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Updated typeshed defs for Galaxy-lib?
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128 files changed

+2746
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‎typeshed/2.7/galaxy/__init__.pyi

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# Stubs for galaxy (Python 3.5)
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# Stubs for galaxy (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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‎typeshed/2.7/galaxy/exceptions/__init__.pyi

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# Stubs for galaxy.exceptions (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any, Optional
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from ..exceptions import error_codes as error_codes
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class MessageException(Exception):
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status_code = ... # type: int
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err_code = ... # type: Any
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err_msg = ... # type: Any
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type = ... # type: Any
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extra_error_info = ... # type: Any
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def __init__(self, err_msg: Optional[Any] = ..., type: str = ..., **extra_error_info) -> None: ...
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class ItemDeletionException(MessageException): ...
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class ObjectInvalid(Exception): ...
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class ActionInputError(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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def __init__(self, err_msg, type: str = ...) -> None: ...
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class DuplicatedSlugException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class DuplicatedIdentifierException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ObjectAttributeInvalidException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ObjectAttributeMissingException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class MalformedId(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class MalformedContents(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class UnknownContentsType(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class RequestParameterMissingException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ToolMetaParameterException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ToolMissingException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class RequestParameterInvalidException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class AuthenticationFailed(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class AuthenticationRequired(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ItemAccessibilityException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ItemOwnershipException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ConfigDoesNotAllowException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class InsufficientPermissionsException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class AdminRequiredException(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ObjectNotFound(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class DeprecatedMethod(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class Conflict(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ConfigurationError(Exception):
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status_code = ... # type: int
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err_code = ... # type: Any
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class InconsistentDatabase(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class InternalServerError(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class NotImplemented(MessageException):
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status_code = ... # type: int
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err_code = ... # type: Any
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class ContainerCLIError(Exception):
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stdout = ... # type: Any
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stderr = ... # type: Any
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returncode = ... # type: Any
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command = ... # type: Any
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subprocess_command = ... # type: Any
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def __init__(self, msg: Optional[Any] = ..., stdout: Optional[Any] = ..., stderr: Optional[Any] = ..., returncode: Optional[Any] = ..., command: Optional[Any] = ..., subprocess_command: Optional[Any] = ..., **kwargs) -> None: ...
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class ContainerNotFound(Exception):
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container_id = ... # type: Any
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def __init__(self, msg: Optional[Any] = ..., container_id: Optional[Any] = ..., **kwargs) -> None: ...
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class ContainerImageNotFound(Exception):
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image = ... # type: Any
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def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., **kwargs) -> None: ...
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class ContainerRunError(Exception):
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image = ... # type: Any
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command = ... # type: Any
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def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., command: Optional[Any] = ..., **kwargs) -> None: ...

‎typeshed/2.7/galaxy/exceptions/error_codes.pyi

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# Stubs for galaxy.exceptions.error_codes (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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UNKNOWN_ERROR_MESSAGE = ... # type: str
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class ErrorCode:
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code = ... # type: Any
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default_error_message = ... # type: Any
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def __init__(self, code, default_error_message) -> None: ...
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def __int__(self): ...
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error_codes_json = ... # type: Any
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name = ... # type: Any
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error_code_obj = ... # type: Any

‎typeshed/2.7/galaxy/jobs/__init__.pyi

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# Stubs for galaxy.jobs (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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‎typeshed/2.7/galaxy/jobs/metrics/__init__.pyi

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# Stubs for galaxy.jobs.metrics (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any, Optional
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from ..metrics import formatting as formatting
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log = ... # type: Any
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DEFAULT_FORMATTER = ... # type: Any
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class JobMetrics:
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plugin_classes = ... # type: Any
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default_job_instrumenter = ... # type: Any
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job_instrumenters = ... # type: Any
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def __init__(self, conf_file: Optional[Any] = ..., **kwargs) -> None: ...
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def format(self, plugin, key, value): ...
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def set_destination_conf_file(self, destination_id, conf_file): ...
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def set_destination_conf_element(self, destination_id, element): ...
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def set_destination_instrumenter(self, destination_id, job_instrumenter: Optional[Any] = ...): ...
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def collect_properties(self, destination_id, job_id, job_directory): ...
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class NullJobInstrumenter:
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def pre_execute_commands(self, job_directory): ...
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def post_execute_commands(self, job_directory): ...
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def collect_properties(self, job_id, job_directory): ...
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NULL_JOB_INSTRUMENTER = ... # type: Any
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class JobInstrumenter:
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extra_kwargs = ... # type: Any
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plugin_classes = ... # type: Any
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plugins = ... # type: Any
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def __init__(self, plugin_classes, plugins_source, **kwargs) -> None: ...
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def pre_execute_commands(self, job_directory): ...
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def post_execute_commands(self, job_directory): ...
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def collect_properties(self, job_id, job_directory): ...
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@staticmethod
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def from_file(plugin_classes, conf_file, **kwargs): ...

‎typeshed/2.7/galaxy/jobs/metrics/collectl/__init__.pyi

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# Stubs for galaxy.jobs.metrics.collectl (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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‎typeshed/2.7/galaxy/jobs/metrics/collectl/cli.pyi

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# Stubs for galaxy.jobs.metrics.collectl.cli (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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class CollectlCli:
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mode = ... # type: Any
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command_args = ... # type: Any
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def __init__(self, **kwargs) -> None: ...
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def build_command_line(self): ...
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def run(self, stdout: Any = ..., stderr: Any = ...): ...

‎typeshed/2.7/galaxy/jobs/metrics/collectl/processes.pyi

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# Stubs for galaxy.jobs.metrics.collectl.processes (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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def generate_process_statistics(collectl_playback_cli, pid, statistics: Any = ...): ...
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class CollectlProcessSummarizer:
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pid = ... # type: Any
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statistics = ... # type: Any
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columns_of_interest = ... # type: Any
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tree_statistics = ... # type: Any
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process_accum_statistics = ... # type: Any
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interval_count = ... # type: int
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def __init__(self, pid, statistics) -> None: ...
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def handle_interval(self, interval): ...
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def get_statistics(self): ...
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class CollectlProcessInterval:
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rows = ... # type: Any
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def __init__(self) -> None: ...
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def row_is_in(self, row): ...
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def add_row(self, row): ...

‎typeshed/2.7/galaxy/jobs/metrics/collectl/stats.pyi

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# Stubs for galaxy.jobs.metrics.collectl.stats (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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from typing import Any
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class StatisticsTracker:
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min = ... # type: Any
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max = ... # type: Any
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count = ... # type: int
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sum = ... # type: int
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def __init__(self) -> None: ...
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def track(self, value): ...
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@property
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def avg(self): ...

‎typeshed/2.7/galaxy/jobs/metrics/collectl/subsystems.pyi

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# Stubs for galaxy.jobs.metrics.collectl.subsystems (Python 3.4)
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#
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# NOTE: This dynamically typed stub was automatically generated by stubgen.
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class CollectlSubsystem:
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@property
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def command_line_arg(self): ...
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@property
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def name(self, job_directory): ...
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class ProcessesSubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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class CpuSubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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class DiskSubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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class NetworkSubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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class EnvironmentSubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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class MemorySubsystem(CollectlSubsystem):
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command_line_arg = ... # type: str
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name = ... # type: str
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def get_subsystem(name): ...

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