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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."""
self.data_id = data_id
# Fetch data instance to get any executor requirements.
self.process = PROCESS
requirements = self.process['requirements']
self.requirements = requirements.get('execu... | python | async def _run(self, data_id, script):
"""Execute the script and save results."""
self.data_id = data_id
# Fetch data instance to get any executor requirements.
self.process = PROCESS
requirements = self.process['requirements']
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DataONEorg/d1_python | gmn/src/d1_gmn/app/local_replica.py | get_total_size_of_queued_replicas | def get_total_size_of_queued_replicas():
"""Return the total number of bytes of requested, unprocessed replicas."""
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) | python | def get_total_size_of_queued_replicas():
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DataONEorg/d1_python | gmn/src/d1_gmn/app/local_replica.py | add_to_replication_queue | def add_to_replication_queue(source_node_urn, sysmeta_pyxb):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/util/standard_args.py | add_arguments | def add_arguments(parser, doc_str, add_base_url=True):
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parser.description = doc_str
parser.formatter_class = argparse.RawDescriptionHelpFormatter
parser.add_argument("--debug", action="store_true", help="Debug level logging")
... | python | def add_arguments(parser, doc_str, add_base_url=True):
"""Add standard arguments for DataONE utilities to a command line parser."""
parser.description = doc_str
parser.formatter_class = argparse.RawDescriptionHelpFormatter
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DataONEorg/d1_python | lib_common/src/d1_common/iter/path.py | path_generator | def path_generator(
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ignore_invalid=False,
default_excludes=True,
return_dir_paths=False,
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DataONEorg/d1_python | gmn/src/d1_gmn/app/resource_map.py | get_resource_map_members | def get_resource_map_members(pid):
"""``pid`` is the PID of a Resource Map or the PID of a member of a Resource Map."""
if d1_gmn.app.did.is_resource_map_db(pid):
return get_resource_map_members_by_map(pid)
elif d1_gmn.app.did.is_resource_map_member(pid):
return get_resource_map_members_by_m... | python | def get_resource_map_members(pid):
"""``pid`` is the PID of a Resource Map or the PID of a member of a Resource Map."""
if d1_gmn.app.did.is_resource_map_db(pid):
return get_resource_map_members_by_map(pid)
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DataONEorg/d1_python | client_cli/src/d1_cli/impl/session.py | Session.set_with_conversion | def set_with_conversion(self, variable, value_string):
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Lets user use values such as True, False and integers. All variables can be set
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | log_setup | def log_setup(is_debug=False, is_multiprocess=False):
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | get_content_type | def get_content_type(content_type):
"""Extract the MIME type value from a content type string.
Removes any subtype and parameter values that may be present in the string.
Args:
content_type: str
String with content type and optional subtype and parameter fields.
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | nested_update | def nested_update(d, u):
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updating such a structure, it may be convenient to present the updated data as a
corresponding recursive structure. This function will then apply the update.
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | save_json | def save_json(py_obj, json_path):
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Args:
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Any object that can be represented in JSON. Some types, such as datetimes are
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | serialize_to_normalized_pretty_json | def serialize_to_normalized_pretty_json(py_obj):
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | serialize_to_normalized_compact_json | def serialize_to_normalized_compact_json(py_obj):
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | format_sec_to_dhm | def format_sec_to_dhm(sec):
"""Format seconds to days, hours, minutes.
Args:
sec: float or int
Number of seconds in a period of time
Returns:
Period of time represented as a string on the form ``0d:00h:00m``.
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Number of seconds in a period of time
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DataONEorg/d1_python | lib_common/src/d1_common/util.py | EventCounter.log_and_count | def log_and_count(self, event_str, msg_str=None, inc_int=None):
"""Count an event and write a message to a logger.
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event_str: str
The name of an event to count. Used as a key in the event dict. The same
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DataONEorg/d1_python | gmn/src/d1_gmn/app/delete.py | delete_all_from_db | def delete_all_from_db():
"""Clear the database.
Used for testing and debugging.
"""
# The models.CASCADE property is set on all ForeignKey fields, so tables can
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for model in django.apps.apps.get_models():
model.objects.all().dele... | python | def delete_all_from_db():
"""Clear the database.
Used for testing and debugging.
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genialis/resolwe | resolwe/elastic/pagination.py | get_query_param | def get_query_param(request, key):
"""Get query parameter uniformly for GET and POST requests."""
value = request.query_params.get(key) or request.data.get(key)
if value is None:
raise KeyError()
return value | python | def get_query_param(request, key):
"""Get query parameter uniformly for GET and POST requests."""
value = request.query_params.get(key) or request.data.get(key)
if value is None:
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genialis/resolwe | resolwe/elastic/pagination.py | LimitOffsetPostPagination.get_limit | def get_limit(self, request):
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genialis/resolwe | resolwe/elastic/pagination.py | LimitOffsetPostPagination.get_offset | def get_offset(self, request):
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DataONEorg/d1_python | dev_tools/src/d1_dev/src-cleanup.py | futurize_module | def futurize_module(module_path, show_diff, write_update):
"""2to3 uses AST, not Baron."""
logging.info('Futurizing module... path="{}"'.format(module_path))
ast_tree = back_to_the_futurize(module_path)
return d1_dev.util.update_module_file_ast(
ast_tree, module_path, show_diff, write_update
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"""2to3 uses AST, not Baron."""
logging.info('Futurizing module... path="{}"'.format(module_path))
ast_tree = back_to_the_futurize(module_path)
return d1_dev.util.update_module_file_ast(
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DataONEorg/d1_python | dev_tools/src/d1_dev/src-cleanup.py | _remove_single_line_import_comments | def _remove_single_line_import_comments(r):
"""We previously used more groups for the import statements and named each group."""
logging.info('Removing single line import comments')
import_r, remaining_r = split_by_last_import(r)
new_import_r = redbaron.NodeList()
for i, v in enumerate(import_r):
... | python | def _remove_single_line_import_comments(r):
"""We previously used more groups for the import statements and named each group."""
logging.info('Removing single line import comments')
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DataONEorg/d1_python | dev_tools/src/d1_dev/src-cleanup.py | _update_init_all | def _update_init_all(module_path, r):
"""Add or update __all__ in __init__.py file."""
module_dir_path = os.path.split(module_path)[0]
module_list = []
for item_name in os.listdir(module_dir_path):
item_path = os.path.join(module_dir_path, item_name)
if os.path.isfile(item_path) and item... | python | def _update_init_all(module_path, r):
"""Add or update __all__ in __init__.py file."""
module_dir_path = os.path.split(module_path)[0]
module_list = []
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return new_r | python | def _remove_init_all(r):
"""Remove any __all__ in __init__.py file."""
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if n.type == 'assignment' and n.target.value == '__all__':
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/gmn.py | get_object_list_json | def get_object_list_json(request):
"""gmn.listObjects(session[, fromDate][, toDate][, formatId]
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GMN specific API for fast retrieval of object sysmeta elements.
"""
# TODO: Add to documentation
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genialis/resolwe | resolwe/flow/executors/logger.py | configure_logging | def configure_logging(emit_list):
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module_base = 'executors'
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"""Configure logging to send log records to the master."""
if 'sphinx' in sys.modules:
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else:
module_base = 'executors'
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data['data_location_id'] = DATA_LOCATION['id']
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genialis/resolwe | resolwe/flow/executors/logger.py | RedisHandler.emit | def emit(self, record):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/sync.py | Command.is_object_synced_to_cn | async def is_object_synced_to_cn(self, client, pid):
"""Check if object with {pid} has successfully synced to the CN.
CNRead.describe() is used as it's a light-weight HTTP HEAD request.
This assumes that the call is being made over a connection that has
been authenticated and has read ... | python | async def is_object_synced_to_cn(self, client, pid):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/sync.py | Command.send_synchronization_request | async def send_synchronization_request(self, client, pid):
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# Skip CN call for debugging
# status = 200
status = await client.synchronize(pid)
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"""Issue a notification and request for sync for object with {pid} to the CN."""
# Skip CN call for debugging
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genialis/resolwe | resolwe/flow/models/secret.py | SecretManager.create_secret | def create_secret(self, value, contributor, metadata=None, expires=None):
"""Create a new secret, returning its handle.
:param value: Secret value to store
:param contributor: User owning the secret
:param metadata: Optional metadata dictionary (must be JSON serializable)
:param... | python | def create_secret(self, value, contributor, metadata=None, expires=None):
"""Create a new secret, returning its handle.
:param value: Secret value to store
:param contributor: User owning the secret
:param metadata: Optional metadata dictionary (must be JSON serializable)
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genialis/resolwe | resolwe/flow/models/secret.py | SecretManager.get_secret | def get_secret(self, handle, contributor):
"""Retrieve an existing secret's value.
:param handle: Secret handle
:param contributor: User instance to perform contributor validation,
which means that only secrets for the given contributor will be
looked up.
"""
... | python | def get_secret(self, handle, contributor):
"""Retrieve an existing secret's value.
:param handle: Secret handle
:param contributor: User instance to perform contributor validation,
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genialis/resolwe | resolwe/flow/models/utils.py | validation_schema | def validation_schema(name):
"""Return json schema for json validation."""
schemas = {
'processor': 'processSchema.json',
'descriptor': 'descriptorSchema.json',
'field': 'fieldSchema.json',
'type': 'typeSchema.json',
}
if name not in schemas:
raise ValueError()
... | python | def validation_schema(name):
"""Return json schema for json validation."""
schemas = {
'processor': 'processSchema.json',
'descriptor': 'descriptorSchema.json',
'field': 'fieldSchema.json',
'type': 'typeSchema.json',
}
if name not in schemas:
raise ValueError()
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genialis/resolwe | resolwe/flow/models/utils.py | validate_schema | def validate_schema(instance, schema, test_required=True, data_location=None,
skip_missing_data=False):
"""Check if DictField values are consistent with our data types.
Perform basic JSON schema validation and our custom validations:
* check that required fields are given (if `test_r... | python | def validate_schema(instance, schema, test_required=True, data_location=None,
skip_missing_data=False):
"""Check if DictField values are consistent with our data types.
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genialis/resolwe | resolwe/flow/models/utils.py | _hydrate_values | def _hydrate_values(output, output_schema, data):
"""Hydrate basic:file and basic:json values.
Find fields with basic:file type and assign a full path to the file.
Find fields with basic:json type and assign a JSON object from storage.
"""
def hydrate_path(file_name):
"""Hydrate file paths... | python | def _hydrate_values(output, output_schema, data):
"""Hydrate basic:file and basic:json values.
Find fields with basic:file type and assign a full path to the file.
Find fields with basic:json type and assign a JSON object from storage.
"""
def hydrate_path(file_name):
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genialis/resolwe | resolwe/flow/models/utils.py | hydrate_input_references | def hydrate_input_references(input_, input_schema, hydrate_values=True):
"""Hydrate ``input_`` with linked data.
Find fields with complex data:<...> types in ``input_``.
Assign an output of corresponding data object to those fields.
"""
from .data import Data # prevent circular import
for fi... | python | def hydrate_input_references(input_, input_schema, hydrate_values=True):
"""Hydrate ``input_`` with linked data.
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genialis/resolwe | resolwe/flow/models/utils.py | hydrate_input_uploads | def hydrate_input_uploads(input_, input_schema, hydrate_values=True):
"""Hydrate input basic:upload types with upload location.
Find basic:upload fields in input.
Add the upload location for relative paths.
"""
from resolwe.flow.managers import manager
files = []
for field_schema, fields ... | python | def hydrate_input_uploads(input_, input_schema, hydrate_values=True):
"""Hydrate input basic:upload types with upload location.
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genialis/resolwe | resolwe/flow/models/utils.py | hydrate_size | def hydrate_size(data, force=False):
"""Add file and dir sizes.
Add sizes to ``basic:file:``, ``list:basic:file``, ``basic:dir:``
and ``list:basic:dir:`` fields.
``force`` parameter is used to recompute file sizes also on objects
that already have these values, e.g. in migrations.
"""
from... | python | def hydrate_size(data, force=False):
"""Add file and dir sizes.
Add sizes to ``basic:file:``, ``list:basic:file``, ``basic:dir:``
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``force`` parameter is used to recompute file sizes also on objects
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genialis/resolwe | resolwe/flow/models/utils.py | render_descriptor | def render_descriptor(data):
"""Render data descriptor.
The rendering is based on descriptor schema and input context.
:param data: data instance
:type data: :class:`resolwe.flow.models.Data` or :class:`dict`
"""
if not data.descriptor_schema:
return
# Set default values
for ... | python | def render_descriptor(data):
"""Render data descriptor.
The rendering is based on descriptor schema and input context.
:param data: data instance
:type data: :class:`resolwe.flow.models.Data` or :class:`dict`
"""
if not data.descriptor_schema:
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# Set default values
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genialis/resolwe | resolwe/flow/models/utils.py | render_template | def render_template(process, template_string, context):
"""Render template using the specified expression engine."""
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expression_engine = process.requirements.get... | python | def render_template(process, template_string, context):
"""Render template using the specified expression engine."""
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genialis/resolwe | resolwe/flow/models/utils.py | json_path_components | def json_path_components(path):
"""Convert JSON path to individual path components.
:param path: JSON path, which can be either an iterable of path
components or a dot-separated string
:return: A list of path components
"""
if isinstance(path, str):
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retur... | python | def json_path_components(path):
"""Convert JSON path to individual path components.
:param path: JSON path, which can be either an iterable of path
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:return: A list of path components
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genialis/resolwe | resolwe/flow/models/utils.py | validate_process_subtype | def validate_process_subtype(supertype_name, supertype, subtype_name, subtype):
"""Perform process subtype validation.
:param supertype_name: Supertype name
:param supertype: Supertype schema
:param subtype_name: Subtype name
:param subtype: Subtype schema
:return: A list of validation error st... | python | def validate_process_subtype(supertype_name, supertype, subtype_name, subtype):
"""Perform process subtype validation.
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genialis/resolwe | resolwe/flow/models/utils.py | validate_process_types | def validate_process_types(queryset=None):
"""Perform process type validation.
:param queryset: Optional process queryset to validate
:return: A list of validation error strings
"""
if not queryset:
from .process import Process
queryset = Process.objects.all()
processes = {}
... | python | def validate_process_types(queryset=None):
"""Perform process type validation.
:param queryset: Optional process queryset to validate
:return: A list of validation error strings
"""
if not queryset:
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queryset = Process.objects.all()
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genialis/resolwe | resolwe/flow/models/utils.py | fill_with_defaults | def fill_with_defaults(process_input, input_schema):
"""Fill empty optional fields in input with default values."""
for field_schema, fields, path in iterate_schema(process_input, input_schema):
if 'default' in field_schema and field_schema['name'] not in fields:
dict_dot(process_input, path... | python | def fill_with_defaults(process_input, input_schema):
"""Fill empty optional fields in input with default values."""
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genialis/resolwe | resolwe/flow/serializers/contributor.py | ContributorSerializer.to_internal_value | def to_internal_value(self, data):
"""Format the internal value."""
# When setting the contributor, it may be passed as an integer.
if isinstance(data, dict) and isinstance(data.get('id', None), int):
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genialis/resolwe | resolwe/flow/elastic_indexes/collection.py | CollectionIndexMixin.extract_descriptor | def extract_descriptor(self, obj):
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genialis/resolwe | resolwe/flow/serializers/data.py | DataSerializer._serialize_items | def _serialize_items(self, serializer, kind, items):
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if self.request and self.request.query_params.get('hydrate_{}'.format(kind), False):
serializer = serializer(items, many=True, read_only=True)
... | python | def _serialize_items(self, serializer, kind, items):
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genialis/resolwe | resolwe/flow/serializers/data.py | DataSerializer.get_entity_names | def get_entity_names(self, data):
"""Return serialized list of entity names on data that user has `view` permission on."""
entities = self._filter_queryset('view_entity', data.entity_set.all())
return list(entities.values_list('name', flat=True)) | python | def get_entity_names(self, data):
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genialis/resolwe | resolwe/flow/serializers/data.py | DataSerializer.get_collections | def get_collections(self, data):
"""Return serialized list of collection objects on data that user has `view` permission on."""
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genialis/resolwe | resolwe/flow/serializers/data.py | DataSerializer.get_entities | def get_entities(self, data):
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genialis/resolwe | resolwe/flow/serializers/data.py | DataSerializer.get_fields | def get_fields(self):
"""Dynamically adapt fields based on the current request."""
fields = super(DataSerializer, self).get_fields()
# Hide collections/entities fields on list views as fetching them may be expensive.
if self.parent is not None:
del fields['collections']
... | python | def get_fields(self):
"""Dynamically adapt fields based on the current request."""
fields = super(DataSerializer, self).get_fields()
# Hide collections/entities fields on list views as fetching them may be expensive.
if self.parent is not None:
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genialis/resolwe | resolwe/flow/management/commands/list_docker_images.py | Command.handle | def handle(self, *args, **options):
"""Handle command list_docker_images."""
verbosity = int(options.get('verbosity'))
# Check that the specified output format is valid
if options['format'] != 'plain' and options['format'] != 'yaml':
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genialis/resolwe | resolwe/flow/views/data.py | DataViewSet.create | def create(self, request, *args, **kwargs):
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collections = request.data.get('collections', [])
# check that user has permissions on all collections that Data
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for collection_id in collections:
try:
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genialis/resolwe | resolwe/flow/views/data.py | DataViewSet.get_or_create | def get_or_create(self, request, *args, **kwargs):
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genialis/resolwe | resolwe/flow/views/data.py | DataViewSet.perform_get_or_create | def perform_get_or_create(self, request, *args, **kwargs):
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serializer = self.get_serializer(data=request.data)
serializer.is_valid(raise_exception=True)
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genialis/resolwe | resolwe/flow/views/data.py | DataViewSet.perform_create | def perform_create(self, serializer):
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process = serializer.validated_data.get('process')
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DataONEorg/d1_python | gmn/src/d1_gmn/app/gmn.py | Startup.ready | def ready(self):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/gmn.py | Startup._assert_dirs_exist | def _assert_dirs_exist(self, setting_name):
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Does not check if the file exists.
"""
v = self._get_setting(setting_name)
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self.raise_config_... | python | def _assert_dirs_exist(self, setting_name):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/gmn.py | Startup._warn_unsafe_for_prod | def _warn_unsafe_for_prod(self):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/gmn.py | Startup._get_setting | def _get_setting(self, setting_dotted_name, default=None):
"""Return the value of a potentially nested dict setting.
E.g., 'DATABASES.default.NAME
"""
name_list = setting_dotted_name.split('.')
setting_obj = getattr(django.conf.settings, name_list[0], default)
# if len(... | python | def _get_setting(self, setting_dotted_name, default=None):
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex._refresh_connection | def _refresh_connection(self):
"""Refresh connection to Elasticsearch when worker is started.
File descriptors (sockets) can be shared between multiple
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same time, this can cause timeouts in some of the pushes. So
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.generate_id | def generate_id(self, obj):
"""Generate unique document id for ElasticSearch."""
object_type = type(obj).__name__.lower()
return '{}_{}'.format(object_type, self.get_object_id(obj)) | python | def generate_id(self, obj):
"""Generate unique document id for ElasticSearch."""
object_type = type(obj).__name__.lower()
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.process_object | def process_object(self, obj):
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.create_mapping | def create_mapping(self):
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try:
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"""Create the mappings in elasticsearch."""
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.build | def build(self, obj=None, queryset=None, push=True):
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex._build | def _build(self, obj=None, queryset=None, push=True):
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.push | def push(self):
"""Push built documents to ElasticSearch."""
self._refresh_connection()
# Check if we need to update mappings as this needs to be done
# before we push anything to the Elasticsearch server.
# This must be done even if the queue is empty, as otherwise ES
#... | python | def push(self):
"""Push built documents to ElasticSearch."""
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.destroy | def destroy(self):
"""Destroy an index."""
self._refresh_connection()
self.push_queue = []
index_name = self.document_class()._get_index() # pylint: disable=protected-access
connections.get_connection().indices.delete(index_name, ignore=404)
self._mapping_created = Fal... | python | def destroy(self):
"""Destroy an index."""
self._refresh_connection()
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.get_permissions | def get_permissions(self, obj):
"""Return users and groups with ``view`` permission on the current object.
Return a dict with two keys - ``users`` and ``groups`` - which
contain list of ids of users/groups with ``view`` permission.
"""
# TODO: Optimize this for bulk running
... | python | def get_permissions(self, obj):
"""Return users and groups with ``view`` permission on the current object.
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genialis/resolwe | resolwe/elastic/indices.py | BaseIndex.remove_object | def remove_object(self, obj):
"""Remove current object from the ElasticSearch."""
obj_id = self.generate_id(obj)
es_obj = self.document_class.get(obj_id, ignore=[404])
# Object may not exist in this index.
if es_obj:
es_obj.delete(refresh=True) | python | def remove_object(self, obj):
"""Remove current object from the ElasticSearch."""
obj_id = self.generate_id(obj)
es_obj = self.document_class.get(obj_id, ignore=[404])
# Object may not exist in this index.
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DataONEorg/d1_python | lib_common/src/d1_common/types/scripts/pyxbgen_all.py | GenerateBindings.generate_pyxb_binding | def generate_pyxb_binding(self, args):
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args:
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pyxbgen_args = []
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pyxbgen_args.append('--binding-root=\'{}\''.format(self.binding_dir))
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args:
"""
cmd = 'pyxbgen {}'.format(' '.join(args))
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os.system(cmd) | python | def run_pyxbgen(self, args):
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DataONEorg/d1_python | lib_common/src/d1_common/types/scripts/pyxbgen_all.py | GenerateVersionFile.generate_version_file | def generate_version_file(self, schema_filename, binding_filename):
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about the schema."""
version_filename = binding_filename + '_version.txt'
version_path = os.path.join(self.binding_dir, version_filename)
... | python | def generate_version_file(self, schema_filename, binding_filename):
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DataONEorg/d1_python | lib_common/src/d1_common/types/scripts/pyxbgen_all.py | GenerateVersionFile.write_version_file | def write_version_file(self, version_file_path, tstamp, svnpath, svnrev, version):
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DataONEorg/d1_python | lib_client/src/d1_client/baseclient_2_0.py | DataONEBaseClient_2_0.updateSystemMetadataResponse | def updateSystemMetadataResponse(self, pid, sysmeta_pyxb, vendorSpecific=None):
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http://jenkins-1.dataone.org/documentation/unstable/API-Documentation-
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genialis/resolwe | resolwe/flow/migrations/0028_add_data_location.py | set_data_location | def set_data_location(apps, schema_editor):
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DataLocation = apps.get_model('flow', 'DataLocation')
for data in Data.objects.all():
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... | python | def set_data_location(apps, schema_editor):
"""Create DataLocation for each Data."""
Data = apps.get_model('flow', 'Data')
DataLocation = apps.get_model('flow', 'DataLocation')
for data in Data.objects.all():
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DataONEorg/d1_python | lib_client/src/d1_client/iter/objectlist.py | ObjectListIterator._loadMore | def _loadMore(self, start=0, trys=0, validation=True):
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self._pageoffs = 0
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DataONEorg/d1_python | lib_common/src/d1_common/ext/mimeparser.py | parse_mime_type | def parse_mime_type(mime_type):
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genialis/resolwe | resolwe/flow/models/data.py | DataQuerySet._delete_chunked | def _delete_chunked(queryset, chunk_size=500):
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genialis/resolwe | resolwe/flow/models/data.py | DataQuerySet.duplicate | def duplicate(self, contributor=None):
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:param contributor: Duplication user
"""
bundle = [
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bundle = rewire_inputs(... | python | def duplicate(self, contributor=None):
"""Duplicate (make a copy) ``Data`` objects.
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genialis/resolwe | resolwe/flow/models/data.py | Data.save_storage | def save_storage(self, instance, schema):
"""Save basic:json values to a Storage collection."""
for field_schema, fields in iterate_fields(instance, schema):
name = field_schema['name']
value = fields[name]
if field_schema.get('type', '').startswith('basic:json:'):
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genialis/resolwe | resolwe/flow/models/data.py | Data.resolve_secrets | def resolve_secrets(self):
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genialis/resolwe | resolwe/flow/models/data.py | Data.save_dependencies | def save_dependencies(self, instance, schema):
"""Save data: and list:data: references as parents."""
def add_dependency(value):
"""Add parent Data dependency."""
try:
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parent=Data.objects.get(pk=value),
... | python | def save_dependencies(self, instance, schema):
"""Save data: and list:data: references as parents."""
def add_dependency(value):
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try:
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genialis/resolwe | resolwe/flow/models/data.py | Data.create_entity | def create_entity(self):
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* Only add `Data object` to `Entity` if process has defined
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genialis/resolwe | resolwe/flow/models/data.py | Data.save | def save(self, render_name=False, *args, **kwargs): # pylint: disable=keyword-arg-before-vararg
"""Save the data model."""
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fill_with_defaults(self.input, self.proc... | python | def save(self, render_name=False, *args, **kwargs): # pylint: disable=keyword-arg-before-vararg
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genialis/resolwe | resolwe/flow/models/data.py | Data.delete | def delete(self, *args, **kwargs):
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storage_ids = list(self.storages.values_list('pk', flat=True)) # pylint: disable=no-member
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genialis/resolwe | resolwe/flow/models/data.py | Data.duplicate | def duplicate(self, contributor=None):
"""Duplicate (make a copy)."""
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genialis/resolwe | resolwe/flow/models/data.py | Data._render_name | def _render_name(self):
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if not self.process.data_name or self.named_by_user: # pylint: disable=no-member
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inputs = copy.deepcopy(self.input)
... | python | def _render_name(self):
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genialis/resolwe | resolwe/flow/models/data.py | DataLocation.get_path | def get_path(self, prefix=None, filename=None):
"""Compose data location path."""
prefix = prefix or settings.FLOW_EXECUTOR['DATA_DIR']
path = os.path.join(prefix, self.subpath)
if filename:
path = os.path.join(path, filename)
return path | python | def get_path(self, prefix=None, filename=None):
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genialis/resolwe | resolwe/flow/serializers/entity.py | EntitySerializer.get_data | def get_data(self, entity):
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genialis/resolwe | resolwe/process/descriptor.py | ProcessDescriptor.validate | def validate(self):
"""Validate process descriptor."""
required_fields = ('slug', 'name', 'process_type', 'version')
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"""Validate process descriptor."""
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genialis/resolwe | resolwe/process/descriptor.py | ProcessDescriptor.to_schema | def to_schema(self):
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genialis/resolwe | resolwe/flow/executors/docker/prepare.py | FlowExecutorPreparer.post_register_hook | def post_register_hook(self, verbosity=1):
"""Pull Docker images needed by processes after registering."""
if not getattr(settings, 'FLOW_DOCKER_DONT_PULL', False):
call_command('list_docker_images', pull=True, verbosity=verbosity) | python | def post_register_hook(self, verbosity=1):
"""Pull Docker images needed by processes after registering."""
if not getattr(settings, 'FLOW_DOCKER_DONT_PULL', False):
call_command('list_docker_images', pull=True, verbosity=verbosity) | [
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genialis/resolwe | resolwe/flow/executors/docker/prepare.py | FlowExecutorPreparer.resolve_data_path | def resolve_data_path(self, data=None, filename=None):
"""Resolve data path for use with the executor.
:param data: Data object instance
:param filename: Filename to resolve
:return: Resolved filename, which can be used to access the
given data file in programs executed usin... | python | def resolve_data_path(self, data=None, filename=None):
"""Resolve data path for use with the executor.
:param data: Data object instance
:param filename: Filename to resolve
:return: Resolved filename, which can be used to access the
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genialis/resolwe | resolwe/flow/executors/docker/prepare.py | FlowExecutorPreparer.resolve_upload_path | def resolve_upload_path(self, filename=None):
"""Resolve upload path for use with the executor.
:param filename: Filename to resolve
:return: Resolved filename, which can be used to access the
given uploaded file in programs executed using this
executor
"""
... | python | def resolve_upload_path(self, filename=None):
"""Resolve upload path for use with the executor.
:param filename: Filename to resolve
:return: Resolved filename, which can be used to access the
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DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | are_equal | def are_equal(a_dt, b_dt, round_sec=1):
"""Determine if two datetimes are equal with fuzz factor.
A naive datetime (no timezone information) is assumed to be in in UTC.
Args:
a_dt: datetime
Timestamp to compare.
b_dt: datetime
Timestamp to compare.
round_sec: int or flo... | python | def are_equal(a_dt, b_dt, round_sec=1):
"""Determine if two datetimes are equal with fuzz factor.
A naive datetime (no timezone information) is assumed to be in in UTC.
Args:
a_dt: datetime
Timestamp to compare.
b_dt: datetime
Timestamp to compare.
round_sec: int or flo... | [
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