@galaxy-tool-util/schema 0.1.0

package/dist/workflow/normalized/toFormat2.js

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+/**
+ * Native → Format2 conversion.
+ *
+ * Port of gxformat2/normalized/_conversion.py to_format2 + helpers.
+ */
+import { normalizedNative } from "./native.js";
+import { flattenCommentData } from "./comments.js";
+import { UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, isUnlabeled, Labels } from "./labels.js";
+// Effect schemas produce deeply-readonly types. We build plain objects
+// and cast — runtime semantics are identical.
+// Step types that represent workflow inputs
+const INPUT_STEP_TYPES = new Set(["data_input", "data_collection_input", "parameter_input"]);
+/**
+ * Convert a native Galaxy workflow to normalized Format2.
+ */
+export function toFormat2(raw) {
+    const wf = normalizedNative(raw);
+    return _buildFormat2Workflow(wf);
+}
+function _buildFormat2Workflow(wf) {
+    // Build label map: step key → label string
+    const labelMap = new Map();
+    for (const [key, step] of Object.entries(wf.steps)) {
+        if (step.label != null) {
+            labelMap.set(String(key), step.label);
+        }
+        else if (INPUT_STEP_TYPES.has(step.type)) {
+            labelMap.set(String(key), `${UNLABELED_INPUT_PREFIX}${step.id}`);
+        }
+        else {
+            labelMap.set(String(key), `${UNLABELED_STEP_PREFIX}${step.id}`);
+        }
+    }
+    // Build workflow outputs from step workflow_outputs
+    const labels = new Labels();
+    const outputParams = [];
+    for (const step of Object.values(wf.steps)) {
+        for (const wo of step.workflow_outputs) {
+            const source = _toSource(wo.output_name, labelMap, step.id);
+            const outputId = labels.ensureNewOutputLabel(wo.label);
+            outputParams.push({ id: outputId, outputSource: source });
+        }
+    }
+    // Separate inputs from non-input steps
+    const inputParams = [];
+    const fmt2Steps = [];
+    for (const step of Object.values(wf.steps)) {
+        if (INPUT_STEP_TYPES.has(step.type)) {
+            inputParams.push(_buildInputParam(step));
+        }
+        else {
+            fmt2Steps.push(_buildFormat2Step(step, labelMap));
+        }
+    }
+    // Replace anonymous subworkflow output references
+    _replaceAnonymousOutputReferences(outputParams, fmt2Steps);
+    // Convert comments
+    const comments = _buildFormat2Comments(wf, labelMap);
+    const wfAny = wf;
+    const result = {
+        class: "GalaxyWorkflow",
+        label: wf.name ?? null,
+        doc: wf.annotation || null,
+        inputs: inputParams,
+        outputs: outputParams,
+        steps: fmt2Steps,
+        tags: wf.tags,
+        uuid: wf.uuid,
+        license: wf.license ?? undefined,
+        release: wf.release ?? undefined,
+        unique_tools: wf.unique_tools,
+    };
+    if (comments)
+        result.comments = comments;
+    if (wfAny.report)
+        result.report = { markdown: wfAny.report.markdown };
+    if (wfAny.creator)
+        result.creator = wfAny.creator;
+    return result;
+}
+// --- Input parameter building ---
+function _nativeInputToFormat2Type(stepType, toolState) {
+    if (stepType === "data_collection_input")
+        return "collection";
+    if (stepType === "data_input")
+        return "data";
+    if (stepType === "parameter_input") {
+        const nativeType = toolState.parameter_type ?? "";
+        let format2Type = nativeType;
+        if (nativeType === "integer")
+            format2Type = "int";
+        else if (nativeType === "text")
+            format2Type = "string";
+        if (toolState.multiple)
+            return [format2Type];
+        return format2Type;
+    }
+    return "data";
+}
+function _buildInputParam(step) {
+    const stepId = step.label ?? `${UNLABELED_INPUT_PREFIX}${step.id}`;
+    const inputType = _nativeInputToFormat2Type(step.type, step.tool_state);
+    const result = { id: stepId, type: inputType };
+    const ts = step.tool_state;
+    for (const key of [
+        "collection_type",
+        "optional",
+        "format",
+        "default",
+        "restrictions",
+        "suggestions",
+        "restrictOnConnections",
+        "fields",
+        "column_definitions",
+    ]) {
+        if (key in ts) {
+            if (key === "format") {
+                const fmt = ts[key];
+                result[key] = typeof fmt === "string" ? [fmt] : fmt;
+            }
+            else {
+                result[key] = ts[key];
+            }
+        }
+    }
+    if (step.annotation)
+        result.doc = step.annotation;
+    if (step.position)
+        result.position = step.position;
+    return result;
+}
+// --- Step identity ---
+function _resolveStepIdentity(step, labelMap) {
+    const rawLabel = step.label ?? labelMap.get(String(step.id));
+    const stepId = rawLabel ?? String(step.id);
+    const displayLabel = rawLabel && isUnlabeled(rawLabel) ? undefined : rawLabel;
+    return { stepId, displayLabel };
+}
+// --- Step building ---
+function _buildFormat2Step(step, labelMap) {
+    const moduleType = step.type;
+    if (moduleType === "subworkflow") {
+        return _buildSubworkflowFormat2Step(step, labelMap);
+    }
+    if (moduleType === "pause") {
+        return _buildPauseFormat2Step(step, labelMap);
+    }
+    if (moduleType === "pick_value") {
+        return _buildPickValueFormat2Step(step, labelMap);
+    }
+    // Default: tool
+    return _buildToolFormat2Step(step, labelMap);
+}
+function _buildToolFormat2Step(step, labelMap) {
+    // User-defined tool: tool_representation with class GalaxyUserTool
+    const toolRep = step.tool_representation;
+    if (toolRep && toolRep.class === "GalaxyUserTool") {
+        return _buildUserToolFormat2Step(step, labelMap);
+    }
+    const inList = _buildFormat2StepInputs(step, labelMap);
+    const outList = _buildFormat2StepOutputs(step);
+    // Tool state: strip __page__ and __rerun_remap_job_id__
+    let toolState = null;
+    const ts = { ...step.tool_state };
+    delete ts.__page__;
+    delete ts.__rerun_remap_job_id__;
+    if (Object.keys(ts).length > 0) {
+        toolState = ts;
+    }
+    const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
+    return {
+        id: stepId,
+        label: displayLabel ?? undefined,
+        doc: step.annotation || undefined,
+        tool_id: step.tool_id ?? undefined,
+        tool_version: step.tool_version ?? undefined,
+        tool_shed_repository: step.tool_shed_repository,
+        in: inList,
+        out: outList,
+        tool_state: toolState,
+        position: step.position,
+        when: step.when ?? undefined,
+        uuid: step.uuid ?? undefined,
+        errors: step.errors ?? undefined,
+    };
+}
+function _buildUserToolFormat2Step(step, labelMap) {
+    const inList = _buildFormat2StepInputs(step, labelMap);
+    const outList = _buildFormat2StepOutputs(step);
+    const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
+    return {
+        id: stepId,
+        label: displayLabel ?? undefined,
+        doc: step.annotation || undefined,
+        run: step.tool_representation,
+        in: inList,
+        out: outList,
+        position: step.position,
+    };
+}
+function _buildSubworkflowFormat2Step(step, labelMap) {
+    const inList = _buildFormat2StepInputs(step, labelMap);
+    const outList = _buildFormat2StepOutputs(step);
+    let run = null;
+    const contentSource = step.content_source;
+    if ((contentSource === "url" || contentSource === "trs_url") && step.content_id) {
+        // URL/TRS reference passes through as string
+        run = step.content_id;
+    }
+    else if (step.subworkflow != null) {
+        run = _buildFormat2Workflow(step.subworkflow);
+    }
+    else if (step.content_id) {
+        // Other content_id (e.g. direct reference)
+        run = step.content_id;
+    }
+    const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
+    return {
+        id: stepId,
+        label: displayLabel ?? undefined,
+        doc: step.annotation || undefined,
+        run,
+        in: inList,
+        out: outList,
+        position: step.position,
+        when: step.when ?? undefined,
+        uuid: step.uuid ?? undefined,
+    };
+}
+function _buildPauseFormat2Step(step, labelMap) {
+    const inList = _buildFormat2StepInputs(step, labelMap);
+    const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
+    return {
+        id: stepId,
+        label: displayLabel ?? undefined,
+        doc: step.annotation || undefined,
+        type: "pause",
+        in: inList,
+        out: [],
+        position: step.position,
+    };
+}
+function _buildPickValueFormat2Step(step, labelMap) {
+    const inList = _buildFormat2StepInputs(step, labelMap);
+    const outList = _buildFormat2StepOutputs(step);
+    const { stepId, displayLabel } = _resolveStepIdentity(step, labelMap);
+    let state;
+    if ("mode" in step.tool_state) {
+        state = { mode: step.tool_state.mode };
+    }
+    return {
+        id: stepId,
+        label: displayLabel ?? undefined,
+        doc: step.annotation || undefined,
+        type: "pick_value",
+        state,
+        in: inList,
+        out: outList,
+        position: step.position,
+    };
+}
+// --- Step inputs from input_connections ---
+function _buildFormat2StepInputs(step, labelMap) {
+    const inList = [];
+    // Preserve existing 'in' defaults
+    const defaults = new Map();
+    if (step.in != null) {
+        for (const [key, value] of Object.entries(step.in)) {
+            if (value && typeof value === "object" && "default" in value) {
+                defaults.set(key, value.default);
+            }
+        }
+    }
+    for (const [inputName, inputDefs] of Object.entries(step.input_connections)) {
+        const defs = Array.isArray(inputDefs) ? inputDefs : [inputDefs];
+        const sources = [];
+        for (const inputDef of defs) {
+            const def = inputDef;
+            const source = _toSource(def.output_name, labelMap, def.id);
+            sources.push(source);
+        }
+        let actualName = inputName;
+        let resolvedSources = sources;
+        if (inputName === "__NO_INPUT_OUTPUT_NAME__") {
+            actualName = "$step";
+            resolvedSources = sources.map((s) => s.includes("/__NO_INPUT_OUTPUT_NAME__") ? s.split("/__NO_INPUT_OUTPUT_NAME__")[0] : s);
+        }
+        const sourceVal = resolvedSources.length === 1 ? resolvedSources[0] : resolvedSources;
+        const def = defaults.get(actualName);
+        defaults.delete(actualName);
+        const entry = { id: actualName, source: sourceVal };
+        if (def !== undefined)
+            entry.default = def;
+        inList.push(entry);
+    }
+    // Add remaining defaults without connections
+    for (const [key, def] of defaults) {
+        inList.push({ id: key, default: def });
+    }
+    return inList;
+}
+// --- Step outputs from post_job_actions ---
+function _buildFormat2StepOutputs(step) {
+    if (!step.post_job_actions || Object.keys(step.post_job_actions).length === 0) {
+        return [];
+    }
+    const outputsByName = new Map();
+    for (const pja of Object.values(step.post_job_actions)) {
+        const actionType = pja.action_type;
+        const outputName = pja.output_name;
+        const actionArgs = (pja.action_arguments ?? {});
+        if (!outputsByName.has(outputName)) {
+            outputsByName.set(outputName, {});
+        }
+        const outputDict = outputsByName.get(outputName);
+        if (actionType === "RenameDatasetAction") {
+            outputDict.rename = actionArgs.newname;
+        }
+        else if (actionType === "HideDatasetAction") {
+            outputDict.hide = true;
+        }
+        else if (actionType === "DeleteIntermediatesAction") {
+            outputDict.delete_intermediate_datasets = true;
+        }
+        else if (actionType === "ChangeDatatypeAction") {
+            outputDict.change_datatype = actionArgs.newtype;
+        }
+        else if (actionType === "TagDatasetAction") {
+            outputDict.add_tags = actionArgs.tags.split(",");
+        }
+        else if (actionType === "RemoveTagDatasetAction") {
+            outputDict.remove_tags = actionArgs.tags.split(",");
+        }
+        else if (actionType === "ColumnSetAction") {
+            if (actionArgs && Object.keys(actionArgs).length > 0) {
+                outputDict.set_columns = actionArgs;
+            }
+        }
+    }
+    const result = [];
+    for (const [name, props] of outputsByName) {
+        result.push({ id: name, ...props });
+    }
+    return result;
+}
+// --- Source reference ---
+function _toSource(outputName, labelMap, stepId) {
+    const outputLabel = labelMap.get(String(stepId)) ?? String(stepId);
+    if (outputName === "output") {
+        return outputLabel;
+    }
+    return `${outputLabel}/${outputName}`;
+}
+// --- Anonymous output reference rewriting ---
+function _replaceAnonymousOutputReferences(outputParams, fmt2Steps) {
+    const runsByLabel = new Map();
+    for (const step of fmt2Steps) {
+        const label = step.label ?? step.id;
+        if (step.run && typeof step.run === "object") {
+            runsByLabel.set(String(label), step.run);
+        }
+    }
+    for (const out of outputParams) {
+        const source = out.outputSource;
+        if (!source || !source.includes("/"))
+            continue;
+        const [stepLabel, outputName] = source.split("/", 2);
+        if (!outputName.includes(":"))
+            continue;
+        const [innerStepId, innerOutputName] = outputName.split(":", 2);
+        const subworkflow = runsByLabel.get(stepLabel);
+        if (!subworkflow)
+            continue;
+        const targetSuffix = `/${innerOutputName}`;
+        for (const subOut of subworkflow.outputs) {
+            const subSrc = subOut.outputSource;
+            if (subSrc && subSrc.endsWith(targetSuffix)) {
+                // Verify the step portion refers to the right inner step
+                const subStepRef = subSrc.slice(0, -targetSuffix.length);
+                if (subStepRef === innerStepId || subStepRef.endsWith(innerStepId)) {
+                    out.outputSource = `${stepLabel}/${subOut.id}`;
+                    break;
+                }
+            }
+        }
+    }
+}
+// --- Comment conversion (native → format2) ---
+function _buildFormat2Comments(wf, labelMap) {
+    const rawComments = wf.comments;
+    if (!rawComments || !Array.isArray(rawComments) || rawComments.length === 0) {
+        return undefined;
+    }
+    const commentLabelMap = new Map();
+    for (let i = 0; i < rawComments.length; i++) {
+        const c = rawComments[i];
+        if (c.label) {
+            commentLabelMap.set(i, c.label);
+        }
+    }
+    const result = [];
+    for (const nativeComment of rawComments) {
+        const fmt2 = flattenCommentData(nativeComment);
+        if (fmt2.type === "frame") {
+            if (fmt2.contains_steps && Array.isArray(fmt2.contains_steps)) {
+                fmt2.contains_steps = fmt2.contains_steps.map((idx) => labelMap.get(String(idx)) ?? idx);
+            }
+            if (fmt2.contains_comments && Array.isArray(fmt2.contains_comments)) {
+                fmt2.contains_comments = fmt2.contains_comments.map((idx) => commentLabelMap.get(idx) ?? idx);
+            }
+        }
+        result.push(fmt2);
+    }
+    return result;
+}
+//# sourceMappingURL=toFormat2.js.map

package/dist/workflow/normalized/toFormat2.js.map

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package/dist/workflow/normalized/toNative.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Format2 → Native conversion.
+ *
+ * Port of gxformat2/normalized/_conversion.py to_native + helpers.
+ */
+import type { NormalizedNativeWorkflow } from "./native.js";
+/**
+ * Convert a Format2 workflow to normalized native Galaxy format.
+ */
+export declare function toNative(raw: unknown): NormalizedNativeWorkflow;
+//# sourceMappingURL=toNative.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"toNative.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toNative.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAwB,MAAM,aAAa,CAAC;AA+FlF;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,OAAO,GAAG,wBAAwB,CAW/D"}