diff --git a/gxformat2/schema/v19_09.py b/gxformat2/schema/v19_09.py index 5d6778e..5268193 100644 --- a/gxformat2/schema/v19_09.py +++ b/gxformat2/schema/v19_09.py @@ -6613,7 +6613,10 @@ def save( booltype, ) ) -uri_strtype_False_True_None_None = _URILoader(strtype, False, True, None, None) +GalaxyWorkflow_classLoader = _EnumLoader(("GalaxyWorkflow",), "GalaxyWorkflow_class") +uri_GalaxyWorkflow_classLoader_False_True_None_None = _URILoader( + GalaxyWorkflow_classLoader, False, True, None, None +) array_of_WorkflowInputParameterLoader = _ArrayLoader(WorkflowInputParameterLoader) idmap_inputs_array_of_WorkflowInputParameterLoader = _IdMapLoader( array_of_WorkflowInputParameterLoader, "id", "type" diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflow.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflow.java index a994b9c..726639d 100644 --- a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflow.java +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflow.java @@ -52,7 +52,7 @@ public interface GalaxyWorkflow extends Process, HasUUID, Saveable { /** * Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
*/ - String getClass_(); + GalaxyWorkflow_class getClass_(); /** * Getter for property https://w3id.org/cwl/cwl#Labeled/label
* diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflowImpl.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflowImpl.java index 204d95a..57753ff 100644 --- a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflowImpl.java +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/GalaxyWorkflowImpl.java @@ -61,12 +61,12 @@ public java.util.Optional getId() { return this.id; } - private String class_; + private GalaxyWorkflow_class class_; /** * Getter for property https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow/class
*/ - public String getClass_() { + public GalaxyWorkflow_class getClass_() { return this.class_; } @@ -310,10 +310,10 @@ public GalaxyWorkflowImpl( } else { __baseUri = (String) id.orElse(null); } - String class_; + GalaxyWorkflow_class class_; try { class_ = - LoaderInstances.uri_StringInstance_False_True_None_None.loadField( + LoaderInstances.uri_GalaxyWorkflow_class_False_True_None_None.loadField( __doc.get("class"), __baseUri, __loadingOptions); } catch (ValidationException e) { class_ = null; // won't be used but prevents compiler from complaining. @@ -487,7 +487,7 @@ public GalaxyWorkflowImpl( this.inputs = (java.util.List) inputs; this.outputs = (java.util.List) outputs; this.uuid = (java.util.Optional) uuid; - this.class_ = (String) class_; + this.class_ = (GalaxyWorkflow_class) class_; this.steps = (java.util.List) steps; this.report = (java.util.Optional) report; this.tags = (java.util.Optional>) tags; diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/ConstantMaps.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/ConstantMaps.java index 9e60c96..f88ca00 100644 --- a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/ConstantMaps.java +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/ConstantMaps.java @@ -14,7 +14,7 @@ public class ConstantMaps { vocab.put("EnumSchema", "https://w3id.org/cwl/salad#EnumSchema"); vocab.put("File", "https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File"); vocab.put("GalaxyType", "https://galaxyproject.org/gxformat2/v19_09#GalaxyType"); - vocab.put("GalaxyWorkflow", "https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow"); + vocab.put("GalaxyWorkflow", "GalaxyWorkflow"); vocab.put("HasStepErrors", "https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors"); vocab.put( "HasStepPosition", "https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition"); @@ -72,7 +72,7 @@ public class ConstantMaps { rvocab.put("https://w3id.org/cwl/salad#EnumSchema", "EnumSchema"); rvocab.put("https://galaxyproject.org/gxformat2/v19_09#GalaxyType/File", "File"); rvocab.put("https://galaxyproject.org/gxformat2/v19_09#GalaxyType", "GalaxyType"); - rvocab.put("https://galaxyproject.org/gxformat2/v19_09#GalaxyWorkflow", "GalaxyWorkflow"); + rvocab.put("GalaxyWorkflow", "GalaxyWorkflow"); rvocab.put( "https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors", "HasStepErrors"); rvocab.put( diff --git a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/LoaderInstances.java b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/LoaderInstances.java index f11bd0d..00452eb 100644 --- a/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/LoaderInstances.java +++ b/java/src/main/java/org/galaxyproject/gxformat2/v19_09/utils/LoaderInstances.java @@ -228,8 +228,10 @@ public class LoaderInstances { false, 2, null); - public static Loader uri_StringInstance_False_True_None_None = - new UriLoader(StringInstance, false, true, null, null); + public static Loader GalaxyWorkflow_class = + new EnumLoader(GalaxyWorkflow_class.class); + public static Loader uri_GalaxyWorkflow_class_False_True_None_None = + new UriLoader(GalaxyWorkflow_class, false, true, null, null); public static Loader> array_of_WorkflowStep = new ArrayLoader(WorkflowStep); public static Loader> idmap_steps_array_of_WorkflowStep = diff --git a/typescript/docs/assets/search.js b/typescript/docs/assets/search.js index 7e64786..6f718c3 100644 --- a/typescript/docs/assets/search.js +++ b/typescript/docs/assets/search.js @@ -1 +1 @@ -window.searchData = JSON.parse("{\"kinds\":{\"8\":\"Enumeration\",\"16\":\"Enumeration member\",\"64\":\"Function\",\"128\":\"Class\",\"256\":\"Interface\",\"512\":\"Constructor\",\"1024\":\"Property\",\"2048\":\"Method\",\"65536\":\"Type 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\ No newline at end of file diff --git a/typescript/docs/classes/ArraySchema.html b/typescript/docs/classes/ArraySchema.html index b17fcad..5fb71c6 100644 --- a/typescript/docs/classes/ArraySchema.html +++ b/typescript/docs/classes/ArraySchema.html @@ -1,10 +1,10 @@ ArraySchema | org.galaxyproject.gxformat2.v19_09
Options
All
  • Public
  • Public/Protected
  • All
Menu

Class ArraySchema

Auto-generated class implementation for https://w3id.org/cwl/salad#ArraySchema

-

Hierarchy

  • Saveable
    • ArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]
+

Hierarchy

  • Saveable
    • ArraySchema

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

  • Parameters

    Returns ArraySchema

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

items

items: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]

Defines the type of the array elements.

-

loadingOptions

loadingOptions: LoadingOptions

type

type: ARRAY
+

loadingOptions

loadingOptions: LoadingOptions

type

type: ARRAY

Must be array

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

  • Used to construct instances of .

    throws

    ValidationException If the document fragment is not a {@link Dictionary} or validation of fields fails.

    diff --git a/typescript/docs/classes/EnumSchema.html b/typescript/docs/classes/EnumSchema.html index 390e90a..5f5b97a 100644 --- a/typescript/docs/classes/EnumSchema.html +++ b/typescript/docs/classes/EnumSchema.html @@ -1,11 +1,11 @@ EnumSchema | org.galaxyproject.gxformat2.v19_09
    Options
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    Menu

    Class EnumSchema

    Auto-generated class implementation for https://w3id.org/cwl/salad#EnumSchema

    Define an enumerated type.

    -

    Hierarchy

    • Saveable
      • EnumSchema

    Implements

    Index

    Constructors

    Properties

    Methods

    Constructors

    constructor

    Properties

    Optional extensionFields

    extensionFields?: Dictionary<any>

    loadingOptions

    loadingOptions: LoadingOptions

    symbols

    symbols: string[]
    +

    Hierarchy

    • Saveable
      • EnumSchema

    Implements

    Index

    Constructors

    Properties

    Methods

    Constructors

    constructor

    • Parameters

      Returns EnumSchema

    Properties

    Optional extensionFields

    extensionFields?: Dictionary<any>

    loadingOptions

    loadingOptions: LoadingOptions

    symbols

    symbols: string[]

    Defines the set of valid symbols.

    -

    type

    type: ENUM
    +

    type

    type: ENUM

    Must be enum

    -

    Static attr

    attr: Set<string> = ...

    Methods

    save

    • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

    • Parameters

      • top: boolean = false
      • baseUrl: string = ''
      • relativeUris: boolean = true

      Returns Dictionary<any>

    Static fromDoc

    • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

    Static attr

    attr: Set<string> = ...

    Methods

    save

    • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

    • Parameters

      • top: boolean = false
      • baseUrl: string = ''
      • relativeUris: boolean = true

      Returns Dictionary<any>

    Static fromDoc

    • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

    • Used to construct instances of .

      throws

      ValidationException If the document fragment is not a {@link Dictionary} or validation of fields fails.

      diff --git a/typescript/docs/classes/GalaxyWorkflow.html b/typescript/docs/classes/GalaxyWorkflow.html index 47f61d1..be1f7d6 100644 --- a/typescript/docs/classes/GalaxyWorkflow.html +++ b/typescript/docs/classes/GalaxyWorkflow.html @@ -12,13 +12,13 @@

      A note about label field.

      users will primarily identify the workflow using. Legacy support - this may also be called 'name' and Galaxy will consume the workflow document fine and treat this attribute correctly - however in order to validate against this workflow definition schema the attribute should be called label.

      -

Hierarchy

  • Saveable
    • GalaxyWorkflow

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: string

Optional creator

creator?: any
+

Hierarchy

  • Saveable
    • GalaxyWorkflow

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

class_

class_: GALAXYWORKFLOW

Optional creator

creator?: any

Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: WorkflowInputParameter[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -29,25 +29,25 @@

A note about label field.

assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional license

license?: string
+

Optional license

license?: string

Must be a valid license listed at https://spdx.org/licenses/

-

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: WorkflowOutputParameter[]
+

loadingOptions

loadingOptions: LoadingOptions

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

-

Optional release

release?: string
+

Optional release

release?: string

If listed should correspond to the release of the workflow in its source reposiory.

-

Optional report

report?: Report
+

Optional report

report?: Report

Workflow invocation report template.

-

steps

steps: WorkflowStep[]
+

steps

steps: WorkflowStep[]

The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled.

-

Optional tags

tags?: string[]
+

Optional tags

tags?: string[]

Tags for the workflow.

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

  • Saveable
    • WorkflowOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

  • Saveable
    • WorkflowOutputParameter

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional outputSource

outputSource?: string
+

loadingOptions

loadingOptions: LoadingOptions

Optional outputSource

outputSource?: string

Specifies workflow parameter that supply the value of to the output parameter.

-

Optional type

type?: GalaxyType
+

Optional type

type?: GalaxyType

Specify valid types of data that may be assigned to this parameter.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

  • Used to construct instances of .

    throws

    ValidationException If the document fragment is not a {@link Dictionary} or validation of fields fails.

    diff --git a/typescript/docs/classes/WorkflowStep.html b/typescript/docs/classes/WorkflowStep.html index 4689ab6..13b482c 100644 --- a/typescript/docs/classes/WorkflowStep.html +++ b/typescript/docs/classes/WorkflowStep.html @@ -14,53 +14,53 @@

    A note about state and tool_state fields.

    Galaxy but shouldn't be written by humans.

    state can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing state this way is defining inputs with default values.

    -

Hierarchy

  • Saveable
    • WorkflowStep

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

  • Saveable
    • WorkflowStep

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

  • Parameters

    Returns WorkflowStep

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional errors

errors?: string
+

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

This field should not be used in human written Galaxy workflow files.

A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional in_

in_?: WorkflowStepInput[]
+

Optional in_

in_?: WorkflowStepInput[]

Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional out

out?: (string | WorkflowStepOutput)[]
+

loadingOptions

loadingOptions: LoadingOptions

Optional out

out?: (string | WorkflowStepOutput)[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema.

-

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow
+

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow

Specifies a subworkflow to run.

-

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any
+

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any

Structured tool state.

-

Optional tool_id

tool_id?: string
+

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_state

tool_state?: any
+

Optional tool_state

tool_state?: any

Unstructured tool state.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

-

Optional type

type?: WorkflowStepType
+

Optional type

type?: WorkflowStepType

Workflow step module's type (defaults to 'tool').

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Optional when

when?: string
+

Optional when

when?: string

If defined, only run the step when the expression evaluates to true. If false the step is skipped. A skipped step produces a null on each output.

Expression should be an ecma5.1 expression.

-

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

  • Saveable
    • WorkflowStepOutput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string
+

Hierarchy

  • Saveable
    • WorkflowStepOutput

Implements

Index

Constructors

Properties

Methods

Constructors

constructor

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string

The unique identifier for this object.

-

loadingOptions

loadingOptions: LoadingOptions

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

loadingOptions

loadingOptions: LoadingOptions

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

Static attr

attr: Set<string> = ...

Methods

save

  • save(top?: boolean, baseUrl?: string, relativeUris?: boolean): Dictionary<any>

  • Parameters

    • top: boolean = false
    • baseUrl: string = ''
    • relativeUris: boolean = true

    Returns Dictionary<any>

Static fromDoc

  • fromDoc(__doc: any, baseuri: string, loadingOptions: LoadingOptions, docRoot?: string): Promise<Saveable>

Hierarchy

Implemented by

Index

Properties

Properties

Optional class_

class_?: string

Optional creator

creator?: any
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional class_

class_?: GALAXYWORKFLOW

Optional creator

creator?: any

Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: WorkflowInputParameter[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -29,22 +29,22 @@

A note about label field.

assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional license

license?: string
+

Optional license

license?: string

Must be a valid license listed at https://spdx.org/licenses/

-

outputs

outputs: WorkflowOutputParameter[]
+

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

-

Optional release

release?: string
+

Optional release

release?: string

If listed should correspond to the release of the workflow in its source reposiory.

-

Optional report

report?: Report
+

Optional report

report?: Report

Workflow invocation report template.

-

steps

steps: WorkflowStep[]
+

steps

steps: WorkflowStep[]

The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled.

-

Optional tags

tags?: string[]
+

Optional tags

tags?: string[]

Tags for the workflow.

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/HasStepErrorsProperties.html b/typescript/docs/interfaces/HasStepErrorsProperties.html index ca20449..293b104 100644 --- a/typescript/docs/interfaces/HasStepErrorsProperties.html +++ b/typescript/docs/interfaces/HasStepErrorsProperties.html @@ -1,6 +1,6 @@ HasStepErrorsProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasStepErrorsProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepErrors

-

Hierarchy

Index

Properties

Properties

Optional errors

errors?: string
+

Hierarchy

Index

Properties

Properties

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

diff --git a/typescript/docs/interfaces/HasStepPositionProperties.html b/typescript/docs/interfaces/HasStepPositionProperties.html index 532e645..c326e4d 100644 --- a/typescript/docs/interfaces/HasStepPositionProperties.html +++ b/typescript/docs/interfaces/HasStepPositionProperties.html @@ -1,3 +1,3 @@ HasStepPositionProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasStepPositionProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasStepPosition

-

Hierarchy

Index

Properties

Properties

Optional position

position?: StepPosition

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

Theme

Generated using TypeDoc

\ No newline at end of file +

Hierarchy

Index

Properties

Properties

Optional position

position?: StepPosition

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/HasUUIDProperties.html b/typescript/docs/interfaces/HasUUIDProperties.html index 5cda86f..4ae4b4f 100644 --- a/typescript/docs/interfaces/HasUUIDProperties.html +++ b/typescript/docs/interfaces/HasUUIDProperties.html @@ -1,5 +1,5 @@ HasUUIDProperties | org.galaxyproject.gxformat2.v19_09
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Interface HasUUIDProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#HasUUID

-

Hierarchy

Index

Properties

Properties

Optional uuid

uuid?: string
+

Hierarchy

Index

Properties

Properties

Optional uuid

uuid?: string

UUID uniquely representing this element.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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\ No newline at end of file diff --git a/typescript/docs/interfaces/IdentifiedProperties.html b/typescript/docs/interfaces/IdentifiedProperties.html index 3fc5cc2..7506f35 100644 --- a/typescript/docs/interfaces/IdentifiedProperties.html +++ b/typescript/docs/interfaces/IdentifiedProperties.html @@ -1,5 +1,5 @@ IdentifiedProperties | org.galaxyproject.gxformat2.v19_09
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Interface IdentifiedProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Identified

-

Hierarchy

Index

Properties

Properties

Optional id

id?: string
+

Hierarchy

Index

Properties

Properties

Optional id

id?: string

The unique identifier for this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/InputParameterProperties.html b/typescript/docs/interfaces/InputParameterProperties.html index 77bea12..200625d 100644 --- a/typescript/docs/interfaces/InputParameterProperties.html +++ b/typescript/docs/interfaces/InputParameterProperties.html @@ -1,14 +1,14 @@ InputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface InputParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#InputParameter

-

Hierarchy

Index

Properties

Properties

Optional default_

default_?: any
+

Hierarchy

Index

Properties

Properties

Optional default_

default_?: any

The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is null. Default values are applied before evaluating expressions (e.g. dependent valueFrom fields).

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

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\ No newline at end of file diff --git a/typescript/docs/interfaces/LabeledProperties.html b/typescript/docs/interfaces/LabeledProperties.html index 8d8c25b..fe4ef14 100644 --- a/typescript/docs/interfaces/LabeledProperties.html +++ b/typescript/docs/interfaces/LabeledProperties.html @@ -1,5 +1,5 @@ LabeledProperties | org.galaxyproject.gxformat2.v19_09
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Interface LabeledProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Labeled

-

Hierarchy

Index

Properties

Properties

Optional label

label?: string
+

Hierarchy

Index

Properties

Properties

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

Theme

Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/OutputParameterProperties.html b/typescript/docs/interfaces/OutputParameterProperties.html index 68a2689..ff3757c 100644 --- a/typescript/docs/interfaces/OutputParameterProperties.html +++ b/typescript/docs/interfaces/OutputParameterProperties.html @@ -1,9 +1,9 @@ OutputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface OutputParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#OutputParameter

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
  • Property
  • Method
  • Static property
  • Static method
  • Property
  • Inherited property

Settings

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/ParameterProperties.html b/typescript/docs/interfaces/ParameterProperties.html index 7f118b5..3d1dc23 100644 --- a/typescript/docs/interfaces/ParameterProperties.html +++ b/typescript/docs/interfaces/ParameterProperties.html @@ -1,10 +1,10 @@ ParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface ParameterProperties

Auto-generated interface for https://w3id.org/cwl/cwl#Parameter

Define an input or output parameter to a process.

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

Legend

  • Constructor
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Settings

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ProcessProperties.html b/typescript/docs/interfaces/ProcessProperties.html index 590e9e8..5614050 100644 --- a/typescript/docs/interfaces/ProcessProperties.html +++ b/typescript/docs/interfaces/ProcessProperties.html @@ -3,11 +3,11 @@

The base executable type in CWL is the Process object defined by the document. Note that the Process object is abstract and cannot be directly executed.

-

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

inputs

inputs: WorkflowInputParameter[]
+

inputs

inputs: WorkflowInputParameter[]

Defines the input parameters of the process. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is @@ -18,9 +18,9 @@ assigned a value of null (or the value of default for that parameter, if provided) for the purposes of validation and evaluation of expressions.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

outputs

outputs: WorkflowOutputParameter[]
+

outputs

outputs: WorkflowOutputParameter[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/RecordFieldProperties.html b/typescript/docs/interfaces/RecordFieldProperties.html index e7b8994..866cf6a 100644 --- a/typescript/docs/interfaces/RecordFieldProperties.html +++ b/typescript/docs/interfaces/RecordFieldProperties.html @@ -1,10 +1,10 @@ RecordFieldProperties | org.galaxyproject.gxformat2.v19_09
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Interface RecordFieldProperties

Auto-generated interface for https://w3id.org/cwl/salad#RecordField

A field of a record.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string

The name of the field

-

type

type: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]
+

type

type: string | ArraySchema | RecordSchema | EnumSchema | (string | ArraySchema | RecordSchema | EnumSchema)[]

The field type

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\ No newline at end of file diff --git a/typescript/docs/interfaces/RecordSchemaProperties.html b/typescript/docs/interfaces/RecordSchemaProperties.html index 94c443b..71b3a23 100644 --- a/typescript/docs/interfaces/RecordSchemaProperties.html +++ b/typescript/docs/interfaces/RecordSchemaProperties.html @@ -1,7 +1,7 @@ RecordSchemaProperties | org.galaxyproject.gxformat2.v19_09
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Interface RecordSchemaProperties

Auto-generated interface for https://w3id.org/cwl/salad#RecordSchema

-

Hierarchy

  • RecordSchemaProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]
+

Hierarchy

  • RecordSchemaProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

Optional fields

fields?: RecordField[]

Defines the fields of the record.

-

type

type: RECORD
+

type

type: RECORD

Must be record

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ReferencesToolProperties.html b/typescript/docs/interfaces/ReferencesToolProperties.html index f35706c..9476965 100644 --- a/typescript/docs/interfaces/ReferencesToolProperties.html +++ b/typescript/docs/interfaces/ReferencesToolProperties.html @@ -1,10 +1,10 @@ ReferencesToolProperties | org.galaxyproject.gxformat2.v19_09
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Interface ReferencesToolProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ReferencesTool

-

Hierarchy

Index

Properties

Properties

Optional tool_id

tool_id?: string
+

Hierarchy

Index

Properties

Properties

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

Legend

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ReportProperties.html b/typescript/docs/interfaces/ReportProperties.html index 22170f5..4c977ea 100644 --- a/typescript/docs/interfaces/ReportProperties.html +++ b/typescript/docs/interfaces/ReportProperties.html @@ -2,6 +2,6 @@

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Report

Definition of an invocation report for this workflow. Currently the only field is 'markdown'.

-

Hierarchy

  • ReportProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

markdown

markdown: string
+

Hierarchy

  • ReportProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

markdown

markdown: string

Galaxy flavored Markdown to define an invocation report.

Legend

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\ No newline at end of file diff --git a/typescript/docs/interfaces/SinkProperties.html b/typescript/docs/interfaces/SinkProperties.html index 447dbd8..07fa198 100644 --- a/typescript/docs/interfaces/SinkProperties.html +++ b/typescript/docs/interfaces/SinkProperties.html @@ -1,6 +1,6 @@ SinkProperties | org.galaxyproject.gxformat2.v19_09
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Interface SinkProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#Sink

-

Hierarchy

Index

Properties

Properties

Optional source

source?: string | string[]
+

Hierarchy

Index

Properties

Properties

Optional source

source?: string | string[]

Specifies one or more workflow parameters that will provide input to the underlying step parameter.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/StepPositionProperties.html b/typescript/docs/interfaces/StepPositionProperties.html index 7425e0c..1215ee6 100644 --- a/typescript/docs/interfaces/StepPositionProperties.html +++ b/typescript/docs/interfaces/StepPositionProperties.html @@ -1,8 +1,8 @@ StepPositionProperties | org.galaxyproject.gxformat2.v19_09
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Interface StepPositionProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#StepPosition

This field specifies the location of the step's node when rendered in the workflow editor.

-

Hierarchy

  • StepPositionProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

left

left: number
+

Hierarchy

  • StepPositionProperties

Implemented by

Index

Properties

Properties

Optional extensionFields

extensionFields?: Dictionary<any>

left

left: number

Relative horizontal position of the step's node when rendered in the workflow editor.

-

top

top: number
+

top

top: number

Relative vertical position of the step's node when rendered in the workflow editor.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/ToolShedRepositoryProperties.html b/typescript/docs/interfaces/ToolShedRepositoryProperties.html index 251cdb5..2a0873d 100644 --- a/typescript/docs/interfaces/ToolShedRepositoryProperties.html +++ b/typescript/docs/interfaces/ToolShedRepositoryProperties.html @@ -1,11 +1,11 @@ ToolShedRepositoryProperties | org.galaxyproject.gxformat2.v19_09
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Interface ToolShedRepositoryProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/gxformat2common#ToolShedRepository

-

Hierarchy

  • ToolShedRepositoryProperties

Implemented by

Index

Properties

Properties

changeset_revision

changeset_revision: string
+

Hierarchy

  • ToolShedRepositoryProperties

Implemented by

Index

Properties

Properties

changeset_revision

changeset_revision: string

The revision of the tool shed repository this tool can be found in.

-

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

name

name: string

The name of the tool shed repository this tool can be found in.

-

owner

owner: string
+

owner

owner: string

The owner of the tool shed repository this tool can be found in.

-

tool_shed

tool_shed: string
+

tool_shed

tool_shed: string

The URI of the tool shed containing the repository this tool can be found in - typically this should be toolshed.g2.bx.psu.edu.

Legend

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Generated using TypeDoc

\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowInputParameterProperties.html b/typescript/docs/interfaces/WorkflowInputParameterProperties.html index 4a4fd17..6aac54c 100644 --- a/typescript/docs/interfaces/WorkflowInputParameterProperties.html +++ b/typescript/docs/interfaces/WorkflowInputParameterProperties.html @@ -1,23 +1,23 @@ WorkflowInputParameterProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowInputParameterProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowInputParameter

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional collection_type

collection_type?: string
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional collection_type

collection_type?: string

Collection type (defaults to list if type is collection). Nested collection types are separated with colons, e.g. list:list:paired.

-

Optional default_

default_?: any
+

Optional default_

default_?: any

The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is null. Default values are applied before evaluating expressions (e.g. dependent valueFrom fields).

-

Optional doc

doc?: string | string[]
+

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string[]
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional format

format?: string[]

Specify datatype extension for valid input datasets.

-

Optional id

id?: string
+

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional optional

optional?: boolean
+

Optional optional

optional?: boolean

If set to true, WorkflowInputParameter is not required to submit the workflow.

-

Optional position

position?: StepPosition

Optional type

type?: GalaxyType | GalaxyType[]
+

Optional position

position?: StepPosition

Optional type

type?: GalaxyType | GalaxyType[]

Specify valid types of data that may be assigned to this parameter.

Legend

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowOutputParameterProperties.html b/typescript/docs/interfaces/WorkflowOutputParameterProperties.html index 63bc05d..d6ba916 100644 --- a/typescript/docs/interfaces/WorkflowOutputParameterProperties.html +++ b/typescript/docs/interfaces/WorkflowOutputParameterProperties.html @@ -4,15 +4,15 @@ connected to one parameter defined in the workflow that will provide the value of the output parameter. It is legal to connect a WorkflowInputParameter to a WorkflowOutputParameter.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional outputSource

outputSource?: string
+

Optional outputSource

outputSource?: string

Specifies workflow parameter that supply the value of to the output parameter.

-

Optional type

type?: GalaxyType
+

Optional type

type?: GalaxyType

Specify valid types of data that may be assigned to this parameter.

Legend

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepInputProperties.html b/typescript/docs/interfaces/WorkflowStepInputProperties.html index 8e8854e..d029a0e 100644 --- a/typescript/docs/interfaces/WorkflowStepInputProperties.html +++ b/typescript/docs/interfaces/WorkflowStepInputProperties.html @@ -1,15 +1,15 @@ WorkflowStepInputProperties | org.galaxyproject.gxformat2.v19_09
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Interface WorkflowStepInputProperties

Auto-generated interface for https://galaxyproject.org/gxformat2/v19_09#WorkflowStepInput

TODO:

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional default_

default_?: any

The default value for this parameter to use if either there is no source field, or the value produced by the source is null. The default must be applied prior to scattering or evaluating valueFrom.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional source

source?: string | string[]
+

Optional source

source?: string | string[]

Specifies one or more workflow parameters that will provide input to the underlying step parameter.

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepOutputProperties.html b/typescript/docs/interfaces/WorkflowStepOutputProperties.html index 53330a3..fc38483 100644 --- a/typescript/docs/interfaces/WorkflowStepOutputProperties.html +++ b/typescript/docs/interfaces/WorkflowStepOutputProperties.html @@ -7,6 +7,6 @@

A unique identifier for this workflow output parameter. This is the identifier to use in the source field of WorkflowStepInput to connect the output value to downstream parameters.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional add_tags

add_tags?: string[]

Optional change_datatype

change_datatype?: string

Optional delete_intermediate_datasets

delete_intermediate_datasets?: boolean

Optional extensionFields

extensionFields?: Dictionary<any>

Optional hide

hide?: boolean

Optional id

id?: string

The unique identifier for this object.

-

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

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\ No newline at end of file +

Optional remove_tags

remove_tags?: string[]

Optional rename

rename?: string

Optional set_columns

set_columns?: string[]

Legend

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\ No newline at end of file diff --git a/typescript/docs/interfaces/WorkflowStepProperties.html b/typescript/docs/interfaces/WorkflowStepProperties.html index 79e2920..f733f2b 100644 --- a/typescript/docs/interfaces/WorkflowStepProperties.html +++ b/typescript/docs/interfaces/WorkflowStepProperties.html @@ -14,48 +14,48 @@

A note about state and tool_state fields.

Galaxy but shouldn't be written by humans.

state can contained a typed map. Repeat values can be represented as YAML arrays. An alternative to representing state this way is defining inputs with default values.

-

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]
+

Hierarchy

Implemented by

Index

Properties

Properties

Optional doc

doc?: string | string[]

A documentation string for this object, or an array of strings which should be concatenated.

-

Optional errors

errors?: string
+

Optional errors

errors?: string

During Galaxy export there may be some problem validating the tool state, tool used, etc.. that will be indicated by this field. The Galaxy user should be warned of these problems before the workflow can be used in Galaxy.

This field should not be used in human written Galaxy workflow files.

A typical problem is the referenced tool is not installed, this can be fixed by installed the tool and re-saving the workflow and then re-exporting it.

-

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string
+

Optional extensionFields

extensionFields?: Dictionary<any>

Optional id

id?: string

The unique identifier for this object.

-

Optional in_

in_?: WorkflowStepInput[]
+

Optional in_

in_?: WorkflowStepInput[]

Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter which is used to validate the input object. It may also be used build a user interface for constructing the input object.

-

Optional label

label?: string
+

Optional label

label?: string

A short, human-readable label of this object.

-

Optional out

out?: (string | WorkflowStepOutput)[]
+

Optional out

out?: (string | WorkflowStepOutput)[]

Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.

This can also be called 'outputs' for legacy reasons - but the resulting workflow document is not a valid instance of this schema.

-

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow
+

Optional position

position?: StepPosition

Optional run

run?: GalaxyWorkflow

Specifies a subworkflow to run.

-

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any
+

Optional runtime_inputs

runtime_inputs?: string[]

Optional state

state?: any

Structured tool state.

-

Optional tool_id

tool_id?: string
+

Optional tool_id

tool_id?: string

The tool ID used to run this step of the workflow (e.g. 'cat1' or 'toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0').

-

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository
+

Optional tool_shed_repository

tool_shed_repository?: ToolShedRepository

The Galaxy Tool Shed repository that should be installed in order to use this tool.

-

Optional tool_state

tool_state?: any
+

Optional tool_state

tool_state?: any

Unstructured tool state.

-

Optional tool_version

tool_version?: string
+

Optional tool_version

tool_version?: string

The tool version corresponding used to run this step of the workflow. For tool shed installed tools, the ID generally uniquely specifies a version and this field is optional.

-

Optional type

type?: WorkflowStepType
+

Optional type

type?: WorkflowStepType

Workflow step module's type (defaults to 'tool').

-

Optional uuid

uuid?: string
+

Optional uuid

uuid?: string

UUID uniquely representing this element.

-

Optional when

when?: string
+

Optional when

when?: string

If defined, only run the step when the expression evaluates to true. If false the step is skipped. A skipped step produces a null on each output.

diff --git a/typescript/docs/modules.html b/typescript/docs/modules.html index 2430719..d7857c9 100644 --- a/typescript/docs/modules.html +++ b/typescript/docs/modules.html @@ -1,4 +1,4 @@ -org.galaxyproject.gxformat2.v19_09
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Functions

loadDocument

loadDocumentByString

shortname

  • shortname(inputId: string): string

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\ No newline at end of file diff --git a/typescript/src/GalaxyWorkflow.ts b/typescript/src/GalaxyWorkflow.ts index ac67084..cd1defe 100644 --- a/typescript/src/GalaxyWorkflow.ts +++ b/typescript/src/GalaxyWorkflow.ts @@ -39,7 +39,7 @@ export class GalaxyWorkflow extends Saveable implements Internal.GalaxyWorkflowP * The unique identifier for this object. */ id?: undefined | string - class_: string + class_: Internal.GalaxyWorkflow_class /** * A short, human-readable label of this object. @@ -114,7 +114,7 @@ export class GalaxyWorkflow extends Saveable implements Internal.GalaxyWorkflowP release?: undefined | string - constructor ({loadingOptions, extensionFields, id, class_ = 'GalaxyWorkflow', label, doc, inputs, outputs, uuid, steps, report, tags, creator, license, release} : {loadingOptions?: LoadingOptions} & Internal.GalaxyWorkflowProperties) { + constructor ({loadingOptions, extensionFields, id, class_ = Internal.GalaxyWorkflow_class.GALAXYWORKFLOW, label, doc, inputs, outputs, uuid, steps, report, tags, creator, license, release} : {loadingOptions?: LoadingOptions} & Internal.GalaxyWorkflowProperties) { super(loadingOptions) this.extensionFields = extensionFields ?? {} this.id = id @@ -177,7 +177,7 @@ export class GalaxyWorkflow extends Saveable implements Internal.GalaxyWorkflowP let class_ try { - class_ = await loadField(_doc.class, LoaderInstances.uristrtypeFalseTrueNoneNone, + class_ = await loadField(_doc.class, LoaderInstances.uriGalaxyWorkflow_classLoaderFalseTrueNoneNone, baseuri, loadingOptions) } catch (e) { if (e instanceof ValidationException) { diff --git a/typescript/src/GalaxyWorkflowProperties.ts b/typescript/src/GalaxyWorkflowProperties.ts index 75b4796..18ddc1a 100644 --- a/typescript/src/GalaxyWorkflowProperties.ts +++ b/typescript/src/GalaxyWorkflowProperties.ts @@ -27,7 +27,7 @@ export interface GalaxyWorkflowProperties extends Internal.ProcessProperties, In * The unique identifier for this object. */ id?: undefined | string - class_?: string + class_?: Internal.GalaxyWorkflow_class /** * A short, human-readable label of this object. diff --git a/typescript/src/index.ts b/typescript/src/index.ts index d18be8d..ffbeed8 100644 --- a/typescript/src/index.ts +++ b/typescript/src/index.ts @@ -12,6 +12,7 @@ export { GalaxyType, GalaxyWorkflow, GalaxyWorkflowProperties, + GalaxyWorkflow_class, HasStepErrorsProperties, HasStepPositionProperties, HasUUIDProperties, diff --git a/typescript/src/util/Internal.ts b/typescript/src/util/Internal.ts index 27e966e..7d092c9 100644 --- a/typescript/src/util/Internal.ts +++ b/typescript/src/util/Internal.ts @@ -29,6 +29,7 @@ export * from '../EnumSchemaProperties' export * from '../GalaxyType' export * from '../GalaxyWorkflow' export * from '../GalaxyWorkflowProperties' +export * from '../GalaxyWorkflow_class' export * from '../HasStepErrorsProperties' export * from '../HasStepPositionProperties' export * from '../HasUUIDProperties' diff --git a/typescript/src/util/LoaderInstances.ts b/typescript/src/util/LoaderInstances.ts index 413f2b7..737e78b 100644 --- a/typescript/src/util/LoaderInstances.ts +++ b/typescript/src/util/LoaderInstances.ts @@ -21,6 +21,7 @@ import { GalaxyType, GalaxyWorkflow, GalaxyWorkflowProperties, + GalaxyWorkflow_class, HasStepErrorsProperties, HasStepPositionProperties, HasUUIDProperties, @@ -133,7 +134,8 @@ export const unionOfundefinedtypeOrGalaxyWorkflowLoader = new _UnionLoader([unde export const uriunionOfundefinedtypeOrGalaxyWorkflowLoaderFalseFalseNoneNone = new _URILoader(unionOfundefinedtypeOrGalaxyWorkflowLoader, false, false, undefined, undefined); export const uriunionOfundefinedtypeOrstrtypeOrarrayOfstrtypeFalseFalse2None = new _URILoader(unionOfundefinedtypeOrstrtypeOrarrayOfstrtype, false, false, 2, undefined); export const unionOfundefinedtypeOrbooltype = new _UnionLoader([undefinedtype, booltype]); -export const uristrtypeFalseTrueNoneNone = new _URILoader(strtype, false, true, undefined, undefined); +export const GalaxyWorkflow_classLoader = new _EnumLoader((Object.keys(GalaxyWorkflow_class) as Array).map(key => GalaxyWorkflow_class[key])); +export const uriGalaxyWorkflow_classLoaderFalseTrueNoneNone = new _URILoader(GalaxyWorkflow_classLoader, false, true, undefined, undefined); export const arrayOfWorkflowInputParameterLoader = new _ArrayLoader([WorkflowInputParameterLoader]); export const idmapinputsarrayOfWorkflowInputParameterLoader = new _IdMapLoader(arrayOfWorkflowInputParameterLoader, 'id', 'type'); export const arrayOfWorkflowOutputParameterLoader = new _ArrayLoader([WorkflowOutputParameterLoader]);