:6:count.txt 3:7:count.txt\n", c.portable_manifest_text())