# 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._



<div data-search-exclude markdown="1">



URI: [tvbo_study:class/StudyFile](https://w3id.org/tvbo/study/class/StudyFile)





```{mermaid}
 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"
    

        
      
```




<!-- no inheritance hierarchy -->

## Slots

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





## Usages

| used by | used in | type | used |
| ---  | --- | --- | --- |
| [StudyLayout](../classes/StudyLayout.qmd) | [files](../slots/files.qmd) | range | [StudyFile](../classes/StudyFile.qmd) |
| [StudyDirectory](../classes/StudyDirectory.qmd) | [files](../slots/files.qmd) | range | [StudyFile](../classes/StudyFile.qmd) |












## 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

<!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->

### Direct

<details>
```yaml
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

```
</details>

### Induced

<details>
```yaml
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

```
</details></div>