cryosparc.spec

Type specifications for CryoSPARC database entities.

Unless otherwise noted, classes defined here represent dictionary instances whose attributes may be accessed with dictionary key syntax.

Examples

Accessing job document details

>>> cs = CryoSPARC()
>>> job = cs.find_job("P3", "J118")
>>> job.doc["output_results"][0]["metafiles"]
[
  "J118/J118_000_particles.cs",
  "J118/J118_001_particles.cs",
  "J118/J118_002_particles.cs",
  "J118/J118_003_particles.cs"
]

Classes:

AssetDetails	Result of job asset files query.
BaseParam	Base parameter specification.
BaseSchedulerTarget	Properties shared by both node and cluster scheduler targets.
Connection	Connection element specified in a Job document's input_slot_groups[].connections list.
ConnectionSlot	Slots specified entry in a Job document's input_slot_groups[].connections[].slots list.
Datafield	Definition of a prefix field within a CS file.
EnumParam	Additional Param keys available for enum params.
EventLogAsset	Dictionary item in a job event log's imgfiles property (in the events collection).
FixedResourceSlots	Available resource slots that only indicate presence, not the amount that may be allocated.
Gpu	GPU details for a target.
InputSlot	Dictionary entry in Job document's input_slot_groups.slots property.
InputSlotGroup	Element specified in a Job document's input_slot_groups list.
JobDocument	Specification for a Job document from the MongoDB database.
JobSection	Specification of available job types of a certain category.
JobSpec	Specification for a Job document from the CryoSPARC's job register.
JobSpecSection	Similar to JobSection, except each item in contains is a detailed JobSpec.
OutputResult	Detailed schema and metadata for a Job document's output_results list.
OutputResultGroup	Elements of a Job document's output_result_groups list.
OutputResultGroupContains	Elements of a Job document's output_result_groups[].contains list.
Param	Specifies possible values for type property.
ParamSection	Param section specification
ParamSpec	Param specification.
PathParam	Additional Param key available for path params.
ProjectDocument	Specification for a project document in the MongoDB database.
ProjectLastAccessed	Details on when a project was last accessed.
ResourceSlots	Listings of available resources on a worker node that may be allocated for scheduling.
SchedulerLane	Description for a CryoSPARC scheduler lane.
SchedulerTargetCluster	Cluster-type scheduler targets.
SchedulerTargetGpuNode	node-type scheduler target that includes GPUs.
SchedulerTargetNode	node-type scheduler target that does not include GPUs.
WorkspaceDocument	Specification for a Workspace document from the MongoDB database.

cryosparc.spec.AssetContentType(*args, **kwargs)

Supported job asset MIME types.

alias of Literal[‘text/plain’, ‘text/csv’, ‘text/html’, ‘application/json’, ‘application/xml’, ‘application/x-troff’] | Literal[‘application/pdf’, ‘image/gif’, ‘image/jpeg’, ‘image/png’, ‘image/svg+xml’] | Literal[‘application/octet-stream’]

class cryosparc.spec.AssetDetails

Result of job asset files query. Keys may be accessed with dictionary syntax.

Examples

>>> print(details['filename'])
image.png

Attributes:

chunkSize	File chunk size in bytes
contentType	Asset content type, e.g., "image/png"
filename	File name
job_uid	Associated job or session UID
length	Size of file in bytes
md5	MD5 hash of asset
project_uid	Associated project UID
uploadDate	ISO 8601-formatted asset upload date

chunkSize: int

File chunk size in bytes

contentType: Literal['text/plain', 'text/csv', 'text/html', 'application/json', 'application/xml', 'application/x-troff', 'application/pdf', 'image/gif', 'image/jpeg', 'image/png', 'image/svg+xml', 'application/octet-stream']

Asset content type, e.g., “image/png”

filename: str

File name

job_uid: str

Associated job or session UID

length: int

Size of file in bytes

md5: str

MD5 hash of asset

project_uid: str

Associated project UID

uploadDate: str

ISO 8601-formatted asset upload date

cryosparc.spec.AssetFormat(*args, **kwargs)

Supported job stream log asset file formats.

alias of Literal[‘txt’, ‘csv’, ‘html’, ‘json’, ‘xml’, ‘bild’, ‘bld’] | Literal[‘pdf’, ‘gif’, ‘jpg’, ‘jpeg’, ‘png’, ‘svg’]

class cryosparc.spec.BaseParam

Base parameter specification.

Attributes:

advanced	True if this is an advanced parameter (hidden unlesss the "Advanced" checkbox is enabled in the Job Builder".
desc	Human-readable parameter description.
hidden	If True, this parameter is always hidden from the interface.
order	Parameter order in the builder list.
section	Parameter section identifier.
title	Human-readable parameter title.
value	Base parameter value.

advanced: bool

True if this is an advanced parameter (hidden unlesss the “Advanced” checkbox is enabled in the Job Builder”.

desc: str

Human-readable parameter description.

hidden: bool

If True, this parameter is always hidden from the interface.

order: int

Parameter order in the builder list.

section: str

Parameter section identifier.

title: str

Human-readable parameter title.

value: bool

Base parameter value. Should not be changed.

class cryosparc.spec.BaseSchedulerTarget

Properties shared by both node and cluster scheduler targets.

Attributes:

cache_path	Path the SSD cache scratch directory, if applicable.
cache_quota_mb	Do not cache more than this amoun on the SSD scrath drive..
cache_reserve_mb	Ensure at least this much space is free on the SSD scratch drive before caching.
desc	Human-readable description for this target.
hostname	Network machine hostname (same as name for for clusters).
lane	Lane name this target belongs to.
name	Identifier for this target.
title	Human-readable title for this target.
worker_bin_path	Path to cryosparc_worker/bin/cryosparcw executable.

cache_path: str | None

Path the SSD cache scratch directory, if applicable.

cache_quota_mb: int

Do not cache more than this amoun on the SSD scrath drive..

cache_reserve_mb: int

Ensure at least this much space is free on the SSD scratch drive before caching.

desc: str | None

Human-readable description for this target.

hostname: str

Network machine hostname (same as name for for clusters).

lane: str

Lane name this target belongs to.

name: str

Identifier for this target.

title: str

Human-readable title for this target.

worker_bin_path: str

Path to cryosparc_worker/bin/cryosparcw executable.

class cryosparc.spec.Connection

Connection element specified in a Job document’s input_slot_groups[].connections list.

Attributes:

group_name	Name of output group in parent job.
job_uid	Parent job UID source of main input group connection.
slots	List of connection specifiers for each slot

group_name: str

Name of output group in parent job. e.g., “particles”

job_uid: str

Parent job UID source of main input group connection.

slots: List[ConnectionSlot]

List of connection specifiers for each slot

class cryosparc.spec.ConnectionSlot

Slots specified entry in a Job document’s input_slot_groups[].connections[].slots list.

Attributes:

group_name	Name of output group in parent job.
job_uid	Parent job UID source of this input slot connection.
result_name	Name of output slot in parent job, e.g., "blob"
result_type	Type of result slot based on entry in cryosparc_compute/jobs/common.py, e.g., "particle.blob"
slot_name	Passthrough slots have slot_name set to None.
version	Version number or specifier to use.

group_name: str

Name of output group in parent job. e.g., “particles”

job_uid: str

Parent job UID source of this input slot connection.

result_name: str

Name of output slot in parent job, e.g., “blob”

result_type: str

Type of result slot based on entry in cryosparc_compute/jobs/common.py, e.g., “particle.blob”

slot_name: str | None

Passthrough slots have slot_name set to None.

version: int | Literal['F']

Version number or specifier to use. Usually “F”

class cryosparc.spec.Datafield

Definition of a prefix field within a CS file.

Examples

>>> field = Datafield(dtype='alignments3D', prefix='alignments_class_0', required=False)
>>> print(field['dtype'])
alignments3D

Attributes:

dtype	Datatype-specific string from based on entry in cryosparc_compute/jobs/common.py.
prefix	where to find field in an associated .cs file.
required	whether this field must necessarily exist in a corresponding input/output.

dtype: str

Datatype-specific string from based on entry in cryosparc_compute/jobs/common.py. e.g., “movie_blob”, “ctf”, “alignments2D”.

prefix: str

where to find field in an associated .cs file. e.g., “alignments_class_1”

required: bool

whether this field must necessarily exist in a corresponding input/output. Assumed to be True if not specified

cryosparc.spec.Datatype(*args, **kwargs)

Supported data types for job inputs and outputs.

alias of Literal[‘exposure’, ‘particle’, ‘template’, ‘volume’, ‘volume_multi’, ‘mask’, ‘live’, ‘ml_model’, ‘symmetry_candidate’, ‘flex_mesh’, ‘flex_model’, ‘hyperparameter’, ‘denoise_model’, ‘annotation_model’]

class cryosparc.spec.EnumParam

Additional Param keys available for enum params. Inherits from BaseParam.

Attributes:

enum_dict	Map from enum key names to their equivalent values.
enum_keys	Possible enum names for display for selection.
type	Possible Parameter type.

enum_dict: Dict[str, Any]

Map from enum key names to their equivalent values.

enum_keys: List[str]

Possible enum names for display for selection. Parameter must be set to one of these values.

type: Literal['enum']

Possible Parameter type.

class cryosparc.spec.EventLogAsset

Dictionary item in a job event log’s imgfiles property (in the events collection). Keys may be accessed with dictionary key syntax.

Examples

>>> print(asset['filename'])
image.png

Attributes:

fileid	Reference to file _id property in GridFS collection
filename	File name
filetype	File content type, e.g., "image/png"

fileid: str

Reference to file _id property in GridFS collection

filename: str

File name

filetype: Literal['text/plain', 'text/csv', 'text/html', 'application/json', 'application/xml', 'application/x-troff', 'application/pdf', 'image/gif', 'image/jpeg', 'image/png', 'image/svg+xml', 'application/octet-stream']

File content type, e.g., “image/png”

class cryosparc.spec.FixedResourceSlots

Available resource slots that only indicate presence, not the amount that may be allocated. (i.e., “SSD is available or not available”)

Attributes:

SSD	Whether this target thas an SSD

SSD: bool

Whether this target thas an SSD

class cryosparc.spec.Gpu

GPU details for a target.

Attributes:

id	Index of GPU.
mem	Amount of memory available on this GPU, in bytes.
name	Identifiable model name for this GPU, e.g.,"GeForce RTX 3090".

id: int

Index of GPU. Generally based on which PCI slot the GPU occupies.

mem: int

Amount of memory available on this GPU, in bytes.

name: str

Identifiable model name for this GPU, e.g.,”GeForce RTX 3090”.

cryosparc.spec.ImageContentType(*args, **kwargs)

Supported job image asset MIME types.

alias of Literal[‘application/pdf’, ‘image/gif’, ‘image/jpeg’, ‘image/png’, ‘image/svg+xml’]

cryosparc.spec.ImageFormat(*args, **kwargs)

Supported job stream log asset file image formats.

alias of Literal[‘pdf’, ‘gif’, ‘jpg’, ‘jpeg’, ‘png’, ‘svg’]

class cryosparc.spec.InputSlot

Dictionary entry in Job document’s input_slot_groups.slots property.

Attributes:

description	Human-readable description
name	Input slot name, e.g., "movie_blob" or "location"
optional	If True, input is not required for the job
title	Human-readable input slot title
type	Cryo-EM native data type, e.g., "exposure", "particle" or "volume"

description: str

Human-readable description

name: str

Input slot name, e.g., “movie_blob” or “location”

optional: bool

If True, input is not required for the job

title: str

Human-readable input slot 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 cryosparc.spec.InputSlotGroup

Element specified in a Job document’s input_slot_groups list.

Attributes:

connections	Connected output for this input group.
count_max	Maximum allowed output groups that may be connected to this input slot.
count_min	Minimum required output groups that may be connected to this input slot.
description	Human-readable input group description.
name	Input group name, e.g., "particles".
repeat_allowed	If True, the same output group may be connected twice.
slots	List of slot definitions in the input group.
title	Human-readable input group title.
type	Possible Cryo-EM data type for this group, e.g., "particle".

connections: List[Connection]

Connected output for this input group.

count_max: int | None

Maximum allowed output groups that may be connected to this input slot. Infinity if not specified.

count_min: int

Minimum required output groups that may be connected to this input slot.

description: str

Human-readable input group description.

name: str

Input group name, e.g., “particles”.

repeat_allowed: bool

If True, the same output group may be connected twice.

slots: List[InputSlot]

List of slot definitions in the input group.

title: str

Human-readable input group title.

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']

Possible Cryo-EM data type for this group, e.g., “particle”.

class cryosparc.spec.JobDocument

Specification for a Job document from the MongoDB database.

Attributes:

children	List of child job UIDs based on output connections.
created_at	Job creation date in ISO 8601 format.
created_by_user_id	Object ID of user account that created this job.
deleted	True if the job has been marked as deleted.
description	Human-readable job markdown description.
input_slot_groups	Input group specifications, including schema and connection information.
job_type	Alias for type key
output_result_groups	Output group specifications.
output_results	Aggregated output results specification (similar to output_result_groups with additional field information).
params_base	Job param specification and their base values.
params_secs	Parameter section definitions
params_spec	User-specified parameter values.
parents	List of parent jobs UIDs based on input connections.
project_uid	Project unique ID, e.g., "P3".
project_uid_num	Project number, e.g., 3.
status	Job scheduling status, e.g., "building", "queued", "running".
title	Human-readable job title.
type	Job type identifier, e.g., "class2d".
uid	Job unique ID, e.g., "J42".
uid_num	Job number, e.g., 42.
workspace_uids	List of workspace UIDs this job belongs to.

children: List[str]

List of child job UIDs based on output connections.

created_at: str

Job creation date in ISO 8601 format.

created_by_user_id: str | None

Object ID of user account that created this job.

deleted: bool

True if the job has been marked as deleted.

description: str

Human-readable job markdown description.

input_slot_groups: List[InputSlotGroup]

Input group specifications, including schema and connection information.

job_type: str

Alias for type key

output_result_groups: List[OutputResultGroup]

Output group specifications.

output_results: List[OutputResult]

Aggregated output results specification (similar to output_result_groups with additional field information).

params_base: Dict[str, Param | EnumParam | PathParam]

Job param specification and their base values. Each key represents a parameter name.

params_secs: Dict[str, ParamSection]

Parameter section definitions

params_spec: Dict[str, ParamSpec]

User-specified parameter values. Each key is a parameter value. Not all keys from params_base are included here, only ones that were explicitly set.

parents: List[str]

List of parent jobs UIDs based on input connections.

project_uid: str

Project unique ID, e.g., “P3”.

project_uid_num: int

Project number, e.g., 3.

status: Literal['building', 'queued', 'launched', 'started', 'running', 'waiting', 'completed', 'killed', 'failed']

Job scheduling status, e.g., “building”, “queued”, “running”.

title: str

Human-readable job title.

type: str

Job type identifier, e.g., “class2d”.

uid: str

Job unique ID, e.g., “J42”.

uid_num: int

Job number, e.g., 42.

workspace_uids: List[str]

List of workspace UIDs this job belongs to.

class cryosparc.spec.JobSection

Specification of available job types of a certain category.

Examples

>>> {
...     "name": "refinement",
...     "title": "3D Refinement",
...     "description: "...",
...     "contains" : [
...         "homo_refine",
...         "hetero_refine",
...         "nonuniform_refine",
...         "homo_reconstruct"
...     ]
... }

Attributes:

contains	List of available job types in this category
description	Human-readable section description.
name	Section identifier.
title	Human-readable section title.

contains: List[str]

List of available job types in this category

description: str

Human-readable section description.

name: str

Section identifier.

title: str

Human-readable section title.

class cryosparc.spec.JobSpec

Specification for a Job document from the CryoSPARC’s job register.

Attributes:

description	Detailed description of job type
develop_only	If True, job is in development and not available to run.
hidden	If True, job is not visible in the interface.
input_slot_groups	Description of available inputs.
is_interactive	If True, this job is requires interaction.
is_lightweight	If True, does job does not require GPUs and requires few-enough resources that it can usually run directly on the master machine.
name	Job's machine-readable type, e.g., 'homo_abinit'.
params_base	Description of available parameters.
params_secs	Description of parameter sections.
shorttitle	Short-version of name, e.g., 'Ab-Initio'.
title	Job's human-readable name, e.g., 'Ab-Initio Reconstruction'.

description: str

Detailed description of job type

develop_only: bool

If True, job is in development and not available to run.

hidden: bool

If True, job is not visible in the interface.

input_slot_groups: List[InputSlotGroup]

Description of available inputs.

is_interactive: bool

If True, this job is requires interaction. “Curate Exposures” and “Select 2D Classes” are examples of interactive jobs.

is_lightweight: bool

If True, does job does not require GPUs and requires few-enough resources that it can usually run directly on the master machine.

name: str

Job’s machine-readable type, e.g., ‘homo_abinit’.

params_base: Dict[str, Param | EnumParam | PathParam]

Description of available parameters.

params_secs: Dict[str, ParamSection]

Description of parameter sections.

shorttitle: str

Short-version of name, e.g., ‘Ab-Initio’.

title: str

Job’s human-readable name, e.g., ‘Ab-Initio Reconstruction’.

class cryosparc.spec.JobSpecSection

Similar to JobSection, except each item in contains is a detailed JobSpec.

Attributes:

contains	List of job details available in this category
description	Human-readable section description.
name	Section identifier.
title	Human-readable section title.

contains: List[JobSpec]

List of job details available in this category

description: str

Human-readable section description.

name: str

Section identifier.

title: str

Human-readable section title.

cryosparc.spec.JobStatus(*args, **kwargs)

Possible job status values.

alias of Literal[‘building’, ‘queued’, ‘launched’, ‘started’, ‘running’, ‘waiting’, ‘completed’, ‘killed’, ‘failed’]

class cryosparc.spec.OutputResult

Detailed schema and metadata for a Job document’s output_results list. Similar to a flattened output_result_groups[].contains but with more details.

Attributes:

description	Human-readable output result description.
group_name	Name of output group, e.g., "particles".
metafiles	List of available intermediate result files (same size as versions).
min_fields	Minimum included dataset field definitions in this result.
name	Name of output result (a.k.a.
num_items	Number of rows in the dataset for this result populated by jobs when they run.
passthrough	If True, this result is passed through as-is from an associated input.
title	Human-readable output result title.
type	Result type based on entry in cryosparc_compute/jobs/common.py, e.g., "particle.alignments3D".
uid	Result unique ID, e.g., "J42-R1".
versions	List of available intermediate result version numbers.

description: str

Human-readable output result description.

group_name: str

Name of output group, e.g., “particles”.

metafiles: List[str]

List of available intermediate result files (same size as versions).

min_fields: List[Tuple[str, str]]

Minimum included dataset field definitions in this result.

name: str

Name of output result (a.k.a. slot), e.g., “alignments_class_1”.

num_items: int

Number of rows in the dataset for this result populated by jobs when they run.

passthrough: bool

If True, this result is passed through as-is from an associated input.

title: str

Human-readable output result title.

type: str

Result type based on entry in cryosparc_compute/jobs/common.py, e.g., “particle.alignments3D”.

uid: str

Result unique ID, e.g., “J42-R1”.

versions: List[int]

List of available intermediate result version numbers.

class cryosparc.spec.OutputResultGroup

Elements of a Job document’s output_result_groups list.

Attributes:

contains	List of specific results (a.k.a.
description	Human-readable output group description.
name	Output group name, e.g., "particles_selected"
num_items	Number of rows in the dataset for this result group populated by jobs when they run.
passthrough	Either False if this is a newly-created output or the name of an input group used to forward passthrough slots for this result group.
summary	Context-specific details about this result populated by jobs when they run.
title	Human-readable output group title.
type	Possible Cryo-EM data type for this group, e.g., "particle".
uid	Ouptut group unique ID, e.g., "J42-G1".

contains: List[OutputResultGroupContains]

List of specific results (a.k.a. slots) in this output group.

description: str

Human-readable output group description.

name: str

Output group name, e.g., “particles_selected”

num_items: int

Number of rows in the dataset for this result group populated by jobs when they run.

passthrough: str | Literal[False]

Either False if this is a newly-created output or the name of an input group used to forward passthrough slots for this result group.

summary: dict

Context-specific details about this result populated by jobs when they run.

title: str

Human-readable output group title.

type: Literal['exposure', 'particle', 'template', 'volume', 'volume_multi', 'mask', 'live', 'ml_model', 'symmetry_candidate', 'flex_mesh', 'flex_model', 'hyperparameter', 'denoise_model', 'annotation_model']

Possible Cryo-EM data type for this group, e.g., “particle”.

uid: str

Ouptut group unique ID, e.g., “J42-G1”.

class cryosparc.spec.OutputResultGroupContains

Elements of a Job document’s output_result_groups[].contains list.

Attributes:

group_name	Name of output group, e.g., "particles".
name	Name of output result (a.k.a.
passthrough	If True, this result is passed through as-is from an associated input.
type	Result type based on entry in cryosparc_compute/jobs/common.py, e.g., "particle.alignments3D".
uid	Result unique ID, e.g., "J42-R1".

group_name: str

Name of output group, e.g., “particles”.

name: str

Name of output result (a.k.a. slot), e.g., “alignments_class_1”.

passthrough: bool

If True, this result is passed through as-is from an associated input.

type: str

Result type based on entry in cryosparc_compute/jobs/common.py, e.g., “particle.alignments3D”.

uid: str

Result unique ID, e.g., “J42-R1”.

class cryosparc.spec.Param

Specifies possible values for type property. Inherits from BaseParam.

Attributes:

type	Possible Parameter type.

type: Literal['number', 'string', 'boolean']

Possible Parameter type.

class cryosparc.spec.ParamSection

Param section specification

Attributes:

desc	Parameter section description
order	Order for this parameter section to appear in the job builder
title	Parameter section title

desc: str

Parameter section description

order: int

Order for this parameter section to appear in the job builder

title: str

Parameter section title

class cryosparc.spec.ParamSpec

Param specification. Dictionary with single "value" key.

Attributes:

value

Value of param.

value: Any

Value of param.

class cryosparc.spec.PathParam

Additional Param key available for path params. Inherits Inherits from BaseParam.

Attributes:

path_dir_allowed	If True, directories may be specified.
path_file_allowed	If True, files may be specified.
path_glob_allowed	If True, a wildcard string that refers to many files may be specified..

path_dir_allowed: bool

If True, directories may be specified.

path_file_allowed: bool

If True, files may be specified.

path_glob_allowed: bool

If True, a wildcard string that refers to many files may be specified..

class cryosparc.spec.ProjectDocument

Specification for a project document in the MongoDB database.

Attributes:

archived	Whether this project has been marked as archived from the inteface.
created_at	Project creation date in ISO 8601 format.
deleted	Whether this project has been deleted from the interface.
description	Human-readable project markdown description.
detached	Whether this project is detached.
generate_intermediate_results_settings	Project settings for generating intermediate results for specific job types.
hidden	Whether this project is hidden.
last_accessed	Details about when the project was last accessed by a user account.
owner_user_id	Object ID of user account that created this project.
project_dir	Project directory on disk.
project_params_pdef	Project-level job parameter default definitions.
project_stats	Computed project statistics.
size	Computed size of project on disk.
title	Human-readable Project title.
uid	Project unique ID, e.g., "J42".
uid_num	Project number, e.g., 42.
users_with_access	Object IDs of user accounts that may access this project.

archived: bool

Whether this project has been marked as archived from the inteface.

created_at: str

Project creation date in ISO 8601 format.

deleted: bool

Whether this project has been deleted from the interface.

description: str

Human-readable project markdown description.

detached: bool

Whether this project is detached.

generate_intermediate_results_settings: dict

Project settings for generating intermediate results for specific job types.

hidden: bool

Whether this project is hidden.

last_accessed: ProjectLastAccessed

Details about when the project was last accessed by a user account.

owner_user_id: str

Object ID of user account that created this project.

project_dir: str

Project directory on disk. May include unresolved shell variables.

project_params_pdef: dict

Project-level job parameter default definitions.

project_stats: dict

Computed project statistics.

size: int

Computed size of project on disk.

title: str

Human-readable Project title.

uid: str

Project unique ID, e.g., “J42”.

uid_num: int

Project number, e.g., 42.

users_with_access: List[str]

Object IDs of user accounts that may access this project.

class cryosparc.spec.ProjectLastAccessed

Details on when a project was last accessed.

Attributes:

accessed_at	Last access date in ISO 8601 format.
name	User account name that accessed this project.

accessed_at: str

Last access date in ISO 8601 format.

name: str

User account name that accessed this project.

class cryosparc.spec.ResourceSlots

Listings of available resources on a worker node that may be allocated for scheduling.

Attributes:

CPU	List of available CPU core indices.
GPU	List of available GPU indices.
RAM	List of available 8GB slots.

CPU: List[int]

List of available CPU core indices.

GPU: List[int]

List of available GPU indices.

RAM: List[int]

List of available 8GB slots.

class cryosparc.spec.SchedulerLane

Description for a CryoSPARC scheduler lane.

Attributes:

desc	Human-readable lane description.
name	Identifier for this lane.
title	Human-readable lane title.
type	What kind of lane this is based on how on what kind of target(s) it contains.

desc: str

Human-readable lane description.

name: str

Identifier for this lane.

title: str

Human-readable lane title.

type: Literal['node', 'cluster']

What kind of lane this is based on how on what kind of target(s) it contains.

cryosparc.spec.SchedulerTarget(*args, **kwargs)

Scheduler target details.

alias of SchedulerTargetNode | SchedulerTargetGpuNode | SchedulerTargetCluster

class cryosparc.spec.SchedulerTargetCluster

Cluster-type scheduler targets. Inherits from BaseSchedulerTarget.

Attributes:

qdel_cmd_tpl	Template command to delete cluster jobs.
qinfo_cmd_tpl	Template command to check cluster queue info.
qstat_cmd_tpl	Template command to check the cluster job by its ID.
qsub_cmd_tpl	Template command to submit jobs to the cluster.
script_tpl	Full cluster submission script Jinja template.
send_cmd_tpl	Template command to access the cluster and running commands.
type	Cluster scheduler targets have type "cluster".

qdel_cmd_tpl: str

Template command to delete cluster jobs.

qinfo_cmd_tpl: str

Template command to check cluster queue info.

qstat_cmd_tpl: str

Template command to check the cluster job by its ID.

qsub_cmd_tpl: str

Template command to submit jobs to the cluster.

script_tpl: str

Full cluster submission script Jinja template.

send_cmd_tpl: str

Template command to access the cluster and running commands.

type: Literal['cluster']

Cluster scheduler targets have type “cluster”.

class cryosparc.spec.SchedulerTargetGpuNode

node-type scheduler target that includes GPUs. Inherits from BaseSchedulerTarget and SchedulerTargetNode.

Attributes:

gpus	Details about GPUs available on this node.

gpus: List[Gpu]

Details about GPUs available on this node.

class cryosparc.spec.SchedulerTargetNode

node-type scheduler target that does not include GPUs. Inherits from BaseSchedulerTarget.

Attributes:

monitor_port	Not used.
resource_fixed	Available fixed resources.
resource_slots	Available compute resources.
ssh_str	Shell command used to access this node, e.g., ssh cryosparcuser@worker.
type	Node scheduler targets have type "node".

monitor_port: int | None

Not used.

resource_fixed: FixedResourceSlots

Available fixed resources.

resource_slots: ResourceSlots

Available compute resources.

ssh_str: str

Shell command used to access this node, e.g., ssh cryosparcuser@worker.

type: Literal['node']

Node scheduler targets have type “node”.

cryosparc.spec.SlotSpec(*args, **kwargs)

A result slot specification for the slots=… argument.

alias of str | Datafield

cryosparc.spec.TextContentType(*args, **kwargs)

Supported job stream log text asset MIME types.

alias of Literal[‘text/plain’, ‘text/csv’, ‘text/html’, ‘application/json’, ‘application/xml’, ‘application/x-troff’]

cryosparc.spec.TextFormat(*args, **kwargs)

Supported job stream log asset file text formats.

alias of Literal[‘txt’, ‘csv’, ‘html’, ‘json’, ‘xml’, ‘bild’, ‘bld’]

class cryosparc.spec.WorkspaceDocument

Specification for a Workspace document from the MongoDB database. Live-related fields are not yet included.

Attributes:

created_at	Workspace creation date in ISO 8601 format.
created_by_user_id	Object ID of user account that created this workspace.
deleted	True if the workspace has been marked as deleted.
description	Human-readable workspace markdown description.
project_uid	Project unique ID, e.g., "P3".
project_uid_num	Project number, e.g., 3.
title	Human-readable workspace title.
uid	Workspace unique ID, e.g., "W1".
uid_num	Workspace number, e.g., 1.
workspace_type	Either "live" or "base".

created_at: str

Workspace creation date in ISO 8601 format.

created_by_user_id: str

Object ID of user account that created this workspace.

deleted: bool

True if the workspace has been marked as deleted.

description: str | None

Human-readable workspace markdown description.

project_uid: str

Project unique ID, e.g., “P3”.

project_uid_num: int

Project number, e.g., 3.

title: str

Human-readable workspace title.

uid: str

Workspace unique ID, e.g., “W1”.

uid_num: int

Workspace number, e.g., 1.

workspace_type: Literal['base', 'live']

Either “live” or “base”.