@galaxy-tool-util/schema 1.1.0 → 1.5.0

package/dist/user-tool-parse/inputs.js

@@ -0,0 +1,565 @@
+/**
+ * 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).
+ */
+const DATA_PARAM_TYPES = new Set([
+    "integer",
+    "float",
+    "text",
+    "boolean",
+    "hidden",
+    "color",
+    "rules",
+    "data",
+    "hidden_data",
+    "data_collection",
+    "select",
+    "drill_down",
+    "data_column",
+    "group_tag",
+    "baseurl",
+    "genomebuild",
+    "directory_uri",
+]);
+export function parseInputs(raw) {
+    const list = normalizeInputList(raw);
+    return list.map(parseInput);
+}
+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 parseInput(input) {
+    const containerType = readContainerType(input);
+    if (containerType === "conditional")
+        return parseConditional(input);
+    if (containerType === "repeat")
+        return parseRepeat(input);
+    if (containerType === "section")
+        return parseSection(input);
+    return parseLeafParam(input);
+}
+function readContainerType(input) {
+    const t = input.type;
+    if (t === "conditional")
+        return "conditional";
+    if (t === "repeat")
+        return "repeat";
+    if (t === "section")
+        return "section";
+    return null;
+}
+function parseConditional(input) {
+    const name = readString(input.name);
+    const testRaw = input.test_parameter;
+    if (!isDict(testRaw)) {
+        throw new Error(`conditional '${name}' must define a 'test_parameter'`);
+    }
+    const testParam = parseLeafParam(testRaw);
+    if (testParam.parameter_type !== "gx_boolean" && testParam.parameter_type !== "gx_select") {
+        throw new Error(`conditional '${name}' test_parameter must be boolean or select (got ${testParam.parameter_type})`);
+    }
+    const whens = parseWhens(input, testParam);
+    return {
+        parameter_type: "gx_conditional",
+        name,
+        hidden: readBool(input.hidden, false),
+        label: readNullableString(input.label),
+        help: readNullableString(input.help),
+        argument: readNullableString(input.argument),
+        is_dynamic: false,
+        test_parameter: testParam,
+        whens,
+    };
+}
+function parseWhens(input, testParam) {
+    const defaultDiscriminator = defaultTestDiscriminator(testParam);
+    const result = [];
+    // YAML supports two shapes: `when: {key: [params], ...}` (map) and `whens:
+    // [{discriminator, parameters: [...]}]` (list).
+    const whenMap = input.when;
+    const whenList = input.whens;
+    if (isDict(whenMap)) {
+        for (const [key, value] of Object.entries(whenMap)) {
+            const params = Array.isArray(value) ? value.filter(isDict) : [];
+            result.push(makeWhen(key, parseInputs(params), defaultDiscriminator, testParam));
+        }
+    }
+    else if (Array.isArray(whenList)) {
+        for (const item of whenList) {
+            if (!isDict(item))
+                continue;
+            const disc = item.discriminator;
+            const params = item.parameters;
+            result.push(makeWhen(disc, parseInputs(params), defaultDiscriminator, testParam));
+        }
+    }
+    return result;
+}
+function defaultTestDiscriminator(testParam) {
+    if (testParam.parameter_type === "gx_boolean") {
+        return testParam.value ?? false;
+    }
+    if (testParam.parameter_type === "gx_select") {
+        const opts = testParam.options;
+        if (!opts)
+            return null;
+        const selected = opts.find((o) => o.selected);
+        return selected ? selected.value : (opts[0]?.value ?? null);
+    }
+    return null;
+}
+function makeWhen(rawDiscriminator, parameters, defaultDiscriminator, testParam) {
+    let typed;
+    if (testParam.parameter_type === "gx_boolean") {
+        typed = coerceBool(rawDiscriminator);
+    }
+    else {
+        typed = rawDiscriminator == null ? "" : String(rawDiscriminator);
+    }
+    const isDefault = typed === defaultDiscriminator;
+    return { discriminator: typed, parameters, is_default_when: isDefault };
+}
+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);
+}
+function parseRepeat(input) {
+    const name = readString(input.name);
+    const innerRaw = input.blocks ?? input.parameters ?? input.inputs;
+    const parameters = parseInputs(innerRaw);
+    return {
+        parameter_type: "gx_repeat",
+        name,
+        hidden: readBool(input.hidden, false),
+        label: readNullableString(input.label),
+        help: readNullableString(input.help),
+        argument: readNullableString(input.argument),
+        is_dynamic: false,
+        parameters,
+        min: readNullableInt(input.min),
+        max: readNullableInt(input.max),
+    };
+}
+function parseSection(input) {
+    const name = readString(input.name);
+    const innerRaw = input.parameters ?? input.inputs;
+    const parameters = parseInputs(innerRaw);
+    return {
+        parameter_type: "gx_section",
+        name,
+        hidden: readBool(input.hidden, false),
+        label: readNullableString(input.label),
+        help: readNullableString(input.help),
+        argument: readNullableString(input.argument),
+        is_dynamic: false,
+        parameters,
+    };
+}
+function parseLeafParam(input) {
+    const paramType = readString(input.type);
+    if (!DATA_PARAM_TYPES.has(paramType)) {
+        throw new Error(`Unknown Galaxy parameter type '${paramType}'`);
+    }
+    const base = baseFields(input);
+    switch (paramType) {
+        case "integer": {
+            const optional = base.optional;
+            const value = parseOptionalNumber(input.value, optional, "integer");
+            return {
+                ...base,
+                parameter_type: "gx_integer",
+                type: "integer",
+                value,
+                min: readNullableInt(input.min),
+                max: readNullableInt(input.max),
+                validators: collectValidators(input.validators, "number"),
+            };
+        }
+        case "float": {
+            const optional = base.optional;
+            const value = parseOptionalNumber(input.value, optional, "float");
+            return {
+                ...base,
+                parameter_type: "gx_float",
+                type: "float",
+                value,
+                min: readNullableFloat(input.min),
+                max: readNullableFloat(input.max),
+                validators: collectValidators(input.validators, "number"),
+            };
+        }
+        case "text": {
+            const optional = textIsOptional(input);
+            return {
+                ...base,
+                optional,
+                parameter_type: "gx_text",
+                type: "text",
+                area: readBool(input.area, false),
+                value: textDefault(input.value, optional),
+                default_options: [],
+                validators: collectValidators(input.validators, "text"),
+            };
+        }
+        case "boolean": {
+            const optional = base.optional;
+            const rawChecked = input.checked;
+            const value = rawChecked == null ? (optional ? false : false) : coerceBool(rawChecked);
+            return {
+                ...base,
+                parameter_type: "gx_boolean",
+                type: "boolean",
+                value,
+                truevalue: readNullableString(input.truevalue),
+                falsevalue: readNullableString(input.falsevalue),
+            };
+        }
+        case "hidden": {
+            return {
+                ...base,
+                parameter_type: "gx_hidden",
+                type: "hidden",
+                value: readNullableString(input.value),
+                validators: collectValidators(input.validators, "text"),
+            };
+        }
+        case "color": {
+            const value = typeof input.value === "string" ? input.value : "#000000";
+            return {
+                ...base,
+                parameter_type: "gx_color",
+                type: "color",
+                value,
+            };
+        }
+        case "rules": {
+            return { ...base, parameter_type: "gx_rules", type: "rules" };
+        }
+        case "data":
+        case "hidden_data": {
+            // hidden_data is broken without optional=true in Python; mirror the
+            // override.
+            const optional = paramType === "data" ? base.optional : true;
+            return {
+                ...base,
+                optional,
+                parameter_type: "gx_data",
+                type: "data",
+                multiple: readBool(input.multiple, false),
+                extensions: parseExtensions(input),
+            };
+        }
+        case "data_collection": {
+            return {
+                ...base,
+                parameter_type: "gx_data_collection",
+                type: "data_collection",
+                collection_type: readNullableString(input.collection_type),
+                extensions: parseExtensions(input),
+                value: input.default ?? input.value ?? null,
+            };
+        }
+        case "select": {
+            const multiple = readBool(input.multiple, false);
+            const optional = base.optional;
+            const options = parseStaticOptions(input);
+            const validators = collectValidators(input.validators, "select");
+            // `no_options` doesn't apply if select is optional (mirrors Python).
+            const filtered = optional ? validators.filter((v) => v.type !== "no_options") : validators;
+            return {
+                ...base,
+                parameter_type: "gx_select",
+                type: "select",
+                multiple,
+                options,
+                validators: filtered,
+            };
+        }
+        case "drill_down": {
+            return {
+                ...base,
+                parameter_type: "gx_drill_down",
+                type: "drill_down",
+                multiple: readBool(input.multiple, false),
+                hierarchy: input.hierarchy === "recurse" ? "recurse" : "exact",
+                options: parseDrillDownOptions(input.options) ?? [],
+            };
+        }
+        case "data_column": {
+            const multiple = readBool(input.multiple, false);
+            const acceptDefault = readBool(input.accept_default, false);
+            let optional = base.optional;
+            let value = input.value;
+            if (!optional && acceptDefault)
+                optional = true;
+            if (acceptDefault && (value === null || value === undefined)) {
+                value = multiple ? [0] : 0;
+            }
+            let coerced;
+            if (value === null || value === undefined) {
+                coerced = null;
+            }
+            else if (multiple) {
+                const arr = Array.isArray(value) ? value : String(value).split(",");
+                coerced = arr.map((v) => Number(v)).filter((v) => !Number.isNaN(v));
+            }
+            else {
+                const n = typeof value === "number" ? value : Number(value);
+                coerced = Number.isNaN(n) ? null : n;
+            }
+            return {
+                ...base,
+                optional,
+                parameter_type: "gx_data_column",
+                type: "data_column",
+                multiple,
+                value: coerced,
+            };
+        }
+        case "group_tag": {
+            return {
+                ...base,
+                parameter_type: "gx_group_tag",
+                type: "group_tag",
+                multiple: readBool(input.multiple, false),
+            };
+        }
+        case "baseurl": {
+            return {
+                ...base,
+                parameter_type: "gx_baseurl",
+                type: "baseurl",
+                value: readNullableString(input.value),
+            };
+        }
+        case "genomebuild": {
+            return {
+                ...base,
+                parameter_type: "gx_genomebuild",
+                type: "genomebuild",
+                multiple: readBool(input.multiple, false),
+                options: [],
+            };
+        }
+        case "directory_uri": {
+            return {
+                ...base,
+                parameter_type: "gx_directory_uri",
+                type: "directory_uri",
+                value: readNullableString(input.value),
+                validators: collectValidators(input.validators, "text"),
+            };
+        }
+        default:
+            throw new Error(`Unknown Galaxy parameter type '${paramType}'`);
+    }
+}
+function baseFields(input) {
+    return {
+        name: readString(input.name),
+        hidden: readBool(input.hidden, false),
+        label: readNullableString(input.label),
+        help: readNullableString(input.help),
+        argument: readNullableString(input.argument),
+        is_dynamic: false,
+        optional: readBool(input.optional, false),
+    };
+}
+function textIsOptional(input) {
+    // Mirrors `text_input_is_optional`: explicit `optional:` wins, otherwise
+    // inferred from `value:` being present.
+    if (input.optional !== undefined && input.optional !== null) {
+        return coerceBool(input.optional);
+    }
+    return input.value === undefined || input.value === null || input.value === "";
+}
+function textDefault(value, optional) {
+    if (typeof value === "string")
+        return value;
+    if (value === undefined || value === null)
+        return optional ? null : "";
+    return String(value);
+}
+function parseExtensions(input) {
+    const explicit = input.extensions;
+    let raw = explicit;
+    if (raw === undefined || raw === null || (Array.isArray(raw) && raw.length === 0)) {
+        raw = 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 !== "");
+}
+function parseStaticOptions(input) {
+    const opts = 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;
+}
+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 parseOptionalNumber(value, optional, kind) {
+    if (value === undefined || value === null || value === "") {
+        return null;
+    }
+    const n = kind === "integer" ? parseInt(String(value), 10) : Number(value);
+    if (Number.isNaN(n)) {
+        if (optional)
+            return null;
+        throw new Error(`invalid ${kind} value: ${JSON.stringify(value)}`);
+    }
+    return n;
+}
+function collectValidators(raw, kind) {
+    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);
+    }
+    if (kind === "number") {
+        return all.filter((v) => v.type === "in_range");
+    }
+    if (kind === "text") {
+        return all.filter((v) => v.type === "length" ||
+            v.type === "regex" ||
+            v.type === "expression" ||
+            v.type === "empty_field");
+    }
+    // select
+    return all.filter((v) => v.type === "no_options");
+}
+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;
+    }
+}
+function isDict(v) {
+    return v != null && typeof v === "object" && !Array.isArray(v);
+}
+function readString(v) {
+    return typeof v === "string" ? v : v == null ? "" : String(v);
+}
+function readNullableString(v) {
+    if (v === undefined || v === null)
+        return null;
+    if (typeof v === "string")
+        return v;
+    return String(v);
+}
+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;
+}
+function readNullableInt(v) {
+    if (v === undefined || v === null || v === "")
+        return null;
+    const n = parseInt(String(v), 10);
+    return Number.isNaN(n) ? null : n;
+}
+function readNullableFloat(v) {
+    if (v === undefined || v === null || v === "")
+        return null;
+    const n = Number(v);
+    return Number.isNaN(n) ? null : n;
+}
+//# sourceMappingURL=inputs.js.map

package/dist/user-tool-parse/inputs.js.map

@@ -0,0 +1 @@
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package/dist/user-tool-parse/outputs.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Inline tool output parser. Mirrors
+ * `galaxy.tool_util.parser.yaml.YamlToolSource.parse_outputs` +
+ * `output_objects.ToolOutput.from_dict` and `output_objects.ToolOutputCollection`.
+ * Produces the `ToolOutput` union from `../schema/parsed-tool.ts` (data /
+ * collection / text / integer / float / boolean).
+ */
+import type { ToolOutput } from "../schema/parsed-tool.js";
+export declare function parseOutputs(raw: unknown): ToolOutput[];
+//# sourceMappingURL=outputs.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"outputs.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/outputs.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAGV,UAAU,EAOX,MAAM,0BAA0B,CAAC;AAwBlC,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,UAAU,EAAE,CAGvD"}