repository_name stringlengths 7 55 | func_path_in_repository stringlengths 4 223 | func_name stringlengths 1 134 | whole_func_string stringlengths 75 104k | language stringclasses 1
value | func_code_string stringlengths 75 104k | func_code_tokens listlengths 19 28.4k | func_documentation_string stringlengths 1 46.9k | func_documentation_tokens listlengths 1 1.97k | split_name stringclasses 1
value | func_code_url stringlengths 87 315 |
|---|---|---|---|---|---|---|---|---|---|---|
DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | http_datetime_str_from_dt | def http_datetime_str_from_dt(dt):
"""Format datetime to HTTP Full Date format.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.
Returns:
str
The returned format is a is fixed-length subset of that defined by RFC 1123 and
... | python | def http_datetime_str_from_dt(dt):
"""Format datetime to HTTP Full Date format.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.
Returns:
str
The returned format is a is fixed-length subset of that defined by RFC 1123 and
... | [
"def",
"http_datetime_str_from_dt",
"(",
"dt",
")",
":",
"epoch_seconds",
"=",
"ts_from_dt",
"(",
"dt",
")",
"return",
"email",
".",
"utils",
".",
"formatdate",
"(",
"epoch_seconds",
",",
"localtime",
"=",
"False",
",",
"usegmt",
"=",
"True",
")"
] | Format datetime to HTTP Full Date format.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.
Returns:
str
The returned format is a is fixed-length subset of that defined by RFC 1123 and
is
the preferred format fo... | [
"Format",
"datetime",
"to",
"HTTP",
"Full",
"Date",
"format",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/date_time.py#L295-L317 |
DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | dt_from_http_datetime_str | def dt_from_http_datetime_str(http_full_datetime):
"""Parse HTTP Full Date formats and return as datetime.
Args:
http_full_datetime : str
Each of the allowed formats are supported:
- Sun, 06 Nov 1994 08:49:37 GMT ; RFC 822, updated by RFC 1123
- Sunday, 06-Nov-94 08:49:37 GMT ; ... | python | def dt_from_http_datetime_str(http_full_datetime):
"""Parse HTTP Full Date formats and return as datetime.
Args:
http_full_datetime : str
Each of the allowed formats are supported:
- Sun, 06 Nov 1994 08:49:37 GMT ; RFC 822, updated by RFC 1123
- Sunday, 06-Nov-94 08:49:37 GMT ; ... | [
"def",
"dt_from_http_datetime_str",
"(",
"http_full_datetime",
")",
":",
"date_parts",
"=",
"list",
"(",
"email",
".",
"utils",
".",
"parsedate",
"(",
"http_full_datetime",
")",
"[",
":",
"6",
"]",
")",
"year",
"=",
"date_parts",
"[",
"0",
"]",
"if",
"year... | Parse HTTP Full Date formats and return as datetime.
Args:
http_full_datetime : str
Each of the allowed formats are supported:
- Sun, 06 Nov 1994 08:49:37 GMT ; RFC 822, updated by RFC 1123
- Sunday, 06-Nov-94 08:49:37 GMT ; RFC 850, obsoleted by RFC 1036
- Sun Nov 6 08:49:... | [
"Parse",
"HTTP",
"Full",
"Date",
"formats",
"and",
"return",
"as",
"datetime",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/date_time.py#L339-L364 |
DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | normalize_datetime_to_utc | def normalize_datetime_to_utc(dt):
"""Adjust datetime to UTC.
Apply the timezone offset to the datetime and set the timezone to UTC.
This is a no-op if the datetime is already in UTC.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.... | python | def normalize_datetime_to_utc(dt):
"""Adjust datetime to UTC.
Apply the timezone offset to the datetime and set the timezone to UTC.
This is a no-op if the datetime is already in UTC.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.... | [
"def",
"normalize_datetime_to_utc",
"(",
"dt",
")",
":",
"return",
"datetime",
".",
"datetime",
"(",
"*",
"dt",
".",
"utctimetuple",
"(",
")",
"[",
":",
"6",
"]",
",",
"microsecond",
"=",
"dt",
".",
"microsecond",
",",
"tzinfo",
"=",
"datetime",
".",
"... | Adjust datetime to UTC.
Apply the timezone offset to the datetime and set the timezone to UTC.
This is a no-op if the datetime is already in UTC.
Args:
dt : datetime
- tz-aware: Used in the formatted string.
- tz-naive: Assumed to be in UTC.
Returns:
datetime
The ... | [
"Adjust",
"datetime",
"to",
"UTC",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/date_time.py#L399-L429 |
DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | cast_naive_datetime_to_tz | def cast_naive_datetime_to_tz(dt, tz=UTC()):
"""If datetime is tz-naive, set it to ``tz``. If datetime is tz-aware, return it
unmodified.
Args:
dt : datetime
tz-naive or tz-aware datetime.
tz : datetime.tzinfo
The timezone to which to adjust tz-naive datetime.
Returns:
... | python | def cast_naive_datetime_to_tz(dt, tz=UTC()):
"""If datetime is tz-naive, set it to ``tz``. If datetime is tz-aware, return it
unmodified.
Args:
dt : datetime
tz-naive or tz-aware datetime.
tz : datetime.tzinfo
The timezone to which to adjust tz-naive datetime.
Returns:
... | [
"def",
"cast_naive_datetime_to_tz",
"(",
"dt",
",",
"tz",
"=",
"UTC",
"(",
")",
")",
":",
"if",
"has_tz",
"(",
"dt",
")",
":",
"return",
"dt",
"return",
"dt",
".",
"replace",
"(",
"tzinfo",
"=",
"tz",
")"
] | If datetime is tz-naive, set it to ``tz``. If datetime is tz-aware, return it
unmodified.
Args:
dt : datetime
tz-naive or tz-aware datetime.
tz : datetime.tzinfo
The timezone to which to adjust tz-naive datetime.
Returns:
datetime
tz-aware datetime.
Warning:... | [
"If",
"datetime",
"is",
"tz",
"-",
"naive",
"set",
"it",
"to",
"tz",
".",
"If",
"datetime",
"is",
"tz",
"-",
"aware",
"return",
"it",
"unmodified",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/date_time.py#L432-L457 |
DataONEorg/d1_python | lib_common/src/d1_common/date_time.py | round_to_nearest | def round_to_nearest(dt, n_round_sec=1.0):
"""Round datetime up or down to nearest divisor.
Round datetime up or down to nearest number of seconds that divides evenly by
the divisor.
Any timezone is preserved but ignored in the rounding.
Args:
dt: datetime
n_round_sec : int or float
... | python | def round_to_nearest(dt, n_round_sec=1.0):
"""Round datetime up or down to nearest divisor.
Round datetime up or down to nearest number of seconds that divides evenly by
the divisor.
Any timezone is preserved but ignored in the rounding.
Args:
dt: datetime
n_round_sec : int or float
... | [
"def",
"round_to_nearest",
"(",
"dt",
",",
"n_round_sec",
"=",
"1.0",
")",
":",
"ts",
"=",
"ts_from_dt",
"(",
"strip_timezone",
"(",
"dt",
")",
")",
"+",
"n_round_sec",
"/",
"2.0",
"res",
"=",
"dt_from_ts",
"(",
"ts",
"-",
"(",
"ts",
"%",
"n_round_sec"... | Round datetime up or down to nearest divisor.
Round datetime up or down to nearest number of seconds that divides evenly by
the divisor.
Any timezone is preserved but ignored in the rounding.
Args:
dt: datetime
n_round_sec : int or float
Divisor for rounding
Examples:
... | [
"Round",
"datetime",
"up",
"or",
"down",
"to",
"nearest",
"divisor",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/date_time.py#L545-L567 |
genialis/resolwe | resolwe/flow/managers/workload_connectors/slurm.py | Connector.submit | def submit(self, data, runtime_dir, argv):
"""Run process with SLURM.
For details, see
:meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`.
"""
limits = data.process.get_resource_limits()
logger.debug(__(
"Connector '{}' running for D... | python | def submit(self, data, runtime_dir, argv):
"""Run process with SLURM.
For details, see
:meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`.
"""
limits = data.process.get_resource_limits()
logger.debug(__(
"Connector '{}' running for D... | [
"def",
"submit",
"(",
"self",
",",
"data",
",",
"runtime_dir",
",",
"argv",
")",
":",
"limits",
"=",
"data",
".",
"process",
".",
"get_resource_limits",
"(",
")",
"logger",
".",
"debug",
"(",
"__",
"(",
"\"Connector '{}' running for Data with id {} ({}).\"",
"... | Run process with SLURM.
For details, see
:meth:`~resolwe.flow.managers.workload_connectors.base.BaseConnector.submit`. | [
"Run",
"process",
"with",
"SLURM",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/managers/workload_connectors/slurm.py#L29-L73 |
genialis/resolwe | resolwe/flow/utils/purge.py | get_purge_files | def get_purge_files(root, output, output_schema, descriptor, descriptor_schema):
"""Get files to purge."""
def remove_file(fn, paths):
"""From paths remove fn and dirs before fn in dir tree."""
while fn:
for i in range(len(paths) - 1, -1, -1):
if fn == paths[i]:
... | python | def get_purge_files(root, output, output_schema, descriptor, descriptor_schema):
"""Get files to purge."""
def remove_file(fn, paths):
"""From paths remove fn and dirs before fn in dir tree."""
while fn:
for i in range(len(paths) - 1, -1, -1):
if fn == paths[i]:
... | [
"def",
"get_purge_files",
"(",
"root",
",",
"output",
",",
"output_schema",
",",
"descriptor",
",",
"descriptor_schema",
")",
":",
"def",
"remove_file",
"(",
"fn",
",",
"paths",
")",
":",
"\"\"\"From paths remove fn and dirs before fn in dir tree.\"\"\"",
"while",
"fn... | Get files to purge. | [
"Get",
"files",
"to",
"purge",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/utils/purge.py#L21-L97 |
genialis/resolwe | resolwe/flow/utils/purge.py | location_purge | def location_purge(location_id, delete=False, verbosity=0):
"""Print and conditionally delete files not referenced by meta data.
:param location_id: Id of the
:class:`~resolwe.flow.models.DataLocation` model that data
objects reference to.
:param delete: If ``True``, then delete unreference... | python | def location_purge(location_id, delete=False, verbosity=0):
"""Print and conditionally delete files not referenced by meta data.
:param location_id: Id of the
:class:`~resolwe.flow.models.DataLocation` model that data
objects reference to.
:param delete: If ``True``, then delete unreference... | [
"def",
"location_purge",
"(",
"location_id",
",",
"delete",
"=",
"False",
",",
"verbosity",
"=",
"0",
")",
":",
"try",
":",
"location",
"=",
"DataLocation",
".",
"objects",
".",
"get",
"(",
"id",
"=",
"location_id",
")",
"except",
"DataLocation",
".",
"D... | Print and conditionally delete files not referenced by meta data.
:param location_id: Id of the
:class:`~resolwe.flow.models.DataLocation` model that data
objects reference to.
:param delete: If ``True``, then delete unreferenced files. | [
"Print",
"and",
"conditionally",
"delete",
"files",
"not",
"referenced",
"by",
"meta",
"data",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/utils/purge.py#L100-L161 |
genialis/resolwe | resolwe/flow/utils/purge.py | _location_purge_all | def _location_purge_all(delete=False, verbosity=0):
"""Purge all data locations."""
if DataLocation.objects.exists():
for location in DataLocation.objects.filter(Q(purged=False) | Q(data=None)):
location_purge(location.id, delete, verbosity)
else:
logger.info("No data locations") | python | def _location_purge_all(delete=False, verbosity=0):
"""Purge all data locations."""
if DataLocation.objects.exists():
for location in DataLocation.objects.filter(Q(purged=False) | Q(data=None)):
location_purge(location.id, delete, verbosity)
else:
logger.info("No data locations") | [
"def",
"_location_purge_all",
"(",
"delete",
"=",
"False",
",",
"verbosity",
"=",
"0",
")",
":",
"if",
"DataLocation",
".",
"objects",
".",
"exists",
"(",
")",
":",
"for",
"location",
"in",
"DataLocation",
".",
"objects",
".",
"filter",
"(",
"Q",
"(",
... | Purge all data locations. | [
"Purge",
"all",
"data",
"locations",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/utils/purge.py#L164-L170 |
genialis/resolwe | resolwe/flow/utils/purge.py | _storage_purge_all | def _storage_purge_all(delete=False, verbosity=0):
"""Purge unreferenced storages."""
orphaned_storages = Storage.objects.filter(data=None)
if verbosity >= 1:
if orphaned_storages.exists():
logger.info(__("Unreferenced storages ({}):", orphaned_storages.count()))
for storage... | python | def _storage_purge_all(delete=False, verbosity=0):
"""Purge unreferenced storages."""
orphaned_storages = Storage.objects.filter(data=None)
if verbosity >= 1:
if orphaned_storages.exists():
logger.info(__("Unreferenced storages ({}):", orphaned_storages.count()))
for storage... | [
"def",
"_storage_purge_all",
"(",
"delete",
"=",
"False",
",",
"verbosity",
"=",
"0",
")",
":",
"orphaned_storages",
"=",
"Storage",
".",
"objects",
".",
"filter",
"(",
"data",
"=",
"None",
")",
"if",
"verbosity",
">=",
"1",
":",
"if",
"orphaned_storages",... | Purge unreferenced storages. | [
"Purge",
"unreferenced",
"storages",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/utils/purge.py#L173-L186 |
genialis/resolwe | resolwe/flow/utils/purge.py | purge_all | def purge_all(delete=False, verbosity=0):
"""Purge all data locations."""
_location_purge_all(delete, verbosity)
_storage_purge_all(delete, verbosity) | python | def purge_all(delete=False, verbosity=0):
"""Purge all data locations."""
_location_purge_all(delete, verbosity)
_storage_purge_all(delete, verbosity) | [
"def",
"purge_all",
"(",
"delete",
"=",
"False",
",",
"verbosity",
"=",
"0",
")",
":",
"_location_purge_all",
"(",
"delete",
",",
"verbosity",
")",
"_storage_purge_all",
"(",
"delete",
",",
"verbosity",
")"
] | Purge all data locations. | [
"Purge",
"all",
"data",
"locations",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/utils/purge.py#L189-L192 |
genialis/resolwe | resolwe/process/parser.py | StaticStringMetadata.get_value | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Str):
raise TypeError("must be a string literal")
return node.s | python | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Str):
raise TypeError("must be a string literal")
return node.s | [
"def",
"get_value",
"(",
"self",
",",
"node",
")",
":",
"if",
"not",
"isinstance",
"(",
"node",
",",
"ast",
".",
"Str",
")",
":",
"raise",
"TypeError",
"(",
"\"must be a string literal\"",
")",
"return",
"node",
".",
"s"
] | Convert value from an AST node. | [
"Convert",
"value",
"from",
"an",
"AST",
"node",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L24-L29 |
genialis/resolwe | resolwe/process/parser.py | StaticEnumMetadata.get_value | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Attribute):
raise TypeError("must be an attribute")
if node.value.id != self.choices.__name__:
raise TypeError("must be an attribute of {}".format(self.choices.__name__))
... | python | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Attribute):
raise TypeError("must be an attribute")
if node.value.id != self.choices.__name__:
raise TypeError("must be an attribute of {}".format(self.choices.__name__))
... | [
"def",
"get_value",
"(",
"self",
",",
"node",
")",
":",
"if",
"not",
"isinstance",
"(",
"node",
",",
"ast",
".",
"Attribute",
")",
":",
"raise",
"TypeError",
"(",
"\"must be an attribute\"",
")",
"if",
"node",
".",
"value",
".",
"id",
"!=",
"self",
"."... | Convert value from an AST node. | [
"Convert",
"value",
"from",
"an",
"AST",
"node",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L39-L47 |
genialis/resolwe | resolwe/process/parser.py | StaticDictMetadata.get_value | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Dict):
raise TypeError("must be a dictionary")
evaluator = SafeEvaluator()
try:
value = evaluator.run(node)
except Exception as ex:
# TODO: Handle err... | python | def get_value(self, node):
"""Convert value from an AST node."""
if not isinstance(node, ast.Dict):
raise TypeError("must be a dictionary")
evaluator = SafeEvaluator()
try:
value = evaluator.run(node)
except Exception as ex:
# TODO: Handle err... | [
"def",
"get_value",
"(",
"self",
",",
"node",
")",
":",
"if",
"not",
"isinstance",
"(",
"node",
",",
"ast",
".",
"Dict",
")",
":",
"raise",
"TypeError",
"(",
"\"must be a dictionary\"",
")",
"evaluator",
"=",
"SafeEvaluator",
"(",
")",
"try",
":",
"value... | Convert value from an AST node. | [
"Convert",
"value",
"from",
"an",
"AST",
"node",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L53-L73 |
genialis/resolwe | resolwe/process/parser.py | ProcessVisitor.visit_field_class | def visit_field_class(self, item, descriptor=None, fields=None):
"""Visit a class node containing a list of field definitions."""
discovered_fields = collections.OrderedDict()
field_groups = {}
for node in item.body:
if isinstance(node, ast.ClassDef):
field_gr... | python | def visit_field_class(self, item, descriptor=None, fields=None):
"""Visit a class node containing a list of field definitions."""
discovered_fields = collections.OrderedDict()
field_groups = {}
for node in item.body:
if isinstance(node, ast.ClassDef):
field_gr... | [
"def",
"visit_field_class",
"(",
"self",
",",
"item",
",",
"descriptor",
"=",
"None",
",",
"fields",
"=",
"None",
")",
":",
"discovered_fields",
"=",
"collections",
".",
"OrderedDict",
"(",
")",
"field_groups",
"=",
"{",
"}",
"for",
"node",
"in",
"item",
... | Visit a class node containing a list of field definitions. | [
"Visit",
"a",
"class",
"node",
"containing",
"a",
"list",
"of",
"field",
"definitions",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L118-L165 |
genialis/resolwe | resolwe/process/parser.py | ProcessVisitor.visit_ClassDef | def visit_ClassDef(self, node): # pylint: disable=invalid-name
"""Visit top-level classes."""
# Resolve everything as root scope contains everything from the process module.
for base in node.bases:
# Cover `from resolwe.process import ...`.
if isinstance(base, ast.Name) ... | python | def visit_ClassDef(self, node): # pylint: disable=invalid-name
"""Visit top-level classes."""
# Resolve everything as root scope contains everything from the process module.
for base in node.bases:
# Cover `from resolwe.process import ...`.
if isinstance(base, ast.Name) ... | [
"def",
"visit_ClassDef",
"(",
"self",
",",
"node",
")",
":",
"# pylint: disable=invalid-name",
"# Resolve everything as root scope contains everything from the process module.",
"for",
"base",
"in",
"node",
".",
"bases",
":",
"# Cover `from resolwe.process import ...`.",
"if",
... | Visit top-level classes. | [
"Visit",
"top",
"-",
"level",
"classes",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L167-L212 |
genialis/resolwe | resolwe/process/parser.py | SafeParser.parse | def parse(self):
"""Parse process.
:return: A list of discovered process descriptors
"""
root = ast.parse(self._source)
visitor = ProcessVisitor(source=self._source)
visitor.visit(root)
return visitor.processes | python | def parse(self):
"""Parse process.
:return: A list of discovered process descriptors
"""
root = ast.parse(self._source)
visitor = ProcessVisitor(source=self._source)
visitor.visit(root)
return visitor.processes | [
"def",
"parse",
"(",
"self",
")",
":",
"root",
"=",
"ast",
".",
"parse",
"(",
"self",
".",
"_source",
")",
"visitor",
"=",
"ProcessVisitor",
"(",
"source",
"=",
"self",
".",
"_source",
")",
"visitor",
".",
"visit",
"(",
"root",
")",
"return",
"visito... | Parse process.
:return: A list of discovered process descriptors | [
"Parse",
"process",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/parser.py#L225-L234 |
genialis/resolwe | resolwe/permissions/loader.py | get_permissions_class | def get_permissions_class(permissions_name=None):
"""Load and cache permissions class.
If ``permissions_name`` is not given, it defaults to permissions
class set in Django ``FLOW_API['PERMISSIONS']`` setting.
"""
def load_permissions(permissions_name):
"""Look for a fully qualified flow per... | python | def get_permissions_class(permissions_name=None):
"""Load and cache permissions class.
If ``permissions_name`` is not given, it defaults to permissions
class set in Django ``FLOW_API['PERMISSIONS']`` setting.
"""
def load_permissions(permissions_name):
"""Look for a fully qualified flow per... | [
"def",
"get_permissions_class",
"(",
"permissions_name",
"=",
"None",
")",
":",
"def",
"load_permissions",
"(",
"permissions_name",
")",
":",
"\"\"\"Look for a fully qualified flow permissions class.\"\"\"",
"try",
":",
"return",
"import_module",
"(",
"'{}'",
".",
"format... | Load and cache permissions class.
If ``permissions_name`` is not given, it defaults to permissions
class set in Django ``FLOW_API['PERMISSIONS']`` setting. | [
"Load",
"and",
"cache",
"permissions",
"class",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/permissions/loader.py#L21-L62 |
genialis/resolwe | resolwe/flow/models/base.py | BaseModel.save | def save(self, *args, **kwargs):
"""Save the model."""
name_max_len = self._meta.get_field('name').max_length
if len(self.name) > name_max_len:
self.name = self.name[:(name_max_len - 3)] + '...'
for _ in range(MAX_SLUG_RETRIES):
try:
# Attempt to ... | python | def save(self, *args, **kwargs):
"""Save the model."""
name_max_len = self._meta.get_field('name').max_length
if len(self.name) > name_max_len:
self.name = self.name[:(name_max_len - 3)] + '...'
for _ in range(MAX_SLUG_RETRIES):
try:
# Attempt to ... | [
"def",
"save",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"name_max_len",
"=",
"self",
".",
"_meta",
".",
"get_field",
"(",
"'name'",
")",
".",
"max_length",
"if",
"len",
"(",
"self",
".",
"name",
")",
">",
"name_max_len",
":... | Save the model. | [
"Save",
"the",
"model",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/models/base.py#L48-L68 |
DataONEorg/d1_python | lib_common/src/d1_common/revision.py | get_identifiers | def get_identifiers(sysmeta_pyxb):
"""Get set of identifiers that provide revision context for SciObj.
Returns: tuple: PID, SID, OBSOLETES_PID, OBSOLETED_BY_PID
"""
pid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'identifier')
sid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'seriesId')
obsoletes... | python | def get_identifiers(sysmeta_pyxb):
"""Get set of identifiers that provide revision context for SciObj.
Returns: tuple: PID, SID, OBSOLETES_PID, OBSOLETED_BY_PID
"""
pid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'identifier')
sid = d1_common.xml.get_opt_val(sysmeta_pyxb, 'seriesId')
obsoletes... | [
"def",
"get_identifiers",
"(",
"sysmeta_pyxb",
")",
":",
"pid",
"=",
"d1_common",
".",
"xml",
".",
"get_opt_val",
"(",
"sysmeta_pyxb",
",",
"'identifier'",
")",
"sid",
"=",
"d1_common",
".",
"xml",
".",
"get_opt_val",
"(",
"sysmeta_pyxb",
",",
"'seriesId'",
... | Get set of identifiers that provide revision context for SciObj.
Returns: tuple: PID, SID, OBSOLETES_PID, OBSOLETED_BY_PID | [
"Get",
"set",
"of",
"identifiers",
"that",
"provide",
"revision",
"context",
"for",
"SciObj",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/revision.py#L23-L33 |
DataONEorg/d1_python | lib_common/src/d1_common/revision.py | topological_sort | def topological_sort(unsorted_dict):
"""Sort objects by dependency.
Sort a dict of obsoleting PID to obsoleted PID to a list of PIDs in order of
obsolescence.
Args:
unsorted_dict : dict
Dict that holds obsolescence information. Each ``key/value`` pair establishes
that the PID in ... | python | def topological_sort(unsorted_dict):
"""Sort objects by dependency.
Sort a dict of obsoleting PID to obsoleted PID to a list of PIDs in order of
obsolescence.
Args:
unsorted_dict : dict
Dict that holds obsolescence information. Each ``key/value`` pair establishes
that the PID in ... | [
"def",
"topological_sort",
"(",
"unsorted_dict",
")",
":",
"sorted_list",
"=",
"[",
"]",
"sorted_set",
"=",
"set",
"(",
")",
"found",
"=",
"True",
"unconnected_dict",
"=",
"unsorted_dict",
".",
"copy",
"(",
")",
"while",
"found",
":",
"found",
"=",
"False"... | Sort objects by dependency.
Sort a dict of obsoleting PID to obsoleted PID to a list of PIDs in order of
obsolescence.
Args:
unsorted_dict : dict
Dict that holds obsolescence information. Each ``key/value`` pair establishes
that the PID in ``key`` identifies an object that obsoletes ... | [
"Sort",
"objects",
"by",
"dependency",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/revision.py#L36-L81 |
DataONEorg/d1_python | lib_common/src/d1_common/revision.py | get_pids_in_revision_chain | def get_pids_in_revision_chain(client, did):
"""Args: client: d1_client.cnclient.CoordinatingNodeClient or
d1_client.mnclient.MemberNodeClient.
did : str
SID or a PID of any object in a revision chain.
Returns:
list of str:
All PIDs in the chain. The returned list is in the sam... | python | def get_pids_in_revision_chain(client, did):
"""Args: client: d1_client.cnclient.CoordinatingNodeClient or
d1_client.mnclient.MemberNodeClient.
did : str
SID or a PID of any object in a revision chain.
Returns:
list of str:
All PIDs in the chain. The returned list is in the sam... | [
"def",
"get_pids_in_revision_chain",
"(",
"client",
",",
"did",
")",
":",
"def",
"_req",
"(",
"p",
")",
":",
"return",
"d1_common",
".",
"xml",
".",
"get_req_val",
"(",
"p",
")",
"def",
"_opt",
"(",
"p",
",",
"a",
")",
":",
"return",
"d1_common",
"."... | Args: client: d1_client.cnclient.CoordinatingNodeClient or
d1_client.mnclient.MemberNodeClient.
did : str
SID or a PID of any object in a revision chain.
Returns:
list of str:
All PIDs in the chain. The returned list is in the same order as the chain. The
initial PID is typ... | [
"Args",
":",
"client",
":",
"d1_client",
".",
"cnclient",
".",
"CoordinatingNodeClient",
"or",
"d1_client",
".",
"mnclient",
".",
"MemberNodeClient",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/revision.py#L84-L114 |
DataONEorg/d1_python | dev_tools/src/d1_dev/src-format-docstrings.py | main | def main():
"""Remove unused imports Unsafe!
Only tested on our codebase, which uses simple absolute imports on the form, "import
a.b.c".
"""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument("path", na... | python | def main():
"""Remove unused imports Unsafe!
Only tested on our codebase, which uses simple absolute imports on the form, "import
a.b.c".
"""
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument("path", na... | [
"def",
"main",
"(",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"description",
"=",
"__doc__",
",",
"formatter_class",
"=",
"argparse",
".",
"RawDescriptionHelpFormatter",
")",
"parser",
".",
"add_argument",
"(",
"\"path\"",
",",
"nargs",
... | Remove unused imports Unsafe!
Only tested on our codebase, which uses simple absolute imports on the form, "import
a.b.c". | [
"Remove",
"unused",
"imports",
"Unsafe!"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/src-format-docstrings.py#L46-L99 |
DataONEorg/d1_python | dev_tools/src/d1_dev/src-format-docstrings.py | get_docstr_list | def get_docstr_list(red):
"""Find all triple-quoted docstrings in module."""
docstr_list = []
for n in red.find_all("string"):
if n.value.startswith('"""'):
docstr_list.append(n)
return docstr_list | python | def get_docstr_list(red):
"""Find all triple-quoted docstrings in module."""
docstr_list = []
for n in red.find_all("string"):
if n.value.startswith('"""'):
docstr_list.append(n)
return docstr_list | [
"def",
"get_docstr_list",
"(",
"red",
")",
":",
"docstr_list",
"=",
"[",
"]",
"for",
"n",
"in",
"red",
".",
"find_all",
"(",
"\"string\"",
")",
":",
"if",
"n",
".",
"value",
".",
"startswith",
"(",
"'\"\"\"'",
")",
":",
"docstr_list",
".",
"append",
... | Find all triple-quoted docstrings in module. | [
"Find",
"all",
"triple",
"-",
"quoted",
"docstrings",
"in",
"module",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/src-format-docstrings.py#L144-L150 |
DataONEorg/d1_python | dev_tools/src/d1_dev/src-format-docstrings.py | unwrap | def unwrap(s, node_indent):
"""Group lines of a docstring to blocks.
For now, only groups markdown list sections.
A block designates a list of consequtive lines that all start at the same
indentation level.
The lines of the docstring are iterated top to bottom. Each line is added to
`block_li... | python | def unwrap(s, node_indent):
"""Group lines of a docstring to blocks.
For now, only groups markdown list sections.
A block designates a list of consequtive lines that all start at the same
indentation level.
The lines of the docstring are iterated top to bottom. Each line is added to
`block_li... | [
"def",
"unwrap",
"(",
"s",
",",
"node_indent",
")",
":",
"def",
"get_indent",
"(",
")",
":",
"if",
"line_str",
".",
"startswith",
"(",
"'\"\"\"'",
")",
":",
"return",
"node_indent",
"return",
"len",
"(",
"re",
".",
"match",
"(",
"r\"^( *)\"",
",",
"lin... | Group lines of a docstring to blocks.
For now, only groups markdown list sections.
A block designates a list of consequtive lines that all start at the same
indentation level.
The lines of the docstring are iterated top to bottom. Each line is added to
`block_list` until a line is encountered tha... | [
"Group",
"lines",
"of",
"a",
"docstring",
"to",
"blocks",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/src-format-docstrings.py#L186-L270 |
DataONEorg/d1_python | dev_tools/src/d1_dev/src-format-docstrings.py | wrap | def wrap(indent_int, unwrap_str):
"""Wrap a single line to one or more lines that start at indent_int and end at the
last word that will fit before WRAP_MARGIN_INT.
If there are no word breaks (spaces) before WRAP_MARGIN_INT, force a break at
WRAP_MARGIN_INT.
"""
with io.StringIO() as str_buf:... | python | def wrap(indent_int, unwrap_str):
"""Wrap a single line to one or more lines that start at indent_int and end at the
last word that will fit before WRAP_MARGIN_INT.
If there are no word breaks (spaces) before WRAP_MARGIN_INT, force a break at
WRAP_MARGIN_INT.
"""
with io.StringIO() as str_buf:... | [
"def",
"wrap",
"(",
"indent_int",
",",
"unwrap_str",
")",
":",
"with",
"io",
".",
"StringIO",
"(",
")",
"as",
"str_buf",
":",
"is_rest_block",
"=",
"unwrap_str",
".",
"startswith",
"(",
"(",
"\"- \"",
",",
"\"* \"",
")",
")",
"while",
"unwrap_str",
":",
... | Wrap a single line to one or more lines that start at indent_int and end at the
last word that will fit before WRAP_MARGIN_INT.
If there are no word breaks (spaces) before WRAP_MARGIN_INT, force a break at
WRAP_MARGIN_INT. | [
"Wrap",
"a",
"single",
"line",
"to",
"one",
"or",
"more",
"lines",
"that",
"start",
"at",
"indent_int",
"and",
"end",
"at",
"the",
"last",
"word",
"that",
"will",
"fit",
"before",
"WRAP_MARGIN_INT",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/src-format-docstrings.py#L273-L297 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | createSimpleResourceMap | def createSimpleResourceMap(ore_pid, scimeta_pid, sciobj_pid_list):
"""Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects.
This creates a document that establishes an association between a Science Metadata
object and any number of Science Data... | python | def createSimpleResourceMap(ore_pid, scimeta_pid, sciobj_pid_list):
"""Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects.
This creates a document that establishes an association between a Science Metadata
object and any number of Science Data... | [
"def",
"createSimpleResourceMap",
"(",
"ore_pid",
",",
"scimeta_pid",
",",
"sciobj_pid_list",
")",
":",
"ore",
"=",
"ResourceMap",
"(",
")",
"ore",
".",
"initialize",
"(",
"ore_pid",
")",
"ore",
".",
"addMetadataDocument",
"(",
"scimeta_pid",
")",
"ore",
".",
... | Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects.
This creates a document that establishes an association between a Science Metadata
object and any number of Science Data objects. The Science Metadata object contains
information that is inde... | [
"Create",
"a",
"simple",
"OAI",
"-",
"ORE",
"Resource",
"Map",
"with",
"one",
"Science",
"Metadata",
"document",
"and",
"any",
"number",
"of",
"Science",
"Data",
"objects",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L66-L96 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | createResourceMapFromStream | def createResourceMapFromStream(in_stream, base_url=d1_common.const.URL_DATAONE_ROOT):
"""Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects, using a stream of PIDs.
Args:
in_stream:
The first non-blank line is the PID of the resourc... | python | def createResourceMapFromStream(in_stream, base_url=d1_common.const.URL_DATAONE_ROOT):
"""Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects, using a stream of PIDs.
Args:
in_stream:
The first non-blank line is the PID of the resourc... | [
"def",
"createResourceMapFromStream",
"(",
"in_stream",
",",
"base_url",
"=",
"d1_common",
".",
"const",
".",
"URL_DATAONE_ROOT",
")",
":",
"pids",
"=",
"[",
"]",
"for",
"line",
"in",
"in_stream",
":",
"pid",
"=",
"line",
".",
"strip",
"(",
")",
"if",
"p... | Create a simple OAI-ORE Resource Map with one Science Metadata document and any
number of Science Data objects, using a stream of PIDs.
Args:
in_stream:
The first non-blank line is the PID of the resource map itself. Second line is
the science metadata PID and remaining lines are science ... | [
"Create",
"a",
"simple",
"OAI",
"-",
"ORE",
"Resource",
"Map",
"with",
"one",
"Science",
"Metadata",
"document",
"and",
"any",
"number",
"of",
"Science",
"Data",
"objects",
"using",
"a",
"stream",
"of",
"PIDs",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L99-L142 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.initialize | def initialize(self, pid, ore_software_id=d1_common.const.ORE_SOFTWARE_ID):
"""Create the basic ORE document structure."""
# Set nice prefixes for the namespaces
for k in list(d1_common.const.ORE_NAMESPACE_DICT.keys()):
self.bind(k, d1_common.const.ORE_NAMESPACE_DICT[k])
# Cr... | python | def initialize(self, pid, ore_software_id=d1_common.const.ORE_SOFTWARE_ID):
"""Create the basic ORE document structure."""
# Set nice prefixes for the namespaces
for k in list(d1_common.const.ORE_NAMESPACE_DICT.keys()):
self.bind(k, d1_common.const.ORE_NAMESPACE_DICT[k])
# Cr... | [
"def",
"initialize",
"(",
"self",
",",
"pid",
",",
"ore_software_id",
"=",
"d1_common",
".",
"const",
".",
"ORE_SOFTWARE_ID",
")",
":",
"# Set nice prefixes for the namespaces",
"for",
"k",
"in",
"list",
"(",
"d1_common",
".",
"const",
".",
"ORE_NAMESPACE_DICT",
... | Create the basic ORE document structure. | [
"Create",
"the",
"basic",
"ORE",
"document",
"structure",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L204-L223 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.serialize_to_transport | def serialize_to_transport(self, doc_format="xml", *args, **kwargs):
"""Serialize ResourceMap to UTF-8 encoded XML document.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
args and kwargs... | python | def serialize_to_transport(self, doc_format="xml", *args, **kwargs):
"""Serialize ResourceMap to UTF-8 encoded XML document.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
args and kwargs... | [
"def",
"serialize_to_transport",
"(",
"self",
",",
"doc_format",
"=",
"\"xml\"",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"return",
"super",
"(",
"ResourceMap",
",",
"self",
")",
".",
"serialize",
"(",
"format",
"=",
"doc_format",
",",
"encod... | Serialize ResourceMap to UTF-8 encoded XML document.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
args and kwargs:
Optional arguments forwarded to rdflib.ConjunctiveGraph.serialize(... | [
"Serialize",
"ResourceMap",
"to",
"UTF",
"-",
"8",
"encoded",
"XML",
"document",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L225-L245 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.serialize_to_display | def serialize_to_display(self, doc_format="pretty-xml", *args, **kwargs):
"""Serialize ResourceMap to an XML doc that is pretty printed for display.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
... | python | def serialize_to_display(self, doc_format="pretty-xml", *args, **kwargs):
"""Serialize ResourceMap to an XML doc that is pretty printed for display.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
... | [
"def",
"serialize_to_display",
"(",
"self",
",",
"doc_format",
"=",
"\"pretty-xml\"",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"return",
"(",
"super",
"(",
"ResourceMap",
",",
"self",
")",
".",
"serialize",
"(",
"format",
"=",
"doc_format",
"... | Serialize ResourceMap to an XML doc that is pretty printed for display.
Args:
doc_format: str
One of: ``xml``, ``n3``, ``turtle``, ``nt``, ``pretty-xml``, ``trix``,
``trig`` and ``nquads``.
args and kwargs:
Optional arguments forwarded to rdflib.Conjunct... | [
"Serialize",
"ResourceMap",
"to",
"an",
"XML",
"doc",
"that",
"is",
"pretty",
"printed",
"for",
"display",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L247-L269 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.deserialize | def deserialize(self, *args, **kwargs):
"""Deserialize Resource Map XML doc.
The source is specified using one of source, location, file or data.
Args:
source: InputSource, file-like object, or string
In the case of a string the string is the location of the source.
... | python | def deserialize(self, *args, **kwargs):
"""Deserialize Resource Map XML doc.
The source is specified using one of source, location, file or data.
Args:
source: InputSource, file-like object, or string
In the case of a string the string is the location of the source.
... | [
"def",
"deserialize",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"self",
".",
"parse",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
"self",
".",
"_ore_initialized",
"=",
"True"
] | Deserialize Resource Map XML doc.
The source is specified using one of source, location, file or data.
Args:
source: InputSource, file-like object, or string
In the case of a string the string is the location of the source.
location: str
String indicating t... | [
"Deserialize",
"Resource",
"Map",
"XML",
"doc",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L272-L305 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.getAggregation | def getAggregation(self):
"""Returns:
str : URIRef of the Aggregation entity
"""
self._check_initialized()
return [
o for o in self.subjects(predicate=rdflib.RDF.type, object=ORE.Aggregation)
][0] | python | def getAggregation(self):
"""Returns:
str : URIRef of the Aggregation entity
"""
self._check_initialized()
return [
o for o in self.subjects(predicate=rdflib.RDF.type, object=ORE.Aggregation)
][0] | [
"def",
"getAggregation",
"(",
"self",
")",
":",
"self",
".",
"_check_initialized",
"(",
")",
"return",
"[",
"o",
"for",
"o",
"in",
"self",
".",
"subjects",
"(",
"predicate",
"=",
"rdflib",
".",
"RDF",
".",
"type",
",",
"object",
"=",
"ORE",
".",
"Agg... | Returns:
str : URIRef of the Aggregation entity | [
"Returns",
":"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L307-L316 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.getObjectByPid | def getObjectByPid(self, pid):
"""
Args:
pid : str
Returns:
str : URIRef of the entry identified by ``pid``."""
self._check_initialized()
opid = rdflib.term.Literal(pid)
res = [o for o in self.subjects(predicate=DCTERMS.identifier, object=opid)]
return res[0] | python | def getObjectByPid(self, pid):
"""
Args:
pid : str
Returns:
str : URIRef of the entry identified by ``pid``."""
self._check_initialized()
opid = rdflib.term.Literal(pid)
res = [o for o in self.subjects(predicate=DCTERMS.identifier, object=opid)]
return res[0] | [
"def",
"getObjectByPid",
"(",
"self",
",",
"pid",
")",
":",
"self",
".",
"_check_initialized",
"(",
")",
"opid",
"=",
"rdflib",
".",
"term",
".",
"Literal",
"(",
"pid",
")",
"res",
"=",
"[",
"o",
"for",
"o",
"in",
"self",
".",
"subjects",
"(",
"pre... | Args:
pid : str
Returns:
str : URIRef of the entry identified by ``pid``. | [
"Args",
":",
"pid",
":",
"str"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L318-L328 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.addResource | def addResource(self, pid):
"""Add a resource to the Resource Map.
Args:
pid : str
"""
self._check_initialized()
try:
# is entry already in place?
self.getObjectByPid(pid)
return
except IndexError:
pass
#... | python | def addResource(self, pid):
"""Add a resource to the Resource Map.
Args:
pid : str
"""
self._check_initialized()
try:
# is entry already in place?
self.getObjectByPid(pid)
return
except IndexError:
pass
#... | [
"def",
"addResource",
"(",
"self",
",",
"pid",
")",
":",
"self",
".",
"_check_initialized",
"(",
")",
"try",
":",
"# is entry already in place?",
"self",
".",
"getObjectByPid",
"(",
"pid",
")",
"return",
"except",
"IndexError",
":",
"pass",
"# Entry not present,... | Add a resource to the Resource Map.
Args:
pid : str | [
"Add",
"a",
"resource",
"to",
"the",
"Resource",
"Map",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L330-L350 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.setDocuments | def setDocuments(self, documenting_pid, documented_pid):
"""Add a CiTO, the Citation Typing Ontology, triple asserting that
``documenting_pid`` documents ``documented_pid``.
Adds assertion: ``documenting_pid cito:documents documented_pid``
Args:
documenting_pid: str
... | python | def setDocuments(self, documenting_pid, documented_pid):
"""Add a CiTO, the Citation Typing Ontology, triple asserting that
``documenting_pid`` documents ``documented_pid``.
Adds assertion: ``documenting_pid cito:documents documented_pid``
Args:
documenting_pid: str
... | [
"def",
"setDocuments",
"(",
"self",
",",
"documenting_pid",
",",
"documented_pid",
")",
":",
"self",
".",
"_check_initialized",
"(",
")",
"documenting_id",
"=",
"self",
".",
"getObjectByPid",
"(",
"documenting_pid",
")",
"documented_id",
"=",
"self",
".",
"getOb... | Add a CiTO, the Citation Typing Ontology, triple asserting that
``documenting_pid`` documents ``documented_pid``.
Adds assertion: ``documenting_pid cito:documents documented_pid``
Args:
documenting_pid: str
PID of a Science Object that documents ``documented_pid``.
... | [
"Add",
"a",
"CiTO",
"the",
"Citation",
"Typing",
"Ontology",
"triple",
"asserting",
"that",
"documenting_pid",
"documents",
"documented_pid",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L352-L369 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.setDocumentedBy | def setDocumentedBy(self, documented_pid, documenting_pid):
"""Add a CiTO, the Citation Typing Ontology, triple asserting that
``documented_pid`` isDocumentedBy ``documenting_pid``.
Adds assertion: ``documented_pid cito:isDocumentedBy documenting_pid``
Args:
documented_pid: s... | python | def setDocumentedBy(self, documented_pid, documenting_pid):
"""Add a CiTO, the Citation Typing Ontology, triple asserting that
``documented_pid`` isDocumentedBy ``documenting_pid``.
Adds assertion: ``documented_pid cito:isDocumentedBy documenting_pid``
Args:
documented_pid: s... | [
"def",
"setDocumentedBy",
"(",
"self",
",",
"documented_pid",
",",
"documenting_pid",
")",
":",
"self",
".",
"_check_initialized",
"(",
")",
"documented_id",
"=",
"self",
".",
"getObjectByPid",
"(",
"documented_pid",
")",
"documenting_id",
"=",
"self",
".",
"get... | Add a CiTO, the Citation Typing Ontology, triple asserting that
``documented_pid`` isDocumentedBy ``documenting_pid``.
Adds assertion: ``documented_pid cito:isDocumentedBy documenting_pid``
Args:
documented_pid: str
PID of a Science Object that is documented by ``document... | [
"Add",
"a",
"CiTO",
"the",
"Citation",
"Typing",
"Ontology",
"triple",
"asserting",
"that",
"documented_pid",
"isDocumentedBy",
"documenting_pid",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L371-L388 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.addDataDocuments | def addDataDocuments(self, scidata_pid_list, scimeta_pid=None):
"""Add Science Data object(s)
Args:
scidata_pid_list : list of str
List of one or more PIDs of Science Data objects
scimeta_pid: str
PID of a Science Metadata object that documents the Science D... | python | def addDataDocuments(self, scidata_pid_list, scimeta_pid=None):
"""Add Science Data object(s)
Args:
scidata_pid_list : list of str
List of one or more PIDs of Science Data objects
scimeta_pid: str
PID of a Science Metadata object that documents the Science D... | [
"def",
"addDataDocuments",
"(",
"self",
",",
"scidata_pid_list",
",",
"scimeta_pid",
"=",
"None",
")",
":",
"mpids",
"=",
"self",
".",
"getAggregatedScienceMetadataPids",
"(",
")",
"if",
"scimeta_pid",
"is",
"None",
":",
"if",
"len",
"(",
"mpids",
")",
">",
... | Add Science Data object(s)
Args:
scidata_pid_list : list of str
List of one or more PIDs of Science Data objects
scimeta_pid: str
PID of a Science Metadata object that documents the Science Data objects. | [
"Add",
"Science",
"Data",
"object",
"(",
"s",
")"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L400-L425 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.getResourceMapPid | def getResourceMapPid(self):
"""Returns:
str : PID of the Resource Map itself.
"""
ore = [
o for o in self.subjects(predicate=rdflib.RDF.type, object=ORE.ResourceMap)
][0]
pid = [str(o) for o in self.objects(predicate=DCTERMS.identifier, subject=ore)][
... | python | def getResourceMapPid(self):
"""Returns:
str : PID of the Resource Map itself.
"""
ore = [
o for o in self.subjects(predicate=rdflib.RDF.type, object=ORE.ResourceMap)
][0]
pid = [str(o) for o in self.objects(predicate=DCTERMS.identifier, subject=ore)][
... | [
"def",
"getResourceMapPid",
"(",
"self",
")",
":",
"ore",
"=",
"[",
"o",
"for",
"o",
"in",
"self",
".",
"subjects",
"(",
"predicate",
"=",
"rdflib",
".",
"RDF",
".",
"type",
",",
"object",
"=",
"ORE",
".",
"ResourceMap",
")",
"]",
"[",
"0",
"]",
... | Returns:
str : PID of the Resource Map itself. | [
"Returns",
":"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L427-L439 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.getAllTriples | def getAllTriples(self):
"""Returns:
list of tuples : Each tuple holds a subject, predicate, object triple
"""
return [(str(s), str(p), str(o)) for s, p, o in self] | python | def getAllTriples(self):
"""Returns:
list of tuples : Each tuple holds a subject, predicate, object triple
"""
return [(str(s), str(p), str(o)) for s, p, o in self] | [
"def",
"getAllTriples",
"(",
"self",
")",
":",
"return",
"[",
"(",
"str",
"(",
"s",
")",
",",
"str",
"(",
"p",
")",
",",
"str",
"(",
"o",
")",
")",
"for",
"s",
",",
"p",
",",
"o",
"in",
"self",
"]"
] | Returns:
list of tuples : Each tuple holds a subject, predicate, object triple | [
"Returns",
":"
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L441-L447 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.getSubjectObjectsByPredicate | def getSubjectObjectsByPredicate(self, predicate):
"""
Args:
predicate : str
Predicate for which to return subject, object tuples.
Returns:
list of subject, object tuples: All subject/objects with ``predicate``.
Notes:
Equivalent SPARQL:
.. highlight: sql
:... | python | def getSubjectObjectsByPredicate(self, predicate):
"""
Args:
predicate : str
Predicate for which to return subject, object tuples.
Returns:
list of subject, object tuples: All subject/objects with ``predicate``.
Notes:
Equivalent SPARQL:
.. highlight: sql
:... | [
"def",
"getSubjectObjectsByPredicate",
"(",
"self",
",",
"predicate",
")",
":",
"return",
"sorted",
"(",
"set",
"(",
"[",
"(",
"str",
"(",
"s",
")",
",",
"str",
"(",
"o",
")",
")",
"for",
"s",
",",
"o",
"in",
"self",
".",
"subject_objects",
"(",
"r... | Args:
predicate : str
Predicate for which to return subject, object tuples.
Returns:
list of subject, object tuples: All subject/objects with ``predicate``.
Notes:
Equivalent SPARQL:
.. highlight: sql
::
SELECT DISTINCT ?s ?o
WHERE {{
?s {0} ... | [
"Args",
":",
"predicate",
":",
"str",
"Predicate",
"for",
"which",
"to",
"return",
"subject",
"object",
"tuples",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L468-L497 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap.parseDoc | def parseDoc(self, doc_str, format="xml"):
"""Parse a OAI-ORE Resource Maps document.
See Also: ``rdflib.ConjunctiveGraph.parse`` for documentation on arguments.
"""
self.parse(data=doc_str, format=format)
self._ore_initialized = True
return self | python | def parseDoc(self, doc_str, format="xml"):
"""Parse a OAI-ORE Resource Maps document.
See Also: ``rdflib.ConjunctiveGraph.parse`` for documentation on arguments.
"""
self.parse(data=doc_str, format=format)
self._ore_initialized = True
return self | [
"def",
"parseDoc",
"(",
"self",
",",
"doc_str",
",",
"format",
"=",
"\"xml\"",
")",
":",
"self",
".",
"parse",
"(",
"data",
"=",
"doc_str",
",",
"format",
"=",
"format",
")",
"self",
".",
"_ore_initialized",
"=",
"True",
"return",
"self"
] | Parse a OAI-ORE Resource Maps document.
See Also: ``rdflib.ConjunctiveGraph.parse`` for documentation on arguments. | [
"Parse",
"a",
"OAI",
"-",
"ORE",
"Resource",
"Maps",
"document",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L606-L614 |
DataONEorg/d1_python | lib_common/src/d1_common/resource_map.py | ResourceMap._pid_to_id | def _pid_to_id(self, pid):
"""Converts a pid to a URI that can be used as an OAI-ORE identifier."""
return d1_common.url.joinPathElements(
self._base_url,
self._version_tag,
"resolve",
d1_common.url.encodePathElement(pid),
) | python | def _pid_to_id(self, pid):
"""Converts a pid to a URI that can be used as an OAI-ORE identifier."""
return d1_common.url.joinPathElements(
self._base_url,
self._version_tag,
"resolve",
d1_common.url.encodePathElement(pid),
) | [
"def",
"_pid_to_id",
"(",
"self",
",",
"pid",
")",
":",
"return",
"d1_common",
".",
"url",
".",
"joinPathElements",
"(",
"self",
".",
"_base_url",
",",
"self",
".",
"_version_tag",
",",
"\"resolve\"",
",",
"d1_common",
".",
"url",
".",
"encodePathElement",
... | Converts a pid to a URI that can be used as an OAI-ORE identifier. | [
"Converts",
"a",
"pid",
"to",
"a",
"URI",
"that",
"can",
"be",
"used",
"as",
"an",
"OAI",
"-",
"ORE",
"identifier",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/resource_map.py#L618-L625 |
DataONEorg/d1_python | utilities/src/d1_util/check_object_checksums.py | make_checksum_validation_script | def make_checksum_validation_script(stats_list):
"""Make batch files required for checking checksums from another machine."""
if not os.path.exists('./hash_check'):
os.mkdir('./hash_check')
with open('./hash_check/curl.sh', 'w') as curl_f, open(
'./hash_check/md5.txt', 'w'
) as md5_f, o... | python | def make_checksum_validation_script(stats_list):
"""Make batch files required for checking checksums from another machine."""
if not os.path.exists('./hash_check'):
os.mkdir('./hash_check')
with open('./hash_check/curl.sh', 'w') as curl_f, open(
'./hash_check/md5.txt', 'w'
) as md5_f, o... | [
"def",
"make_checksum_validation_script",
"(",
"stats_list",
")",
":",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"'./hash_check'",
")",
":",
"os",
".",
"mkdir",
"(",
"'./hash_check'",
")",
"with",
"open",
"(",
"'./hash_check/curl.sh'",
",",
"'w'",
... | Make batch files required for checking checksums from another machine. | [
"Make",
"batch",
"files",
"required",
"for",
"checking",
"checksums",
"from",
"another",
"machine",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/utilities/src/d1_util/check_object_checksums.py#L113-L160 |
MarkusH/django-osm-field | osm_field/fields.py | LatitudeField.formfield | def formfield(self, **kwargs):
"""
:returns: A :class:`~django.forms.FloatField` with ``max_value`` 90 and
``min_value`` -90.
"""
kwargs.update({
'max_value': 90,
'min_value': -90,
})
return super(LatitudeField, self).formfield(**kwargs... | python | def formfield(self, **kwargs):
"""
:returns: A :class:`~django.forms.FloatField` with ``max_value`` 90 and
``min_value`` -90.
"""
kwargs.update({
'max_value': 90,
'min_value': -90,
})
return super(LatitudeField, self).formfield(**kwargs... | [
"def",
"formfield",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"kwargs",
".",
"update",
"(",
"{",
"'max_value'",
":",
"90",
",",
"'min_value'",
":",
"-",
"90",
",",
"}",
")",
"return",
"super",
"(",
"LatitudeField",
",",
"self",
")",
".",
"for... | :returns: A :class:`~django.forms.FloatField` with ``max_value`` 90 and
``min_value`` -90. | [
":",
"returns",
":",
"A",
":",
"class",
":",
"~django",
".",
"forms",
".",
"FloatField",
"with",
"max_value",
"90",
"and",
"min_value",
"-",
"90",
"."
] | train | https://github.com/MarkusH/django-osm-field/blob/00e6613a93162e781a2b7d404b582ce83802f19a/osm_field/fields.py#L78-L87 |
MarkusH/django-osm-field | osm_field/fields.py | LongitudeField.formfield | def formfield(self, **kwargs):
"""
:returns: A :class:`~django.forms.FloatField` with ``max_value`` 180 and
``min_value`` -180.
"""
kwargs.update({
'max_value': 180,
'min_value': -180,
})
return super(LongitudeField, self).formfield(**k... | python | def formfield(self, **kwargs):
"""
:returns: A :class:`~django.forms.FloatField` with ``max_value`` 180 and
``min_value`` -180.
"""
kwargs.update({
'max_value': 180,
'min_value': -180,
})
return super(LongitudeField, self).formfield(**k... | [
"def",
"formfield",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"kwargs",
".",
"update",
"(",
"{",
"'max_value'",
":",
"180",
",",
"'min_value'",
":",
"-",
"180",
",",
"}",
")",
"return",
"super",
"(",
"LongitudeField",
",",
"self",
")",
".",
"... | :returns: A :class:`~django.forms.FloatField` with ``max_value`` 180 and
``min_value`` -180. | [
":",
"returns",
":",
"A",
":",
"class",
":",
"~django",
".",
"forms",
".",
"FloatField",
"with",
"max_value",
"180",
"and",
"min_value",
"-",
"180",
"."
] | train | https://github.com/MarkusH/django-osm-field/blob/00e6613a93162e781a2b7d404b582ce83802f19a/osm_field/fields.py#L106-L115 |
MarkusH/django-osm-field | osm_field/fields.py | OSMField.formfield | def formfield(self, **kwargs):
"""
:returns: A :class:`~osm_field.forms.OSMFormField` with a
:class:`~osm_field.widgets.OSMWidget`.
"""
widget_kwargs = {
'lat_field': self.latitude_field_name,
'lon_field': self.longitude_field_name,
}
... | python | def formfield(self, **kwargs):
"""
:returns: A :class:`~osm_field.forms.OSMFormField` with a
:class:`~osm_field.widgets.OSMWidget`.
"""
widget_kwargs = {
'lat_field': self.latitude_field_name,
'lon_field': self.longitude_field_name,
}
... | [
"def",
"formfield",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"widget_kwargs",
"=",
"{",
"'lat_field'",
":",
"self",
".",
"latitude_field_name",
",",
"'lon_field'",
":",
"self",
".",
"longitude_field_name",
",",
"}",
"if",
"self",
".",
"data_field_name... | :returns: A :class:`~osm_field.forms.OSMFormField` with a
:class:`~osm_field.widgets.OSMWidget`. | [
":",
"returns",
":",
"A",
":",
"class",
":",
"~osm_field",
".",
"forms",
".",
"OSMFormField",
"with",
"a",
":",
"class",
":",
"~osm_field",
".",
"widgets",
".",
"OSMWidget",
"."
] | train | https://github.com/MarkusH/django-osm-field/blob/00e6613a93162e781a2b7d404b582ce83802f19a/osm_field/fields.py#L199-L218 |
MarkusH/django-osm-field | osm_field/fields.py | OSMField.latitude_field_name | def latitude_field_name(self):
"""
The name of the related :class:`LatitudeField`.
"""
if self._lat_field_name is None:
self._lat_field_name = self.name + '_lat'
return self._lat_field_name | python | def latitude_field_name(self):
"""
The name of the related :class:`LatitudeField`.
"""
if self._lat_field_name is None:
self._lat_field_name = self.name + '_lat'
return self._lat_field_name | [
"def",
"latitude_field_name",
"(",
"self",
")",
":",
"if",
"self",
".",
"_lat_field_name",
"is",
"None",
":",
"self",
".",
"_lat_field_name",
"=",
"self",
".",
"name",
"+",
"'_lat'",
"return",
"self",
".",
"_lat_field_name"
] | The name of the related :class:`LatitudeField`. | [
"The",
"name",
"of",
"the",
"related",
":",
"class",
":",
"LatitudeField",
"."
] | train | https://github.com/MarkusH/django-osm-field/blob/00e6613a93162e781a2b7d404b582ce83802f19a/osm_field/fields.py#L221-L227 |
MarkusH/django-osm-field | osm_field/fields.py | OSMField.longitude_field_name | def longitude_field_name(self):
"""
The name of the related :class:`LongitudeField`.
"""
if self._lon_field_name is None:
self._lon_field_name = self.name + '_lon'
return self._lon_field_name | python | def longitude_field_name(self):
"""
The name of the related :class:`LongitudeField`.
"""
if self._lon_field_name is None:
self._lon_field_name = self.name + '_lon'
return self._lon_field_name | [
"def",
"longitude_field_name",
"(",
"self",
")",
":",
"if",
"self",
".",
"_lon_field_name",
"is",
"None",
":",
"self",
".",
"_lon_field_name",
"=",
"self",
".",
"name",
"+",
"'_lon'",
"return",
"self",
".",
"_lon_field_name"
] | The name of the related :class:`LongitudeField`. | [
"The",
"name",
"of",
"the",
"related",
":",
"class",
":",
"LongitudeField",
"."
] | train | https://github.com/MarkusH/django-osm-field/blob/00e6613a93162e781a2b7d404b582ce83802f19a/osm_field/fields.py#L230-L236 |
genialis/resolwe | resolwe/flow/migrations/0005_data_dependency_3.py | update_dependency_kinds | def update_dependency_kinds(apps, schema_editor):
"""Update historical dependency kinds as they may be wrong."""
DataDependency = apps.get_model('flow', 'DataDependency')
for dependency in DataDependency.objects.all():
# Assume dependency is of subprocess kind.
dependency.kind = 'subprocess'... | python | def update_dependency_kinds(apps, schema_editor):
"""Update historical dependency kinds as they may be wrong."""
DataDependency = apps.get_model('flow', 'DataDependency')
for dependency in DataDependency.objects.all():
# Assume dependency is of subprocess kind.
dependency.kind = 'subprocess'... | [
"def",
"update_dependency_kinds",
"(",
"apps",
",",
"schema_editor",
")",
":",
"DataDependency",
"=",
"apps",
".",
"get_model",
"(",
"'flow'",
",",
"'DataDependency'",
")",
"for",
"dependency",
"in",
"DataDependency",
".",
"objects",
".",
"all",
"(",
")",
":",... | Update historical dependency kinds as they may be wrong. | [
"Update",
"historical",
"dependency",
"kinds",
"as",
"they",
"may",
"be",
"wrong",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/migrations/0005_data_dependency_3.py#L10-L35 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | Environment.escape | def escape(self, value):
"""Escape given value."""
value = soft_unicode(value)
if self._engine._escape is None: # pylint: disable=protected-access
return value
return self._engine._escape(value) | python | def escape(self, value):
"""Escape given value."""
value = soft_unicode(value)
if self._engine._escape is None: # pylint: disable=protected-access
return value
return self._engine._escape(value) | [
"def",
"escape",
"(",
"self",
",",
"value",
")",
":",
"value",
"=",
"soft_unicode",
"(",
"value",
")",
"if",
"self",
".",
"_engine",
".",
"_escape",
"is",
"None",
":",
"# pylint: disable=protected-access",
"return",
"value",
"return",
"self",
".",
"_engine",... | Escape given value. | [
"Escape",
"given",
"value",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L70-L77 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | ExpressionEngine._wrap_jinja_filter | def _wrap_jinja_filter(self, function):
"""Propagate exceptions as undefined values filter."""
def wrapper(*args, **kwargs):
"""Filter wrapper."""
try:
return function(*args, **kwargs)
except Exception: # pylint: disable=broad-except
r... | python | def _wrap_jinja_filter(self, function):
"""Propagate exceptions as undefined values filter."""
def wrapper(*args, **kwargs):
"""Filter wrapper."""
try:
return function(*args, **kwargs)
except Exception: # pylint: disable=broad-except
r... | [
"def",
"_wrap_jinja_filter",
"(",
"self",
",",
"function",
")",
":",
"def",
"wrapper",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"\"\"\"Filter wrapper.\"\"\"",
"try",
":",
"return",
"function",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
... | Propagate exceptions as undefined values filter. | [
"Propagate",
"exceptions",
"as",
"undefined",
"values",
"filter",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L115-L129 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | ExpressionEngine._register_custom_filters | def _register_custom_filters(self):
"""Register any custom filter modules."""
custom_filters = self.settings.get('CUSTOM_FILTERS', [])
if not isinstance(custom_filters, list):
raise KeyError("`CUSTOM_FILTERS` setting must be a list.")
for filter_module_name in custom_filters... | python | def _register_custom_filters(self):
"""Register any custom filter modules."""
custom_filters = self.settings.get('CUSTOM_FILTERS', [])
if not isinstance(custom_filters, list):
raise KeyError("`CUSTOM_FILTERS` setting must be a list.")
for filter_module_name in custom_filters... | [
"def",
"_register_custom_filters",
"(",
"self",
")",
":",
"custom_filters",
"=",
"self",
".",
"settings",
".",
"get",
"(",
"'CUSTOM_FILTERS'",
",",
"[",
"]",
")",
"if",
"not",
"isinstance",
"(",
"custom_filters",
",",
"list",
")",
":",
"raise",
"KeyError",
... | Register any custom filter modules. | [
"Register",
"any",
"custom",
"filter",
"modules",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L131-L154 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | ExpressionEngine._evaluation_context | def _evaluation_context(self, escape, safe_wrapper):
"""Configure the evaluation context."""
self._escape = escape
self._safe_wrapper = safe_wrapper
try:
yield
finally:
self._escape = None
self._safe_wrapper = None | python | def _evaluation_context(self, escape, safe_wrapper):
"""Configure the evaluation context."""
self._escape = escape
self._safe_wrapper = safe_wrapper
try:
yield
finally:
self._escape = None
self._safe_wrapper = None | [
"def",
"_evaluation_context",
"(",
"self",
",",
"escape",
",",
"safe_wrapper",
")",
":",
"self",
".",
"_escape",
"=",
"escape",
"self",
".",
"_safe_wrapper",
"=",
"safe_wrapper",
"try",
":",
"yield",
"finally",
":",
"self",
".",
"_escape",
"=",
"None",
"se... | Configure the evaluation context. | [
"Configure",
"the",
"evaluation",
"context",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L157-L166 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | ExpressionEngine.evaluate_block | def evaluate_block(self, template, context=None, escape=None, safe_wrapper=None):
"""Evaluate a template block."""
if context is None:
context = {}
try:
with self._evaluation_context(escape, safe_wrapper):
template = self._environment.from_string(template... | python | def evaluate_block(self, template, context=None, escape=None, safe_wrapper=None):
"""Evaluate a template block."""
if context is None:
context = {}
try:
with self._evaluation_context(escape, safe_wrapper):
template = self._environment.from_string(template... | [
"def",
"evaluate_block",
"(",
"self",
",",
"template",
",",
"context",
"=",
"None",
",",
"escape",
"=",
"None",
",",
"safe_wrapper",
"=",
"None",
")",
":",
"if",
"context",
"is",
"None",
":",
"context",
"=",
"{",
"}",
"try",
":",
"with",
"self",
".",... | Evaluate a template block. | [
"Evaluate",
"a",
"template",
"block",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L168-L180 |
genialis/resolwe | resolwe/flow/expression_engines/jinja/__init__.py | ExpressionEngine.evaluate_inline | def evaluate_inline(self, expression, context=None, escape=None, safe_wrapper=None):
"""Evaluate an inline expression."""
if context is None:
context = {}
try:
with self._evaluation_context(escape, safe_wrapper):
compiled = self._environment.compile_expre... | python | def evaluate_inline(self, expression, context=None, escape=None, safe_wrapper=None):
"""Evaluate an inline expression."""
if context is None:
context = {}
try:
with self._evaluation_context(escape, safe_wrapper):
compiled = self._environment.compile_expre... | [
"def",
"evaluate_inline",
"(",
"self",
",",
"expression",
",",
"context",
"=",
"None",
",",
"escape",
"=",
"None",
",",
"safe_wrapper",
"=",
"None",
")",
":",
"if",
"context",
"is",
"None",
":",
"context",
"=",
"{",
"}",
"try",
":",
"with",
"self",
"... | Evaluate an inline expression. | [
"Evaluate",
"an",
"inline",
"expression",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/expression_engines/jinja/__init__.py#L182-L192 |
DataONEorg/d1_python | dev_tools/src/d1_dev/util.py | update_module_file | def update_module_file(redbaron_tree, module_path, show_diff=False, dry_run=False):
"""Set show_diff to False to overwrite module_path with a new file generated from
``redbaron_tree``.
Returns True if tree is different from source.
"""
with tempfile.NamedTemporaryFile() as tmp_file:
tmp_fi... | python | def update_module_file(redbaron_tree, module_path, show_diff=False, dry_run=False):
"""Set show_diff to False to overwrite module_path with a new file generated from
``redbaron_tree``.
Returns True if tree is different from source.
"""
with tempfile.NamedTemporaryFile() as tmp_file:
tmp_fi... | [
"def",
"update_module_file",
"(",
"redbaron_tree",
",",
"module_path",
",",
"show_diff",
"=",
"False",
",",
"dry_run",
"=",
"False",
")",
":",
"with",
"tempfile",
".",
"NamedTemporaryFile",
"(",
")",
"as",
"tmp_file",
":",
"tmp_file",
".",
"write",
"(",
"red... | Set show_diff to False to overwrite module_path with a new file generated from
``redbaron_tree``.
Returns True if tree is different from source. | [
"Set",
"show_diff",
"to",
"False",
"to",
"overwrite",
"module_path",
"with",
"a",
"new",
"file",
"generated",
"from",
"redbaron_tree",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/util.py#L54-L71 |
DataONEorg/d1_python | dev_tools/src/d1_dev/util.py | find_repo_root_by_path | def find_repo_root_by_path(path):
"""Given a path to an item in a git repository, find the root of the repository."""
repo = git.Repo(path, search_parent_directories=True)
repo_path = repo.git.rev_parse('--show-toplevel')
logging.info('Repository: {}'.format(repo_path))
return repo_path | python | def find_repo_root_by_path(path):
"""Given a path to an item in a git repository, find the root of the repository."""
repo = git.Repo(path, search_parent_directories=True)
repo_path = repo.git.rev_parse('--show-toplevel')
logging.info('Repository: {}'.format(repo_path))
return repo_path | [
"def",
"find_repo_root_by_path",
"(",
"path",
")",
":",
"repo",
"=",
"git",
".",
"Repo",
"(",
"path",
",",
"search_parent_directories",
"=",
"True",
")",
"repo_path",
"=",
"repo",
".",
"git",
".",
"rev_parse",
"(",
"'--show-toplevel'",
")",
"logging",
".",
... | Given a path to an item in a git repository, find the root of the repository. | [
"Given",
"a",
"path",
"to",
"an",
"item",
"in",
"a",
"git",
"repository",
"find",
"the",
"root",
"of",
"the",
"repository",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/dev_tools/src/d1_dev/util.py#L181-L186 |
DataONEorg/d1_python | client_cli/src/d1_cli/impl/operation_formatter.py | OperationFormatter._format_value | def _format_value(self, operation, key, indent):
"""A value that exists in the operation but has value None is displayed.
A value that does not exist in the operation is left out entirely. The value
name in the operation must match the value name in the template, but the
location does n... | python | def _format_value(self, operation, key, indent):
"""A value that exists in the operation but has value None is displayed.
A value that does not exist in the operation is left out entirely. The value
name in the operation must match the value name in the template, but the
location does n... | [
"def",
"_format_value",
"(",
"self",
",",
"operation",
",",
"key",
",",
"indent",
")",
":",
"v",
"=",
"self",
".",
"_find_value",
"(",
"operation",
",",
"key",
")",
"if",
"v",
"==",
"\"NOT_FOUND\"",
":",
"return",
"[",
"]",
"if",
"not",
"isinstance",
... | A value that exists in the operation but has value None is displayed.
A value that does not exist in the operation is left out entirely. The value
name in the operation must match the value name in the template, but the
location does not have to match. | [
"A",
"value",
"that",
"exists",
"in",
"the",
"operation",
"but",
"has",
"value",
"None",
"is",
"displayed",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/client_cli/src/d1_cli/impl/operation_formatter.py#L94-L121 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/views/headers.py | add_cors_headers | def add_cors_headers(response, request):
"""Add Cross-Origin Resource Sharing (CORS) headers to response.
- ``method_list`` is a list of HTTP methods that are allowed for the endpoint that
was called. It should not include "OPTIONS", which is included automatically
since it's allowed for all endpoi... | python | def add_cors_headers(response, request):
"""Add Cross-Origin Resource Sharing (CORS) headers to response.
- ``method_list`` is a list of HTTP methods that are allowed for the endpoint that
was called. It should not include "OPTIONS", which is included automatically
since it's allowed for all endpoi... | [
"def",
"add_cors_headers",
"(",
"response",
",",
"request",
")",
":",
"opt_method_list",
"=",
"\",\"",
".",
"join",
"(",
"request",
".",
"allowed_method_list",
"+",
"[",
"\"OPTIONS\"",
"]",
")",
"response",
"[",
"\"Allow\"",
"]",
"=",
"opt_method_list",
"respo... | Add Cross-Origin Resource Sharing (CORS) headers to response.
- ``method_list`` is a list of HTTP methods that are allowed for the endpoint that
was called. It should not include "OPTIONS", which is included automatically
since it's allowed for all endpoints. | [
"Add",
"Cross",
"-",
"Origin",
"Resource",
"Sharing",
"(",
"CORS",
")",
"headers",
"to",
"response",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/views/headers.py#L69-L82 |
genialis/resolwe | resolwe/process/runtime.py | Process.run_process | def run_process(self, slug, inputs):
"""Run a new process from a running process."""
def export_files(value):
"""Export input files of spawned process."""
if isinstance(value, str) and os.path.isfile(value):
# TODO: Use the protocol to export files and get the
... | python | def run_process(self, slug, inputs):
"""Run a new process from a running process."""
def export_files(value):
"""Export input files of spawned process."""
if isinstance(value, str) and os.path.isfile(value):
# TODO: Use the protocol to export files and get the
... | [
"def",
"run_process",
"(",
"self",
",",
"slug",
",",
"inputs",
")",
":",
"def",
"export_files",
"(",
"value",
")",
":",
"\"\"\"Export input files of spawned process.\"\"\"",
"if",
"isinstance",
"(",
"value",
",",
"str",
")",
"and",
"os",
".",
"path",
".",
"i... | Run a new process from a running process. | [
"Run",
"a",
"new",
"process",
"from",
"a",
"running",
"process",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/runtime.py#L177-L193 |
genialis/resolwe | resolwe/process/runtime.py | Process.info | def info(self, *args):
"""Log informational message."""
report = resolwe_runtime_utils.info(' '.join([str(x) for x in args]))
# TODO: Use the protocol to report progress.
print(report) | python | def info(self, *args):
"""Log informational message."""
report = resolwe_runtime_utils.info(' '.join([str(x) for x in args]))
# TODO: Use the protocol to report progress.
print(report) | [
"def",
"info",
"(",
"self",
",",
"*",
"args",
")",
":",
"report",
"=",
"resolwe_runtime_utils",
".",
"info",
"(",
"' '",
".",
"join",
"(",
"[",
"str",
"(",
"x",
")",
"for",
"x",
"in",
"args",
"]",
")",
")",
"# TODO: Use the protocol to report progress.",... | Log informational message. | [
"Log",
"informational",
"message",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/runtime.py#L204-L208 |
genialis/resolwe | resolwe/process/runtime.py | Process.get_data_id_by_slug | def get_data_id_by_slug(self, slug):
"""Find data object ID for given slug.
This method queries the Resolwe API and requires network access.
"""
resolwe_host = os.environ.get('RESOLWE_HOST_URL')
url = urllib.parse.urljoin(resolwe_host, '/api/data?slug={}&fields=id'.format(slug))... | python | def get_data_id_by_slug(self, slug):
"""Find data object ID for given slug.
This method queries the Resolwe API and requires network access.
"""
resolwe_host = os.environ.get('RESOLWE_HOST_URL')
url = urllib.parse.urljoin(resolwe_host, '/api/data?slug={}&fields=id'.format(slug))... | [
"def",
"get_data_id_by_slug",
"(",
"self",
",",
"slug",
")",
":",
"resolwe_host",
"=",
"os",
".",
"environ",
".",
"get",
"(",
"'RESOLWE_HOST_URL'",
")",
"url",
"=",
"urllib",
".",
"parse",
".",
"urljoin",
"(",
"resolwe_host",
",",
"'/api/data?slug={}&fields=id... | Find data object ID for given slug.
This method queries the Resolwe API and requires network access. | [
"Find",
"data",
"object",
"ID",
"for",
"given",
"slug",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/runtime.py#L222-L238 |
genialis/resolwe | resolwe/process/runtime.py | Process.requirements | def requirements(self):
"""Process requirements."""
class dotdict(dict): # pylint: disable=invalid-name
"""Dot notation access to dictionary attributes."""
def __getattr__(self, attr):
value = self.get(attr)
return dotdict(value) if isinstance(va... | python | def requirements(self):
"""Process requirements."""
class dotdict(dict): # pylint: disable=invalid-name
"""Dot notation access to dictionary attributes."""
def __getattr__(self, attr):
value = self.get(attr)
return dotdict(value) if isinstance(va... | [
"def",
"requirements",
"(",
"self",
")",
":",
"class",
"dotdict",
"(",
"dict",
")",
":",
"# pylint: disable=invalid-name",
"\"\"\"Dot notation access to dictionary attributes.\"\"\"",
"def",
"__getattr__",
"(",
"self",
",",
"attr",
")",
":",
"value",
"=",
"self",
".... | Process requirements. | [
"Process",
"requirements",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/runtime.py#L245-L254 |
genialis/resolwe | resolwe/process/runtime.py | Process.start | def start(self, inputs):
"""Start the process.
:param inputs: An instance of `Inputs` describing the process inputs
:return: An instance of `Outputs` describing the process outputs
"""
self.logger.info("Process is starting")
outputs = Outputs(self._meta.outputs)
... | python | def start(self, inputs):
"""Start the process.
:param inputs: An instance of `Inputs` describing the process inputs
:return: An instance of `Outputs` describing the process outputs
"""
self.logger.info("Process is starting")
outputs = Outputs(self._meta.outputs)
... | [
"def",
"start",
"(",
"self",
",",
"inputs",
")",
":",
"self",
".",
"logger",
".",
"info",
"(",
"\"Process is starting\"",
")",
"outputs",
"=",
"Outputs",
"(",
"self",
".",
"_meta",
".",
"outputs",
")",
"self",
".",
"logger",
".",
"info",
"(",
"\"Proces... | Start the process.
:param inputs: An instance of `Inputs` describing the process inputs
:return: An instance of `Outputs` describing the process outputs | [
"Start",
"the",
"process",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/process/runtime.py#L256-L279 |
genialis/resolwe | resolwe/flow/execution_engines/python/__init__.py | ExecutionEngine.discover_process | def discover_process(self, path):
"""Perform process discovery in given path.
This method will be called during process registration and
should return a list of dictionaries with discovered process
schemas.
"""
if not path.lower().endswith('.py'):
return []
... | python | def discover_process(self, path):
"""Perform process discovery in given path.
This method will be called during process registration and
should return a list of dictionaries with discovered process
schemas.
"""
if not path.lower().endswith('.py'):
return []
... | [
"def",
"discover_process",
"(",
"self",
",",
"path",
")",
":",
"if",
"not",
"path",
".",
"lower",
"(",
")",
".",
"endswith",
"(",
"'.py'",
")",
":",
"return",
"[",
"]",
"parser",
"=",
"SafeParser",
"(",
"open",
"(",
"path",
")",
".",
"read",
"(",
... | Perform process discovery in given path.
This method will be called during process registration and
should return a list of dictionaries with discovered process
schemas. | [
"Perform",
"process",
"discovery",
"in",
"given",
"path",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/execution_engines/python/__init__.py#L30-L42 |
genialis/resolwe | resolwe/flow/execution_engines/python/__init__.py | ExecutionEngine.evaluate | def evaluate(self, data):
"""Evaluate the code needed to compute a given Data object."""
return 'PYTHONPATH="{runtime}" python3 -u -m resolwe.process {program} --slug {slug} --inputs {inputs}'.format(
runtime=PYTHON_RUNTIME_VOLUME,
program=PYTHON_PROGRAM_VOLUME,
slug=... | python | def evaluate(self, data):
"""Evaluate the code needed to compute a given Data object."""
return 'PYTHONPATH="{runtime}" python3 -u -m resolwe.process {program} --slug {slug} --inputs {inputs}'.format(
runtime=PYTHON_RUNTIME_VOLUME,
program=PYTHON_PROGRAM_VOLUME,
slug=... | [
"def",
"evaluate",
"(",
"self",
",",
"data",
")",
":",
"return",
"'PYTHONPATH=\"{runtime}\" python3 -u -m resolwe.process {program} --slug {slug} --inputs {inputs}'",
".",
"format",
"(",
"runtime",
"=",
"PYTHON_RUNTIME_VOLUME",
",",
"program",
"=",
"PYTHON_PROGRAM_VOLUME",
",... | Evaluate the code needed to compute a given Data object. | [
"Evaluate",
"the",
"code",
"needed",
"to",
"compute",
"a",
"given",
"Data",
"object",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/execution_engines/python/__init__.py#L44-L51 |
genialis/resolwe | resolwe/flow/execution_engines/python/__init__.py | ExecutionEngine.prepare_runtime | def prepare_runtime(self, runtime_dir, data):
"""Prepare runtime directory."""
# Copy over Python process runtime (resolwe.process).
import resolwe.process as runtime_package
src_dir = os.path.dirname(inspect.getsourcefile(runtime_package))
dest_package_dir = os.path.join(runtim... | python | def prepare_runtime(self, runtime_dir, data):
"""Prepare runtime directory."""
# Copy over Python process runtime (resolwe.process).
import resolwe.process as runtime_package
src_dir = os.path.dirname(inspect.getsourcefile(runtime_package))
dest_package_dir = os.path.join(runtim... | [
"def",
"prepare_runtime",
"(",
"self",
",",
"runtime_dir",
",",
"data",
")",
":",
"# Copy over Python process runtime (resolwe.process).",
"import",
"resolwe",
".",
"process",
"as",
"runtime_package",
"src_dir",
"=",
"os",
".",
"path",
".",
"dirname",
"(",
"inspect"... | Prepare runtime directory. | [
"Prepare",
"runtime",
"directory",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/execution_engines/python/__init__.py#L53-L96 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | get_subject_with_local_validation | def get_subject_with_local_validation(jwt_bu64, cert_obj):
"""Validate the JWT and return the subject it contains.
- The JWT is validated by checking that it was signed with a CN certificate.
- The returned subject can be trusted for authz and authn operations.
- Possible validation errors include:
... | python | def get_subject_with_local_validation(jwt_bu64, cert_obj):
"""Validate the JWT and return the subject it contains.
- The JWT is validated by checking that it was signed with a CN certificate.
- The returned subject can be trusted for authz and authn operations.
- Possible validation errors include:
... | [
"def",
"get_subject_with_local_validation",
"(",
"jwt_bu64",
",",
"cert_obj",
")",
":",
"try",
":",
"jwt_dict",
"=",
"validate_and_decode",
"(",
"jwt_bu64",
",",
"cert_obj",
")",
"except",
"JwtException",
"as",
"e",
":",
"return",
"log_jwt_bu64_info",
"(",
"loggin... | Validate the JWT and return the subject it contains.
- The JWT is validated by checking that it was signed with a CN certificate.
- The returned subject can be trusted for authz and authn operations.
- Possible validation errors include:
- A trusted (TLS/SSL) connection could not be made to the C... | [
"Validate",
"the",
"JWT",
"and",
"return",
"the",
"subject",
"it",
"contains",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L54-L88 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | get_subject_with_remote_validation | def get_subject_with_remote_validation(jwt_bu64, base_url):
"""Same as get_subject_with_local_validation() except that the signing certificate
is automatically downloaded from the CN.
- Additional possible validations errors:
- The certificate could not be retrieved from the root CN.
"""
ce... | python | def get_subject_with_remote_validation(jwt_bu64, base_url):
"""Same as get_subject_with_local_validation() except that the signing certificate
is automatically downloaded from the CN.
- Additional possible validations errors:
- The certificate could not be retrieved from the root CN.
"""
ce... | [
"def",
"get_subject_with_remote_validation",
"(",
"jwt_bu64",
",",
"base_url",
")",
":",
"cert_obj",
"=",
"d1_common",
".",
"cert",
".",
"x509",
".",
"download_as_obj",
"(",
"base_url",
")",
"return",
"get_subject_with_local_validation",
"(",
"jwt_bu64",
",",
"cert_... | Same as get_subject_with_local_validation() except that the signing certificate
is automatically downloaded from the CN.
- Additional possible validations errors:
- The certificate could not be retrieved from the root CN. | [
"Same",
"as",
"get_subject_with_local_validation",
"()",
"except",
"that",
"the",
"signing",
"certificate",
"is",
"automatically",
"downloaded",
"from",
"the",
"CN",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L91-L101 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | get_subject_with_file_validation | def get_subject_with_file_validation(jwt_bu64, cert_path):
"""Same as get_subject_with_local_validation() except that the signing certificate
is read from a local PEM file."""
cert_obj = d1_common.cert.x509.deserialize_pem_file(cert_path)
return get_subject_with_local_validation(jwt_bu64, cert_obj) | python | def get_subject_with_file_validation(jwt_bu64, cert_path):
"""Same as get_subject_with_local_validation() except that the signing certificate
is read from a local PEM file."""
cert_obj = d1_common.cert.x509.deserialize_pem_file(cert_path)
return get_subject_with_local_validation(jwt_bu64, cert_obj) | [
"def",
"get_subject_with_file_validation",
"(",
"jwt_bu64",
",",
"cert_path",
")",
":",
"cert_obj",
"=",
"d1_common",
".",
"cert",
".",
"x509",
".",
"deserialize_pem_file",
"(",
"cert_path",
")",
"return",
"get_subject_with_local_validation",
"(",
"jwt_bu64",
",",
"... | Same as get_subject_with_local_validation() except that the signing certificate
is read from a local PEM file. | [
"Same",
"as",
"get_subject_with_local_validation",
"()",
"except",
"that",
"the",
"signing",
"certificate",
"is",
"read",
"from",
"a",
"local",
"PEM",
"file",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L104-L108 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | get_subject_without_validation | def get_subject_without_validation(jwt_bu64):
"""Extract subject from the JWT without validating the JWT.
- The extracted subject cannot be trusted for authn or authz.
Args:
jwt_bu64: bytes
JWT, encoded using a a URL safe flavor of Base64.
Returns:
str: The subject contained in th... | python | def get_subject_without_validation(jwt_bu64):
"""Extract subject from the JWT without validating the JWT.
- The extracted subject cannot be trusted for authn or authz.
Args:
jwt_bu64: bytes
JWT, encoded using a a URL safe flavor of Base64.
Returns:
str: The subject contained in th... | [
"def",
"get_subject_without_validation",
"(",
"jwt_bu64",
")",
":",
"try",
":",
"jwt_dict",
"=",
"get_jwt_dict",
"(",
"jwt_bu64",
")",
"except",
"JwtException",
"as",
"e",
":",
"return",
"log_jwt_bu64_info",
"(",
"logging",
".",
"error",
",",
"str",
"(",
"e",
... | Extract subject from the JWT without validating the JWT.
- The extracted subject cannot be trusted for authn or authz.
Args:
jwt_bu64: bytes
JWT, encoded using a a URL safe flavor of Base64.
Returns:
str: The subject contained in the JWT. | [
"Extract",
"subject",
"from",
"the",
"JWT",
"without",
"validating",
"the",
"JWT",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L111-L131 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | get_jwt_dict | def get_jwt_dict(jwt_bu64):
"""Parse Base64 encoded JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict containing Unicode strings.
- In addition, a SHA1 hash is added to the dict for convenience.
Args:
jwt_bu64:... | python | def get_jwt_dict(jwt_bu64):
"""Parse Base64 encoded JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict containing Unicode strings.
- In addition, a SHA1 hash is added to the dict for convenience.
Args:
jwt_bu64:... | [
"def",
"get_jwt_dict",
"(",
"jwt_bu64",
")",
":",
"jwt_tup",
"=",
"get_jwt_tup",
"(",
"jwt_bu64",
")",
"try",
":",
"jwt_dict",
"=",
"json",
".",
"loads",
"(",
"jwt_tup",
"[",
"0",
"]",
".",
"decode",
"(",
"'utf-8'",
")",
")",
"jwt_dict",
".",
"update",... | Parse Base64 encoded JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict containing Unicode strings.
- In addition, a SHA1 hash is added to the dict for convenience.
Args:
jwt_bu64: bytes
JWT, encoded using a... | [
"Parse",
"Base64",
"encoded",
"JWT",
"and",
"return",
"as",
"a",
"dict",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L181-L203 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | validate_and_decode | def validate_and_decode(jwt_bu64, cert_obj):
"""Validate the JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict.
Args:
jwt_bu64: bytes
The JWT encoded using a a URL safe flavor of Base64.
cert_obj: cr... | python | def validate_and_decode(jwt_bu64, cert_obj):
"""Validate the JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict.
Args:
jwt_bu64: bytes
The JWT encoded using a a URL safe flavor of Base64.
cert_obj: cr... | [
"def",
"validate_and_decode",
"(",
"jwt_bu64",
",",
"cert_obj",
")",
":",
"try",
":",
"return",
"jwt",
".",
"decode",
"(",
"jwt_bu64",
".",
"strip",
"(",
")",
",",
"cert_obj",
".",
"public_key",
"(",
")",
",",
"algorithms",
"=",
"[",
"'RS256'",
"]",
",... | Validate the JWT and return as a dict.
- JWTs contain a set of values serialized to a JSON dict. This decodes the JWT and
returns it as a dict.
Args:
jwt_bu64: bytes
The JWT encoded using a a URL safe flavor of Base64.
cert_obj: cryptography.Certificate
Public certificate us... | [
"Validate",
"the",
"JWT",
"and",
"return",
"as",
"a",
"dict",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L206-L231 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | log_jwt_dict_info | def log_jwt_dict_info(log, msg_str, jwt_dict):
"""Dump JWT to log.
Args:
log: Logger
Logger to which to write the message.
msg_str: str
A message to write to the log before the JWT values.
jwt_dict: dict
JWT containing values to log.
Returns:
None
"""... | python | def log_jwt_dict_info(log, msg_str, jwt_dict):
"""Dump JWT to log.
Args:
log: Logger
Logger to which to write the message.
msg_str: str
A message to write to the log before the JWT values.
jwt_dict: dict
JWT containing values to log.
Returns:
None
"""... | [
"def",
"log_jwt_dict_info",
"(",
"log",
",",
"msg_str",
",",
"jwt_dict",
")",
":",
"d",
"=",
"ts_to_str",
"(",
"jwt_dict",
")",
"# Log known items in specific order, then the rest just sorted",
"log_list",
"=",
"[",
"(",
"b",
",",
"d",
".",
"pop",
"(",
"a",
")... | Dump JWT to log.
Args:
log: Logger
Logger to which to write the message.
msg_str: str
A message to write to the log before the JWT values.
jwt_dict: dict
JWT containing values to log.
Returns:
None | [
"Dump",
"JWT",
"to",
"log",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L234-L261 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | ts_to_str | def ts_to_str(jwt_dict):
"""Convert timestamps in JWT to human readable dates.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with human readable
dates.
"""
d = ts_to_dt(jwt_dict)
f... | python | def ts_to_str(jwt_dict):
"""Convert timestamps in JWT to human readable dates.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with human readable
dates.
"""
d = ts_to_dt(jwt_dict)
f... | [
"def",
"ts_to_str",
"(",
"jwt_dict",
")",
":",
"d",
"=",
"ts_to_dt",
"(",
"jwt_dict",
")",
"for",
"k",
",",
"v",
"in",
"list",
"(",
"d",
".",
"items",
"(",
")",
")",
":",
"if",
"isinstance",
"(",
"v",
",",
"datetime",
".",
"datetime",
")",
":",
... | Convert timestamps in JWT to human readable dates.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with human readable
dates. | [
"Convert",
"timestamps",
"in",
"JWT",
"to",
"human",
"readable",
"dates",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L284-L300 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | ts_to_dt | def ts_to_dt(jwt_dict):
"""Convert timestamps in JWT to datetime objects.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with
datetime.datetime() objects.
"""
d = jwt_dict.copy()
fo... | python | def ts_to_dt(jwt_dict):
"""Convert timestamps in JWT to datetime objects.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with
datetime.datetime() objects.
"""
d = jwt_dict.copy()
fo... | [
"def",
"ts_to_dt",
"(",
"jwt_dict",
")",
":",
"d",
"=",
"jwt_dict",
".",
"copy",
"(",
")",
"for",
"k",
",",
"v",
"in",
"[",
"v",
"[",
":",
"2",
"]",
"for",
"v",
"in",
"CLAIM_LIST",
"if",
"v",
"[",
"2",
"]",
"]",
":",
"if",
"k",
"in",
"jwt_d... | Convert timestamps in JWT to datetime objects.
Args:
jwt_dict: dict
JWT with some keys containing timestamps.
Returns:
dict: Copy of input dict where timestamps have been replaced with
datetime.datetime() objects. | [
"Convert",
"timestamps",
"in",
"JWT",
"to",
"datetime",
"objects",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L303-L319 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | encode_bu64 | def encode_bu64(b):
"""Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of decode_bu64().
Args:
b: bytes
Bytes to Base64 encode.
Returns:
bytes: URL safe Base64 encoded version of input.
"""
s = base64.standard_b64encode(b)
s = s.rstrip('=')
s =... | python | def encode_bu64(b):
"""Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of decode_bu64().
Args:
b: bytes
Bytes to Base64 encode.
Returns:
bytes: URL safe Base64 encoded version of input.
"""
s = base64.standard_b64encode(b)
s = s.rstrip('=')
s =... | [
"def",
"encode_bu64",
"(",
"b",
")",
":",
"s",
"=",
"base64",
".",
"standard_b64encode",
"(",
"b",
")",
"s",
"=",
"s",
".",
"rstrip",
"(",
"'='",
")",
"s",
"=",
"s",
".",
"replace",
"(",
"'+'",
",",
"'-'",
")",
"s",
"=",
"s",
".",
"replace",
... | Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of decode_bu64().
Args:
b: bytes
Bytes to Base64 encode.
Returns:
bytes: URL safe Base64 encoded version of input. | [
"Encode",
"bytes",
"to",
"a",
"URL",
"safe",
"flavor",
"of",
"Base64",
"used",
"by",
"JWTs",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L322-L339 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/jwt.py | decode_bu64 | def decode_bu64(b):
"""Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of encode_bu64().
Args:
b: bytes
URL safe Base64 encoded bytes to encode.
Returns:
bytes: Decoded bytes.
"""
s = b
s = s.replace(b'-', b'+')
s = s.replace(b'_', b'/')
p ... | python | def decode_bu64(b):
"""Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of encode_bu64().
Args:
b: bytes
URL safe Base64 encoded bytes to encode.
Returns:
bytes: Decoded bytes.
"""
s = b
s = s.replace(b'-', b'+')
s = s.replace(b'_', b'/')
p ... | [
"def",
"decode_bu64",
"(",
"b",
")",
":",
"s",
"=",
"b",
"s",
"=",
"s",
".",
"replace",
"(",
"b'-'",
",",
"b'+'",
")",
"s",
"=",
"s",
".",
"replace",
"(",
"b'_'",
",",
"b'/'",
")",
"p",
"=",
"len",
"(",
"s",
")",
"%",
"4",
"if",
"p",
"=="... | Encode bytes to a URL safe flavor of Base64 used by JWTs.
- Reverse of encode_bu64().
Args:
b: bytes
URL safe Base64 encoded bytes to encode.
Returns:
bytes: Decoded bytes. | [
"Encode",
"bytes",
"to",
"a",
"URL",
"safe",
"flavor",
"of",
"Base64",
"used",
"by",
"JWTs",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/jwt.py#L342-L367 |
genialis/resolwe | resolwe/flow/execution_engines/bash/__init__.py | ExecutionEngine.evaluate | def evaluate(self, data):
"""Evaluate the code needed to compute a given Data object."""
try:
inputs = copy.deepcopy(data.input)
hydrate_input_references(inputs, data.process.input_schema)
hydrate_input_uploads(inputs, data.process.input_schema)
# Include... | python | def evaluate(self, data):
"""Evaluate the code needed to compute a given Data object."""
try:
inputs = copy.deepcopy(data.input)
hydrate_input_references(inputs, data.process.input_schema)
hydrate_input_uploads(inputs, data.process.input_schema)
# Include... | [
"def",
"evaluate",
"(",
"self",
",",
"data",
")",
":",
"try",
":",
"inputs",
"=",
"copy",
".",
"deepcopy",
"(",
"data",
".",
"input",
")",
"hydrate_input_references",
"(",
"inputs",
",",
"data",
".",
"process",
".",
"input_schema",
")",
"hydrate_input_uplo... | Evaluate the code needed to compute a given Data object. | [
"Evaluate",
"the",
"code",
"needed",
"to",
"compute",
"a",
"given",
"Data",
"object",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/execution_engines/bash/__init__.py#L54-L87 |
genialis/resolwe | resolwe/flow/execution_engines/bash/__init__.py | ExecutionEngine._escape | def _escape(self, value):
"""Escape given value unless it is safe."""
if isinstance(value, SafeString):
return value
return shellescape.quote(value) | python | def _escape(self, value):
"""Escape given value unless it is safe."""
if isinstance(value, SafeString):
return value
return shellescape.quote(value) | [
"def",
"_escape",
"(",
"self",
",",
"value",
")",
":",
"if",
"isinstance",
"(",
"value",
",",
"SafeString",
")",
":",
"return",
"value",
"return",
"shellescape",
".",
"quote",
"(",
"value",
")"
] | Escape given value unless it is safe. | [
"Escape",
"given",
"value",
"unless",
"it",
"is",
"safe",
"."
] | train | https://github.com/genialis/resolwe/blob/f7bb54932c81ec0cfc5b5e80d238fceaeaa48d86/resolwe/flow/execution_engines/bash/__init__.py#L89-L94 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | open_sciobj_file_by_pid_ctx | def open_sciobj_file_by_pid_ctx(pid, write=False):
"""Open the file containing the Science Object bytes of ``pid`` in the default
location within the tree of the local SciObj store.
If ``write`` is True, the file is opened for writing and any missing directories are
created. Return the file handle and ... | python | def open_sciobj_file_by_pid_ctx(pid, write=False):
"""Open the file containing the Science Object bytes of ``pid`` in the default
location within the tree of the local SciObj store.
If ``write`` is True, the file is opened for writing and any missing directories are
created. Return the file handle and ... | [
"def",
"open_sciobj_file_by_pid_ctx",
"(",
"pid",
",",
"write",
"=",
"False",
")",
":",
"abs_path",
"=",
"get_abs_sciobj_file_path_by_pid",
"(",
"pid",
")",
"with",
"open_sciobj_file_by_path_ctx",
"(",
"abs_path",
",",
"write",
")",
"as",
"sciobj_file",
":",
"yiel... | Open the file containing the Science Object bytes of ``pid`` in the default
location within the tree of the local SciObj store.
If ``write`` is True, the file is opened for writing and any missing directories are
created. Return the file handle and file_url with the file location in a suitable
form for... | [
"Open",
"the",
"file",
"containing",
"the",
"Science",
"Object",
"bytes",
"of",
"pid",
"in",
"the",
"default",
"location",
"within",
"the",
"tree",
"of",
"the",
"local",
"SciObj",
"store",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L74-L87 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | open_sciobj_file_by_path_ctx | def open_sciobj_file_by_path_ctx(abs_path, write=False):
"""Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem.
If ``write`` is True, the file is opened for writing and any missing directores are
created. Return the file handle and file_url wit... | python | def open_sciobj_file_by_path_ctx(abs_path, write=False):
"""Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem.
If ``write`` is True, the file is opened for writing and any missing directores are
created. Return the file handle and file_url wit... | [
"def",
"open_sciobj_file_by_path_ctx",
"(",
"abs_path",
",",
"write",
"=",
"False",
")",
":",
"if",
"write",
":",
"d1_common",
".",
"utils",
".",
"filesystem",
".",
"create_missing_directories_for_file",
"(",
"abs_path",
")",
"try",
":",
"with",
"open",
"(",
"... | Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem.
If ``write`` is True, the file is opened for writing and any missing directores are
created. Return the file handle and file_url with the file location in a suitable
form for storing in the DB... | [
"Open",
"the",
"file",
"containing",
"the",
"Science",
"Object",
"bytes",
"at",
"the",
"custom",
"location",
"abs_path",
"in",
"the",
"local",
"filesystem",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L91-L109 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | open_sciobj_file_by_pid | def open_sciobj_file_by_pid(pid, write=False):
"""Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem for read."""
abs_path = get_abs_sciobj_file_path_by_pid(pid)
if write:
d1_common.utils.filesystem.create_missing_directories_for_file(ab... | python | def open_sciobj_file_by_pid(pid, write=False):
"""Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem for read."""
abs_path = get_abs_sciobj_file_path_by_pid(pid)
if write:
d1_common.utils.filesystem.create_missing_directories_for_file(ab... | [
"def",
"open_sciobj_file_by_pid",
"(",
"pid",
",",
"write",
"=",
"False",
")",
":",
"abs_path",
"=",
"get_abs_sciobj_file_path_by_pid",
"(",
"pid",
")",
"if",
"write",
":",
"d1_common",
".",
"utils",
".",
"filesystem",
".",
"create_missing_directories_for_file",
"... | Open the file containing the Science Object bytes at the custom location
``abs_path`` in the local filesystem for read. | [
"Open",
"the",
"file",
"containing",
"the",
"Science",
"Object",
"bytes",
"at",
"the",
"custom",
"location",
"abs_path",
"in",
"the",
"local",
"filesystem",
"for",
"read",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L134-L140 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | open_sciobj_file_by_path | def open_sciobj_file_by_path(abs_path, write=False):
"""Open a SciObj file for read or write. If opened for write, create any missing
directories. For a SciObj stored in the default SciObj store, the path includes the
PID hash based directory levels.
This is the only method in GMN that opens SciObj fil... | python | def open_sciobj_file_by_path(abs_path, write=False):
"""Open a SciObj file for read or write. If opened for write, create any missing
directories. For a SciObj stored in the default SciObj store, the path includes the
PID hash based directory levels.
This is the only method in GMN that opens SciObj fil... | [
"def",
"open_sciobj_file_by_path",
"(",
"abs_path",
",",
"write",
"=",
"False",
")",
":",
"if",
"write",
":",
"d1_common",
".",
"utils",
".",
"filesystem",
".",
"create_missing_directories_for_file",
"(",
"abs_path",
")",
"return",
"open",
"(",
"abs_path",
",",
... | Open a SciObj file for read or write. If opened for write, create any missing
directories. For a SciObj stored in the default SciObj store, the path includes the
PID hash based directory levels.
This is the only method in GMN that opens SciObj files, so can be modified to
customize the SciObj storage l... | [
"Open",
"a",
"SciObj",
"file",
"for",
"read",
"or",
"write",
".",
"If",
"opened",
"for",
"write",
"create",
"any",
"missing",
"directories",
".",
"For",
"a",
"SciObj",
"stored",
"in",
"the",
"default",
"SciObj",
"store",
"the",
"path",
"includes",
"the",
... | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L143-L158 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | get_rel_sciobj_file_path | def get_rel_sciobj_file_path(pid):
"""Get the relative local path to the file holding an object's bytes.
- The path is relative to settings.OBJECT_STORE_PATH
- There is a one-to-one mapping between pid and path
- The path is based on a SHA1 hash. It's now possible to craft SHA1 collisions, but
it... | python | def get_rel_sciobj_file_path(pid):
"""Get the relative local path to the file holding an object's bytes.
- The path is relative to settings.OBJECT_STORE_PATH
- There is a one-to-one mapping between pid and path
- The path is based on a SHA1 hash. It's now possible to craft SHA1 collisions, but
it... | [
"def",
"get_rel_sciobj_file_path",
"(",
"pid",
")",
":",
"hash_str",
"=",
"hashlib",
".",
"sha1",
"(",
"pid",
".",
"encode",
"(",
"'utf-8'",
")",
")",
".",
"hexdigest",
"(",
")",
"return",
"os",
".",
"path",
".",
"join",
"(",
"hash_str",
"[",
":",
"2... | Get the relative local path to the file holding an object's bytes.
- The path is relative to settings.OBJECT_STORE_PATH
- There is a one-to-one mapping between pid and path
- The path is based on a SHA1 hash. It's now possible to craft SHA1 collisions, but
it's so unlikely that we ignore it for now
... | [
"Get",
"the",
"relative",
"local",
"path",
"to",
"the",
"file",
"holding",
"an",
"object",
"s",
"bytes",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L161-L172 |
DataONEorg/d1_python | gmn/src/d1_gmn/app/sciobj_store.py | get_abs_sciobj_file_path_by_url | def get_abs_sciobj_file_path_by_url(file_url):
"""Get the absolute path to the file holding an object's bytes.
- ``file_url`` is an absolute or relative file:// url as stored in the DB.
"""
assert_sciobj_store_exists()
m = re.match(r'file://(.*?)/(.*)', file_url, re.IGNORECASE)
if m.group(1) =... | python | def get_abs_sciobj_file_path_by_url(file_url):
"""Get the absolute path to the file holding an object's bytes.
- ``file_url`` is an absolute or relative file:// url as stored in the DB.
"""
assert_sciobj_store_exists()
m = re.match(r'file://(.*?)/(.*)', file_url, re.IGNORECASE)
if m.group(1) =... | [
"def",
"get_abs_sciobj_file_path_by_url",
"(",
"file_url",
")",
":",
"assert_sciobj_store_exists",
"(",
")",
"m",
"=",
"re",
".",
"match",
"(",
"r'file://(.*?)/(.*)'",
",",
"file_url",
",",
"re",
".",
"IGNORECASE",
")",
"if",
"m",
".",
"group",
"(",
"1",
")"... | Get the absolute path to the file holding an object's bytes.
- ``file_url`` is an absolute or relative file:// url as stored in the DB. | [
"Get",
"the",
"absolute",
"path",
"to",
"the",
"file",
"holding",
"an",
"object",
"s",
"bytes",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/gmn/src/d1_gmn/app/sciobj_store.py#L254-L265 |
DataONEorg/d1_python | utilities/src/d1_util/find_gmn_instances.py | get_gmn_version | def get_gmn_version(base_url):
"""Return the version currently running on a GMN instance.
(is_gmn, version_or_error)
"""
home_url = d1_common.url.joinPathElements(base_url, 'home')
try:
response = requests.get(home_url, verify=False)
except requests.exceptions.ConnectionError as e:
... | python | def get_gmn_version(base_url):
"""Return the version currently running on a GMN instance.
(is_gmn, version_or_error)
"""
home_url = d1_common.url.joinPathElements(base_url, 'home')
try:
response = requests.get(home_url, verify=False)
except requests.exceptions.ConnectionError as e:
... | [
"def",
"get_gmn_version",
"(",
"base_url",
")",
":",
"home_url",
"=",
"d1_common",
".",
"url",
".",
"joinPathElements",
"(",
"base_url",
",",
"'home'",
")",
"try",
":",
"response",
"=",
"requests",
".",
"get",
"(",
"home_url",
",",
"verify",
"=",
"False",
... | Return the version currently running on a GMN instance.
(is_gmn, version_or_error) | [
"Return",
"the",
"version",
"currently",
"running",
"on",
"a",
"GMN",
"instance",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/utilities/src/d1_util/find_gmn_instances.py#L179-L199 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | extract_subjects | def extract_subjects(subject_info_xml, primary_str):
"""Extract a set of authenticated subjects from a DataONE SubjectInfo.
- See subject_info_tree for details.
Args:
subject_info_xml : str
A SubjectInfo XML document.
primary_str : str
A DataONE subject, typically ... | python | def extract_subjects(subject_info_xml, primary_str):
"""Extract a set of authenticated subjects from a DataONE SubjectInfo.
- See subject_info_tree for details.
Args:
subject_info_xml : str
A SubjectInfo XML document.
primary_str : str
A DataONE subject, typically ... | [
"def",
"extract_subjects",
"(",
"subject_info_xml",
",",
"primary_str",
")",
":",
"subject_info_pyxb",
"=",
"deserialize_subject_info",
"(",
"subject_info_xml",
")",
"subject_info_tree",
"=",
"gen_subject_info_tree",
"(",
"subject_info_pyxb",
",",
"primary_str",
")",
"ret... | Extract a set of authenticated subjects from a DataONE SubjectInfo.
- See subject_info_tree for details.
Args:
subject_info_xml : str
A SubjectInfo XML document.
primary_str : str
A DataONE subject, typically a DataONE compliant serialization of the DN of
t... | [
"Extract",
"a",
"set",
"of",
"authenticated",
"subjects",
"from",
"a",
"DataONE",
"SubjectInfo",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L144-L249 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | deserialize_subject_info | def deserialize_subject_info(subject_info_xml):
"""Deserialize SubjectInfo XML doc to native object.
Args:
subject_info_xml: str
SubjectInfo XML doc
Returns:
SubjectInfo PyXB object
"""
try:
return d1_common.xml.deserialize(subject_info_xml)
except ValueErr... | python | def deserialize_subject_info(subject_info_xml):
"""Deserialize SubjectInfo XML doc to native object.
Args:
subject_info_xml: str
SubjectInfo XML doc
Returns:
SubjectInfo PyXB object
"""
try:
return d1_common.xml.deserialize(subject_info_xml)
except ValueErr... | [
"def",
"deserialize_subject_info",
"(",
"subject_info_xml",
")",
":",
"try",
":",
"return",
"d1_common",
".",
"xml",
".",
"deserialize",
"(",
"subject_info_xml",
")",
"except",
"ValueError",
"as",
"e",
":",
"raise",
"d1_common",
".",
"types",
".",
"exceptions",
... | Deserialize SubjectInfo XML doc to native object.
Args:
subject_info_xml: str
SubjectInfo XML doc
Returns:
SubjectInfo PyXB object | [
"Deserialize",
"SubjectInfo",
"XML",
"doc",
"to",
"native",
"object",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L252-L271 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | gen_subject_info_tree | def gen_subject_info_tree(subject_info_pyxb, authn_subj, include_duplicates=False):
"""Convert the flat, self referential lists in the SubjectInfo to a tree structure.
Args:
subject_info_pyxb: SubjectInfo PyXB object
authn_subj: str
The authenticated subject that becomes the root s... | python | def gen_subject_info_tree(subject_info_pyxb, authn_subj, include_duplicates=False):
"""Convert the flat, self referential lists in the SubjectInfo to a tree structure.
Args:
subject_info_pyxb: SubjectInfo PyXB object
authn_subj: str
The authenticated subject that becomes the root s... | [
"def",
"gen_subject_info_tree",
"(",
"subject_info_pyxb",
",",
"authn_subj",
",",
"include_duplicates",
"=",
"False",
")",
":",
"class",
"State",
":",
"\"\"\"self.\"\"\"",
"pass",
"state",
"=",
"State",
"(",
")",
"state",
".",
"subject_info_pyxb",
"=",
"subject_in... | Convert the flat, self referential lists in the SubjectInfo to a tree structure.
Args:
subject_info_pyxb: SubjectInfo PyXB object
authn_subj: str
The authenticated subject that becomes the root subject in the tree of
subjects built from the SubjectInfo.
Only su... | [
"Convert",
"the",
"flat",
"self",
"referential",
"lists",
"in",
"the",
"SubjectInfo",
"to",
"a",
"tree",
"structure",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L275-L318 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | _trim_tree | def _trim_tree(state):
"""Trim empty leaf nodes from the tree.
- To simplify the tree conversion, empty nodes are added before it is known if they
will contain items that connect back to the authenticated subject. If there are
no connections, the nodes remain empty, which causes them to be removed ... | python | def _trim_tree(state):
"""Trim empty leaf nodes from the tree.
- To simplify the tree conversion, empty nodes are added before it is known if they
will contain items that connect back to the authenticated subject. If there are
no connections, the nodes remain empty, which causes them to be removed ... | [
"def",
"_trim_tree",
"(",
"state",
")",
":",
"for",
"n",
"in",
"list",
"(",
"state",
".",
"tree",
".",
"leaf_node_gen",
")",
":",
"if",
"n",
".",
"type_str",
"==",
"TYPE_NODE_TAG",
":",
"n",
".",
"parent",
".",
"child_list",
".",
"remove",
"(",
"n",
... | Trim empty leaf nodes from the tree.
- To simplify the tree conversion, empty nodes are added before it is known if they
will contain items that connect back to the authenticated subject. If there are
no connections, the nodes remain empty, which causes them to be removed here.
- Removing a leaf n... | [
"Trim",
"empty",
"leaf",
"nodes",
"from",
"the",
"tree",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L378-L392 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | SubjectInfoNode.add_child | def add_child(self, label_str, type_str):
"""Add a child node."""
child_node = SubjectInfoNode(label_str, type_str)
child_node.parent = self
self.child_list.append(child_node)
return child_node | python | def add_child(self, label_str, type_str):
"""Add a child node."""
child_node = SubjectInfoNode(label_str, type_str)
child_node.parent = self
self.child_list.append(child_node)
return child_node | [
"def",
"add_child",
"(",
"self",
",",
"label_str",
",",
"type_str",
")",
":",
"child_node",
"=",
"SubjectInfoNode",
"(",
"label_str",
",",
"type_str",
")",
"child_node",
".",
"parent",
"=",
"self",
"self",
".",
"child_list",
".",
"append",
"(",
"child_node",... | Add a child node. | [
"Add",
"a",
"child",
"node",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L413-L418 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | SubjectInfoNode.get_path_str | def get_path_str(self, sep=os.path.sep, type_str=None):
"""Get path from root to this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
type_str:
SU... | python | def get_path_str(self, sep=os.path.sep, type_str=None):
"""Get path from root to this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
type_str:
SU... | [
"def",
"get_path_str",
"(",
"self",
",",
"sep",
"=",
"os",
".",
"path",
".",
"sep",
",",
"type_str",
"=",
"None",
")",
":",
"return",
"sep",
".",
"join",
"(",
"list",
"(",
"reversed",
"(",
"[",
"v",
".",
"label_str",
"for",
"v",
"in",
"self",
"."... | Get path from root to this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
... | [
"Get",
"path",
"from",
"root",
"to",
"this",
"node",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L452-L478 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | SubjectInfoNode.get_leaf_node_path_list | def get_leaf_node_path_list(self, sep=os.path.sep, type_str=None):
"""Get paths for all leaf nodes for the tree rooted at this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
... | python | def get_leaf_node_path_list(self, sep=os.path.sep, type_str=None):
"""Get paths for all leaf nodes for the tree rooted at this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
... | [
"def",
"get_leaf_node_path_list",
"(",
"self",
",",
"sep",
"=",
"os",
".",
"path",
".",
"sep",
",",
"type_str",
"=",
"None",
")",
":",
"return",
"[",
"v",
".",
"get_path_str",
"(",
"sep",
",",
"type_str",
")",
"for",
"v",
"in",
"self",
".",
"leaf_nod... | Get paths for all leaf nodes for the tree rooted at this node.
Args:
sep: str
One or more characters to insert between each element in the path.
Defaults to "/" on Unix and "\" on Windows.
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None... | [
"Get",
"paths",
"for",
"all",
"leaf",
"nodes",
"for",
"the",
"tree",
"rooted",
"at",
"this",
"node",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L480-L496 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | SubjectInfoNode.get_path_list | def get_path_list(self, type_str=None):
"""Get list of the labels of the nodes leading up to this node from the root.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
... | python | def get_path_list(self, type_str=None):
"""Get list of the labels of the nodes leading up to this node from the root.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
... | [
"def",
"get_path_list",
"(",
"self",
",",
"type_str",
"=",
"None",
")",
":",
"return",
"list",
"(",
"reversed",
"(",
"[",
"v",
".",
"label_str",
"for",
"v",
"in",
"self",
".",
"parent_gen",
"if",
"type_str",
"in",
"(",
"None",
",",
"v",
".",
"type_st... | Get list of the labels of the nodes leading up to this node from the root.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
list of str: The labels of the nodes leading up... | [
"Get",
"list",
"of",
"the",
"labels",
"of",
"the",
"nodes",
"leading",
"up",
"to",
"this",
"node",
"from",
"the",
"root",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L498-L514 |
DataONEorg/d1_python | lib_common/src/d1_common/cert/subject_info.py | SubjectInfoNode.get_label_set | def get_label_set(self, type_str=None):
"""Get a set of label_str for the tree rooted at this node.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
set: The label... | python | def get_label_set(self, type_str=None):
"""Get a set of label_str for the tree rooted at this node.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
set: The label... | [
"def",
"get_label_set",
"(",
"self",
",",
"type_str",
"=",
"None",
")",
":",
"return",
"{",
"v",
".",
"label_str",
"for",
"v",
"in",
"self",
".",
"node_gen",
"if",
"type_str",
"in",
"(",
"None",
",",
"v",
".",
"type_str",
")",
"}"
] | Get a set of label_str for the tree rooted at this node.
Args:
type_str:
SUBJECT_NODE_TAG, TYPE_NODE_TAG or None. If set, only include
information from nodes of that type.
Returns:
set: The labels of the nodes leading up to this node from the roo... | [
"Get",
"a",
"set",
"of",
"label_str",
"for",
"the",
"tree",
"rooted",
"at",
"this",
"node",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/cert/subject_info.py#L521-L533 |
DataONEorg/d1_python | lib_common/src/d1_common/utils/progress_logger.py | ProgressLogger.start_task_type | def start_task_type(self, task_type_str, total_task_count):
"""Call when about to start processing a new type of task, typically just before
entering a loop that processes many task of the given type.
Args:
task_type_str (str):
The name of the task, used as a dict ke... | python | def start_task_type(self, task_type_str, total_task_count):
"""Call when about to start processing a new type of task, typically just before
entering a loop that processes many task of the given type.
Args:
task_type_str (str):
The name of the task, used as a dict ke... | [
"def",
"start_task_type",
"(",
"self",
",",
"task_type_str",
",",
"total_task_count",
")",
":",
"assert",
"(",
"task_type_str",
"not",
"in",
"self",
".",
"_task_dict",
")",
",",
"\"Task type has already been started\"",
"self",
".",
"_task_dict",
"[",
"task_type_str... | Call when about to start processing a new type of task, typically just before
entering a loop that processes many task of the given type.
Args:
task_type_str (str):
The name of the task, used as a dict key and printed in the progress
updates.
tot... | [
"Call",
"when",
"about",
"to",
"start",
"processing",
"a",
"new",
"type",
"of",
"task",
"typically",
"just",
"before",
"entering",
"a",
"loop",
"that",
"processes",
"many",
"task",
"of",
"the",
"given",
"type",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/utils/progress_logger.py#L126-L151 |
DataONEorg/d1_python | lib_common/src/d1_common/utils/progress_logger.py | ProgressLogger.end_task_type | def end_task_type(self, task_type_str):
"""Call when processing of all tasks of the given type is completed, typically
just after exiting a loop that processes many tasks of the given type.
Progress messages logged at intervals will typically not include the final entry
which shows that... | python | def end_task_type(self, task_type_str):
"""Call when processing of all tasks of the given type is completed, typically
just after exiting a loop that processes many tasks of the given type.
Progress messages logged at intervals will typically not include the final entry
which shows that... | [
"def",
"end_task_type",
"(",
"self",
",",
"task_type_str",
")",
":",
"assert",
"(",
"task_type_str",
"in",
"self",
".",
"_task_dict",
")",
",",
"\"Task type has not been started yet: {}\"",
".",
"format",
"(",
"task_type_str",
")",
"self",
".",
"_log_progress",
"(... | Call when processing of all tasks of the given type is completed, typically
just after exiting a loop that processes many tasks of the given type.
Progress messages logged at intervals will typically not include the final entry
which shows that processing is 100% complete, so a final progress m... | [
"Call",
"when",
"processing",
"of",
"all",
"tasks",
"of",
"the",
"given",
"type",
"is",
"completed",
"typically",
"just",
"after",
"exiting",
"a",
"loop",
"that",
"processes",
"many",
"tasks",
"of",
"the",
"given",
"type",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/utils/progress_logger.py#L155-L168 |
DataONEorg/d1_python | lib_common/src/d1_common/utils/progress_logger.py | ProgressLogger.start_task | def start_task(self, task_type_str, current_task_index=None):
"""Call when processing is about to start on a single task of the given task
type, typically at the top inside of the loop that processes the tasks.
Args:
task_type_str (str):
The name of the task, used as... | python | def start_task(self, task_type_str, current_task_index=None):
"""Call when processing is about to start on a single task of the given task
type, typically at the top inside of the loop that processes the tasks.
Args:
task_type_str (str):
The name of the task, used as... | [
"def",
"start_task",
"(",
"self",
",",
"task_type_str",
",",
"current_task_index",
"=",
"None",
")",
":",
"assert",
"(",
"task_type_str",
"in",
"self",
".",
"_task_dict",
")",
",",
"\"Task type has not been started yet: {}\"",
".",
"format",
"(",
"task_type_str",
... | Call when processing is about to start on a single task of the given task
type, typically at the top inside of the loop that processes the tasks.
Args:
task_type_str (str):
The name of the task, used as a dict key and printed in the progress
updates.
... | [
"Call",
"when",
"processing",
"is",
"about",
"to",
"start",
"on",
"a",
"single",
"task",
"of",
"the",
"given",
"task",
"type",
"typically",
"at",
"the",
"top",
"inside",
"of",
"the",
"loop",
"that",
"processes",
"the",
"tasks",
"."
] | train | https://github.com/DataONEorg/d1_python/blob/3ac4d4f3ca052d3e8641a6a329cab526c8ddcb0d/lib_common/src/d1_common/utils/progress_logger.py#L171-L193 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.