@galaxy-tool-util/schema 1.10.0 → 1.12.0

package/dist/user-tool-parse/input-source.js

@@ -0,0 +1,271 @@
+/**
+ * `InputSource` / `PageSource` seam — the TS mirror of Galaxy's
+ * `galaxy.tool_util.parser.interface.InputSource` / `PageSource`. Decouples the
+ * input-tree walk (who reads the source) from the parameter-model factory in
+ * `./inputs.ts` (the `_from_input_source_galaxy` + `input_models_for_page`
+ * equivalent), so an XML-backed source in `@galaxy-tool-util/tool-xml` can feed
+ * the same factory.
+ *
+ * This module is the dependency-free interface plus the inline/YAML dict
+ * implementation (`DictInputSource` / `DictPageSource`), mirroring Galaxy's
+ * `YamlInputSource` / `YamlPageSource`. Coercion here is dict-native (native
+ * YAML bools/numbers pass through `get`; string coercion matches the previous
+ * inline reads) — it deliberately does NOT adopt XML's `string_as_bool`
+ * semantics, which live on the XML source in `tool-xml`.
+ *
+ * Only the methods the current factory consumes are on the interface. Further
+ * Galaxy accessors (dynamic options, `get_bool_or_none`, conversion tuples,
+ * sanitizers) land with the feature slices that need them.
+ */
+export class DictPageSource {
+    raw;
+    constructor(raw) {
+        this.raw = raw;
+    }
+    parseInputSources() {
+        return normalizeInputList(this.raw).map((d) => new DictInputSource(d));
+    }
+}
+export class DictInputSource {
+    input;
+    constructor(input) {
+        this.input = input;
+    }
+    get(key, defaultValue) {
+        const v = this.input[key];
+        return v === undefined ? defaultValue : v;
+    }
+    getBool(key, defaultValue) {
+        return readBool(this.input[key], defaultValue);
+    }
+    parseInputType() {
+        const t = this.input.type;
+        if (t === "conditional")
+            return "conditional";
+        if (t === "repeat")
+            return "repeat";
+        return "param";
+    }
+    parseName() {
+        return readString(this.input.name);
+    }
+    parseLabel() {
+        return readNullableString(this.input.label);
+    }
+    parseHelp() {
+        return readNullableString(this.input.help);
+    }
+    parseOptional(defaultValue = false) {
+        return readBool(this.input.optional, defaultValue);
+    }
+    parseExtensions() {
+        const explicit = this.input.extensions;
+        let raw = explicit;
+        if (raw === undefined || raw === null || (Array.isArray(raw) && raw.length === 0)) {
+            raw = this.input.format ?? "data";
+        }
+        let list;
+        if (Array.isArray(raw)) {
+            list = raw;
+        }
+        else if (typeof raw === "string") {
+            list = raw.split(",");
+        }
+        else {
+            list = ["data"];
+        }
+        return list.map((v) => String(v).trim().toLowerCase()).filter((v) => v !== "");
+    }
+    hasDynamicOptions() {
+        // YAML/inline selects are always static (Galaxy's base `parse_dynamic_options`
+        // returns `None`; `YamlInputSource` does not override it).
+        return false;
+    }
+    hasDrillDownDynamicOptions() {
+        // As with `hasDynamicOptions`, the inline/YAML source is always static.
+        return false;
+    }
+    parseStaticOptions() {
+        const opts = this.input.options;
+        if (!Array.isArray(opts))
+            return null;
+        const out = [];
+        for (const item of opts) {
+            if (!isDict(item))
+                continue;
+            const value = item.value;
+            if (value === undefined)
+                continue;
+            const valueStr = String(value);
+            const label = typeof item.label === "string" ? item.label : valueStr;
+            const selected = readBool(item.selected, false);
+            out.push({ label, value: valueStr, selected });
+        }
+        return out;
+    }
+    parseDrillDownStaticOptions() {
+        return parseDrillDownOptions(this.input.options);
+    }
+    parseValidators() {
+        const raw = this.input.validators;
+        if (!Array.isArray(raw))
+            return [];
+        const all = [];
+        for (const entry of raw) {
+            if (!isDict(entry))
+                continue;
+            const v = parseValidatorDict(entry);
+            if (v)
+                all.push(v);
+        }
+        return all;
+    }
+    parseNestedInputsSource() {
+        const inner = this.input.blocks ?? this.input.parameters ?? this.input.inputs;
+        return new DictPageSource(inner);
+    }
+    parseTestInputSource() {
+        const testRaw = this.input.test_parameter;
+        if (!isDict(testRaw)) {
+            throw new Error(`conditional '${this.parseName()}' must define a 'test_parameter'`);
+        }
+        return new DictInputSource(testRaw);
+    }
+    parseWhenInputSources() {
+        const out = [];
+        // YAML supports two shapes: `when: {key: [params], ...}` (map) and `whens:
+        // [{discriminator, parameters: [...]}]` (list).
+        const whenMap = this.input.when;
+        const whenList = this.input.whens;
+        if (isDict(whenMap)) {
+            for (const [key, value] of Object.entries(whenMap)) {
+                out.push([key, new DictPageSource(Array.isArray(value) ? value : [])]);
+            }
+        }
+        else if (Array.isArray(whenList)) {
+            for (const item of whenList) {
+                if (!isDict(item))
+                    continue;
+                out.push([item.discriminator, new DictPageSource(item.parameters)]);
+            }
+        }
+        return out;
+    }
+    parseDefault() {
+        return this.input.default;
+    }
+}
+function normalizeInputList(raw) {
+    if (Array.isArray(raw)) {
+        return raw.filter(isDict);
+    }
+    if (raw && typeof raw === "object") {
+        const out = [];
+        for (const [k, v] of Object.entries(raw)) {
+            if (isDict(v)) {
+                const merged = { ...v };
+                if (merged.name == null)
+                    merged.name = k;
+                out.push(merged);
+            }
+        }
+        return out;
+    }
+    return [];
+}
+function parseDrillDownOptions(raw) {
+    if (!Array.isArray(raw))
+        return null;
+    return raw.filter(isDict).map(parseDrillDownOption);
+}
+function parseDrillDownOption(entry) {
+    return {
+        value: String(entry.value ?? ""),
+        name: String(entry.name ?? entry.value ?? ""),
+        options: parseDrillDownOptions(entry.options) ?? [],
+        selected: readBool(entry.selected, false),
+    };
+}
+function parseValidatorDict(entry) {
+    const type = readString(entry.type);
+    const negate = readBool(entry.negate, false);
+    switch (type) {
+        case "in_range":
+            return {
+                type: "in_range",
+                min: readNullableFloat(entry.min),
+                max: readNullableFloat(entry.max),
+                exclude_min: readBool(entry.exclude_min, false),
+                exclude_max: readBool(entry.exclude_max, false),
+                negate,
+                message: readNullableString(entry.message),
+            };
+        case "regex":
+            return { type: "regex", expression: readString(entry.expression), negate };
+        case "length":
+            return {
+                type: "length",
+                min: readNullableInt(entry.min),
+                max: readNullableInt(entry.max),
+                negate,
+            };
+        case "expression":
+            return { type: "expression", expression: readString(entry.expression), negate };
+        case "empty_field":
+            return { type: "empty_field", negate };
+        case "no_options":
+            return { type: "no_options", negate };
+        default:
+            return null;
+    }
+}
+// --- Shared dict coercion helpers (also used by the factory in ./inputs.ts). ---
+export function isDict(v) {
+    return v != null && typeof v === "object" && !Array.isArray(v);
+}
+export function readString(v) {
+    return typeof v === "string" ? v : v == null ? "" : String(v);
+}
+export function readNullableString(v) {
+    if (v === undefined || v === null)
+        return null;
+    if (typeof v === "string")
+        return v;
+    return String(v);
+}
+export function readBool(v, fallback) {
+    if (typeof v === "boolean")
+        return v;
+    if (typeof v === "string") {
+        const lower = v.toLowerCase();
+        if (lower === "true" || lower === "yes" || lower === "1")
+            return true;
+        if (lower === "false" || lower === "no" || lower === "0")
+            return false;
+    }
+    return fallback;
+}
+export function coerceBool(v) {
+    if (typeof v === "boolean")
+        return v;
+    if (typeof v === "string") {
+        const lower = v.toLowerCase();
+        if (lower === "true" || lower === "yes" || lower === "1")
+            return true;
+        return false;
+    }
+    return Boolean(v);
+}
+export function readNullableInt(v) {
+    if (v === undefined || v === null || v === "")
+        return null;
+    const n = parseInt(String(v), 10);
+    return Number.isNaN(n) ? null : n;
+}
+export function readNullableFloat(v) {
+    if (v === undefined || v === null || v === "")
+        return null;
+    const n = Number(v);
+    return Number.isNaN(n) ? null : n;
+}
+//# sourceMappingURL=input-source.js.map

package/dist/user-tool-parse/input-source.js.map

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package/dist/user-tool-parse/inputs.d.ts

@@ -1,13 +1,20 @@
 /**
- * Inline tool input parser. Mirrors
- * `galaxy.tool_util.parameters.factory._from_input_source_galaxy`, normalized
- * to the YAML pathway only (no XML). Produces the Galaxy `ToolParameterModel`
- * union from `bundle-types.ts`. Validator handling is best-effort: we read
- * `validators: [{type, ...}]` entries verbatim, mirroring
- * `static_validators(parse_dict_validators(...))` once you've stripped the XML
- * shorthand handling and the `in_range` synthesis from `min`/`max` (which is
- * what Python does too).
+ * Tool input factory. Mirrors
+ * `galaxy.tool_util.parameters.factory._from_input_source_galaxy` +
+ * `input_models_for_page`: it consumes an `InputSource` (see `./input-source.ts`)
+ * rather than a raw dict, so both the inline/YAML source and an XML source in
+ * `@galaxy-tool-util/tool-xml` build the same `ToolParameterModel` union from
+ * `bundle-types.ts`. Validator handling is best-effort: `parse_validators`
+ * returns every parsed validator and the factory keeps the ones valid for the
+ * parameter type (mirrors `static_validators(...)`).
  */
 import type { ToolParameterModel } from "../schema/bundle-types.js";
+import type { PageSource } from "./input-source.js";
 export declare function parseInputs(raw: unknown): ToolParameterModel[];
+/**
+ * Mirror of `factory.input_models_for_page`: build the `ToolParameterModel`
+ * list for one `PageSource`, whatever backs it (the inline/YAML `DictPageSource`
+ * or an XML page source in `@galaxy-tool-util/tool-xml`).
+ */
+export declare function inputModelsForPage(page: PageSource): ToolParameterModel[];
 //# sourceMappingURL=inputs.d.ts.map

package/dist/user-tool-parse/inputs.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"inputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/inputs.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAKV,kBAAkB,EASnB,MAAM,2BAA2B,CAAC;AAEnC,OAAO,KAAK,EAAe,UAAU,EAAE,MAAM,mBAAmB,CAAC;AA8BjE,wBAAgB,WAAW,CAAC,GAAG,EAAE,OAAO,GAAG,kBAAkB,EAAE,CAE9D;AAED;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,UAAU,GAAG,kBAAkB,EAAE,CASzE"}