@galaxy-tool-util/schema 1.1.0 → 1.5.0

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

@@ -0,0 +1,231 @@
+/**
+ * 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).
+ */
+const DEFAULT_EXTRA_FILENAME_PATTERN = String.raw `primary_DATASET_ID_(?P<designation>[^_]+)_(?P<visible>[^_]+)_(?P<ext>[^_]+)(_(?P<dbkey>[^_]+))?`;
+const NAMED_PATTERNS = {
+    __default__: DEFAULT_EXTRA_FILENAME_PATTERN,
+    __name__: String.raw `(?P<name>.*)`,
+    __designation__: String.raw `(?P<designation>.*)`,
+    __name_and_ext__: String.raw `(?P<name>.*)\.(?P<ext>[^\.]+)?`,
+    __designation_and_ext__: String.raw `(?P<designation>.*)\.(?P<ext>[^\._]+)?`,
+};
+const DEFAULT_SORT_BY = "filename";
+const DEFAULT_SORT_COMP = "lexical";
+const VALID_SORT_KEYS = new Set([
+    "filename",
+    "name",
+    "designation",
+    "dbkey",
+]);
+export function parseOutputs(raw) {
+    const list = normalizeOutputList(raw);
+    return list.map(parseOutput);
+}
+function normalizeOutputList(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 parseOutput(entry) {
+    const type = typeof entry.type === "string" ? entry.type : "data";
+    if (type === "collection")
+        return parseOutputCollection(entry);
+    if (type === "data")
+        return parseOutputData(entry);
+    if (type === "integer")
+        return baseScalar(entry, "integer");
+    if (type === "float")
+        return baseScalar(entry, "float");
+    if (type === "boolean")
+        return baseScalar(entry, "boolean");
+    if (type === "text")
+        return baseScalar(entry, "text");
+    throw new Error(`Unknown output_type '${type}'`);
+}
+function parseOutputData(entry) {
+    return {
+        name: readString(entry.name),
+        label: readNullableString(entry.label),
+        hidden: readBool(entry.hidden, false),
+        type: "data",
+        format: readString(entry.format) || "data",
+        format_source: readNullableString(entry.format_source),
+        metadata_source: readNullableString(entry.metadata_source),
+        discover_datasets: parseDiscoverDatasets(entry.discover_datasets),
+        from_work_dir: readNullableString(entry.from_work_dir),
+        precreate_directory: readBool(entry.precreate_directory, false),
+    };
+}
+function baseScalar(entry, type) {
+    return {
+        name: readString(entry.name),
+        label: readNullableString(entry.label),
+        hidden: readBool(entry.hidden, false),
+        type,
+    };
+}
+function parseOutputCollection(entry) {
+    return {
+        name: readString(entry.name),
+        label: readNullableString(entry.label),
+        hidden: readBool(entry.hidden, false),
+        type: "collection",
+        structure: parseStructure(entry),
+    };
+}
+function parseStructure(entry) {
+    // YAML lets you put `collection_type`, `type_source`, `structured_like`
+    // either at the output root or under `structure: {...}`. Prefer explicit
+    // `structure` if present (mirrors `ToolOutputCollectionStructure.from_dict`),
+    // otherwise read from the entry itself.
+    const sourceDict = isDict(entry.structure) ? entry.structure : entry;
+    const collectionType = readNullableString(sourceDict.collection_type);
+    const collectionTypeSource = readNullableString(sourceDict.collection_type_source ?? sourceDict.type_source);
+    const collectionTypeFromRules = readNullableString(sourceDict.collection_type_from_rules);
+    const structuredLike = readNullableString(sourceDict.structured_like);
+    const discoverDatasets = parseDiscoverDatasets(sourceDict.discover_datasets);
+    return {
+        collection_type: collectionType,
+        collection_type_source: collectionTypeSource,
+        collection_type_from_rules: collectionTypeFromRules,
+        structured_like: structuredLike,
+        discover_datasets: discoverDatasets,
+    };
+}
+function parseDiscoverDatasets(raw) {
+    let list;
+    if (raw === undefined || raw === null)
+        return null;
+    if (Array.isArray(raw))
+        list = raw;
+    else if (isDict(raw))
+        list = [raw];
+    else
+        return null;
+    const out = list.filter(isDict).map(parseDiscoverDataset);
+    // Mirrors `_validate_collectors`: more than one collector forbids
+    // `tool_provided_metadata`.
+    if (out.length > 1 && out.some((d) => d.discover_via === "tool_provided_metadata")) {
+        throw new Error("Cannot specify more than one discover dataset condition if any of them specify tool_provided_metadata.");
+    }
+    return out;
+}
+function parseDiscoverDataset(entry) {
+    const fromProvidedMetadata = readBool(entry.from_provided_metadata, false);
+    const discoverVia = typeof entry.discover_via === "string"
+        ? entry.discover_via
+        : fromProvidedMetadata
+            ? "tool_provided_metadata"
+            : "pattern";
+    const base = {
+        format: readNullableString(entry.format ?? entry.ext),
+        visible: readBool(entry.visible, false),
+        assign_primary_output: readBool(entry.assign_primary_output, false),
+        directory: readNullableString(entry.directory),
+        recurse: readBool(entry.recurse, false),
+        match_relative_path: readBool(entry.match_relative_path, false),
+    };
+    if (discoverVia === "tool_provided_metadata") {
+        if (entry.pattern || entry.sort_by) {
+            throw new Error("Cannot specify attribute [pattern] or [sort_by] if from_provided_metadata is True");
+        }
+        const desc = {
+            discover_via: "tool_provided_metadata",
+            ...base,
+        };
+        return desc;
+    }
+    const pattern = resolvePattern(entry);
+    const [sortKey, sortComp, sortReverse] = resolveSortFields(entry);
+    const desc = {
+        discover_via: "pattern",
+        ...base,
+        pattern,
+        sort_key: sortKey,
+        sort_comp: sortComp,
+        sort_reverse: sortReverse,
+    };
+    return desc;
+}
+function resolvePattern(entry) {
+    const raw = entry.pattern;
+    const pattern = typeof raw === "string" && raw ? raw : "__default__";
+    return NAMED_PATTERNS[pattern] ?? pattern;
+}
+function resolveSortFields(entry) {
+    if (entry.sort_by == null &&
+        typeof entry.sort_key === "string" &&
+        typeof entry.sort_comp === "string" &&
+        entry.sort_reverse !== undefined) {
+        return [
+            validateSortKey(entry.sort_key),
+            entry.sort_comp === "numeric" ? "numeric" : "lexical",
+            readBool(entry.sort_reverse, false),
+        ];
+    }
+    let sortBy = typeof entry.sort_by === "string" ? entry.sort_by : DEFAULT_SORT_BY;
+    let sortReverse = false;
+    if (sortBy.startsWith("reverse_")) {
+        sortReverse = true;
+        sortBy = sortBy.slice("reverse_".length);
+    }
+    let sortComp = DEFAULT_SORT_COMP;
+    if (sortBy.includes("_")) {
+        const idx = sortBy.indexOf("_");
+        const compPart = sortBy.slice(0, idx);
+        if (compPart === "lexical" || compPart === "numeric") {
+            sortComp = compPart;
+            sortBy = sortBy.slice(idx + 1);
+        }
+    }
+    return [validateSortKey(sortBy), sortComp, sortReverse];
+}
+function validateSortKey(value) {
+    if (VALID_SORT_KEYS.has(value)) {
+        return value;
+    }
+    throw new Error(`Invalid sort key '${value}'`);
+}
+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;
+}
+//# sourceMappingURL=outputs.js.map

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

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

@@ -0,0 +1,12 @@
+/**
+ * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
+ * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
+ * for the parameter / output trees.
+ */
+import type { ParsedTool } from "../schema/parsed-tool.js";
+export type InlineRepresentation = Record<string, unknown>;
+export declare class InlineToolParseError extends Error {
+}
+export declare function parseInlineTool(repr: InlineRepresentation): ParsedTool;
+//# sourceMappingURL=parse.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../src/user-tool-parse/parse.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAmC,MAAM,0BAA0B,CAAC;AAK5F,MAAM,MAAM,oBAAoB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;AAE3D,qBAAa,oBAAqB,SAAQ,KAAK;CAAG;AAElD,wBAAgB,eAAe,CAAC,IAAI,EAAE,oBAAoB,GAAG,UAAU,CA8BtE"}

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

@@ -0,0 +1,98 @@
+/**
+ * Inline GalaxyUserTool → ParsedTool conversion. Mirrors
+ * `galaxy.tool_util.model_factory.parse_tool(YamlToolSource(repr))` for the
+ * fields surfaced on the TS `ParsedTool`. See `./inputs.ts` and `./outputs.ts`
+ * for the parameter / output trees.
+ */
+import { parseInputs } from "./inputs.js";
+import { parseOutputs } from "./outputs.js";
+export class InlineToolParseError extends Error {
+}
+export function parseInlineTool(repr) {
+    if (!repr || typeof repr !== "object" || Array.isArray(repr)) {
+        throw new InlineToolParseError("inline tool representation must be an object");
+    }
+    if (repr.class !== "GalaxyUserTool") {
+        throw new InlineToolParseError(`inline tool representation must have class 'GalaxyUserTool' (got ${JSON.stringify(repr.class)})`);
+    }
+    const id = typeof repr.id === "string" ? repr.id : "";
+    const version = repr.version == null ? null : String(repr.version);
+    const name = (typeof repr.name === "string" && repr.name) || id || "";
+    const description = typeof repr.description === "string" ? repr.description : "";
+    return {
+        id,
+        version,
+        name,
+        description: description === "" ? null : description,
+        inputs: parseInputs(repr.inputs),
+        outputs: parseOutputs(repr.outputs),
+        citations: parseCitations(repr.citations),
+        license: typeof repr.license === "string" ? repr.license : null,
+        profile: parseProfile(repr.profile),
+        edam_operations: parseStringList(repr.edam_operations),
+        edam_topics: parseStringList(repr.edam_topics),
+        xrefs: parseXrefs(repr.xrefs),
+        help: parseHelp(repr.help),
+    };
+}
+function parseStringList(raw) {
+    if (!Array.isArray(raw))
+        return [];
+    return raw.filter((v) => typeof v === "string");
+}
+function parseProfile(raw) {
+    if (typeof raw === "string" && raw)
+        return raw;
+    if (typeof raw === "number")
+        return String(raw);
+    // Matches `YamlToolSource.parse_profile` default.
+    return "24.2";
+}
+function parseCitations(raw) {
+    if (!Array.isArray(raw))
+        return [];
+    const out = [];
+    for (const entry of raw) {
+        if (!entry || typeof entry !== "object")
+            continue;
+        const e = entry;
+        const type = typeof e.type === "string" ? e.type : null;
+        const content = typeof e.content === "string" ? e.content : null;
+        if (type && content !== null)
+            out.push({ type, content });
+    }
+    return out;
+}
+function parseXrefs(raw) {
+    if (!Array.isArray(raw))
+        return [];
+    const out = [];
+    for (const entry of raw) {
+        if (!entry || typeof entry !== "object")
+            continue;
+        const e = entry;
+        const value = typeof e.value === "string" ? e.value : null;
+        const type = typeof e.type === "string" ? e.type : null;
+        // YamlToolSource skips xrefs without a `type`; mirror that here.
+        if (value !== null && type)
+            out.push({ value, type });
+    }
+    return out;
+}
+function parseHelp(raw) {
+    if (raw == null)
+        return null;
+    if (typeof raw === "string") {
+        return { format: "markdown", content: raw };
+    }
+    if (typeof raw === "object" && !Array.isArray(raw)) {
+        const e = raw;
+        const content = typeof e.content === "string" ? e.content : null;
+        if (content === null)
+            return null;
+        const format = typeof e.format === "string" ? e.format : "markdown";
+        return { format, content };
+    }
+    return null;
+}
+//# sourceMappingURL=parse.js.map

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

@@ -0,0 +1 @@
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package/dist/user-tool-source/index.d.ts

@@ -0,0 +1,3 @@
+export { validateUserToolSource, userToolSourceSchema, type UserToolSourceDiagnostic, type ValidateUserToolSourceOptions, } from "./validate.js";
+export { runSemanticChecks } from "./semantic.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/user-tool-source/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/user-tool-source/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,oBAAoB,EACpB,KAAK,wBAAwB,EAC7B,KAAK,6BAA6B,GACnC,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,iBAAiB,EAAE,MAAM,eAAe,CAAC"}

package/dist/user-tool-source/index.js

@@ -0,0 +1,3 @@
+export { validateUserToolSource, userToolSourceSchema, } from "./validate.js";
+export { runSemanticChecks } from "./semantic.js";
+//# sourceMappingURL=index.js.map

package/dist/user-tool-source/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/user-tool-source/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GAGrB,MAAM,eAAe,CAAC;AACvB,OAAO,EAAE,iBAAiB,EAAE,MAAM,eAAe,CAAC"}