@galaxy-tool-util/schema 0.4.0 → 1.1.0

package/dist/index.d.ts

@@ -31,7 +31,7 @@ type GalaxyParameterModel,
 /** Union of container parameter types (section, repeat, conditional). */
 type ContainerParameterModel, 
 /** Base fields shared by all leaf Galaxy parameter types. */
-type BaseGalaxyParameterModel, type SelectParameterModel, type GenomeBuildParameterModel, type DrillDownParameterModel, type BooleanParameterModel, type SectionParameterModel, type RepeatParameterModel, type ConditionalParameterModel, 
+type BaseGalaxyParameterModel, type IntegerParameterModel, type FloatParameterModel, type TextParameterModel, type SelectParameterModel, type GenomeBuildParameterModel, type DrillDownParameterModel, type BooleanParameterModel, type SectionParameterModel, type RepeatParameterModel, type ConditionalParameterModel, 
 /** A single branch of a ConditionalParameterModel. */
 type ConditionalWhen, 
 /** A label/value pair used in select and genomebuild options. */
@@ -39,6 +39,7 @@ type LabelValue, } from "./schema/bundle-types.js";
 export { 
 /** True for gx_select, gx_genomebuild, gx_drill_down — params with an options list. */
 isSelectLikeParam, isBooleanParam, isSectionParam, isRepeatParam, isConditionalParam, } from "./schema/type-guards.js";
+export { ParsedTool, HelpContent, XrefDict, Citation } from "./schema/parsed-tool.js";
 export { type GalaxyWorkflow, 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
 GalaxyWorkflowSchema, type NativeGalaxyWorkflow, 
@@ -52,6 +53,16 @@ normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, To
 injectConnectionsIntoState, 
 /** Strip ConnectedValue markers from state using parameter tree. */
 stripConnectedValues, 
+/** Expand defaults into a tool state dict (port of Python fill_static_defaults). */
+expandToolStateDefaults, 
+/** Build the minimal `tool_state` for a freshly inserted step. Today returns `{}`; designated extension point. */
+buildMinimalToolState, 
+/** Build a native (.ga) step skeleton for an inserted tool. */
+buildNativeStep, 
+/** Build a format2 (.gxwf.yml) step skeleton for an inserted tool. */
+buildFormat2Step, 
+/** Build a step skeleton for an inserted tool; dispatches on format. */
+buildStep, type StepSkeletonInputs, 
 /** Flatten a nested parameter path to a dot-separated string. */
 flatStatePath, keysStartingWith, 
 /** Convert repeat block inputs to arrays. */
@@ -87,7 +98,7 @@ roundtripValidate, type RoundtripResult, type RoundtripStrictOptions, type StepR
 /** Scan native workflow tool_state for legacy parameter encoding signals. */
 scanToolState, type LegacyEncodingClassification, type LegacyEncodingHit, type LegacyEncodingScanResult, 
 /** Clean a workflow — strip stale keys, decode legacy tool_state encoding. */
-cleanWorkflow, type CleanWorkflowResult, 
+cleanWorkflow, type CleanWorkflowResult, workflowToMermaid, type MermaidOptions, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, type WorkflowFormat, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -24,6 +24,7 @@ collectValidatorTypes, } from "./schema/index.js";
 export { 
 /** True for gx_select, gx_genomebuild, gx_drill_down — params with an options list. */
 isSelectLikeParam, isBooleanParam, isSectionParam, isRepeatParam, isConditionalParam, } from "./schema/type-guards.js";
+export { ParsedTool, HelpContent, XrefDict, Citation } from "./schema/parsed-tool.js";
 export { 
 /** Union schema accepting any Galaxy workflow format (format2 or native). */
 GalaxyWorkflowSchema, 
@@ -37,6 +38,16 @@ normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, To
 injectConnectionsIntoState, 
 /** Strip ConnectedValue markers from state using parameter tree. */
 stripConnectedValues, 
+/** Expand defaults into a tool state dict (port of Python fill_static_defaults). */
+expandToolStateDefaults, 
+/** Build the minimal `tool_state` for a freshly inserted step. Today returns `{}`; designated extension point. */
+buildMinimalToolState, 
+/** Build a native (.ga) step skeleton for an inserted tool. */
+buildNativeStep, 
+/** Build a format2 (.gxwf.yml) step skeleton for an inserted tool. */
+buildFormat2Step, 
+/** Build a step skeleton for an inserted tool; dispatches on format. */
+buildStep, 
 /** Flatten a nested parameter path to a dot-separated string. */
 flatStatePath, keysStartingWith, 
 /** Convert repeat block inputs to arrays. */
@@ -72,7 +83,7 @@ roundtripValidate,
 /** Scan native workflow tool_state for legacy parameter encoding signals. */
 scanToolState, 
 /** Clean a workflow — strip stale keys, decode legacy tool_state encoding. */
-cleanWorkflow, 
+cleanWorkflow, workflowToMermaid, 
 /** Detect whether a workflow dict is native (.ga) or format2 (.gxwf.yml). */
 detectFormat, 
 /** Format-aware workflow serializer (JSON/YAML, configurable indent and newline). */

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO;AACL,0FAA0F;AAC1F,gBAAgB;AAEhB,4CAA4C;AAC5C,qBAAqB;AACrB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,wEAAwE;AACxE,yBAAyB;AACzB,6DAA6D;AAC7D,wBAAwB;AACxB,gEAAgE;AAChE,qBAAqB;AACrB,gEAAgE;AAChE,qBAAqB,GACtB,MAAM,mBAAmB,CAAC;AA6B3B,OAAO;AACL,uFAAuF;AACvF,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,aAAa,EACb,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AAEjC,OAAO,EAAE,UAAU,EAAE,WAAW,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,yBAAyB,CAAC;AAEtF,OAAO;AAEL,6EAA6E;AAC7E,oBAAoB;AAEpB,oDAAoD;AACpD,0BAA0B;AAC1B,mFAAmF;AACnF,iBAAiB,EACjB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC;AAOjC,wFAAwF;AACxF,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB;AAInB,iEAAiE;AACjE,0BAA0B;AAC1B,oEAAoE;AACpE,oBAAoB;AACpB,oFAAoF;AACpF,uBAAuB;AACvB,kHAAkH;AAClH,qBAAqB;AACrB,+DAA+D;AAC/D,eAAe;AACf,sEAAsE;AACtE,gBAAgB;AAChB,wEAAwE;AACxE,SAAS;AAET,iEAAiE;AACjE,aAAa,EACb,gBAAgB;AAChB,6CAA6C;AAC7C,mBAAmB;AACnB,qEAAqE;AACrE,eAAe;AACf,6DAA6D;AAC7D,mBAAmB;AACnB,gFAAgF;AAChF,eAAe;AACf,+EAA+E;AAC/E,cAAc;AACd,mEAAmE;AACnE,QAAQ,EACR,mBAAmB;AAOnB,qDAAqD;AACrD,SAAS;AACT,qDAAqD;AACrD,QAAQ;AACR,0EAA0E;AAC1E,iBAAiB;AACjB,0EAA0E;AAC1E,gBAAgB;AAMhB,+EAA+E;AAC/E,sBAAsB,EACtB,kBAAkB;AAGlB,4EAA4E;AAC5E,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB;AACxB,6EAA6E;AAC7E,8BAA8B;AAE9B,kFAAkF;AAClF,eAAe;AAEf,yFAAyF;AACzF,iBAAiB;AAMjB,6EAA6E;AAC7E,aAAa;AAIb,8EAA8E;AAC9E,aAAa,EAEb,iBAAiB;AAEjB,6EAA6E;AAC7E,YAAY;AAEZ,qFAAqF;AACrF,iBAAiB;AAEjB,uFAAuF;AACvF,aAAa;AACb,6EAA6E;AAC7E,WAAW;AACX,0EAA0E;AAC1E,WAAW;AACX,+CAA+C;AAC/C,MAAM,EACN,WAAW,EACX,UAAU;AACV,kDAAkD;AAClD,UAAU;AACV,yDAAyD;AACzD,WAAW;AACX,8CAA8C;AAC9C,YAAY;AACZ,yDAAyD;AACzD,wBAAwB;AACxB,wDAAwD;AACxD,uBAAuB;AAKvB,2CAA2C;AAC3C,uBAAuB;AACvB,gEAAgE;AAChE,iBAAiB,EACjB,gBAAgB,EAChB,eAAe,EACf,UAAU,EACV,sBAAsB,EACtB,iBAAiB;AAEjB,2GAA2G;AAC3G,sBAAsB,EACtB,uBAAuB,EACvB,mBAAmB;AACnB,kFAAkF;AAClF,oBAAoB;AACpB,uGAAuG;AACvG,SAAS;AACT,0EAA0E;AAC1E,eAAe,EACf,qBAAqB,EACrB,cAAc,EACd,oBAAoB,EACpB,mBAAmB,EAGnB,aAAa,EA0Cb,iBAAiB,EACjB,kBAAkB,EAClB,iBAAiB,EACjB,UAAU,EACV,eAAe,EACf,2BAA2B,EAC3B,qBAAqB,EACrB,sBAAsB,EACtB,6BAA6B,EAC7B,uBAAuB,EACvB,wBAAwB,EACxB,yBAAyB,EACzB,mBAAmB,EACnB,oBAAoB,EACpB,yBAAyB,EACzB,qBAAqB,EACrB,2BAA2B,EAC3B,uBAAuB,EACvB,wBAAwB,GAEzB,MAAM,qBAAqB,CAAC;AAE7B,OAAO,EAAE,kBAAkB,EAA4B,MAAM,2BAA2B,CAAC;AAEzF,OAAO;AACL,yEAAyE;AACzE,iBAAiB;AACjB,0FAA0F;AAC1F,WAAW;AAUX,wEAAwE;AACxE,qBAAqB;AACrB,yEAAyE;AACzE,sBAAsB;AACtB,0EAA0E;AAC1E,oBAAoB,EACpB,qBAAqB;AACrB,iFAAiF;AACjF,mBAAmB,EACnB,oBAAoB;AACpB,6GAA6G;AAC7G,gBAAgB;AAChB,mFAAmF;AACnF,QAAQ;AACR,sFAAsF;AACtF,yBAAyB,GAC1B,MAAM,wBAAwB,CAAC"}

package/dist/schema/parameter-defaults.d.ts

@@ -0,0 +1,36 @@
+/**
+ * Per-parameter-type default emission.
+ *
+ * Port of scalar branches of `galaxy.tool_util.parameters.convert._fill_default_for`.
+ * Container types (conditional, repeat, section) are handled by the walker in
+ * `workflow/fill-defaults.ts`, not here.
+ */
+import type { ToolParameterModel } from "./bundle-types.js";
+/** Sentinel: return from scalarParameterDefault to leave the key absent. */
+export declare const NO_DEFAULT: unique symbol;
+/**
+ * Return the default value to emit for a scalar (leaf) parameter when the key
+ * is absent from tool state, or NO_DEFAULT to leave the key absent.
+ *
+ * Mirrors `_fill_default_for` scalar branches in convert.py. Container types
+ * (gx_conditional, gx_repeat, gx_section) are not handled here — they are
+ * the walker's concern. CWL parameter types fall through to NO_DEFAULT.
+ *
+ * Dynamic-options selects (`options === null`) return NO_DEFAULT; the value
+ * is resolved at runtime.
+ *
+ * Never emits placeholder values (e.g. RuntimeValue) for data / data_column /
+ * data_collection-nonoptional / baseurl / color / directory_uri / group_tag /
+ * rules — those keys stay absent so the caller wires them explicitly, rather
+ * than mimicking the Galaxy UI's runtime-value scaffolding.
+ */
+export declare function scalarParameterDefault(param: ToolParameterModel): unknown | typeof NO_DEFAULT;
+/**
+ * Text-null coercion: if a text parameter is present with `null` and is
+ * non-optional, coerce to default_value ?? "". This is the only place
+ * expand-defaults mutates a present key. Idempotent because "" stays "".
+ *
+ * Returns the coerced value, or the sentinel to signal "no coercion needed".
+ */
+export declare function coerceTextNullIfNeeded(param: ToolParameterModel, value: unknown): unknown | typeof NO_DEFAULT;
+//# sourceMappingURL=parameter-defaults.d.ts.map

package/dist/schema/parameter-defaults.d.ts.map

@@ -0,0 +1 @@
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package/dist/schema/parameter-defaults.js

@@ -0,0 +1,128 @@
+/**
+ * Per-parameter-type default emission.
+ *
+ * Port of scalar branches of `galaxy.tool_util.parameters.convert._fill_default_for`.
+ * Container types (conditional, repeat, section) are handled by the walker in
+ * `workflow/fill-defaults.ts`, not here.
+ */
+/** Sentinel: return from scalarParameterDefault to leave the key absent. */
+export const NO_DEFAULT = Symbol("NO_DEFAULT");
+/**
+ * First selected option value (single-select), else first option when required,
+ * else null. Mirrors `SelectParameterModel.default_value` in Python.
+ */
+function selectDefaultSingle(param) {
+    if (!param.options || param.options.length === 0)
+        return null;
+    for (const opt of param.options) {
+        if (opt.selected)
+            return opt.value;
+    }
+    if (!param.optional)
+        return param.options[0].value;
+    return null;
+}
+/** Selected option values (multi-select). Mirrors `default_values` in Python. */
+function selectDefaultMultiple(param) {
+    if (!param.options)
+        return null;
+    return param.options.filter((o) => o.selected).map((o) => o.value);
+}
+/** Walk drill-down option tree collecting values of selected nodes (any depth). */
+function selectedDrillDownOptions(options) {
+    const out = [];
+    const walk = (opts) => {
+        for (const opt of opts) {
+            if (opt.selected && opt.value)
+                out.push(opt.value);
+            if (opt.options && opt.options.length > 0)
+                walk(opt.options);
+        }
+    };
+    walk(options);
+    return out;
+}
+function drillDownDefaultSingle(param) {
+    const selected = selectedDrillDownOptions(param.options);
+    return selected.length > 0 ? selected[0] : null;
+}
+function drillDownDefaultMultiple(param) {
+    if (!param.options || param.options.length === 0)
+        return null;
+    return selectedDrillDownOptions(param.options);
+}
+/**
+ * Return the default value to emit for a scalar (leaf) parameter when the key
+ * is absent from tool state, or NO_DEFAULT to leave the key absent.
+ *
+ * Mirrors `_fill_default_for` scalar branches in convert.py. Container types
+ * (gx_conditional, gx_repeat, gx_section) are not handled here — they are
+ * the walker's concern. CWL parameter types fall through to NO_DEFAULT.
+ *
+ * Dynamic-options selects (`options === null`) return NO_DEFAULT; the value
+ * is resolved at runtime.
+ *
+ * Never emits placeholder values (e.g. RuntimeValue) for data / data_column /
+ * data_collection-nonoptional / baseurl / color / directory_uri / group_tag /
+ * rules — those keys stay absent so the caller wires them explicitly, rather
+ * than mimicking the Galaxy UI's runtime-value scaffolding.
+ */
+export function scalarParameterDefault(param) {
+    switch (param.parameter_type) {
+        case "gx_boolean":
+            // TS schema types value as non-nullable boolean; Python tolerates None and
+            // coerces via `value or False` (convert.py:348).
+            return param.value;
+        case "gx_integer":
+        case "gx_float":
+        case "gx_hidden":
+            return param.value;
+        case "gx_genomebuild":
+            return param.optional ? null : NO_DEFAULT;
+        case "gx_select": {
+            if (param.options === null)
+                return NO_DEFAULT; // dynamic
+            if (param.multiple) {
+                const values = selectDefaultMultiple(param);
+                return values && values.length > 0 ? values : null;
+            }
+            return selectDefaultSingle(param);
+        }
+        case "gx_drill_down": {
+            if (param.multiple) {
+                const opts = drillDownDefaultMultiple(param);
+                return opts !== null ? opts : NO_DEFAULT;
+            }
+            const opt = drillDownDefaultSingle(param);
+            return opt !== null ? opt : NO_DEFAULT;
+        }
+        case "gx_data_collection":
+            return param.optional ? null : NO_DEFAULT;
+        case "gx_text":
+            if (!param.optional)
+                return param.value ?? "";
+            return param.value;
+        default:
+            // gx_data, gx_data_column, gx_baseurl, gx_color, gx_directory_uri,
+            // gx_group_tag, gx_rules, cwl_*, and containers (which shouldn't reach
+            // here via the walker leaf callback) all fall through.
+            return NO_DEFAULT;
+    }
+}
+/**
+ * Text-null coercion: if a text parameter is present with `null` and is
+ * non-optional, coerce to default_value ?? "". This is the only place
+ * expand-defaults mutates a present key. Idempotent because "" stays "".
+ *
+ * Returns the coerced value, or the sentinel to signal "no coercion needed".
+ */
+export function coerceTextNullIfNeeded(param, value) {
+    if (param.parameter_type !== "gx_text")
+        return NO_DEFAULT;
+    if (value !== null)
+        return NO_DEFAULT;
+    if (param.optional)
+        return NO_DEFAULT;
+    return param.value ?? "";
+}
+//# sourceMappingURL=parameter-defaults.js.map

package/dist/schema/parameter-defaults.js.map

@@ -0,0 +1 @@
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package/dist/schema/parsed-tool.d.ts

@@ -0,0 +1,47 @@
+import * as S from "effect/Schema";
+import type { ToolParameterModel } from "./bundle-types.js";
+/** Tool help content with format (rst, markdown, etc.) and rendered content. */
+export declare const HelpContent: S.Struct<{
+    format: typeof S.String;
+    content: typeof S.String;
+}>;
+/** External reference (e.g. bio.tools ID, bioconductor package). */
+export declare const XrefDict: S.Struct<{
+    value: typeof S.String;
+    type: typeof S.String;
+}>;
+/** Tool citation entry (bibtex, doi, etc.). */
+export declare const Citation: S.Struct<{
+    type: typeof S.String;
+    content: typeof S.String;
+}>;
+/**
+ * Effect Schema for parsed Galaxy tool metadata as returned by the ToolShed TRS API
+ * or Galaxy's /api/tools/:id/parsed endpoint.
+ */
+export declare const ParsedTool: S.Struct<{
+    id: typeof S.String;
+    version: S.NullOr<typeof S.String>;
+    name: typeof S.String;
+    description: S.transform<S.NullOr<typeof S.String>, S.NullOr<typeof S.String>>;
+    inputs: S.Array$<S.Schema<ToolParameterModel, ToolParameterModel, never>>;
+    outputs: S.Array$<typeof S.Unknown>;
+    citations: S.Array$<S.Struct<{
+        type: typeof S.String;
+        content: typeof S.String;
+    }>>;
+    license: S.NullOr<typeof S.String>;
+    profile: S.NullOr<typeof S.String>;
+    edam_operations: S.Array$<typeof S.String>;
+    edam_topics: S.Array$<typeof S.String>;
+    xrefs: S.Array$<S.Struct<{
+        value: typeof S.String;
+        type: typeof S.String;
+    }>>;
+    help: S.optional<S.Union<[S.Struct<{
+        format: typeof S.String;
+        content: typeof S.String;
+    }>, typeof S.Null]>>;
+}>;
+export type ParsedTool = S.Schema.Type<typeof ParsedTool>;
+//# sourceMappingURL=parsed-tool.d.ts.map

package/dist/schema/parsed-tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parsed-tool.d.ts","sourceRoot":"","sources":["../../src/schema/parsed-tool.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AAEnC,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AAE5D,gFAAgF;AAChF,eAAO,MAAM,WAAW;;;EAGtB,CAAC;AAEH,oEAAoE;AACpE,eAAO,MAAM,QAAQ;;;EAGnB,CAAC;AAEH,+CAA+C;AAC/C,eAAO,MAAM,QAAQ;;;EAGnB,CAAC;AAoBH;;;GAGG;AACH,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;EAcrB,CAAC;AAEH,MAAM,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,UAAU,CAAC,CAAC"}

package/dist/schema/parsed-tool.js

@@ -0,0 +1,49 @@
+import * as S from "effect/Schema";
+/** Tool help content with format (rst, markdown, etc.) and rendered content. */
+export const HelpContent = S.Struct({
+    format: S.String,
+    content: S.String,
+});
+/** External reference (e.g. bio.tools ID, bioconductor package). */
+export const XrefDict = S.Struct({
+    value: S.String,
+    type: S.String,
+});
+/** Tool citation entry (bibtex, doi, etc.). */
+export const Citation = S.Struct({
+    type: S.String,
+    content: S.String,
+});
+/** Normalize empty string to null for description field. */
+const NullableDescription = S.transform(S.NullOr(S.String), S.NullOr(S.String), {
+    decode: (val) => (val === "" ? null : val),
+    encode: (val) => val,
+});
+/**
+ * Trusted-peer schema for a single tool input parameter. Effect Schema does
+ * not describe the full `ToolParameterModel` discriminated union (that lives
+ * as plain TS interfaces in `bundle-types.ts`), so we use a permissive
+ * object-shaped guard here and supply the TS type via the generic parameter.
+ * `ParsedTool` payloads come from Python's `model_dump()` — already trusted.
+ */
+const ToolParameterModelSchema = S.declare((input) => typeof input === "object" && input !== null && !Array.isArray(input));
+/**
+ * Effect Schema for parsed Galaxy tool metadata as returned by the ToolShed TRS API
+ * or Galaxy's /api/tools/:id/parsed endpoint.
+ */
+export const ParsedTool = S.Struct({
+    id: S.String,
+    version: S.NullOr(S.String),
+    name: S.String,
+    description: NullableDescription,
+    inputs: S.Array(ToolParameterModelSchema),
+    outputs: S.Array(S.Unknown),
+    citations: S.Array(Citation),
+    license: S.NullOr(S.String),
+    profile: S.NullOr(S.String),
+    edam_operations: S.Array(S.String),
+    edam_topics: S.Array(S.String),
+    xrefs: S.Array(XrefDict),
+    help: S.optional(S.Union(HelpContent, S.Null)),
+});
+//# sourceMappingURL=parsed-tool.js.map

package/dist/schema/parsed-tool.js.map

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