def __init__(self,
executor_uri,
cpu_limit,
mem_limit,
push_registry,
staging_uri,
stream=False,
verbose=False,
repository=None,
pull_registry=None,
docker_host=None,
container_image=None,
insecure_registries=False,
max_retries=3):
self.executor_uri = executor_uri
self.cpu = float(cpu_limit)
self.mem = int(mem_limit)
self.push_registry = push_registry
self.pull_registry = pull_registry
self.staging_uri = staging_uri
self.stream = stream
self.verbose = verbose
self.repository = repository
self.docker_host = docker_host
self.container_image = container_image
self.insecure_registries = insecure_registries
self.max_retries = max_retries
self.pending = 0
self.running = 0
self.finished = 0
self.failed = 0
self.queued_tasks = []
self.task_status = defaultdict(lambda: None)
self.task_history = {}
self.task_retries = defaultdict(int)
self.blacklist = set()
self._processing_offers = threading.Lock()
self._processing_queue = threading.Lock()
# Ensure the staging directory exists
self.filesystem = None
if self.staging_uri:
staging_uri = urlparse(self.staging_uri)
staging_fs = opener.opendir(
"%s://%s/" % (staging_uri.scheme, staging_uri.netloc))
staging_fs.makedir(staging_uri.path.lstrip("/"),
recursive=True,
allow_recreate=True)
self.filesystem = opener.opendir(self.staging_uri)
self.cleanup = TaskCleanupThread(self.filesystem)
self.cleanup.start()
def put(self):
filename = parse_options_header(
request.headers.get('Content-Disposition', ''))[1].get('filename')
d = Document.create({'deleted': False})
opener.opendir(directory_name(d), create_dir=True)
d.setcontents(
request.stream,
name=lambda s: os.path.join(directory_name(s),
secure_filename(filename))
)
return d.dumps()
def __init__(self,
tasks,
executor_uri,
cpu_limit,
mem_limit,
push_registry,
staging_uri,
stream=False,
verbose=False,
repository=None,
pull_registry=None,
docker_host=None,
container_image=None,
insecure_registries=False):
self.executor_uri = executor_uri
self.cpu = float(cpu_limit)
self.mem = int(mem_limit)
self.push_registry = push_registry
self.pull_registry = pull_registry
self.staging_uri = staging_uri
self.stream = stream
self.verbose = verbose
self.repository = repository
self.docker_host = docker_host
self.container_image = container_image
self.insecure_registries = insecure_registries
self.queued_tasks = []
for path, tags in tasks:
dockerfile = parse_dockerfile(path, registry=pull_registry)
self.queued_tasks.append((path, dockerfile, tags))
self.pending = len(self.queued_tasks)
self.running = 0
self.finished = 0
self.failed = 0
self.task_ids = {}
self.processing_offers = threading.Lock()
# Ensure the staging directory exists
self.filesystem = None
if self.staging_uri:
staging_uri = urlparse(self.staging_uri)
staging_fs = opener.opendir(
"%s://%s/" % (staging_uri.scheme, staging_uri.netloc))
staging_fs.makedir(staging_uri.path.lstrip("/"),
recursive=True,
allow_recreate=True)
self.filesystem = opener.opendir(self.staging_uri)
def put(self, oauth):
filename = parse_options_header(
request.headers.get('Content-Disposition', ''))[1].get('filename')
d = Document.create({'deleted': False})
opener.opendir(directory_name(d), create_dir=True)
d.setcontents(
request.stream,
name=lambda s: os.path.join(directory_name(s),
secure_filename(filename))
)
return d.dumps()
def __init__(self, executor_uri, cpu_limit, mem_limit, push_registry,
staging_uri, stream=False, verbose=False, repository=None,
pull_registry=None, docker_host=None, container_image=None,
insecure_registries=False, max_retries=3):
self.executor_uri = executor_uri
self.cpu = float(cpu_limit)
self.mem = int(mem_limit)
self.push_registry = push_registry
self.pull_registry = pull_registry
self.staging_uri = staging_uri
self.stream = stream
self.verbose = verbose
self.repository = repository
self.docker_host = docker_host
self.container_image = container_image
self.insecure_registries = insecure_registries
self.max_retries = max_retries
self.pending = 0
self.running = 0
self.finished = 0
self.failed = 0
self.queued_tasks = []
self.task_status = defaultdict(lambda: None)
self.task_history = {}
self.task_retries = defaultdict(int)
self.blacklist = set()
self._processing_offers = threading.Lock()
self._processing_queue = threading.Lock()
# Ensure the staging directory exists
self.filesystem = None
if self.staging_uri:
staging_uri = urlparse(self.staging_uri)
staging_fs = opener.opendir(
"%s://%s/" % (staging_uri.scheme, staging_uri.netloc)
)
staging_fs.makedir(
staging_uri.path.lstrip("/"),
recursive=True,
allow_recreate=True
)
self.filesystem = opener.opendir(self.staging_uri)
self.cleanup = TaskCleanupThread(self.filesystem)
self.cleanup.start()
def __init__(self, tasks, executor_uri, cpu_limit, mem_limit, push_registry,
staging_uri, stream=False, verbose=False, repository=None,
pull_registry=None, docker_host=None, container_image=None,
insecure_registries=False):
self.executor_uri = executor_uri
self.cpu = float(cpu_limit)
self.mem = int(mem_limit)
self.push_registry = push_registry
self.pull_registry = pull_registry
self.staging_uri = staging_uri
self.stream = stream
self.verbose = verbose
self.repository = repository
self.docker_host = docker_host
self.container_image = container_image
self.insecure_registries = insecure_registries
self.queued_tasks = []
for path, tags in tasks:
dockerfile = parse_dockerfile(path, registry=pull_registry)
self.queued_tasks.append((path, dockerfile, tags))
self.pending = len(self.queued_tasks)
self.running = 0
self.finished = 0
self.failed = 0
self.task_ids = {}
self._processing_offers = threading.Lock()
# Ensure the staging directory exists
self.filesystem = None
if self.staging_uri:
staging_uri = urlparse(self.staging_uri)
staging_fs = opener.opendir(
"%s://%s/" % (staging_uri.scheme, staging_uri.netloc)
)
staging_fs.makedir(
staging_uri.path.lstrip("/"),
recursive=True,
allow_recreate=True
)
self.filesystem = opener.opendir(self.staging_uri)
self.cleanup = TaskCleanupThread(self.filesystem)
self.cleanup.start()
def _get_fs(self, create_dir=True):
"""."""
filedir = dirname(self.fileurl)
filename = basename(self.fileurl)
return (opener.opendir(filedir, writeable=True,
create_dir=create_dir), filename)
def test_verify_remote_scroll(self):
pyfs = opener.opendir(settings.config['fs_path'])
signing_key = crypto.generate_signing_key()
scroll_id = sha1_hexdigest
s = scroll.RemoteScroll(pyfs,
scroll_id,
signing_key.verify_key.encode(crypto.HexEncoder))
s.get_verify_key = lambda y: signing_key.verify_key
items = []
for i in range(10):
item_hash = HASH(i)
s.add(item_hash)
items.append(item_hash)
four, five = s.slice(4, 2)
self.assertEqual(four, HASH(4))
self.assertEqual(five, HASH(5))
new_item_hash = HASH(i)
new_state = HASH(s.state + new_item_hash)
update = new_item_hash + new_state
signed_update = signing_key.sign(update)
self.assertEqual(s.verify_update(signed_update), update)
def test_put_get_pool(self):
my_data = "B"*20
scroll_id = sha1_hexdigest
pyfs = opener.opendir(settings.config['fs_path'])
p = pool.Pool(pyfs)
hash_bytes = p.put(my_data)
self.assertEqual(p.get(hash_bytes), my_data)
def archive_fs(locations):
"""Fixture to check the BagIt file generation."""
archive_path = locations['archive'].uri
fs = opener.opendir(archive_path, writeable=False, create_dir=True)
yield fs
for d in fs.listdir():
fs.removedir(d, force=True)
def test_put_get_pool(self):
my_data = "B" * 20
scroll_id = sha1_hexdigest
pyfs = opener.opendir(settings.config['fs_path'])
p = pool.Pool(pyfs)
hash_bytes = p.put(my_data)
self.assertEqual(p.get(hash_bytes), my_data)
def _get_fs(self, create_dir=True):
"""Return tuple with filesystem and filename."""
filedir = dirname(self.fileurl)
filename = basename(self.fileurl)
return (opener.opendir(filedir, writeable=True,
create_dir=create_dir), filename)
def archive_fs(locations):
"""Fixture to check the BagIt file generation."""
archive_path = locations['archive'].uri
fs = opener.opendir(archive_path, writeable=False, create_dir=True)
yield fs
for d in fs.listdir():
fs.removedir(d, force=True)
def test_verify_remote_scroll(self):
pyfs = opener.opendir(settings.config['fs_path'])
signing_key = crypto.generate_signing_key()
scroll_id = sha1_hexdigest
s = scroll.RemoteScroll(
pyfs, scroll_id, signing_key.verify_key.encode(crypto.HexEncoder))
s.get_verify_key = lambda y: signing_key.verify_key
items = []
for i in range(10):
item_hash = bytes_hash_int(i)
s.add(item_hash)
items.append(item_hash)
four, five = s.slice(4, 2)
self.assertEqual(four, bytes_hash_int(4))
self.assertEqual(five, bytes_hash_int(5))
new_item_hash = bytes_hash_int(i)
new_state = settings.HASH(s.state + new_item_hash)
update = new_item_hash + new_state
signed_update = signing_key.sign(update)
self.assertEqual(s.verify_update(signed_update), update)
def test_add_one(self):
scroll_id = 'test_add'
data1 = HASH( '1' )
pyfs = opener.opendir(settings.config['fs_path'])
s = scroll.Scroll(pyfs, scroll_id)
s.add(data1)
contents = pyfs.getcontents(scroll_id + '.scroll')
self.assertEqual(contents, data1)
def test_save_scroll(self):
item_hash = twenty_bytes
scroll_id = sha1_hexdigest
pyfs = opener.opendir(settings.config['fs_path'])
s = scroll.Scroll(pyfs, scroll_id)
s.add(item_hash)
self.assertTrue(s.has(item_hash))
contents = pyfs.getcontents(scroll_id + '.scroll')
self.assertEqual(contents, item_hash)
def _get_fs(self, create_dir=True):
"""."""
filedir = dirname(self.fileurl)
filename = basename(self.fileurl)
return (
opener.opendir(filedir, writeable=True, create_dir=create_dir),
filename
)
def _get_fs(self, create_dir=True):
"""Return tuple with filesystem and filename."""
filedir = dirname(self.fileurl)
filename = basename(self.fileurl)
return (
opener.opendir(filedir, writeable=True, create_dir=create_dir),
filename
)
def test_sign(self):
my_message = 'Do it Like La La La!'
pyfs = opener.opendir(settings.config['fs_path'])
fingerprint = notary.Notary.generate(pyfs)
publisher = None
n = notary.Notary(publisher, pyfs, fingerprint)
signed_message = n.signing_key.sign(my_message)
verify_key = n.signing_key.verify_key
self.assertEqual(verify_key.verify(signed_message), my_message)
def test_sign(self):
my_message = 'Do it Like La La La!'
pyfs = opener.opendir(settings.config['fs_path'])
fingerprint = notary.Notary.generate(pyfs)
publisher = None
n = notary.Notary(publisher, pyfs, fingerprint)
signed_message = n.signing_key.sign(my_message)
verify_key = n.signing_key.verify_key
self.assertEqual(verify_key.verify(signed_message), my_message)
def _process_files(self, metadata):
"""Transfer files in a list from one ``fs`` object to another.
All tranferer files will maintain the same filename.
"""
# FS object created at the folder of where the record specific bag is
fs_dest = opener.opendir(self.folder, "files", create_dir=True)
files_to_upload = []
for file_to_upload in metadata.get("files", []):
dirname_ = os.path.dirname(file_to_upload["path"])
basename_ = os.path.basename(file_to_upload["path"])
fs_src = opener.opendir(dirname_)
copyfile(fs_src, basename_, fs_dest, basename_)
file_to_upload["path"] = os.path.join("files", basename_)
del file_to_upload["url"]
files_to_upload.append(file_to_upload)
metadata["files_to_upload"] = files_to_upload
return metadata
def test_load_scroll(self):
item_hash = twenty_bytes
scroll_id = sha1_hexdigest
pyfs = opener.opendir(settings.config['fs_path'])
with open(scroll_id + '.scroll', 'w+') as f:
f.write(item_hash)
s = scroll.Scroll(pyfs, scroll_id)
s.load()
self.assertTrue(s.has(item_hash))
def save(self, incoming_stream, size=None, chunk_size=None):
"""Save file in the file system."""
uri = self.obj.bucket.location.uri
path = self.make_path()
with opener.opendir(uri) as fs:
dest_file = fs.makeopendir(path, recursive=True).open('data', 'wb')
bytes_written, checksum = self._save_stream(
incoming_stream, dest_file, chunk_size=chunk_size)
dest_file.close()
return join(uri, path, 'data'), bytes_written, checksum
def transfer_data_files(self):
"""Transfer files in a list from one ``fs`` object to another.
All tranferer files will maintain the same filename.
"""
# FS object created at the folder of where the record specific bag is
fs_dest = opener.opendir(self.bagit_folder_path, create_dir=True)
try:
for docfile in self.docfiles:
fs_src = opener.opendir(os.path.dirname(docfile.get_path()))
copyfile(fs_src, os.path.basename(docfile.get_path()),
fs_dest, os.path.basename(docfile.get_path()))
except Exception:
raise ArchiverError("Error while copying %s to %s"
% (docfile.get_path(),
os.path.join(self.bagit_folder_path,
docfile.name +
docfile.format)))
return True
def test_slice(self):
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
s = scroll.Scroll(pyfs, scroll_id)
items = []
for i in range(10):
item_hash = HASH(i)
s.add(item_hash)
items.append(item_hash)
four, five = s.slice(4, 2)
self.assertEqual(four, HASH(4))
self.assertEqual(five, HASH(5))
def test_slice(self):
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
s = scroll.Scroll(pyfs, scroll_id)
items = []
for i in range(10):
item_hash = bytes_hash_int(i)
s.add(item_hash)
items.append(item_hash)
four, five = s.slice(4, 2)
self.assertEqual(four, bytes_hash_int(4))
self.assertEqual(five, bytes_hash_int(5))
def test_put_error(client, bucket):
"""Test upload - cancelled by user."""
object_url = url_for('invenio_files_rest.object_api',
bucket_id=bucket.id,
key='test.txt')
pytest.raises(ValueError,
client.put,
object_url,
input_stream=BadBytesIO(b'a' * 128))
assert FileInstance.query.count() == 0
assert ObjectVersion.query.count() == 0
# Ensure that the file was removed.
assert len(list(opener.opendir(bucket.location.uri).walk('.'))) == 3
def test_load(self):
scroll_id = 'test_load'
pyfs = opener.opendir(settings.config['fs_path'])
data1 = HASH( '2' )
data2 = HASH( '3' )
with open(scroll_id + '.scroll', 'w+') as f:
f.write( data1 + data2 )
s = scroll.Scroll(pyfs, scroll_id)
self.assertTrue(s.has(data1))
self.assertTrue(s.has(data2))
self.assertFalse(s.has('1'))
self.assertFalse(s.has(''))
expected_state = HASH( HASH( HASH( scroll_id ) + data1 ) + data2 )
self.assertEqual(s.state, expected_state)
def save(self, incoming_stream, chunk_size=None, progress_callback=None):
"""Save file in the file system."""
fs = opener.opendir(self.file.uri or self.make_path(), create_dir=True)
fp = fs.open(self.filename, 'wb')
try:
bytes_written, checksum = self._write_stream(
incoming_stream, fp, chunk_size=chunk_size,
progress_callback=progress_callback)
finally:
fp.close()
uri = fs.getpathurl(self.filename, allow_none=True) or \
fs.getsyspath(self.filename, allow_none=True)
return uri, bytes_written, checksum
def test_put_error(client, bucket):
"""Test upload - cancelled by user."""
object_url = url_for(
'invenio_files_rest.object_api', bucket_id=bucket.id, key='test.txt')
pytest.raises(
ValueError,
client.put,
object_url,
input_stream=BadBytesIO(b'a' * 128)
)
assert FileInstance.query.count() == 0
assert ObjectVersion.query.count() == 0
# Ensure that the file was removed.
assert len(list(opener.opendir(bucket.location.uri).walk('.'))) == 3
def test_save_big_scroll(self):
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
s = scroll.Scroll(pyfs, scroll_id)
items = []
for i in range(100):
item_hash = bytes_hash_int(i)
s.add(item_hash)
items.append(item_hash)
for item_hash in items:
self.assertTrue(s.has(item_hash))
contents = pyfs.getcontents(scroll_id + '.scroll')
self.assertEqual(contents, ''.join(items))
def test_add(self):
my_data = "B"*20
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
chissel_set_id = 'spam'
fingerprint = notary.Notary.generate(pyfs)
chisel_set = notary.ChiselSet(pyfs, chissel_set_id, fingerprint)
hash_bytes = chisel_set.add(my_data)
self.assertEqual(chisel_set.pool.get(hash_bytes), my_data)
self.assertTrue(chisel_set.scroll.has(hash_bytes))
self.assertTrue(chisel_set.has(hash_bytes))
def test_add_many(self):
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
s = scroll.Scroll(pyfs, scroll_id)
items = []
for i in range(100):
item_hash = HASH(i)
s.add(item_hash)
items.append(item_hash)
for item_hash in items:
self.assertTrue(s.has(item_hash))
contents = pyfs.getcontents(scroll_id + '.scroll')
self.assertEqual(contents, ''.join(items))
def test_add(self):
my_data = "B" * 20
pyfs = opener.opendir(settings.config['fs_path'])
scroll_id = sha1_hexdigest
chissel_set_id = 'spam'
fingerprint = notary.Notary.generate(pyfs)
chisel_set = notary.ChiselSet(pyfs, chissel_set_id, fingerprint)
hash_bytes = chisel_set.add(my_data)
self.assertEqual(chisel_set.pool.get(hash_bytes), my_data)
self.assertTrue(chisel_set.scroll.has(hash_bytes))
self.assertTrue(chisel_set.has(hash_bytes))
def test_load_artificial(self):
"""
This test writes its own scroll to test scroll loading
"""
scroll_id = 'test_load'
data1 = HASH( '2' )
data2 = HASH( '3' )
expected_state = HASH( HASH( HASH( scroll_id ) + data1 ) + data2 )
pyfs = opener.opendir(settings.config['fs_path'])
with open(scroll_id + '.scroll', 'w+') as f:
f.write( data1 + data2 )
with open(scroll_id + '.state', 'w') as f:
f.write( expected_state )
s = scroll.Scroll(pyfs, scroll_id)
self.assertTrue(s.has(data1))
self.assertTrue(s.has(data2))
self.assertFalse(s.has('1'))
self.assertFalse(s.has(''))
self.assertEqual(s.state, expected_state)
def path_to_fs(path):
"""Convert path to an FS object."""
return opener.opendir(path)
def archive_fs(locations):
"""File system for the archive location."""
archive_path = locations['archive']
fs = opener.opendir(archive_path, writeable=False, create_dir=True)
return fs
def archive_fs(locations):
"""File system for the archive location."""
archive_path = locations['archive']
fs = opener.opendir(archive_path, writeable=False, create_dir=True)
return fs
def loadNotary():
pyfs = opener.opendir(settings.config['fs_path'])
chissel_set_id = 'spam'
notary_fingerprint = notary.Notary.generate(pyfs)
return notary.Notary(SubscribeHandler, pyfs, notary_fingerprint)
def test_generate(self):
pyfs = opener.opendir(settings.config['fs_path'])
fingerprint = notary.Notary.generate(pyfs)
publisher = None
n = notary.Notary(publisher, pyfs, fingerprint)
def get_sample_project_mapping(basepath,
samplesheet=None,
suffix='.fastq.gz',
absolute_paths=False,
catch_undetermined=True):
"""
Given a path containing fastq.gz files, possibily nested in Project/Sample
directories, return a data structure mapping fastq-samples to projects.
TODO: The SampleSheet.csv may be used as a hint but is not required.
:param basepath: Path to directory tree of fastq.gz files - eg, bcl2fastq
output directory
:type basepath: str
:return: Dictionary lists, {project_id : [relative fastq.gz paths]}
:rtype: OrderedDict
"""
from fs.opener import opener
fq_files = []
with opener.opendir(basepath) as vfs:
for fn in vfs.walkfiles():
if suffix in fn:
fq_files.append(fn.lstrip('/').lstrip('\\'))
fq_files = sorted(fq_files)
project_mapping = OrderedDict()
for fqpath in fq_files:
project = ''
fqfile = fqpath
parts = Path(fqpath).parts
if len(parts) == 3:
project, sample_id, fqfile = map(str, parts)
if len(parts) == 2:
project, fqfile = map(str, parts)
if len(parts) == 1:
fqfile = str(parts[0])
if catch_undetermined and 'Undetermined' in fqfile:
project = u'Undetermined_indices'
# TODO: we currently don't deal with Project_ prefixes, really
# the project ID doesn't include Project_. If we strip
# this here, maybe we need to include the project directory
# in the fastq paths so we can know the path and project id
# - will require fixes to downstream code that
# does join(bcl2fastq_output_dir, project_id, fastq_file)
# TODO: also incorporate sample_id in this datastructure
if project not in project_mapping:
project_mapping[project] = []
if absolute_paths:
fqpath = join(basepath, fqpath)
project_mapping[project].append(fqpath)
# TODO: Use the SampleSheet.csv to validate or hint
# TODO: Also assign sample_id, sample_name, lane, read, etc
# we could use parse_sample_info_from_filename for this,
# and/or use the FASTQ header(s)
return project_mapping
def _make_bag(self, **kwargs):
"""Turn a folder into bagit form and compress it."""
opener.opendir(self.folder, create_dir=True)
info = {'Bagging-Date': datetime.now().strftime("%Y-%m-%d")}
info.update(kwargs)
return make_bag(self.folder, info)
def loadNotary():
pyfs = opener.opendir(settings.config['fs_path'])
chissel_set_id = 'spam'
notary_fingerprint = notary.Notary.generate(pyfs)
return notary.Notary(SubscribeHandler, pyfs, notary_fingerprint)
def test_generate(self):
pyfs = opener.opendir(settings.config['fs_path'])
fingerprint = notary.Notary.generate(pyfs)
publisher = None
n = notary.Notary(publisher, pyfs, fingerprint)
def test_opendir(tmppath):
"""Test opendir."""
rooturl = mkurl(tmppath)
fs = opener.opendir(rooturl + "/data")
assert fs.listdir()
count, new = 0,0
for dirPath, filename in remote.walkFiles():
count += 1
if not self.has( filename, 0 ):
new += 1
self.put( remote._fs.getcontents( "%s/%s" % (dirPath, filename) ) )
print "Saw %s files; copied %s that are new" % (count, new)
if __name__ == "__main__":
if len(sys.argv) < 2:
print "usage: %s [put|ls|cat|test]" % os.path.basename( sys.argv[0] )
else:
cmd = sys.argv[1]
if cmd == 'test':
print doctest.testmod( )
else:
from fs.opener import opener
chisel = Chisel( opener.opendir( sys.argv[2] ) )
if cmd == 'put':
chisel.put( sys.stdin.read(), *map(int, sys.argv[3:]) )
elif cmd == 'ls':
print "\n".join( "%s/%s" % (a,b) for a,b in chisel.walkFiles( *map(int, sys.argv[3:]) ) ),
elif cmd == 'cat':
print "".join( chisel.get( *map(int, sys.argv[3:]) ) ),
elif cmd == 'sync':
chisel.sync( Chisel( opener.opendir( sys.argv[3] ) ), *map(int, sys.argv[4:]) )
else:
print "unknown command %s" % (cmd,)
