@galaxy-tool-util/schema 1.2.0 → 1.6.0

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

@@ -1 +1 @@
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package/dist/workflow/raw/native.js.map

@@ -1 +1 @@
-{"version":3,"file":"native.js","sourceRoot":"","sources":["../../../src/workflow/raw/native.ts"],"names":[],"mappings":"AAAA,8DAA8D;AAye9D,MAAM,UAAU,qBAAqB,CACnC,CAAkD;IAElD,OAAO,CAAC,EAAE,KAAK,KAAK,QAAQ,CAAC;AAC/B,CAAC;AAED,MAAM,UAAU,2BAA2B,CACzC,CAAkD;IAElD,OAAO,CAAC,EAAE,KAAK,KAAK,cAAc,CAAC;AACrC,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,MAAM,CAAC;AAC5B,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,UAAU,CAAC;AAChC,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,OAAO,CAAC;AAC7B,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,UAAU,CAAC;AAChC,CAAC"}
+{"version":3,"file":"native.js","sourceRoot":"","sources":["../../../src/workflow/raw/native.ts"],"names":[],"mappings":"AAAA,8DAA8D;AAoiB9D,MAAM,UAAU,qBAAqB,CACnC,CAAkD;IAElD,OAAO,CAAC,EAAE,KAAK,KAAK,QAAQ,CAAC;AAC/B,CAAC;AAED,MAAM,UAAU,2BAA2B,CACzC,CAAkD;IAElD,OAAO,CAAC,EAAE,KAAK,KAAK,cAAc,CAAC;AACrC,CAAC;AAED,MAAM,UAAU,mBAAmB,CACjC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,MAAM,CAAC;AAC5B,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,UAAU,CAAC;AAChC,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,OAAO,CAAC;AAC7B,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,CAAyF;IAEzF,OAAO,CAAC,EAAE,IAAI,KAAK,UAAU,CAAC;AAChC,CAAC"}

package/dist/workflow/report-models.d.ts

@@ -8,6 +8,8 @@
  * Hierarchy:
  *   Step-level  →  Single-workflow wrappers  →  Tree-level reports
  */
+import type { DraftValidationResult, DropReason, ExtractResult } from "./draft-checks.js";
+import type { PromoteFullyConcreteDraftsResult } from "./promote-draft.js";
 export type StepStatus = "ok" | "fail" | "skip_tool_not_found" | "skip_replacement_params";
 export declare const SKIP_STATUSES: ReadonlySet<StepStatus>;
 export interface ValidationStepResult {
@@ -112,6 +114,104 @@ export interface SingleCleanReport {
     before_content?: string | null;
     after_content?: string | null;
 }
+export interface DraftValidationDiagnosticReport {
+    /** Step path; empty array `[]` for workflow-level diagnostics. */
+    path: string[];
+    message: string;
+}
+export interface DraftSurveyReport {
+    is_draft: boolean;
+    todo_count: number;
+    /** Distinct step paths carrying at least one TODO sentinel, in walk order. */
+    todo_paths: string[][];
+    /** Distinct step paths carrying at least one `_plan_*` field, in walk order. */
+    plan_step_paths: string[][];
+}
+/**
+ * Result of `--concrete` validation pass: extract the concrete subset, then
+ * run the regular `gxwf validate` checks on it. The set of populated buckets
+ * depends on which flags were forwarded (cache-dir / no-tool-state /
+ * connections / strict-*). Empty arrays mean the check ran cleanly; absence
+ * of the buckets below means the check was skipped.
+ */
+export interface ConcreteValidationReport {
+    /** Class on the outermost workflow after extract + strip + promote. */
+    class_after: "GalaxyWorkflow" | "GalaxyWorkflowDraft";
+    /**
+     * Reason concrete decode was skipped (e.g., "subset is still a draft —
+     * not fully promoted"). null when decode actually ran.
+     */
+    skipped_reason: string | null;
+    /** Effect Schema decode errors against `GalaxyWorkflowSchema`. */
+    structure_errors: string[];
+    /** Strict-structure check errors. Present only when --strict-structure (or --strict) was set. */
+    strict_structure_errors?: string[];
+    /** Strict-encoding check errors. Present only when --strict-encoding (or --strict) was set. */
+    strict_encoding_errors?: string[];
+    /** Strict-state errors — skipped steps treated as failures. Present only when --strict-state (or --strict) was set. */
+    strict_state_errors?: string[];
+    /** Per-step tool-state validation. Present only when tool-state validation ran. */
+    tool_state?: {
+        results: ValidationStepResult[];
+        summary: {
+            ok: number;
+            fail: number;
+            skip: number;
+        };
+    };
+    /** Connection-type compatibility report. Present only when --connections was set. */
+    connection_report?: ConnectionValidationReport;
+    /**
+     * Tri-state: `true` if every check that ran came back clean, `false` if any
+     * failed, `null` if the concrete pass was skipped (`skipped_reason !== null`).
+     * Consumers must distinguish `null` from `true` — a skipped pass is **not**
+     * an endorsement that the subset would have validated.
+     */
+    ok: boolean | null;
+}
+export interface SingleDraftValidationReport {
+    workflow: string;
+    ok: boolean;
+    structure_errors: DraftValidationDiagnosticReport[];
+    topology_errors: DraftValidationDiagnosticReport[];
+    semantic_errors: DraftValidationDiagnosticReport[];
+    warnings: DraftValidationDiagnosticReport[];
+    survey: DraftSurveyReport;
+    /** Present only when --concrete was requested. */
+    concrete?: ConcreteValidationReport;
+    summary: string;
+}
+export interface DraftExtractDropReport {
+    /** Step path; for workflow-output drops, `[]` for top-level or `[outerStep, ...]` for inner. */
+    path: string[];
+    /** Output label, present only on `dropped_outputs` entries. */
+    label?: string;
+    reason: DropReason;
+}
+export interface DraftExtractRewriteReport {
+    /** Step path of the rewritten step. */
+    path: string[];
+    /** `in:` key on that step whose source was rewritten. */
+    in_key: string;
+    /** Refs removed because their source step / port went away. */
+    removed_refs: string[];
+    /** Refs that survived the rewrite. Empty when only a `default:` keeps the entry alive. */
+    surviving_refs: string[];
+}
+export interface SingleDraftExtractReport {
+    /** Input file path. */
+    workflow: string;
+    /** `-o` destination, or null when the trimmed workflow was written to stdout. */
+    output: string | null;
+    dropped_steps: DraftExtractDropReport[];
+    dropped_outputs: DraftExtractDropReport[];
+    rewritten_step_inputs: DraftExtractRewriteReport[];
+    /** Step paths whose (sub)workflow was flipped from `GalaxyWorkflowDraft` to `GalaxyWorkflow`; `[]` = outermost. */
+    promoted_paths: string[][];
+    /** Class on the outermost workflow after extract + strip + promote. */
+    class_after: "GalaxyWorkflowDraft" | "GalaxyWorkflow";
+    summary: string;
+}
 export type DiffType = "value_mismatch" | "missing_in_roundtrip" | "missing_in_original" | "connection_mismatch" | "position_mismatch" | "label_mismatch" | "annotation_mismatch" | "comment_mismatch" | "step_missing";
 export type DiffSeverity = "error" | "benign";
 export interface BenignArtifact {
@@ -330,6 +430,8 @@ export declare function buildSingleLintReport(workflow: string, lint_errors: num
     lint_warning_messages?: string[];
 }): SingleLintReport;
 export declare function buildSingleCleanReport(workflow: string, results: CleanStepResult[]): SingleCleanReport;
+export declare function buildSingleDraftValidationReport(workflow: string, result: DraftValidationResult, concrete?: ConcreteValidationReport): SingleDraftValidationReport;
+export declare function buildSingleDraftExtractReport(workflow: string, output: string | null, extract: ExtractResult, promote: PromoteFullyConcreteDraftsResult, classAfter: "GalaxyWorkflowDraft" | "GalaxyWorkflow"): SingleDraftExtractReport;
 export declare function buildWorkflowValidationResult(relativePath: string, stepResults: ValidationStepResult[], opts?: {
     error?: string | null;
     skipped_reason?: SkipWorkflowReason | null;

package/dist/workflow/report-models.d.ts.map

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package/dist/workflow/report-models.js

@@ -116,6 +116,104 @@ export function buildSingleCleanReport(workflow, results) {
         steps_with_removals: results.filter((r) => r.removed_keys.length > 0).length,
     };
 }
+export function buildSingleDraftValidationReport(workflow, result, concrete) {
+    const errorCount = result.structureErrors.length +
+        result.topologyErrors.length +
+        result.semanticErrors.length +
+        (concrete ? concreteErrorCount(concrete) : 0);
+    const warnCount = result.warnings.length;
+    const summary = errorCount === 0
+        ? `draft valid${warnCount > 0 ? ` (${warnCount} warning${warnCount === 1 ? "" : "s"})` : ""}`
+        : `${errorCount} error${errorCount === 1 ? "" : "s"}${warnCount > 0 ? `, ${warnCount} warning${warnCount === 1 ? "" : "s"}` : ""}`;
+    // Skipped concrete (ok === null) does NOT drag the aggregate down — it's
+    // informational. Only explicit `false` counts as a failure.
+    const ok = result.ok && concrete?.ok !== false;
+    const report = {
+        workflow,
+        ok,
+        structure_errors: result.structureErrors.map(diagnosticToReport),
+        topology_errors: result.topologyErrors.map(diagnosticToReport),
+        semantic_errors: result.semanticErrors.map(diagnosticToReport),
+        warnings: result.warnings.map(diagnosticToReport),
+        survey: buildDraftSurveyReport(result.survey),
+        summary,
+    };
+    if (concrete)
+        report.concrete = concrete;
+    return report;
+}
+function diagnosticToReport(d) {
+    return { path: [...d.path], message: d.message };
+}
+function concreteErrorCount(c) {
+    return (c.structure_errors.length +
+        (c.strict_structure_errors?.length ?? 0) +
+        (c.strict_encoding_errors?.length ?? 0) +
+        (c.strict_state_errors?.length ?? 0) +
+        (c.tool_state?.summary.fail ?? 0) +
+        (c.connection_report && !c.connection_report.valid ? 1 : 0));
+}
+export function buildSingleDraftExtractReport(workflow, output, extract, promote, classAfter) {
+    const dropped_steps = extract.dropped_steps.map((d) => ({
+        path: [...d.path],
+        reason: d.reason,
+    }));
+    const dropped_outputs = extract.dropped_outputs.map((d) => ({
+        path: [...d.path],
+        label: d.label,
+        reason: d.reason,
+    }));
+    const rewritten_step_inputs = extract.rewritten_step_inputs.map((r) => ({
+        path: [...r.path],
+        in_key: r.in_key,
+        removed_refs: [...r.removed_refs],
+        surviving_refs: [...r.surviving_refs],
+    }));
+    const promoted_paths = promote.promotedPaths.map((p) => [...p]);
+    const stepsWord = dropped_steps.length === 1 ? "step" : "steps";
+    const outputsWord = dropped_outputs.length === 1 ? "output" : "outputs";
+    const rewritesWord = rewritten_step_inputs.length === 1 ? "input rewrite" : "input rewrites";
+    const summary = `${dropped_steps.length} ${stepsWord} dropped, ${dropped_outputs.length} ${outputsWord} dropped,` +
+        ` ${rewritten_step_inputs.length} ${rewritesWord};` +
+        ` class_after=${classAfter}` +
+        (promoted_paths.length > 0 ? ` (${promoted_paths.length} promoted)` : "");
+    return {
+        workflow,
+        output,
+        dropped_steps,
+        dropped_outputs,
+        rewritten_step_inputs,
+        promoted_paths,
+        class_after: classAfter,
+        summary,
+    };
+}
+function buildDraftSurveyReport(survey) {
+    const todoSeen = new Set();
+    const todoPaths = [];
+    for (const hit of survey.todos) {
+        const key = hit.path.join("/");
+        if (todoSeen.has(key))
+            continue;
+        todoSeen.add(key);
+        todoPaths.push([...hit.path]);
+    }
+    const planSeen = new Set();
+    const planStepPaths = [];
+    for (const hit of survey.planFields) {
+        const key = hit.path.join("/");
+        if (planSeen.has(key))
+            continue;
+        planSeen.add(key);
+        planStepPaths.push([...hit.path]);
+    }
+    return {
+        is_draft: survey.isDraft,
+        todo_count: survey.todos.length,
+        todo_paths: todoPaths,
+        plan_step_paths: planStepPaths,
+    };
+}
 // ── Tree workflow-level result builders ──────────────────────────────
 export function buildWorkflowValidationResult(relativePath, stepResults, opts) {
     const hasError = !!(opts?.error || opts?.skipped_reason);

package/dist/workflow/report-models.js.map

@@ -1 +1 @@
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package/dist/workflow/semantic-validators.d.ts

@@ -0,0 +1,18 @@
+/**
+ * Cross-field semantic checks for Format2 input parameters.
+ *
+ * Effect Schema validates structural shape but not cross-field constraints
+ * (e.g. "column_definitions only on sample_sheet collection inputs"). These
+ * checks run after structural validation and throw on violation. Mirrors
+ * gxformat2/_semantic_validators.py.
+ *
+ * Separate from `lint.ts` (style/best-practice) and `stateful-validate.ts`
+ * (runtime tool-state validation): these are structural-but-cross-field
+ * Format2 rules.
+ */
+/**
+ * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
+ * Recurses into inline subworkflows under step.run.
+ */
+export declare function validateWorkflowSemantics(workflow: unknown): void;
+//# sourceMappingURL=semantic-validators.d.ts.map

package/dist/workflow/semantic-validators.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAuGH;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA4BjE"}

package/dist/workflow/semantic-validators.js

@@ -0,0 +1,137 @@
+/**
+ * Cross-field semantic checks for Format2 input parameters.
+ *
+ * Effect Schema validates structural shape but not cross-field constraints
+ * (e.g. "column_definitions only on sample_sheet collection inputs"). These
+ * checks run after structural validation and throw on violation. Mirrors
+ * gxformat2/_semantic_validators.py.
+ *
+ * Separate from `lint.ts` (style/best-practice) and `stateful-validate.ts`
+ * (runtime tool-state validation): these are structural-but-cross-field
+ * Format2 rules.
+ */
+const COLUMN_NAME_RE = /^[\w\-_ ?]*$/;
+const TEXT_TYPE_VALUES = new Set(["text", "string"]);
+const COLLECTION_TYPE_VALUES = new Set(["collection", "data_collection", "data_collection_input"]);
+function _columnDefaultMatchesType(columnType, value) {
+    if (value == null)
+        return true;
+    if (columnType === "string" || columnType === "element_identifier")
+        return typeof value === "string";
+    if (columnType === "int")
+        return typeof value === "number" && Number.isInteger(value) && typeof value !== "boolean";
+    if (columnType === "float")
+        return typeof value === "number" && typeof value !== "boolean";
+    if (columnType === "boolean")
+        return typeof value === "boolean";
+    return true;
+}
+function validateColumnDefinition(column) {
+    if (!column || typeof column !== "object")
+        return;
+    const col = column;
+    const name = col.name;
+    if (typeof name === "string" && !COLUMN_NAME_RE.test(name)) {
+        throw new Error(`Sample sheet column name '${name}' contains disallowed characters`);
+    }
+    const columnType = col.type;
+    const defaultValue = col.default_value;
+    if (!_columnDefaultMatchesType(columnType, defaultValue)) {
+        throw new Error(`Sample sheet column '${String(name)}' default_value ${JSON.stringify(defaultValue)} does not match column type ${JSON.stringify(columnType)}`);
+    }
+    for (const field of ["restrictions", "suggestions"]) {
+        const values = col[field];
+        if (!Array.isArray(values))
+            continue;
+        for (const v of values) {
+            if (!_columnDefaultMatchesType(columnType, v)) {
+                throw new Error(`Sample sheet column '${String(name)}' ${field} entry ${JSON.stringify(v)} does not match column type ${JSON.stringify(columnType)}`);
+            }
+        }
+    }
+}
+function _typeList(typeValue) {
+    if (Array.isArray(typeValue))
+        return typeValue.map(String);
+    if (typeValue == null)
+        return [];
+    return [String(typeValue)];
+}
+function validateInputParameter(inputParam) {
+    if (!inputParam || typeof inputParam !== "object")
+        return;
+    const data = inputParam;
+    const typeValues = _typeList(data.type);
+    const isTextOnly = typeValues.length > 0 && typeValues.every((t) => TEXT_TYPE_VALUES.has(t));
+    const isCollectionOnly = typeValues.length > 0 && typeValues.every((t) => COLLECTION_TYPE_VALUES.has(t));
+    const columnDefinitions = data.column_definitions;
+    if (Array.isArray(columnDefinitions) && columnDefinitions.length > 0) {
+        if (!isCollectionOnly && typeValues.length > 0) {
+            throw new Error(`column_definitions is only valid on collection inputs, got type=${JSON.stringify(data.type)}`);
+        }
+        const collectionType = typeof data.collection_type === "string" ? data.collection_type : "";
+        if (!collectionType.startsWith("sample_sheet")) {
+            throw new Error(`column_definitions requires collection_type starting with 'sample_sheet', got ${JSON.stringify(collectionType)}`);
+        }
+        for (const column of columnDefinitions) {
+            validateColumnDefinition(column);
+        }
+    }
+    for (const field of ["restrictions", "suggestions", "restrictOnConnections"]) {
+        const value = data[field];
+        if (value == null)
+            continue;
+        if (Array.isArray(value) && value.length === 0)
+            continue;
+        if (value === false)
+            continue;
+        if (typeValues.length > 0 && !isTextOnly) {
+            throw new Error(`${field} is only valid on text/string inputs, got type=${JSON.stringify(data.type)}`);
+        }
+    }
+    // Record-input fields validation (mirrors gxformat2 #216).
+    const fields = data.fields;
+    if (Array.isArray(fields) && fields.length > 0) {
+        const collectionType = typeof data.collection_type === "string" ? data.collection_type : "";
+        if (!collectionType.split(":").some((part) => part === "record")) {
+            throw new Error(`fields is only valid on record-typed collection inputs, got collection_type=${JSON.stringify(data.collection_type)}`);
+        }
+    }
+}
+/**
+ * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
+ * Recurses into inline subworkflows under step.run.
+ */
+export function validateWorkflowSemantics(workflow) {
+    if (!workflow || typeof workflow !== "object")
+        return;
+    const data = workflow;
+    const inputs = data.inputs;
+    let iterInputs = [];
+    if (Array.isArray(inputs))
+        iterInputs = inputs;
+    else if (inputs && typeof inputs === "object")
+        iterInputs = Object.values(inputs);
+    for (const inp of iterInputs) {
+        if (typeof inp === "string")
+            continue;
+        validateInputParameter(inp);
+    }
+    const steps = data.steps;
+    let iterSteps = [];
+    if (Array.isArray(steps))
+        iterSteps = steps;
+    else if (steps && typeof steps === "object")
+        iterSteps = Object.values(steps);
+    for (const step of iterSteps) {
+        if (!step || typeof step !== "object")
+            continue;
+        const run = step.run;
+        if (run &&
+            typeof run === "object" &&
+            run.class === "GalaxyWorkflow") {
+            validateWorkflowSemantics(run);
+        }
+    }
+}
+//# sourceMappingURL=semantic-validators.js.map

package/dist/workflow/semantic-validators.js.map

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