Reference·Classes

Class: StudyFile

One file a study layout accounts for. name may interpolate {study}, the dataset’s own name, which is how the entry recipe is named without the layout knowing any particular study.

URI: tvbo_study:class/StudyFile

 classDiagram
    class StudyFile
    click StudyFile href "./StudyFile.html"
      StudyFile : bids
        
          
    
        
        
        StudyFile --> "0..1" BidsDirectoryStatus : bids
        click BidsDirectoryStatus href "../../enums/BidsDirectoryStatus.html"
    

        
      StudyFile : description
        
          
    
        
        
        StudyFile --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : expires_with
        
          
    
        
        
        StudyFile --> "0..1" String : expires_with
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : generated
        
          
    
        
        
        StudyFile --> "0..1" Boolean : generated
        click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
    

        
      StudyFile : in_templates
        
          
    
        
        
        StudyFile --> "*" String : in_templates
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : level
        
          
    
        
        
        StudyFile --> "0..1" RequirementLevel : level
        click RequirementLevel href "../../enums/RequirementLevel.html"
    

        
      StudyFile : name
        
          
    
        
        
        StudyFile --> "1" String : name
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : not_in_templates
        
          
    
        
        
        StudyFile --> "*" String : not_in_templates
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : role
        
          
    
        
        
        StudyFile --> "0..1" StudyFileRole : role
        click StudyFileRole href "../../enums/StudyFileRole.html"
    

        
      StudyFile : template
        
          
    
        
        
        StudyFile --> "0..1" String : template
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      StudyFile : template_variants
        
          
    
        
        
        StudyFile --> "*" LayoutTemplateVariant : template_variants
        click LayoutTemplateVariant href "./LayoutTemplateVariant.html"
    

        
      StudyFile : tracked
        
          
    
        
        
        StudyFile --> "0..1" TrackedContent : tracked
        click TrackedContent href "../../enums/TrackedContent.html"
    

        
      

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string	Globally unique identifier for the entity	direct
description	0..1 xsd:string		direct
role	0..1 StudyFileRole	Semantic key this file is resolved by	direct
level	0..1 RequirementLevel		direct
bids	0..1 BidsDirectoryStatus	Standing with the BIDS standard; an unsanctioned file needs a | direct | | [expires_with](../slots/expires_with.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | For an unsanctioned or proposed file, what would retire its	direct
tracked	0..1 TrackedContent		direct
template	0..1 xsd:string	Asset that seeds the file at tvbo study init, resolved against the scaffo…	direct
generated	0..1 xsd:boolean	Written by tooling and overwritten on the next run, so it is never hand-edite…	direct
in_templates	* xsd:string	Init templates that include this file	direct
not_in_templates	* xsd:string	Init templates that do not get this file, though every other kind does	direct
template_variants	* LayoutTemplateVariant	Seeds that supersede template for one init variant, keyed by variant name	direct

Usages

used by	used in	type	used
StudyLayout	files	range	StudyFile
StudyDirectory	files	range	StudyFile

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo/study

Mappings

Mapping Type	Mapped Value
self	tvbo_study:StudyFile
native	tvbo_study:StudyFile

LinkML Source

Direct

name: StudyFile
description: One file a study layout accounts for. ``name`` may interpolate ``{study}``,
  the dataset's own name, which is how the entry recipe is named without the layout
  knowing any particular study.
from_schema: https://w3id.org/tvbo/study
slots:
- name
- description
attributes:
  role:
    name: role
    description: Semantic key this file is resolved by.
    from_schema: https://w3id.org/tvbo/study
    domain_of:
    - StudyDirectory
    - StudyFile
    - SoftwareRequirement
    range: StudyFileRole
  level:
    name: level
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(optional)
    domain_of:
    - StudyDirectory
    - StudyFile
    range: RequirementLevel
  bids:
    name: bids
    description: Standing with the BIDS standard; an unsanctioned file needs a ``.bidsignore``
      entry.
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(sanctioned)
    domain_of:
    - StudyDirectory
    - StudyFile
    - Network
    range: BidsDirectoryStatus
  expires_with:
    name: expires_with
    description: For an unsanctioned or proposed file, what would retire its ``.bidsignore``
      entry.
    from_schema: https://w3id.org/tvbo/study
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
  tracked:
    name: tracked
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(all)
    domain_of:
    - StudyDirectory
    - StudyFile
    range: TrackedContent
  template:
    name: template
    description: Asset that seeds the file at ``tvbo study init``, resolved against
      the scaffolder's template directory. Absent means the file is written from the
      layout record itself, or left to the author.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyFile
    - LayoutTemplateVariant
    - Surface
    - BidsEntities
    range: string
  generated:
    name: generated
    description: Written by tooling and overwritten on the next run, so it is never
      hand-edited.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    ifabsent: 'false'
    domain_of:
    - StudyFile
    range: boolean
  in_templates:
    name: in_templates
    description: Init templates that include this file. Absent means every study gets
      it.
    from_schema: https://w3id.org/tvbo/study
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
    multivalued: true
  not_in_templates:
    name: not_in_templates
    description: 'Init templates that do *not* get this file, though every other kind
      does. The complement of ``in_templates``, for a file the general study has and
      one kind replaces rather than adds to: a collection''s document stands in for
      a single study''s report, so naming the kinds that keep the report would leave
      every kind added later to be edited in here as well.'
    from_schema: https://w3id.org/tvbo/study
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
    multivalued: true
  template_variants:
    name: template_variants
    description: Seeds that supersede ``template`` for one init variant, keyed by
      variant name. A file every study gets may still need different starting text
      once the variant says what kind of study this is — a replication's provenance
      note names a paper, and a general study has no paper to name — so stating only
      the difference keeps one entry per file rather than two that drift apart. The
      first selected variant naming a seed wins; absent means every variant starts
      from ``template``.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    domain_of:
    - StudyFile
    range: LayoutTemplateVariant
    multivalued: true
    inlined: true

Induced

name: StudyFile
description: One file a study layout accounts for. ``name`` may interpolate ``{study}``,
  the dataset's own name, which is how the entry recipe is named without the layout
  knowing any particular study.
from_schema: https://w3id.org/tvbo/study
attributes:
  role:
    name: role
    description: Semantic key this file is resolved by.
    from_schema: https://w3id.org/tvbo/study
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    - SoftwareRequirement
    range: StudyFileRole
  level:
    name: level
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(optional)
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    range: RequirementLevel
  bids:
    name: bids
    description: Standing with the BIDS standard; an unsanctioned file needs a ``.bidsignore``
      entry.
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(sanctioned)
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    - Network
    range: BidsDirectoryStatus
  expires_with:
    name: expires_with
    description: For an unsanctioned or proposed file, what would retire its ``.bidsignore``
      entry.
    from_schema: https://w3id.org/tvbo/study
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
  tracked:
    name: tracked
    from_schema: https://w3id.org/tvbo/study
    ifabsent: string(all)
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    range: TrackedContent
  template:
    name: template
    description: Asset that seeds the file at ``tvbo study init``, resolved against
      the scaffolder's template directory. Absent means the file is written from the
      layout record itself, or left to the author.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyFile
    domain_of:
    - StudyFile
    - LayoutTemplateVariant
    - Surface
    - BidsEntities
    range: string
  generated:
    name: generated
    description: Written by tooling and overwritten on the next run, so it is never
      hand-edited.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    ifabsent: 'false'
    owner: StudyFile
    domain_of:
    - StudyFile
    range: boolean
  in_templates:
    name: in_templates
    description: Init templates that include this file. Absent means every study gets
      it.
    from_schema: https://w3id.org/tvbo/study
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
    multivalued: true
  not_in_templates:
    name: not_in_templates
    description: 'Init templates that do *not* get this file, though every other kind
      does. The complement of ``in_templates``, for a file the general study has and
      one kind replaces rather than adds to: a collection''s document stands in for
      a single study''s report, so naming the kinds that keep the report would leave
      every kind added later to be edited in here as well.'
    from_schema: https://w3id.org/tvbo/study
    owner: StudyFile
    domain_of:
    - StudyDirectory
    - StudyFile
    range: string
    multivalued: true
  template_variants:
    name: template_variants
    description: Seeds that supersede ``template`` for one init variant, keyed by
      variant name. A file every study gets may still need different starting text
      once the variant says what kind of study this is — a replication's provenance
      note names a paper, and a general study has no paper to name — so stating only
      the difference keeps one entry per file rather than two that drift apart. The
      first selected variant naming a seed wins; absent means every variant starts
      from ``template``.
    from_schema: https://w3id.org/tvbo/study
    rank: 1000
    owner: StudyFile
    domain_of:
    - StudyFile
    range: LayoutTemplateVariant
    multivalued: true
    inlined: true
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: StudyFile
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Event
    - Tractogram
    - ResultEntity
    - Activity
    - CachedArray
    - MeasureSpec
    - NamedArray
    - GraphGenerator
    - Binding
    - ProcedureStep
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - EnvironmentVariable
    - SchedulerDirective
    - Reducer
    range: string
    required: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: StudyFile
    domain_of:
    - CommonCoordinateSpace
    - Dataset
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - ResultEntity
    - Activity
    - Phenotype
    - MeasureSpec
    - NamedArray
    - Network
    - GraphGenerator
    - ProcedureStep
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - AlgorithmStage
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - Study
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    - Reducer
    range: string