@galaxy-tool-util/schema 0.1.0 → 0.4.0

package/dist/workflow/raw/gxformat2.effect.js

@@ -37,6 +37,14 @@ export const DocumentedSchema = Schema.Struct({
     /** A documentation string for this object, or an array of strings which should be concatenated. */
     doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
 });
+export const RecordSchemaSchema = Schema.Struct({
+    /** Defines the fields of the record. */
+    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema).annotations({
+        identifier: "RecordFieldSchema",
+    })))),
+    /** Must be `record` */
+    type: Schema.Literal("record"),
+});
 /**
  * Define an enumerated type.
  */
@@ -46,15 +54,13 @@ export const EnumSchemaSchema = Schema.Struct({
     /** Must be `enum` */
     type: Schema.Literal("enum"),
 });
-export const RecordSchemaSchema = Schema.Struct({
-    /** Defines the fields of the record. */
-    fields: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.suspend(() => RecordFieldSchema)))),
-    /** Must be `record` */
-    type: Schema.Literal("record"),
-});
 export const ArraySchemaSchema = Schema.Struct({
     /** Defines the type of the array elements. */
-    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema), Schema.String))),
+    items: Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String, Schema.Array(Schema.Union(PrimitiveTypeSchema, RecordSchemaSchema, EnumSchemaSchema, Schema.suspend(() => ArraySchemaSchema).annotations({
+        identifier: "ArraySchemaSchema",
+    }), Schema.String))),
     /** Must be `array` */
     type: Schema.Literal("array"),
 });
@@ -104,25 +110,6 @@ export const OutputParameterSchema = Schema.Struct({
     /** A documentation string for this object, or an array of strings which should be concatenated. */
     doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
 });
-/**
- * Describe an output parameter of a workflow.  The parameter must be
-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.
- */
-export const WorkflowOutputParameterSchema = Schema.Struct({
-    ...OutputParameterSchema.fields,
-    /** The unique identifier for this object. */
-    id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** A short, human-readable label of this object. */
-    label: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** A documentation string for this object, or an array of strings which should be concatenated. */
-    doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
-    /** Specifies workflow parameter that supply the value of to the output parameter. */
-    outputSource: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Specify valid types of data that may be assigned to this parameter. */
-    type: Schema.optional(Schema.Union(Schema.Null, GalaxyTypeSchema)),
-});
 /**
  * This field specifies the location of the step's node when rendered in the workflow editor.
  */
@@ -153,6 +140,25 @@ export const WorkflowInputParameterSchema = Schema.Struct({
     /** Collection type (defaults to `list` if `type` is `collection`). Nested collection types are separated with colons, e.g. `list:list:paired`. */
     collection_type: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
+/**
+ * Describe an output parameter of a workflow.  The parameter must be
+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.
+ */
+export const WorkflowOutputParameterSchema = Schema.Struct({
+    ...OutputParameterSchema.fields,
+    /** The unique identifier for this object. */
+    id: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** A short, human-readable label of this object. */
+    label: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** A documentation string for this object, or an array of strings which should be concatenated. */
+    doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
+    /** Specifies workflow parameter that supply the value of to the output parameter. */
+    outputSource: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Specify valid types of data that may be assigned to this parameter. */
+    type: Schema.optional(Schema.Union(Schema.Null, GalaxyTypeSchema)),
+});
 /**
  * The base executable type in CWL is the `Process` object defined by the
 document.  Note that the `Process` object is abstract and cannot be
@@ -199,40 +205,6 @@ export const ReferencesToolSchema = Schema.Struct({
     /** 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. */
     tool_version: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
-/**
- * Associate an output parameter of the underlying process with a workflow
-parameter.  The workflow parameter (given in the `id` field) be may be used
-as a `source` to connect with input parameters of other workflow steps, or
-with an output parameter of the process.
-
-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.
- */
-export const WorkflowStepOutputSchema = Schema.Struct({
-    ...IdentifiedSchema.fields,
-    add_tags: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.String))),
-    change_datatype: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    delete_intermediate_datasets: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
-    hide: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
-    remove_tags: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.String))),
-    rename: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    set_columns: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: Schema.Unknown }), Schema.Null)),
-});
-export const SinkSchema = Schema.Struct({
-    /** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
-    source: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
-});
-/**
- * TODO:
- */
-export const WorkflowStepInputSchema = Schema.Struct({
-    ...IdentifiedSchema.fields,
-    ...SinkSchema.fields,
-    ...LabeledSchema.fields,
-    /** 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 `va... */
-    default: Schema.optional(Schema.Union(Schema.Null, Schema.Unknown)),
-});
 /**
  * Definition of an invocation report for this workflow. Currently the only
 field is 'markdown'.
@@ -254,32 +226,6 @@ export const BaseCommentSchema = Schema.Struct({
     /** Optional label for referencing this comment from frame ``contains_comments`` fields or for use as a map key when comments are represented as a mapping. */
     label: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
-/**
- * A plain text annotation in the workflow editor.
- */
-export const TextCommentSchema = Schema.Struct({
-    ...BaseCommentSchema.fields,
-    /** Comment type (``text``). */
-    type: Schema.Literal("text"),
-    /** The text content. */
-    text: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-    /** Whether the text is displayed in bold. */
-    bold: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
-    /** Whether the text is displayed in italic. */
-    italic: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
-    /** Font size of the text. */
-    text_size: Schema.optional(Schema.Union(Schema.Null, Schema.Number)),
-});
-/**
- * A Markdown-rendered annotation in the workflow editor.
- */
-export const MarkdownCommentSchema = Schema.Struct({
-    ...BaseCommentSchema.fields,
-    /** Comment type (``markdown``). */
-    type: Schema.Literal("markdown"),
-    /** Markdown content. */
-    text: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
-});
 /**
  * A freehand drawn line on the editor canvas.
  */
@@ -335,6 +281,22 @@ export const CreatorPersonSchema = Schema.Struct({
     /** Job title or role. */
     jobTitle: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
+/**
+ * A plain text annotation in the workflow editor.
+ */
+export const TextCommentSchema = Schema.Struct({
+    ...BaseCommentSchema.fields,
+    /** Comment type (``text``). */
+    type: Schema.Literal("text"),
+    /** The text content. */
+    text: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    /** Whether the text is displayed in bold. */
+    bold: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
+    /** Whether the text is displayed in italic. */
+    italic: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
+    /** Font size of the text. */
+    text_size: Schema.optional(Schema.Union(Schema.Null, Schema.Number)),
+});
 /**
  * A rectangular grouping box that visually contains steps and other comments.
  */
@@ -349,6 +311,16 @@ export const FrameCommentSchema = Schema.Struct({
     /** Comment labels or indices contained within this frame. */
     contains_comments: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.Union(Schema.String, Schema.Number)))),
 });
+/**
+ * A Markdown-rendered annotation in the workflow editor.
+ */
+export const MarkdownCommentSchema = Schema.Struct({
+    ...BaseCommentSchema.fields,
+    /** Comment type (``markdown``). */
+    type: Schema.Literal("markdown"),
+    /** Markdown content. */
+    text: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+});
 /**
  * An organization that created or contributed to the workflow.
 Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
@@ -383,9 +355,13 @@ export const GalaxyWorkflowSchema = Schema.Struct({
     /** A documentation string for this object, or an array of strings which should be concatenated. */
     doc: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
     /** The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled. */
-    steps: Schema.Union(Schema.Array(Schema.suspend(() => WorkflowStepSchema)), Schema.Record({
+    steps: Schema.Union(Schema.Array(Schema.suspend(() => WorkflowStepSchema).annotations({
+        identifier: "WorkflowStepSchema",
+    })), Schema.Record({
         key: Schema.String,
-        value: Schema.suspend(() => WorkflowStepSchema),
+        value: Schema.suspend(() => WorkflowStepSchema).annotations({
+            identifier: "WorkflowStepSchema",
+        }),
     })),
     /** Workflow invocation report template. */
     report: Schema.optional(Schema.Union(Schema.Null, ReportSchema)),
@@ -403,6 +379,40 @@ export const GalaxyWorkflowSchema = Schema.Struct({
     /** If listed should correspond to the release of the workflow in its source reposiory. */
     release: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
 });
+/**
+ * Associate an output parameter of the underlying process with a workflow
+parameter.  The workflow parameter (given in the `id` field) be may be used
+as a `source` to connect with input parameters of other workflow steps, or
+with an output parameter of the process.
+
+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.
+ */
+export const WorkflowStepOutputSchema = Schema.Struct({
+    ...IdentifiedSchema.fields,
+    add_tags: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.String))),
+    change_datatype: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    delete_intermediate_datasets: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
+    hide: Schema.optional(Schema.Union(Schema.Null, Schema.Boolean)),
+    remove_tags: Schema.optional(Schema.Union(Schema.Null, Schema.Array(Schema.String))),
+    rename: Schema.optional(Schema.Union(Schema.Null, Schema.String)),
+    set_columns: Schema.optional(Schema.Union(Schema.Record({ key: Schema.String, value: Schema.Unknown }), Schema.Null)),
+});
+export const SinkSchema = Schema.Struct({
+    /** Specifies one or more workflow parameters that will provide input to the underlying step parameter. */
+    source: Schema.optional(Schema.Union(Schema.Null, Schema.String, Schema.Array(Schema.String))),
+});
+/**
+ * TODO:
+ */
+export const WorkflowStepInputSchema = Schema.Struct({
+    ...IdentifiedSchema.fields,
+    ...SinkSchema.fields,
+    ...LabeledSchema.fields,
+    /** 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 `va... */
+    default: Schema.optional(Schema.Union(Schema.Null, Schema.Unknown)),
+});
 /**
  * This represents a non-input step a Galaxy Workflow.
 

package/dist/workflow/raw/gxformat2.effect.js.map

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package/dist/workflow/raw/native.d.ts

@@ -396,9 +396,9 @@ export interface NativeGalaxyWorkflow extends HasUUID {
     name?: null | string;
     class: "NativeGalaxyWorkflow";
     /** Format marker. Always the string ``"true"``. */
-    a_galaxy_workflow: string;
+    a_galaxy_workflow: "true";
     /** Format version. Always ``"0.1"`` currently. In the JSON document this field is written as ``format-version``. */
-    "format-version": string;
+    "format-version": "0.1";
     /** Human-readable workflow description. */
     annotation?: null | string;
     /** Classification tags for the workflow. */

package/dist/workflow/raw/native.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/raw/native.effect.d.ts

@@ -31,13 +31,6 @@ export declare const DocumentedSchema: Schema.Struct<{
     doc: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String, Schema.Array$<typeof Schema.String>]>>;
 }>;
 export type Documented = typeof DocumentedSchema.Type;
-export declare const RecordSchemaSchema: Schema.Struct<{
-    /** Defines the fields of the record. */
-    fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.suspend<any, any, never>>]>>;
-    /** Must be `record` */
-    type: Schema.Literal<["record"]>;
-}>;
-export type RecordSchema = typeof RecordSchemaSchema.Type;
 /**
  * Define an enumerated type.
  */
@@ -48,6 +41,13 @@ export declare const EnumSchemaSchema: Schema.Struct<{
     type: Schema.Literal<["enum"]>;
 }>;
 export type EnumSchema = typeof EnumSchemaSchema.Type;
+export declare const RecordSchemaSchema: Schema.Struct<{
+    /** Defines the fields of the record. */
+    fields: Schema.optional<Schema.Union<[typeof Schema.Null, Schema.Array$<Schema.suspend<any, any, never>>]>>;
+    /** Must be `record` */
+    type: Schema.Literal<["record"]>;
+}>;
+export type RecordSchema = typeof RecordSchemaSchema.Type;
 export declare const ArraySchemaSchema: Schema.Struct<{
     /** Defines the type of the array elements. */
     items: Schema.Union<[Schema.Literal<["null", "boolean", "int", "long", "float", "double", "string"]>, Schema.Struct<{
@@ -417,28 +417,6 @@ export declare const NativeFreehandCommentSchema: Schema.Struct<{
     color: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
 }>;
 export type NativeFreehandComment = typeof NativeFreehandCommentSchema.Type;
-/**
- * Provenance tracking for workflows imported from external sources.
-Contains either a direct URL or TRS (Tool Registry Service) metadata,
-depending on how the workflow was imported.
-
-For URL imports, only ``url`` is set. For TRS imports (Dockstore,
-WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
-are set, with ``trs_server`` optionally identifying the server.
- */
-export declare const NativeSourceMetadataSchema: Schema.Struct<{
-    /** URL from which the workflow was directly imported. */
-    url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
-    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
-    trs_tool_id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
-    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
-    trs_version_id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
-    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
-    trs_server: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
-    /** Complete TRS API endpoint URL for this workflow version. */
-    trs_url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
-}>;
-export type NativeSourceMetadata = typeof NativeSourceMetadataSchema.Type;
 /**
  * Workflow invocation report template.
  */
@@ -500,6 +478,28 @@ export declare const NativeCreatorPersonSchema: Schema.Struct<{
     faxNumber: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
 }>;
 export type NativeCreatorPerson = typeof NativeCreatorPersonSchema.Type;
+/**
+ * Provenance tracking for workflows imported from external sources.
+Contains either a direct URL or TRS (Tool Registry Service) metadata,
+depending on how the workflow was imported.
+
+For URL imports, only ``url`` is set. For TRS imports (Dockstore,
+WorkflowHub), ``trs_tool_id``, ``trs_version_id``, and ``trs_url``
+are set, with ``trs_server`` optionally identifying the server.
+ */
+export declare const NativeSourceMetadataSchema: Schema.Struct<{
+    /** URL from which the workflow was directly imported. */
+    url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    /** Tool identifier in the Tool Registry Service (e.g. ``"#workflow/github.com/user/repo/workflow"`` or ``"109"``). */
+    trs_tool_id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    /** Version identifier in the TRS (e.g. ``"master"``, ``"5"``). */
+    trs_version_id: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    /** TRS server name (e.g. ``"dockstore"``, ``"workflowhub"``). Optional even for TRS imports. */
+    trs_server: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    /** Complete TRS API endpoint URL for this workflow version. */
+    trs_url: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+}>;
+export type NativeSourceMetadata = typeof NativeSourceMetadataSchema.Type;
 /**
  * An organization that created or contributed to the workflow.
 Corresponds to a `schema.org Organization <https://schema.org/Organization>`_.
@@ -534,9 +534,9 @@ export declare const NativeGalaxyWorkflowSchema: Schema.Struct<{
     name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
     class: Schema.Literal<["NativeGalaxyWorkflow"]>;
     /** Format marker. Always the string ``"true"``. */
-    a_galaxy_workflow: typeof Schema.String;
+    a_galaxy_workflow: Schema.Literal<["true"]>;
     /** Format version. Always ``"0.1"`` currently. In the JSON document this field is written as ``format-version``. */
-    "format-version": typeof Schema.String;
+    "format-version": Schema.Literal<["0.1"]>;
     /** Human-readable workflow description. */
     annotation: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
     /** Classification tags for the workflow. */
@@ -769,9 +769,9 @@ export declare const NativeStepSchema: Schema.Struct<{
         name: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
         class: Schema.Literal<["NativeGalaxyWorkflow"]>;
         /** Format marker. Always the string ``"true"``. */
-        a_galaxy_workflow: typeof Schema.String;
+        a_galaxy_workflow: Schema.Literal<["true"]>;
         /** Format version. Always ``"0.1"`` currently. In the JSON document this field is written as ``format-version``. */
-        "format-version": typeof Schema.String;
+        "format-version": Schema.Literal<["0.1"]>;
         /** Human-readable workflow description. */
         annotation: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
         /** Classification tags for the workflow. */

package/dist/workflow/raw/native.effect.d.ts.map

@@ -1 +1 @@
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