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DataONEorg/d1_python | lib_common/src/d1_common/multipart.py | is_multipart | def is_multipart(header_dict):
"""
Args:
header_dict : CaseInsensitiveDict
Returns:
bool: ``True`` if ``header_dict`` has a Content-Type key (case insensitive) with
value that begins with 'multipart'.
"""
return (
{k.lower(): v for k, v in header_dict.items()}
.get('content-ty... | python | def is_multipart(header_dict):
"""
Args:
header_dict : CaseInsensitiveDict
Returns:
bool: ``True`` if ``header_dict`` has a Content-Type key (case insensitive) with
value that begins with 'multipart'.
"""
return (
{k.lower(): v for k, v in header_dict.items()}
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/resolver/object_tree_resolver.py | Resolver._split_path_by_reserved_name | def _split_path_by_reserved_name(self, path):
"""Return: object_tree_path, resolver, controlled_path."""
for i, e in enumerate(path):
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raise d1_onedrive.impl.onedrive_e... | python | def _split_path_by_reserved_name(self, path):
"""Return: object_tree_path, resolver, controlled_path."""
for i, e in enumerate(path):
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/resolver/object_tree_resolver.py | Resolver._generate_readme_text | def _generate_readme_text(self, object_tree_path):
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wdef_folder = self._object_tree.get_source_tree_folder(object_tree_path)
res = StringIO()
if len(object_tree_path):
folder_name = object_tree_path[-1]... | python | def _generate_readme_text(self, object_tree_path):
"""Generate a human readable description of the folder in text format."""
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res = StringIO()
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genialis/resolwe | resolwe/flow/serializers/collection.py | CollectionSerializer._serialize_data | def _serialize_data(self, data):
"""Return serialized data or list of ids, depending on `hydrate_data` query param."""
if self.request and self.request.query_params.get('hydrate_data', False):
serializer = DataSerializer(data, many=True, read_only=True)
serializer.bind('data', se... | python | def _serialize_data(self, data):
"""Return serialized data or list of ids, depending on `hydrate_data` query param."""
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genialis/resolwe | resolwe/flow/serializers/collection.py | CollectionSerializer._filter_queryset | def _filter_queryset(self, perms, queryset):
"""Filter object objects by permissions of user in request."""
user = self.request.user if self.request else AnonymousUser()
return get_objects_for_user(user, perms, queryset) | python | def _filter_queryset(self, perms, queryset):
"""Filter object objects by permissions of user in request."""
user = self.request.user if self.request else AnonymousUser()
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genialis/resolwe | resolwe/flow/serializers/collection.py | CollectionSerializer.get_data | def get_data(self, collection):
"""Return serialized list of data objects on collection that user has `view` permission on."""
data = self._filter_queryset('view_data', collection.data.all())
return self._serialize_data(data) | python | def get_data(self, collection):
"""Return serialized list of data objects on collection that user has `view` permission on."""
data = self._filter_queryset('view_data', collection.data.all())
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genialis/resolwe | resolwe/flow/serializers/collection.py | CollectionSerializer.get_fields | def get_fields(self):
"""Dynamically adapt fields based on the current request."""
fields = super(CollectionSerializer, self).get_fields()
if self.request.method == "GET":
fields['data'] = serializers.SerializerMethodField()
else:
fields['data'] = serializers.Pri... | python | def get_fields(self):
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genialis/resolwe | resolwe/flow/engine.py | load_engines | def load_engines(manager, class_name, base_module, engines, class_key='ENGINE', engine_type='engine'):
"""Load engines."""
loaded_engines = {}
for module_name_or_dict in engines:
if not isinstance(module_name_or_dict, dict):
module_name_or_dict = {
class_key: module_name... | python | def load_engines(manager, class_name, base_module, engines, class_key='ENGINE', engine_type='engine'):
"""Load engines."""
loaded_engines = {}
for module_name_or_dict in engines:
if not isinstance(module_name_or_dict, dict):
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | is_sysmeta_pyxb | def is_sysmeta_pyxb(sysmeta_pyxb):
"""Args: sysmeta_pyxb: Object that may or may not be a SystemMetadata PyXB object.
Returns:
bool:
- ``True`` if ``sysmeta_pyxb`` is a SystemMetadata PyXB object.
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"""Args: sysmeta_pyxb: Object that may or may not be a SystemMetadata PyXB object.
Returns:
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | normalize_in_place | def normalize_in_place(sysmeta_pyxb, reset_timestamps=False):
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Args:
sysmeta_pyxb:
SystemMetadata PyXB object to normalize.
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sysmeta_pyxb:
SystemMetadata PyXB object to normalize.
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | are_equivalent_pyxb | def are_equivalent_pyxb(a_pyxb, b_pyxb, ignore_timestamps=False):
"""Determine if SystemMetadata PyXB objects are semantically equivalent.
Normalize then compare SystemMetadata PyXB objects for equivalency.
Args:
a_pyxb, b_pyxb : SystemMetadata PyXB objects to compare
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... | python | def are_equivalent_pyxb(a_pyxb, b_pyxb, ignore_timestamps=False):
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | are_equivalent_xml | def are_equivalent_xml(a_xml, b_xml, ignore_timestamps=False):
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Normalize then compare SystemMetadata XML docs for equivalency.
Args:
a_xml, b_xml: bytes
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | clear_elements | def clear_elements(sysmeta_pyxb, clear_replica=True, clear_serial_version=True):
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{clear_replica} ignores any differences in replica information, as this information
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"""
if clear_r... | python | def clear_elements(sysmeta_pyxb, clear_replica=True, clear_serial_version=True):
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DataONEorg/d1_python | lib_common/src/d1_common/system_metadata.py | update_elements | def update_elements(dst_pyxb, src_pyxb, el_list):
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genialis/resolwe | resolwe/permissions/utils.py | get_full_perm | def get_full_perm(perm, obj):
"""Join action with the content type of ``obj``.
Permission is returned in the format of ``<action>_<object_type>``.
"""
ctype = ContentType.objects.get_for_model(obj)
# Camel case class names are converted into a space-separated
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"""Join action with the content type of ``obj``.
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genialis/resolwe | resolwe/permissions/utils.py | copy_permissions | def copy_permissions(src_obj, dest_obj):
"""Copy permissions form ``src_obj`` to ``dest_obj``."""
def _process_permission(codename, user_or_group, dest_obj, relabel):
"""Process single permission."""
if relabel:
codename = change_perm_ctype(codename, dest_obj)
if codename... | python | def copy_permissions(src_obj, dest_obj):
"""Copy permissions form ``src_obj`` to ``dest_obj``."""
def _process_permission(codename, user_or_group, dest_obj, relabel):
"""Process single permission."""
if relabel:
codename = change_perm_ctype(codename, dest_obj)
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genialis/resolwe | resolwe/permissions/utils.py | fetch_user | def fetch_user(query):
"""Get user by ``pk`` or ``username``. Raise error if it doesn't exist."""
user_filter = {'pk': query} if query.isdigit() else {'username': query}
user_model = get_user_model()
try:
return user_model.objects.get(**user_filter)
except user_model.DoesNotExist:
r... | python | def fetch_user(query):
"""Get user by ``pk`` or ``username``. Raise error if it doesn't exist."""
user_filter = {'pk': query} if query.isdigit() else {'username': query}
user_model = get_user_model()
try:
return user_model.objects.get(**user_filter)
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genialis/resolwe | resolwe/permissions/utils.py | fetch_group | def fetch_group(query):
"""Get group by ``pk`` or ``name``. Raise error if it doesn't exist."""
group_filter = {'pk': query} if query.isdigit() else {'name': query}
try:
return Group.objects.get(**group_filter)
except Group.DoesNotExist:
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"""Get group by ``pk`` or ``name``. Raise error if it doesn't exist."""
group_filter = {'pk': query} if query.isdigit() else {'name': query}
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genialis/resolwe | resolwe/permissions/utils.py | check_owner_permission | def check_owner_permission(payload, allow_user_owner):
"""Raise ``PermissionDenied``if ``owner`` found in ``data``."""
for entity_type in ['users', 'groups']:
for perm_type in ['add', 'remove']:
for perms in payload.get(entity_type, {}).get(perm_type, {}).values():
if 'owner'... | python | def check_owner_permission(payload, allow_user_owner):
"""Raise ``PermissionDenied``if ``owner`` found in ``data``."""
for entity_type in ['users', 'groups']:
for perm_type in ['add', 'remove']:
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genialis/resolwe | resolwe/permissions/utils.py | check_public_permissions | def check_public_permissions(payload):
"""Raise ``PermissionDenied`` if public permissions are too open."""
allowed_public_permissions = ['view', 'add', 'download']
for perm_type in ['add', 'remove']:
for perm in payload.get('public', {}).get(perm_type, []):
if perm not in allowed_public... | python | def check_public_permissions(payload):
"""Raise ``PermissionDenied`` if public permissions are too open."""
allowed_public_permissions = ['view', 'add', 'download']
for perm_type in ['add', 'remove']:
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genialis/resolwe | resolwe/permissions/utils.py | check_user_permissions | def check_user_permissions(payload, user_pk):
"""Raise ``PermissionDenied`` if ``payload`` includes ``user_pk``."""
for perm_type in ['add', 'remove']:
user_pks = payload.get('users', {}).get(perm_type, {}).keys()
if user_pk in user_pks:
raise exceptions.PermissionDenied("You cannot ... | python | def check_user_permissions(payload, user_pk):
"""Raise ``PermissionDenied`` if ``payload`` includes ``user_pk``."""
for perm_type in ['add', 'remove']:
user_pks = payload.get('users', {}).get(perm_type, {}).keys()
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genialis/resolwe | resolwe/permissions/utils.py | remove_permission | def remove_permission(payload, permission):
"""Remove all occurrences of ``permission`` from ``payload``."""
payload = copy.deepcopy(payload)
for entity_type in ['users', 'groups']:
for perm_type in ['add', 'remove']:
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"""Remove all occurrences of ``permission`` from ``payload``."""
payload = copy.deepcopy(payload)
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for perm_type in ['add', 'remove']:
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genialis/resolwe | resolwe/permissions/utils.py | update_permission | def update_permission(obj, data):
"""Update object permissions."""
full_permissions = get_all_perms(obj)
def apply_perm(perm_func, perms, entity):
"""Apply permissions using given ``perm_func``.
``perm_func`` is intended to be ``assign_perms`` or
``remove_perms`` shortcut function ... | python | def update_permission(obj, data):
"""Update object permissions."""
full_permissions = get_all_perms(obj)
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genialis/resolwe | resolwe/permissions/utils.py | assign_contributor_permissions | def assign_contributor_permissions(obj, contributor=None):
"""Assign all permissions to object's contributor."""
for permission in get_all_perms(obj):
assign_perm(permission, contributor if contributor else obj.contributor, obj) | python | def assign_contributor_permissions(obj, contributor=None):
"""Assign all permissions to object's contributor."""
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genialis/resolwe | resolwe/flow/executors/local/run.py | FlowExecutor.start | async def start(self):
"""Start process execution."""
# Workaround for pylint issue #1469
# (https://github.com/PyCQA/pylint/issues/1469).
self.proc = await subprocess.create_subprocess_exec( # pylint: disable=no-member
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"""Start process execution."""
# Workaround for pylint issue #1469
# (https://github.com/PyCQA/pylint/issues/1469).
self.proc = await subprocess.create_subprocess_exec( # pylint: disable=no-member
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genialis/resolwe | resolwe/flow/executors/local/run.py | FlowExecutor.run_script | async def run_script(self, script):
"""Execute the script and save results."""
script = os.linesep.join(['set -x', 'set +B', script, 'exit']) + os.linesep
self.proc.stdin.write(script.encode('utf-8'))
await self.proc.stdin.drain()
self.proc.stdin.close() | python | async def run_script(self, script):
"""Execute the script and save results."""
script = os.linesep.join(['set -x', 'set +B', script, 'exit']) + os.linesep
self.proc.stdin.write(script.encode('utf-8'))
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genialis/resolwe | resolwe/flow/executors/local/run.py | FlowExecutor.terminate | async def terminate(self):
"""Terminate a running script."""
self.proc.terminate()
await asyncio.wait_for(self.proc.wait(), self.kill_delay)
if self.proc.returncode is None:
self.proc.kill()
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await super().terminate() | python | async def terminate(self):
"""Terminate a running script."""
self.proc.terminate()
await asyncio.wait_for(self.proc.wait(), self.kill_delay)
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self.proc.kill()
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener._make_connection | async def _make_connection(self):
"""Construct a connection to Redis."""
return await aioredis.create_redis(
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self._redis_params.get('host', 'localhost'),
self._redis_params.get('port', 6379)
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"""Construct a connection to Redis."""
return await aioredis.create_redis(
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener._call_redis | async def _call_redis(self, meth, *args, **kwargs):
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while True:
try:
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self._redis = await self._make_connection()
return await meth(self._redis, *args, **kwargs)
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"""Perform a Redis call and handle connection dropping."""
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try:
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self._redis = await self._make_connection()
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.clear_queue | async def clear_queue(self):
"""Reset the executor queue channel to an empty state."""
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"""
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.terminate | def terminate(self):
"""Stop the standalone manager."""
logger.info(__(
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state.MANAGER_EXECUTOR_CHANNELS.queue
))
self._should_stop = True | python | def terminate(self):
"""Stop the standalone manager."""
logger.info(__(
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener._queue_response_channel | def _queue_response_channel(self, obj):
"""Generate the feedback channel name from the object's id.
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return '{}.{}'.format(state.MANAGER_EXECUTOR_CHANNELS.queue_response, obj[ExecutorProtocol.DATA_ID]) | python | def _queue_response_channel(self, obj):
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener._send_reply | async def _send_reply(self, obj, reply):
"""Send a reply with added standard fields back to executor.
:param obj: The original Channels message object to which we're
replying.
:param reply: The message contents dictionary. The data id is
added automatically (``reply`` is... | python | async def _send_reply(self, obj, reply):
"""Send a reply with added standard fields back to executor.
:param obj: The original Channels message object to which we're
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:param reply: The message contents dictionary. The data id is
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.hydrate_spawned_files | def hydrate_spawned_files(self, exported_files_mapper, filename, data_id):
"""Pop the given file's map from the exported files mapping.
:param exported_files_mapper: The dict of file mappings this
process produced.
:param filename: The filename to format and remove from the
... | python | def hydrate_spawned_files(self, exported_files_mapper, filename, data_id):
"""Pop the given file's map from the exported files mapping.
:param exported_files_mapper: The dict of file mappings this
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.handle_update | def handle_update(self, obj, internal_call=False):
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.. code-block:: none
{
'command': 'update',
'data_id': [id of th... | python | def handle_update(self, obj, internal_call=False):
"""Handle an incoming ``Data`` object update request.
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.. code-block:: none
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.handle_finish | def handle_finish(self, obj):
"""Handle an incoming ``Data`` finished processing request.
:param obj: The Channels message object. Command object format:
.. code-block:: none
{
'command': 'finish',
'data_id': [id of the :class:`~reso... | python | def handle_finish(self, obj):
"""Handle an incoming ``Data`` finished processing request.
:param obj: The Channels message object. Command object format:
.. code-block:: none
{
'command': 'finish',
'data_id': [id of the :class:`~reso... | [
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.handle_abort | def handle_abort(self, obj):
"""Handle an incoming ``Data`` abort processing request.
.. IMPORTANT::
This only makes manager's state consistent and doesn't
affect Data object in any way. Any changes to the Data
must be applied over ``handle_update`` method.
... | python | def handle_abort(self, obj):
"""Handle an incoming ``Data`` abort processing request.
.. IMPORTANT::
This only makes manager's state consistent and doesn't
affect Data object in any way. Any changes to the Data
must be applied over ``handle_update`` method.
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.handle_log | def handle_log(self, obj):
"""Handle an incoming log processing request.
:param obj: The Channels message object. Command object format:
.. code-block:: none
{
'command': 'log',
'message': [log message]
}
"""
... | python | def handle_log(self, obj):
"""Handle an incoming log processing request.
:param obj: The Channels message object. Command object format:
.. code-block:: none
{
'command': 'log',
'message': [log message]
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.push_stats | async def push_stats(self):
"""Push current stats to Redis."""
snapshot = self._make_stats()
try:
serialized = json.dumps(snapshot)
await self._call_redis(aioredis.Redis.set, state.MANAGER_LISTENER_STATS, serialized)
await self._call_redis(aioredis.Redis.expir... | python | async def push_stats(self):
"""Push current stats to Redis."""
snapshot = self._make_stats()
try:
serialized = json.dumps(snapshot)
await self._call_redis(aioredis.Redis.set, state.MANAGER_LISTENER_STATS, serialized)
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.check_critical_load | def check_critical_load(self):
"""Check for critical load and log an error if necessary."""
if self.load_avg.intervals['1m'].value > 1:
if self.last_load_level == 1 and time.time() - self.last_load_log < 30:
return
self.last_load_log = time.time()
self... | python | def check_critical_load(self):
"""Check for critical load and log an error if necessary."""
if self.load_avg.intervals['1m'].value > 1:
if self.last_load_level == 1 and time.time() - self.last_load_log < 30:
return
self.last_load_log = time.time()
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genialis/resolwe | resolwe/flow/managers/listener.py | ExecutorListener.run | async def run(self):
"""Run the main listener run loop.
Doesn't return until :meth:`terminate` is called.
"""
logger.info(__(
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state.MANAGER_EXECUTOR_CHANNELS.queue
))
while not self._should_stop:
... | python | async def run(self):
"""Run the main listener run loop.
Doesn't return until :meth:`terminate` is called.
"""
logger.info(__(
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state.MANAGER_EXECUTOR_CHANNELS.queue
))
while not self._should_stop:
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.dokanMain | def dokanMain(self, dokanOptions, dokanOperations):
"""Issue callback to start dokan drive.
:param DokanOptions: drive options
:type DokanOptions: DOKAN_OPTIONS
:param DokanOperations: pointers implemented file system calls
:type DokanOperations: DokanOperations
:return:... | python | def dokanMain(self, dokanOptions, dokanOperations):
"""Issue callback to start dokan drive.
:param DokanOptions: drive options
:type DokanOptions: DOKAN_OPTIONS
:param DokanOperations: pointers implemented file system calls
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.createFile | def createFile(
self,
fileName,
desiredAccess,
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creationDisposition,
flagsAndAttributes,
dokanFileInfo,
):
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:param fileName: name of file to create
:type fileName: ctypes.c_wchar_p
:param desiredAcce... | python | def createFile(
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desiredAccess,
shareMode,
creationDisposition,
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.readFile | def readFile(
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buffer,
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numberOfBytesRead,
offset,
dokanFileInfo,
):
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:param fileName: name of file to read
:type fileName: ctypes.c_wchar_p
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numberOfBytesToRead,
numberOfBytesRead,
offset,
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):
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.writeFile | def writeFile(
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fileName,
buffer,
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numberOfBytesWritten,
offset,
dokanFileInfo,
):
"""Read a file.
:param fileName: name of file to write
:type fileName: ctypes.c_wchar_p
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numberOfBytesWritten,
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.findFilesWithPattern | def findFilesWithPattern(
self, fileName, searchPattern, fillFindData, dokanFileInfo
):
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:param fileName: path to search
:type fileName: ctypes.c_wchar_p
:param searchPattern: pattern to search for
:type s... | python | def findFilesWithPattern(
self, fileName, searchPattern, fillFindData, dokanFileInfo
):
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.setFileTime | def setFileTime(
self, fileName, creationTime, lastAccessTime, lastWriteTime, dokanFileInfo
):
"""Set time values for a file.
:param fileName: name of file to set time values for
:type fileName: ctypes.c_wchar_p
:param creationTime: creation time of file
:type creati... | python | def setFileTime(
self, fileName, creationTime, lastAccessTime, lastWriteTime, dokanFileInfo
):
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.moveFile | def moveFile(self, existingFileName, newFileName, replaceExisiting, dokanFileInfo):
"""Move a file.
:param existingFileName: name of file to move
:type existingFileName: ctypes.c_wchar_p
:param newFileName: new name of file
:type newFileName: ctypes.c_wchar_p
:param repl... | python | def moveFile(self, existingFileName, newFileName, replaceExisiting, dokanFileInfo):
"""Move a file.
:param existingFileName: name of file to move
:type existingFileName: ctypes.c_wchar_p
:param newFileName: new name of file
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.lockFile | def lockFile(self, fileName, byteOffset, length, dokanFileInfo):
"""Lock a file.
:param fileName: name of file to lock
:type fileName: ctypes.c_wchar_p
:param byteOffset: location to start lock
:type byteOffset: ctypes.c_longlong
:param length: number of bytes to lock
... | python | def lockFile(self, fileName, byteOffset, length, dokanFileInfo):
"""Lock a file.
:param fileName: name of file to lock
:type fileName: ctypes.c_wchar_p
:param byteOffset: location to start lock
:type byteOffset: ctypes.c_longlong
:param length: number of bytes to lock
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.unlockFile | def unlockFile(self, fileName, byteOffset, length, dokanFileInfo):
"""Unlock a file.
:param fileName: name of file to unlock
:type fileName: ctypes.c_wchar_p
:param byteOffset: location to start unlock
:type byteOffset: ctypes.c_longlong
:param length: number of bytes to... | python | def unlockFile(self, fileName, byteOffset, length, dokanFileInfo):
"""Unlock a file.
:param fileName: name of file to unlock
:type fileName: ctypes.c_wchar_p
:param byteOffset: location to start unlock
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.getDiskFreeSpace | def getDiskFreeSpace(
self,
freeBytesAvailable,
totalNumberOfBytes,
totalNumberOfFreeBytes,
dokanFileInfo,
):
"""Get the amount of free space on this volume.
:param freeBytesAvailable: pointer for free bytes available
:type freeBytesAvailable: ctypes.... | python | def getDiskFreeSpace(
self,
freeBytesAvailable,
totalNumberOfBytes,
totalNumberOfFreeBytes,
dokanFileInfo,
):
"""Get the amount of free space on this volume.
:param freeBytesAvailable: pointer for free bytes available
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.getVolumeInformation | def getVolumeInformation(
self,
volumeNameBuffer,
volumeNameSize,
volumeSerialNumber,
maximumComponentLength,
fileSystemFlags,
fileSystemNameBuffer,
fileSystemNameSize,
dokanFileInfo,
):
"""Get information about the volume.
:pa... | python | def getVolumeInformation(
self,
volumeNameBuffer,
volumeNameSize,
volumeSerialNumber,
maximumComponentLength,
fileSystemFlags,
fileSystemNameBuffer,
fileSystemNameSize,
dokanFileInfo,
):
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.getFileSecurity | def getFileSecurity(
self,
fileName,
securityInformation,
securityDescriptor,
lengthSecurityDescriptorBuffer,
lengthNeeded,
dokanFileInfo,
):
"""Get security attributes of a file.
:param fileName: name of file to get security for
:type... | python | def getFileSecurity(
self,
fileName,
securityInformation,
securityDescriptor,
lengthSecurityDescriptorBuffer,
lengthNeeded,
dokanFileInfo,
):
"""Get security attributes of a file.
:param fileName: name of file to get security for
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/drivers/dokan/dokan.py | Dokan.setFileSecurity | def setFileSecurity(
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securityInformation,
securityDescriptor,
lengthSecurityDescriptorBuffer,
dokanFileInfo,
):
"""Set security attributes of a file.
:param fileName: name of file to set security for
:type fileName: ctypes.c_wc... | python | def setFileSecurity(
self,
fileName,
securityInformation,
securityDescriptor,
lengthSecurityDescriptorBuffer,
dokanFileInfo,
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DataONEorg/d1_python | utilities/src/d1_util/generate_data_package_from_stream.py | createSimpleResourceMap | def createSimpleResourceMap(ore_pid, sci_meta_pid, data_pids):
"""Create a simple resource map with one metadata document and n data objects."""
ore = ResourceMap()
ore.initialize(ore_pid)
ore.addMetadataDocument(sci_meta_pid)
ore.addDataDocuments(data_pids, sci_meta_pid)
return ore | python | def createSimpleResourceMap(ore_pid, sci_meta_pid, data_pids):
"""Create a simple resource map with one metadata document and n data objects."""
ore = ResourceMap()
ore.initialize(ore_pid)
ore.addMetadataDocument(sci_meta_pid)
ore.addDataDocuments(data_pids, sci_meta_pid)
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DataONEorg/d1_python | utilities/src/d1_util/generate_data_package_from_stream.py | pids2ore | def pids2ore(in_stream, fmt='xml', base_url='https://cn.dataone.org/cn'):
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first pid is the ore_pid second is the sci meta pid remainder are data pids
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first pid is the ore_pid second is the sci meta pid remainder are data pids
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genialis/resolwe | resolwe/flow/managers/workload_connectors/celery.py | Connector.submit | def submit(self, data, runtime_dir, argv):
"""Run process.
For details, see
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"""
queue = 'ordinary'
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queue = ... | python | def submit(self, data, runtime_dir, argv):
"""Run process.
For details, see
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"""
queue = 'ordinary'
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/object_tree.py | ObjectTree.refresh | def refresh(self):
"""Synchronize the local tree of Solr records for DataONE identifiers and
queries with the reference tree."""
if self._source_tree.cache_is_stale():
self._source_tree.refresh()
logging.info('Refreshing object tree')
self._init_cache()
... | python | def refresh(self):
"""Synchronize the local tree of Solr records for DataONE identifiers and
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if self._source_tree.cache_is_stale():
self._source_tree.refresh()
logging.info('Refreshing object tree')
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/object_tree.py | ObjectTree.get_object_record | def get_object_record(self, pid):
"""Get an object that has already been cached in the object tree.
Caching happens when the object tree is refreshed.
"""
try:
return self._cache['records'][pid]
except KeyError:
raise d1_onedrive.impl.onedrive_exceptions... | python | def get_object_record(self, pid):
"""Get an object that has already been cached in the object tree.
Caching happens when the object tree is refreshed.
"""
try:
return self._cache['records'][pid]
except KeyError:
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/object_tree.py | ObjectTree.get_object_record_with_sync | def get_object_record_with_sync(self, pid):
"""Get an object that may not currently be in the cache.
If the object is not in the cache, an attempt is made to retrieve the record
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"""Get an object that may not currently be in the cache.
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DataONEorg/d1_python | client_onedrive/src/d1_onedrive/impl/object_tree.py | ObjectTree._create_cache_item_for_pid | def _create_cache_item_for_pid(self, cache_folder, pid):
"""The source tree can contain identifiers that are no longer valid (or were
never valid).
Any items for which a Solr record cannot be retrieved are silently skipped.
"""
try:
record = self._solr_client.get_so... | python | def _create_cache_item_for_pid(self, cache_folder, pid):
"""The source tree can contain identifiers that are no longer valid (or were
never valid).
Any items for which a Solr record cannot be retrieved are silently skipped.
"""
try:
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | dependency_status | def dependency_status(data):
"""Return abstracted status of dependencies.
- ``STATUS_ERROR`` .. one dependency has error status or was deleted
- ``STATUS_DONE`` .. all dependencies have done status
- ``None`` .. other
"""
parents_statuses = set(
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... | python | def dependency_status(data):
"""Return abstracted status of dependencies.
- ``STATUS_ERROR`` .. one dependency has error status or was deleted
- ``STATUS_DONE`` .. all dependencies have done status
- ``None`` .. other
"""
parents_statuses = set(
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.discover_engines | def discover_engines(self, executor=None):
"""Discover configured engines.
:param executor: Optional executor module override
"""
if executor is None:
executor = getattr(settings, 'FLOW_EXECUTOR', {}).get('NAME', 'resolwe.flow.executors.local')
self.executor = self.l... | python | def discover_engines(self, executor=None):
"""Discover configured engines.
:param executor: Optional executor module override
"""
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executor = getattr(settings, 'FLOW_EXECUTOR', {}).get('NAME', 'resolwe.flow.executors.local')
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.reset | def reset(self, keep_state=False):
"""Reset the shared state and drain Django Channels.
:param keep_state: If ``True``, do not reset the shared manager
state (useful in tests, where the settings overrides need to
be kept). Defaults to ``False``.
"""
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"""Reset the shared state and drain Django Channels.
:param keep_state: If ``True``, do not reset the shared manager
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._marshal_settings | def _marshal_settings(self):
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:return: The serialized settings.
:rtype: dict
"""
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"""Marshal Django settings into a serializable object.
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._include_environment_variables | def _include_environment_variables(self, program, executor_vars):
"""Define environment variables."""
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}
set_env = self.settings_actual.get('FLOW_EXECUTOR', {}).get('SET_ENV', {})
... | python | def _include_environment_variables(self, program, executor_vars):
"""Define environment variables."""
env_vars = {
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.run | def run(self, data, runtime_dir, argv):
"""Select a concrete connector and run the process through it.
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:param runtime_dir: The directory the executor is run from.
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._get_per_data_dir | def _get_per_data_dir(self, dir_base, subpath):
"""Extend the given base directory with a per-data component.
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._prepare_data_dir | def _prepare_data_dir(self, data):
"""Prepare destination directory where the data will live.
:param data: The :class:`~resolwe.flow.models.Data` object for
which to prepare the private execution directory.
:return: The prepared data directory path.
:rtype: str
"""
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._prepare_executor | def _prepare_executor(self, data, executor):
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:param data: The :class:`~resolwe.flow.models.Data` object being
prepared for.
:param executor: The fully qualified name of the executor that
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._prepare_script | def _prepare_script(self, dest_dir, program):
"""Copy the script into the destination directory.
:param dest_dir: The target directory where the script will be
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:param program: The script text to be saved.
:return: The name of the script file.
:rtype: str
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.handle_control_event | async def handle_control_event(self, message):
"""Handle an event from the Channels layer.
Channels layer callback, do not call directly.
"""
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logger.debug(__("Manager worker got channel command '{}'.", cmd))
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._ensure_counter | def _ensure_counter(self):
"""Ensure the sync counter is a valid non-dummy object."""
if not isinstance(self.sync_counter, self._SynchronizationManager):
self.sync_counter = self._SynchronizationManager() | python | def _ensure_counter(self):
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.execution_barrier | async def execution_barrier(self):
"""Wait for executors to finish.
At least one must finish after this point to avoid a deadlock.
"""
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.communicate | async def communicate(self, data_id=None, run_sync=False, save_settings=True):
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._data_execute | def _data_execute(self, data, program, executor):
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager._data_scan | def _data_scan(self, data_id=None, executor='resolwe.flow.executors.local', **kwargs):
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.get_expression_engine | def get_expression_engine(self, name):
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genialis/resolwe | resolwe/flow/managers/dispatcher.py | Manager.load_executor | def load_executor(self, executor_name):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.get_queryset | def get_queryset(self): # pylint: disable=method-hidden
"""Return queryset."""
if self.request and self.request.query_params.get('hydrate_data', False):
return self.queryset.prefetch_related('data__entity_set')
return self.queryset | python | def get_queryset(self): # pylint: disable=method-hidden
"""Return queryset."""
if self.request and self.request.query_params.get('hydrate_data', False):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet._get_entities | def _get_entities(self, user, ids):
"""Return entities queryset based on provided entity ids."""
queryset = get_objects_for_user(user, 'view_entity', Entity.objects.filter(id__in=ids))
actual_ids = queryset.values_list('id', flat=True)
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queryset = get_objects_for_user(user, 'view_entity', Entity.objects.filter(id__in=ids))
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.set_content_permissions | def set_content_permissions(self, user, obj, payload):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.destroy | def destroy(self, request, *args, **kwargs):
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obj = self.get_object()
user = request.user
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.add_to_collection | def add_to_collection(self, request, pk=None):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.add_data | def add_data(self, request, pk=None):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.move_to_collection | def move_to_collection(self, request, *args, **kwargs):
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genialis/resolwe | resolwe/flow/views/entity.py | EntityViewSet.update | def update(self, request, *args, **kwargs):
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genialis/resolwe | resolwe/flow/executors/docker/run.py | FlowExecutor.start | async def start(self):
"""Start process execution."""
# arguments passed to the Docker command
command_args = {
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# Get limit defaults.
... | python | async def start(self):
"""Start process execution."""
# arguments passed to the Docker command
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genialis/resolwe | resolwe/flow/executors/docker/run.py | FlowExecutor.run_script | async def run_script(self, script):
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genialis/resolwe | resolwe/flow/executors/docker/run.py | FlowExecutor.end | async def end(self):
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genialis/resolwe | resolwe/flow/executors/docker/run.py | FlowExecutor.terminate | async def terminate(self):
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] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/executors/docker/run.py#L330-L340 |
genialis/resolwe | resolwe/flow/executors/run.py | iterjson | def iterjson(text):
"""Decode JSON stream."""
decoder = json.JSONDecoder()
while text:
obj, ndx = decoder.raw_decode(text)
if not isinstance(obj, dict):
raise ValueError()
text = text[ndx:].lstrip('\r\n')
yield obj | python | def iterjson(text):
"""Decode JSON stream."""
decoder = json.JSONDecoder()
while text:
obj, ndx = decoder.raw_decode(text)
if not isinstance(obj, dict):
raise ValueError()
text = text[ndx:].lstrip('\r\n')
yield obj | [
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genialis/resolwe | resolwe/flow/executors/run.py | BaseFlowExecutor._send_manager_command | async def _send_manager_command(self, *args, **kwargs):
"""Send an update to manager and terminate the process if it fails."""
resp = await send_manager_command(*args, **kwargs)
if resp is False:
await self.terminate() | python | async def _send_manager_command(self, *args, **kwargs):
"""Send an update to manager and terminate the process if it fails."""
resp = await send_manager_command(*args, **kwargs)
if resp is False:
await self.terminate() | [
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genialis/resolwe | resolwe/flow/executors/run.py | BaseFlowExecutor.update_data_status | async def update_data_status(self, **kwargs):
"""Update (PATCH) Data object.
:param kwargs: The dictionary of
:class:`~resolwe.flow.models.Data` attributes to be changed.
"""
await self._send_manager_command(ExecutorProtocol.UPDATE, extra_fields={
ExecutorProtoco... | python | async def update_data_status(self, **kwargs):
"""Update (PATCH) Data object.
:param kwargs: The dictionary of
:class:`~resolwe.flow.models.Data` attributes to be changed.
"""
await self._send_manager_command(ExecutorProtocol.UPDATE, extra_fields={
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genialis/resolwe | resolwe/flow/executors/run.py | BaseFlowExecutor.run | async def run(self, data_id, script):
"""Execute the script and save results."""
logger.debug("Executor for Data with id {} has started.".format(data_id))
try:
finish_fields = await self._run(data_id, script)
except SystemExit as ex:
raise ex
except Except... | python | async def run(self, data_id, script):
"""Execute the script and save results."""
logger.debug("Executor for Data with id {} has started.".format(data_id))
try:
finish_fields = await self._run(data_id, script)
except SystemExit as ex:
raise ex
except Except... | [
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genialis/resolwe | resolwe/flow/executors/run.py | BaseFlowExecutor._create_file | def _create_file(self, filename):
"""Ensure a new file is created and opened for writing."""
file_descriptor = os.open(filename, os.O_WRONLY | os.O_CREAT | os.O_EXCL)
return os.fdopen(file_descriptor, 'w') | python | def _create_file(self, filename):
"""Ensure a new file is created and opened for writing."""
file_descriptor = os.open(filename, os.O_WRONLY | os.O_CREAT | os.O_EXCL)
return os.fdopen(file_descriptor, 'w') | [
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