@galaxy-tool-util/schema 1.14.0 → 1.15.0

package/dist/workflow/lint.js

@@ -9,7 +9,9 @@ import { normalizedNative } from "./normalized/native.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
 import { detectFormat } from "./detect-format.js";
 import { LintContext } from "./linting.js";
-import { nativeInputLabel, nativeStepLabel } from "./normalized/toNative.js";
+import { format2InputStepType, nativeInputLabel, nativeStepLabel } from "./normalized/toNative.js";
+import { resolveSourceReference } from "./normalized/labels.js";
+import { nativeInputToFormat2Type } from "./normalized/toFormat2.js";
 import { NativeStepKeyNotInteger, StepLabelNotUnique } from "./lint-rules.js";
 export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, } from "./linting.js";
 function toLintResult(ctx) {
@@ -125,6 +127,7 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
         lintStepErrors(ctx, step.errors);
         lintToolIfPresent(ctx, step.tool_id);
     }
+    lintNativeInputDefaults(ctx, nnw);
     validateReport(ctx, nnw.report);
     if (!foundOutputs) {
         ctx.warn("Workflow contained no outputs");
@@ -169,28 +172,68 @@ function validateOutputSources(ctx, nf2) {
 }
 function validateInputTypes(ctx, nf2) {
     for (const inp of nf2.inputs) {
-        if (inp.default == null)
+        lintInputDefault(ctx, inp.id, inp.type, inp.default);
+    }
+}
+function lintNativeInputDefaults(ctx, nnw) {
+    for (const [key, step] of Object.entries(nnw.steps)) {
+        if (step.type !== "parameter_input")
             continue;
-        const inputType = inp.type;
-        if (Array.isArray(inputType))
-            continue; // array types — skip
-        if (inputType === "int" || inputType === "integer") {
-            if (typeof inp.default !== "number" || !Number.isInteger(inp.default)) {
-                ctx.error("Input default is of invalid type");
-            }
-        }
-        else if (inputType === "float" || inputType === "double") {
-            if (typeof inp.default !== "number") {
-                ctx.error("Input default is of invalid type");
-            }
-        }
-        else if (inputType === "string" || inputType === "text") {
-            if (typeof inp.default !== "string") {
-                ctx.error("Input default is of invalid type");
-            }
+        const inputType = nativeInputToFormat2Type(step.type, step.tool_state);
+        lintInputDefault(nativeStepContext(ctx, key), step.label || key, inputType, step.tool_state.default);
+    }
+}
+const STRING_DEFAULT = {
+    typeName: "string",
+    expected: "a string",
+    expectedList: "a string or a list of strings",
+    isValid: (value) => typeof value === "string",
+};
+const INTEGER_DEFAULT = {
+    typeName: "int",
+    expected: "an integer",
+    expectedList: "an integer or a list of integers",
+    isValid: (value) => typeof value === "number" && Number.isInteger(value),
+};
+const FLOAT_DEFAULT = {
+    typeName: "float",
+    expected: "a number",
+    expectedList: "a number or a list of numbers",
+    isValid: (value) => typeof value === "number",
+};
+const DEFAULT_CHECKS = {
+    string: STRING_DEFAULT,
+    text: STRING_DEFAULT,
+    int: INTEGER_DEFAULT,
+    integer: INTEGER_DEFAULT,
+    float: FLOAT_DEFAULT,
+    double: FLOAT_DEFAULT,
+    color: { ...STRING_DEFAULT, typeName: "color" },
+    directory_uri: { ...STRING_DEFAULT, typeName: "directory_uri" },
+};
+function defaultCheck(inputType) {
+    return Object.hasOwn(DEFAULT_CHECKS, inputType) ? DEFAULT_CHECKS[inputType] : undefined;
+}
+function lintInputDefault(ctx, label, inputType, defaultValue) {
+    if (defaultValue == null || inputType == null)
+        return;
+    if (Array.isArray(inputType)) {
+        // Galaxy wraps a bare default for multiple parameter inputs.
+        const check = inputType.length === 1 ? defaultCheck(inputType[0]) : undefined;
+        const values = Array.isArray(defaultValue) ? defaultValue : [defaultValue];
+        if (check && !values.every(check.isValid)) {
+            invalidDefault(ctx, label, `[${check.typeName}]`, check.expectedList);
         }
+        return;
+    }
+    const check = defaultCheck(inputType);
+    if (check && !check.isValid(defaultValue)) {
+        invalidDefault(ctx, label, check.typeName, check.expected);
     }
 }
+function invalidDefault(ctx, label, inputType, expected) {
+    ctx.error(`Input default is of invalid type. Input ${label} is ${inputType}; its default must be ${expected}.`);
+}
 function lintFormat2Workflow(ctx, nf2, rawDict) {
     if (rawDict != null) {
         if (!("steps" in rawDict)) {
@@ -278,18 +321,57 @@ export function lintWorkflow(workflowDict) {
 // ---------------------------------------------------------------------------
 // Best practices linting
 // ---------------------------------------------------------------------------
-const UNTYPED_PARAM_RE = /\$\{.+?\}/;
-function checkJsonForUntypedParams(value) {
-    if (Array.isArray(value)) {
-        return value.some(checkJsonForUntypedParams);
-    }
-    if (value !== null && typeof value === "object") {
-        return Object.values(value).some(checkJsonForUntypedParams);
-    }
+// Galaxy's informal replacement parameter syntax (`get_informal_replacement_parameters`).
+const UNTYPED_PARAMETER_PATTERN = /\$\{(.+?)\}/g;
+const RENAME_ACTION = "RenameDatasetAction";
+const DATA_INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input"]);
+/** Rename `#{...}` reference for a step input; Galaxy reads nested `a|b` as `a.b`. */
+function inputReference(inputName) {
+    return inputName.replaceAll("|", ".");
+}
+/** Distinct `${name}` references anywhere in a JSON-like value, in order. */
+function untypedParameterNames(value) {
     if (typeof value === "string") {
-        return UNTYPED_PARAM_RE.test(value);
+        return Array.from(value.matchAll(UNTYPED_PARAMETER_PATTERN), (m) => m[1]);
+    }
+    const items = Array.isArray(value)
+        ? value
+        : value !== null && typeof value === "object"
+            ? Object.values(value)
+            : [];
+    return [...new Set(items.flatMap(untypedParameterNames))];
+}
+function lintUntypedToolState(ctx, stepId, toolState) {
+    for (const name of untypedParameterNames(toolState)) {
+        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter as an input. \${${name}} is filled only by ` +
+            "the expanded run form, never via the API; connect a workflow parameter input instead.");
+    }
+}
+/** Warn for `${name}` references Galaxy won't fill from a declared parameter input. */
+function lintUntypedPja(ctx, stepId, outputName, action, value, isRename, scope) {
+    const target = outputName ? `output ${outputName}` : "all outputs";
+    for (const name of untypedParameterNames(value)) {
+        let detail;
+        if (!isRename) {
+            detail = "stays literal; Galaxy substitutes parameters only in renames.";
+        }
+        else if (scope.parameterLabels.has(name)) {
+            continue;
+        }
+        else if (scope.dataLabels.has(name)) {
+            const ref = scope.connectedInputs.get(name) ?? "input_name";
+            detail =
+                "names a data input, but Galaxy fills ${...} only from parameter inputs; " +
+                    `use #{${ref}} for that dataset's name.`;
+        }
+        else {
+            detail =
+                "is not a parameter input label, so Galaxy prompts for it at run time and leaves it literal via " +
+                    `the API; add a parameter input labelled ${name}, or use #{input_name} for an input dataset's name.`;
+        }
+        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions. ` +
+            `\${${name}} in ${action} of ${target} ${detail}`);
     }
-    return false;
 }
 const SKIP_DISCONNECTED_NATIVE_TYPES = new Set([
     "data_input",
@@ -297,7 +379,7 @@ const SKIP_DISCONNECTED_NATIVE_TYPES = new Set([
     "parameter_input",
     "pause",
 ]);
-function lintStepBestPractices(ctx, step) {
+function lintStepBestPractices(ctx, step, scope) {
     const stepId = step.label || step.id;
     // disconnected inputs
     for (const stepInput of step.in) {
@@ -313,21 +395,21 @@ function lintStepBestPractices(ctx, step) {
     if (!step.label) {
         ctx.warn(`Workflow step ${stepId} has no label.`);
     }
-    // untyped params in state
-    const toolState = step.state || step.tool_state;
-    if (toolState && checkJsonForUntypedParams(toolState)) {
-        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter as an input.`);
-    }
-    // untyped params in outputs (PJA equivalents)
-    if (step.out && step.out.length > 0 && checkJsonForUntypedParams(step.out)) {
-        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
+    lintUntypedToolState(ctx, stepId, step.state || step.tool_state);
+    // format2 step outputs carry the post-job actions as fields
+    for (const out of step.out ?? []) {
+        for (const [field, value] of Object.entries(out)) {
+            if (field !== "id" && value != null) {
+                lintUntypedPja(ctx, stepId, out.id, field, value, field === "rename", scope);
+            }
+        }
     }
 }
 /**
  * Native step best-practice checks on native fields, so messages reference
  * native ids / labels rather than format2 sentinels like `_unlabeled_step_1`.
  */
-function lintNativeStepBestPractices(ctx, step) {
+function lintNativeStepBestPractices(ctx, step, scope) {
     const stepId = step.label || step.annotation || String(step.id);
     // disconnected inputs
     if (!step.type || !SKIP_DISCONNECTED_NATIVE_TYPES.has(step.type)) {
@@ -344,7 +426,6 @@ function lintNativeStepBestPractices(ctx, step) {
     if (!step.label) {
         ctx.warn(`Workflow step ${stepId} has no label.`);
     }
-    // untyped params in tool_state
     let toolState = step.tool_state;
     if (typeof toolState === "string") {
         try {
@@ -354,13 +435,12 @@ function lintNativeStepBestPractices(ctx, step) {
             toolState = {};
         }
     }
-    if (toolState && typeof toolState === "object" && checkJsonForUntypedParams(toolState)) {
-        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter as an input.`);
-    }
-    // untyped params in post_job_actions
-    if (step.post_job_actions && Object.keys(step.post_job_actions).length > 0) {
-        if (checkJsonForUntypedParams(step.post_job_actions)) {
-            ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
+    lintUntypedToolState(ctx, stepId, toolState);
+    for (const pja of Object.values(step.post_job_actions ?? {})) {
+        for (const [argument, value] of Object.entries(pja.action_arguments ?? {})) {
+            const isRename = pja.action_type === RENAME_ACTION && argument === "newname";
+            const action = isRename ? "rename" : pja.action_type;
+            lintUntypedPja(ctx, stepId, pja.output_name, action, value, isRename, scope);
         }
     }
 }
@@ -410,8 +490,20 @@ export function lintBestPracticesFormat2(workflowDict) {
     }
     if (nf2) {
         lintWorkflowTopLevel(ctx, nf2, workflowDict);
+        const inputTypes = nf2.inputs
+            .filter((inp) => inp.id)
+            .map((inp) => [inp.id, format2InputStepType(inp)]);
+        const parameterLabels = new Set(inputTypes.filter(([, t]) => t === "parameter_input").map(([label]) => label));
+        const dataLabels = new Set(inputTypes.filter(([, t]) => t && DATA_INPUT_STEP_TYPES.has(t)).map(([label]) => label));
         for (const step of nf2.steps) {
-            lintStepBestPractices(ctx, step);
+            const connectedInputs = new Map();
+            for (const stepInput of step.in) {
+                const sources = stepInput.source == null ? [] : [stepInput.source].flat();
+                for (const source of sources) {
+                    connectedInputs.set(resolveSourceReference(source, dataLabels)[0], inputReference(stepInput.id));
+                }
+            }
+            lintStepBestPractices(ctx, step, { parameterLabels, dataLabels, connectedInputs });
         }
     }
     return toLintResult(ctx);
@@ -440,8 +532,22 @@ export function lintBestPracticesNative(workflowDict) {
         nnw = null;
     }
     if (nnw) {
-        for (const step of Object.values(nnw.steps)) {
-            lintNativeStepBestPractices(ctx, step);
+        const steps = Object.values(nnw.steps);
+        const labels = new Map(steps.filter((s) => s.label).map((s) => [s.id, s.label]));
+        const parameterLabels = new Set(steps.filter((s) => s.type === "parameter_input" && s.label).map((s) => s.label));
+        const dataLabels = new Set(steps
+            .filter((s) => DATA_INPUT_STEP_TYPES.has(s.type) && s.label)
+            .map((s) => s.label));
+        for (const step of steps) {
+            const connectedInputs = new Map();
+            for (const [inputName, connections] of Object.entries(step.input_connections)) {
+                for (const connection of connections) {
+                    const label = connection.id == null ? undefined : labels.get(connection.id);
+                    if (label)
+                        connectedInputs.set(label, inputReference(inputName));
+                }
+            }
+            lintNativeStepBestPractices(ctx, step, { parameterLabels, dataLabels, connectedInputs });
         }
     }
     return toLintResult(ctx);

package/dist/workflow/lint.js.map

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package/dist/workflow/mermaid.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAAuB,KAAK,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA6B9F,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAwJR"}
+{"version":3,"file":"mermaid.d.ts","sourceRoot":"","sources":["../../src/workflow/mermaid.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAOtD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAAuB,KAAK,yBAAyB,EAAE,MAAM,yBAAyB,CAAC;AA8B9F,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB;;;OAGG;IACH,eAAe,CAAC,EAAE,GAAG,CAAC,MAAM,EAAE,cAAc,CAAC,CAAC;IAC9C;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,YAAY,GAAG,IAAI,CAAC;CACpC;AA+CD,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,OAAO,GAAG,yBAAyB,EAC7C,IAAI,GAAE,cAAmB,GACxB,MAAM,CAwJR"}

package/dist/workflow/mermaid.js

@@ -20,6 +20,7 @@ const STEP_TYPE_SHAPES = {
     text: SHAPE_PARAM,
     boolean: SHAPE_PARAM,
     color: SHAPE_PARAM,
+    directory_uri: SHAPE_PARAM,
     input: SHAPE_INPUT,
     tool: SHAPE_TOOL,
     subworkflow: SHAPE_SUBWORKFLOW,

package/dist/workflow/mermaid.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/native.js

@@ -136,16 +136,17 @@ function _normalizePosition(position) {
     return { top: position.top, left: position.left };
 }
 function _parseToolState(raw) {
-    if (typeof raw === "string") {
+    let value = raw;
+    if (typeof value === "string") {
         try {
-            return JSON.parse(raw);
+            value = JSON.parse(value);
         }
         catch {
             return {};
         }
     }
-    if (raw != null && typeof raw === "object") {
-        return raw;
+    if (value != null && typeof value === "object" && !Array.isArray(value)) {
+        return value;
     }
     return {};
 }

package/dist/workflow/normalized/native.js.map

@@ -1 +1 @@
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package/dist/workflow/normalized/toFormat2.d.ts

@@ -27,4 +27,5 @@ export interface ToFormat2Options {
  * Convert a native Galaxy workflow to normalized Format2.
  */
 export declare function toFormat2(raw: unknown, options?: ToFormat2Options): NormalizedFormat2Workflow;
+export declare function nativeInputToFormat2Type(stepType: string, toolState: Record<string, unknown>): string | string[];
 //# sourceMappingURL=toFormat2.d.ts.map

package/dist/workflow/normalized/toFormat2.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAStB,eAAO,MAAM,gBAAgB,aAAsE,CAAC;AAEpG;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F"}
+{"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAA4B,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAElF,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAYtB,eAAO,MAAM,gBAAgB,aAAsE,CAAC;AAEpG;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7B;AAED,MAAM,WAAW,gBAAgB;IAC/B;;;;OAIG;IACH,oBAAoB,CAAC,EAAE,CAAC,UAAU,EAAE,oBAAoB,KAAK,oBAAoB,GAAG,IAAI,CAAC;CAC1F;AAED;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,gBAAgB,GAAG,yBAAyB,CAG7F;AAmED,wBAAgB,wBAAwB,CACtC,QAAQ,EAAE,MAAM,EAChB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACjC,MAAM,GAAG,MAAM,EAAE,CAYnB"}

package/dist/workflow/normalized/toFormat2.js

@@ -7,6 +7,8 @@ import { normalizedNative } from "./native.js";
 import { isGalaxyUserToolRun } from "./format2.js";
 import { flattenCommentData } from "./comments.js";
 import { isUnlabeled, Labels, unlabeledNodeId } from "./labels.js";
+import { inputTypesDeclaring } from "../input-parameter.js";
+const REGEX_VALIDATOR_TYPES = inputTypesDeclaring("validators");
 // Effect schemas produce deeply-readonly types. We build plain objects
 // and cast — runtime semantics are identical.
 // Step types that represent workflow inputs
@@ -72,7 +74,7 @@ function _buildFormat2Workflow(wf, options) {
     return result;
 }
 // --- Input parameter building ---
-function _nativeInputToFormat2Type(stepType, toolState) {
+export function nativeInputToFormat2Type(stepType, toolState) {
     if (stepType === "data_collection_input")
         return "collection";
     if (stepType === "data_input")
@@ -90,9 +92,22 @@ function _nativeInputToFormat2Type(stepType, toolState) {
     }
     return "data";
 }
+function _nativeTextValidatorToFormat2(validator) {
+    if (!validator || typeof validator !== "object")
+        return [];
+    const v = validator;
+    if (v.type !== "regex")
+        return [];
+    const result = { type: "regex", expression: v.expression };
+    if (v.message != null)
+        result.message = v.message;
+    if (v.negate)
+        result.negate = true;
+    return [result];
+}
 function _buildInputParam(step) {
     const stepId = unlabeledNodeId(step.label, step.id, true);
-    const inputType = _nativeInputToFormat2Type(step.type, step.tool_state);
+    const inputType = nativeInputToFormat2Type(step.type, step.tool_state);
     const result = { id: stepId, type: inputType };
     const ts = step.tool_state;
     for (const key of [
@@ -133,6 +148,13 @@ function _buildInputParam(step) {
             }
         }
     }
+    else if ((Array.isArray(inputType) && inputType[0] === "string") ||
+        (typeof inputType === "string" && REGEX_VALIDATOR_TYPES.has(inputType))) {
+        const validators = Array.isArray(ts.validators) ? ts.validators : [];
+        const textValidators = validators.flatMap(_nativeTextValidatorToFormat2);
+        if (textValidators.length > 0)
+            result.validators = textValidators;
+    }
     if (step.annotation)
         result.doc = step.annotation;
     if (step.position)