job_spec

job_spec#

Classes:

`Connection`	Job input connection details.
`Input`	Job input connection details.
`InputResult`	Concrete job input result connection to an output result.
`InputSlot`	Specification of an input slot in the job configuration.
`InputSpec`	Input specification.
`InputSpecs`	Dictionary of input specifications, where each key is the input name.
`Inputs`	Dictionary of job input connection details, where each key is the input name.
`JobBuildError`
`JobRegisterError`	Error that occurs when loading a developer job register.
`JobSpec`	Job's unique specification details.
`Output`	Job output details.
`OutputRef`	Minimal name reference to a specific job output
`OutputResult`	Concrete job output.
`OutputSlot`	Specification of an output slot in the job configuration.
`OutputSpec`	Used for outputs with some generated data based on data forwarded from input inheritance
`OutputSpecs`	Dictionary of output specifications, where each key is the output name.
`Outputs`	Dictionary of job output details, where each key is the output name.
`Params`	Job parameter specifications.

BuilderTag(*args, **kwargs)#

Visual indicators for jobs in the builder.

alias of Literal[‘new’, ‘interactive’, ‘gpuEnabled’, ‘multiGpu’, ‘utility’, ‘import’, ‘live’, ‘benchmark’, ‘wrapper’]

Category(*args, **kwargs)#

Section under which to group a job in the builder.

alias of Literal[‘import’, ‘motion_correction’, ‘ctf_estimation’, ‘exposure_curation’, ‘particle_picking’, ‘extraction’, ‘deep_picker’, ‘particle_curation’, ‘reconstruction’, ‘refinement’, ‘ctf_refinement’, ‘variability’, ‘flexibility’, ‘postprocessing’, ‘local_refinement’, ‘helix’, ‘utilities’, ‘simulations’, ‘live’, ‘instance_testing’, ‘workflows’]

class Connection#

Job input connection details.

Attributes:

`job_uid`	Connected parent output job uid.
`output`	Name of output on connected parent output job.
`results`	Specific results from parent job.

job_uid: str#: Connected parent output job uid.

output: str#: Name of output on connected parent output job.

results: List[InputResult]#: Specific results from parent job. Some slots may have a different job UID.

class Input#

Job input connection details.

Attributes:

`connections`	Connected output details
`count_max`	Maximum number of connections supported for this input.
`count_min`	Minimum number of connections to this input.
`description`	Detailed description.
`repeat_allowed`	Whether repeated connections to the same output allowed for this input.
`slots`	Expected low-level input definitions
`title`	Human-readable title
`type`	Cryo-EM native data type, e.g., "exposure", "particle" or "volume"

connections: List[Connection]#: Connected output details

count_max: int | Literal['inf']#: Maximum number of connections supported for this input. Should be any integer >= 0 and <= 500. Inputs with a count_max set to "inf" also support a maximum of 500 connections.

count_min: int#: Minimum number of connections to this input.

description: str#: Detailed description.

repeat_allowed: bool#: Whether repeated connections to the same output allowed for this input.

slots: List[InputSlot]#: Expected low-level input definitions

title: str#: Human-readable title

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']#: Cryo-EM native data type, e.g., “exposure”, “particle” or “volume”

class InputResult#

Concrete job input result connection to an output result.

Attributes:

`dtype`	Datatype-specific string from data_registry.py.
`job_uid`	Parent job UID source of this input slot connection.
`name`	Input slot name.
`output`	Name of output in parent job.
`result`	Name of output result slot in parent job, e.g., "blob".
`version`	Version number or specifier to use.

dtype: str#: Datatype-specific string from data_registry.py. e.g., stat_blob, ctf, alignments2D.

job_uid: str#: Parent job UID source of this input slot connection.

name: str | None#: Input slot name. Passthrough slots have name set to None.

output: str#: Name of output in parent job. e.g., “particles”

result: str#: Name of output result slot in parent job, e.g., “blob”. Usually the same as “name” but may differ if there are multiple outputs of the same type

version: int | Literal['F']#: Version number or specifier to use. Usually “F”

class InputSlot#

Specification of an input slot in the job configuration. Each input includes one or more.

Attributes:

`dtype`	Datatype-specific string from data_registry.py.
`name`	where to find field in a corresponding .cs file e.g., background_blob
`required`	whether this field must necessarily exist in acorresponding input/output

dtype: str#: Datatype-specific string from data_registry.py. e.g., stat_blob, ctf, alignments2D.

name: str#: where to find field in a corresponding .cs file e.g., background_blob

required: bool#: whether this field must necessarily exist in acorresponding input/output

class InputSpec#

Input specification. Used to define the expected connections to a job input.

Attributes:

`count_max`	Maximum number of connections supported for this input.
`count_min`	Minimum number of connections to this input.
`description`	Detailed description.
`repeat_allowed`	Whether repeated connections to the same output allowed for this input.
`slots`	Expected input/output result slots.
`title`	Human-readable title
`type`	Cryo-EM native data type, e.g., "exposure", "particle" or "volume"

count_max: int | Literal['inf']#: Maximum number of connections supported for this input. Should be any integer >= 0 and <= 500. Inputs with a count_max set to "inf" also support a maximum of 500 connections.

count_min: int#: Minimum number of connections to this input.

description: str#: Detailed description.

repeat_allowed: bool#: Whether repeated connections to the same output allowed for this input.

slots: List[InputSlot | str]#

Expected input/output result slots.

“str” is a shortcut for Slot(dtype="str", "prefix="str")

For input specs: “str” is a shortcut for InputSlot(dtype="str", "prefix="str", required=True) “?str” is a shortcut for InputSlot(dtype="str", "prefix="str", required=False)

title: str#: Human-readable title

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']#: Cryo-EM native data type, e.g., “exposure”, “particle” or “volume”

class InputSpecs#

Dictionary of input specifications, where each key is the input name.

Attributes:

root

Dictionary of input specifications, where each key is the input name.

root: Dict[str, InputSpec]#: Dictionary of input specifications, where each key is the input name.

class Inputs#

Dictionary of job input connection details, where each key is the input name.

Attributes:

root

Dictionary of job input connection details, where each key is the input name.

root: Dict[str, Input]#: Dictionary of job input connection details, where each key is the input name.

class JobBuildError#

Attributes:

`ctx`	error context for pydantic
`input`	value of the invalid property - must be serializable
`input_type`
`loc`	path to the invalid property
`type`	//docs.pydantic.dev/latest/errors/validation_errors

ctx: Dict[str, Any]#: error context for pydantic

input: Any#: value of the invalid property - must be serializable

input_type: str#

loc: List[str | int]#: path to the invalid property

type: Literal['no_such_attribute', 'json_invalid', 'json_type', 'needs_python_object', 'recursion_loop', 'missing', 'frozen_field', 'frozen_instance', 'extra_forbidden', 'invalid_key', 'get_attribute_error', 'model_type', 'model_attributes_type', 'dataclass_type', 'dataclass_exact_type', 'none_required', 'greater_than', 'greater_than_equal', 'less_than', 'less_than_equal', 'multiple_of', 'finite_number', 'too_short', 'too_long', 'iterable_type', 'iteration_error', 'string_type', 'string_sub_type', 'string_unicode', 'string_too_short', 'string_too_long', 'string_pattern_mismatch', 'enum', 'dict_type', 'mapping_type', 'list_type', 'tuple_type', 'set_type', 'set_item_not_hashable', 'bool_type', 'bool_parsing', 'int_type', 'int_parsing', 'int_parsing_size', 'int_from_float', 'float_type', 'float_parsing', 'bytes_type', 'bytes_too_short', 'bytes_too_long', 'bytes_invalid_encoding', 'value_error', 'assertion_error', 'literal_error', 'date_type', 'date_parsing', 'date_from_datetime_parsing', 'date_from_datetime_inexact', 'date_past', 'date_future', 'time_type', 'time_parsing', 'datetime_type', 'datetime_parsing', 'datetime_object_invalid', 'datetime_from_date_parsing', 'datetime_past', 'datetime_future', 'timezone_naive', 'timezone_aware', 'timezone_offset', 'time_delta_type', 'time_delta_parsing', 'frozen_set_type', 'is_instance_of', 'is_subclass_of', 'callable_type', 'union_tag_invalid', 'union_tag_not_found', 'arguments_type', 'missing_argument', 'unexpected_keyword_argument', 'missing_keyword_only_argument', 'unexpected_positional_argument', 'missing_positional_only_argument', 'multiple_argument_values', 'url_type', 'url_parsing', 'url_syntax_violation', 'url_too_long', 'url_scheme', 'uuid_type', 'uuid_parsing', 'uuid_version', 'decimal_type', 'decimal_parsing', 'decimal_max_digits', 'decimal_max_places', 'decimal_whole_digits', 'complex_type', 'complex_str_parsing']#

//docs.pydantic.dev/latest/errors/validation_errors

Type:: values based on https

class JobRegisterError#

Error that occurs when loading a developer job register.

Attributes:

`message`
`traceback`
`type`

message: str#

traceback: str#

type: str#

class JobSpec#

Job’s unique specification details. Defines the parameters, inputs, outputs and required resources. Contents vary by job type, configured parameters and connected inputs.

Attributes:

`inputs`	Connected inputs
`outputs`	Available outputs.
`params`	Parameters for job, attributes vary per job type.
`resource_spec`	Compute resource requirements for this job.
`type`	Job type key, e.g., "import_particles" or "class_2D_new"
`ui_tile_height`	Number of vertical tiles this job should take in the UI.
`ui_tile_width`	Number of horizontal tiles this job should take in the UI.

inputs: Inputs#: Connected inputs

outputs: Outputs#: Available outputs. Empty when job has not run.

params: Params#

Parameters for job, attributes vary per job type.

NOTE: After changing a job parameter, the spec may need to be refreshed. Instead of directly modifying this field with job.params.foo = … , use job.set_param(“foo”, …) instead.

resource_spec: ResourceSpec#: Compute resource requirements for this job.

type: str#: Job type key, e.g., “import_particles” or “class_2D_new”

ui_tile_height: int#: Number of vertical tiles this job should take in the UI.

ui_tile_width: int#: Number of horizontal tiles this job should take in the UI.

class Output#

Job output details. Includes saved dataset paths and summary statistics.

Attributes:

`description`	Detailed description.
`image`	Asset ID of thumbnail for this output
`latest_summary_stats`	Additional context-specific summary statistics
`num_items`	Number of items in final version file
`passthrough`	Associated passthrough input name
`results`	All individial outputs based on available output slots
`slots`	Low-level output result definitions.
`summary`	Result dataset summary data
`title`	Human-readable title
`type`	Cryo-EM native data type, e.g., "exposure", "particle" or "volume"

description: str#: Detailed description.

image: str | None#: Asset ID of thumbnail for this output

latest_summary_stats: Dict[str, Any]#: Additional context-specific summary statistics

num_items: int#: Number of items in final version file

passthrough: str | None#: Associated passthrough input name

results: List[OutputResult]#: All individial outputs based on available output slots

slots: List[OutputSlot]#: Low-level output result definitions.

summary: Dict[str, Any]#: Result dataset summary data

title: str#: Human-readable title

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']#: Cryo-EM native data type, e.g., “exposure”, “particle” or “volume”

class OutputRef#

Minimal name reference to a specific job output

Attributes:

`job_uid`	Connected parent output job uid.
`output`	Name of output on connected parent output job.

job_uid: str#: Connected parent output job uid.

output: str#: Name of output on connected parent output job.

class OutputResult#

Concrete job output.

Attributes:

`dtype`	Datatype-specific string from data_registry.py.
`metafiles`	List of available intermediate result files (same size as `versions`).
`name`	where to find field in a corresponding .cs file e.g., background_blob
`num_items`	Number of rows in each metafile
`passthrough`	If True, this result is passed through as-is from an associated input.
`versions`	List of available intermediate result version numbers.

dtype: str#: Datatype-specific string from data_registry.py. e.g., stat_blob, ctf, alignments2D.

metafiles: List[str]#: List of available intermediate result files (same size as versions).

name: str#: where to find field in a corresponding .cs file e.g., background_blob

num_items: List[int]#: Number of rows in each metafile

passthrough: bool#: If True, this result is passed through as-is from an associated input.

versions: List[int]#: List of available intermediate result version numbers.

class OutputSlot#

Specification of an output slot in the job configuration. Each output includes one or more.

Attributes:

`dtype`	Datatype-specific string from data_registry.py.
`name`	where to find field in a corresponding .cs file e.g., background_blob

dtype: str#: Datatype-specific string from data_registry.py. e.g., stat_blob, ctf, alignments2D.

name: str#: where to find field in a corresponding .cs file e.g., background_blob

class OutputSpec#

Used for outputs with some generated data based on data forwarded from input inheritance

Attributes:

`description`	Detailed description.
`passthrough`	Associated passthrough input name
`slots`	Expected input/output result slots.
`title`	Human-readable title
`type`	Cryo-EM native data type, e.g., "exposure", "particle" or "volume"

description: str#: Detailed description.

passthrough: str | None#: Associated passthrough input name

slots: List[OutputSlot | str]#

Expected input/output result slots.

“str” is a shortcut for Slot(dtype="str", "prefix="str")

For input specs: “str” is a shortcut for InputSlot(dtype="str", "prefix="str", required=True) “?str” is a shortcut for InputSlot(dtype="str", "prefix="str", required=False)

title: str#: Human-readable title

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']#: Cryo-EM native data type, e.g., “exposure”, “particle” or “volume”

class OutputSpecs#

Dictionary of output specifications, where each key is the output name.

Attributes:

root

Dictionary of output specifications, where each key is the output name.

root: Dict[str, OutputSpec]#: Dictionary of output specifications, where each key is the output name.

class Outputs#

Dictionary of job output details, where each key is the output name.

Attributes:

root

Dictionary of job output details, where each key is the output name.

root: Dict[str, Output]#: Dictionary of job output details, where each key is the output name.

class Params#: Job parameter specifications. See API function projects.get_job_register for allowed parameters based on job spec type.

Stability(*args, **kwargs)#

Lifecycle/development stage for a job. Jobs will change stabilities as they are continually developed or replaced with other jobs.

alias of Literal[‘develop’, ‘beta’, ‘stable’, ‘legacy’, ‘obsolete’]