@morscherlab/mint-sdk 1.2.0-beta.3 → 1.2.0-beta.4

package/dist/{useProtocolTemplates-Cv0ca1AM.js → useProtocolTemplates-BWhQIWV5.js}

@@ -1,9 +1,9 @@
 import { d as resolveExperimentCode } from "./experiment-utils-CLnzPPq5.js";
 import { r as useRequestSyncState } from "./EmptyState-p90quq8Z.js";
-import { A as useConcentrationUnits, H as parseExperimentId, U as resolveCurrentExperimentId, V as getInjectedPlatformContext, u as useControlWorkspace } from "./useControlSchema-Ds4VeFxt.js";
-import { o as useSettingsStore, r as useApi } from "./useApi-yE0re8k-.js";
-import { t as useExperimentStore } from "./experiment-D08H_TIH.js";
-import { B as toBioTemplateComponentProps, F as getBioTemplateComponentProps$1, H as toBioTemplateComponentPropsById, Jt as getBioTemplatePresetInfo, L as toBioTemplateComponentBindings, P as getBioTemplateComponentBindings, Qt as getBioTemplatePackInfo, R as toBioTemplateComponentBindingsById, U as toBioTemplateComponentSnippets, V as toBioTemplateComponentPropsByComponent$1, W as toBioTemplateComponentUsage, d as createBioTemplatePresetCollectionFromControls, dn as extractTemplateCollection, i as createBioTemplateControlToolkit, p as createBioTemplatePackCollection, sn as createTemplateCollection, u as createBioTemplatePresetCollection, un as ensureTemplateFromCollection, z as toBioTemplateComponentImports } from "./templates-Pbxjdqlh.js";
+import { A as useConcentrationUnits, H as parseExperimentId, J as isActiveJobStatus, Q as normalizeJobState, U as resolveCurrentExperimentId, V as getInjectedPlatformContext, u as useControlWorkspace } from "./useControlSchema-CXhxTul7.js";
+import { o as useSettingsStore, r as useApi } from "./useApi-CDBq6z23.js";
+import { t as useExperimentStore } from "./experiment-Y9Iz7KYi.js";
+import { B as toBioTemplateComponentProps, F as getBioTemplateComponentProps$1, H as toBioTemplateComponentPropsById, Jt as getBioTemplatePresetInfo, L as toBioTemplateComponentBindings, P as getBioTemplateComponentBindings, Qt as getBioTemplatePackInfo, R as toBioTemplateComponentBindingsById, U as toBioTemplateComponentSnippets, V as toBioTemplateComponentPropsByComponent$1, W as toBioTemplateComponentUsage, d as createBioTemplatePresetCollectionFromControls, dn as extractTemplateCollection, i as createBioTemplateControlToolkit, p as createBioTemplatePackCollection, sn as createTemplateCollection, u as createBioTemplatePresetCollection, un as ensureTemplateFromCollection, z as toBioTemplateComponentImports } from "./templates-BTJ9C9Kb.js";
 import { computed, effectScope, getCurrentScope, inject, onMounted, onScopeDispose, onUnmounted, provide, reactive, readonly, ref, shallowRef, toRaw, toValue, unref, watch } from "vue";
 //#region src/composables/useSortedItems.ts
 /** Shared sorting for SDK tables and lists with stable empty-value handling. */
@@ -528,32 +528,85 @@ function useMobileSupportGate(options = {}) {
 	};
 }
 //#endregion
-//#region src/jobs.ts
-var ACTIVE_JOB_STATUSES = new Set([
-	"awaiting_input",
-	"queued",
-	"running"
-]);
-/** Clamp invalid or out-of-range progress values for safe display. */
-function normalizeJobPercent(value) {
-	if (!Number.isFinite(value)) return 0;
-	return Math.min(100, Math.max(0, value));
-}
-function isActiveJobStatus(status) {
-	return ACTIVE_JOB_STATUSES.has(status);
-}
-function jobStatusLabel(status) {
-	return {
-		awaiting_input: "Waiting for input",
-		queued: "Queued",
-		running: "Running",
-		completed: "Completed",
-		failed: "Failed",
-		cancelled: "Cancelled"
-	}[status];
-}
-//#endregion
 //#region src/composables/useJobsStatusTray.ts
+/**
+* Combines independent job runtimes without copying their reactive state.
+*
+* Job ids must be globally unique across the sources. A duplicate id throws
+* when jobs are read or an id-routed action is requested, rather than silently
+* dispatching a mutation to the wrong owner.
+*/
+function combinePluginJobSources(sources) {
+	const jobs = computed(() => {
+		const combined = [];
+		const owners = /* @__PURE__ */ new Set();
+		for (const source of sources) for (const job of toValue(source.jobs)) {
+			if (owners.has(job.job_id)) throw duplicatePluginJobId(job.job_id);
+			owners.add(job.job_id);
+			combined.push(job);
+		}
+		return combined;
+	});
+	function ownerFor(jobId) {
+		let owner;
+		for (const source of sources) {
+			if (!toValue(source.jobs).some((job) => job.job_id === jobId)) continue;
+			if (owner) throw duplicatePluginJobId(jobId);
+			owner = source;
+		}
+		if (!owner) throw new Error(`Unknown plugin job id: ${jobId}`);
+		return owner;
+	}
+	const combined = { jobs };
+	if (sources.some((source) => source.refreshJobs)) combined.refreshJobs = async () => {
+		await Promise.all(sources.map((source) => source.refreshJobs?.()));
+		return jobs.value;
+	};
+	if (sources.some((source) => source.cancelJob)) combined.cancelJob = async (jobId) => {
+		const owner = ownerFor(jobId);
+		if (!owner.cancelJob) throw new Error(`Job ${jobId} cannot be cancelled by its source`);
+		return owner.cancelJob(jobId);
+	};
+	if (sources.length > 0 && sources.every((source) => source.deleteJob)) combined.deleteJob = async (jobId) => {
+		const owner = ownerFor(jobId);
+		if (!owner.deleteJob) throw new Error(`Job ${jobId} cannot be deleted by its source`);
+		return owner.deleteJob(jobId);
+	};
+	if (sources.length > 0 && sources.every((source) => source.clearFinishedJobs)) combined.clearFinishedJobs = async () => {
+		const results = await Promise.all(sources.map((source) => source.clearFinishedJobs()));
+		return results.every((result) => typeof result === "number") ? results.reduce((total, result) => total + result, 0) : void 0;
+	};
+	if (sources.some((source) => source.dispose)) combined.dispose = () => {
+		const errors = [];
+		for (const source of sources) try {
+			source.dispose?.();
+		} catch (cause) {
+			errors.push(cause);
+		}
+		if (errors.length === 1) throw errors[0];
+		if (errors.length > 1) throw new PluginJobSourceDisposeError(errors);
+	};
+	return combined;
+}
+var PluginJobSourceDisposeError = class extends Error {
+	cause;
+	errors;
+	constructor(errors) {
+		super("Failed to dispose plugin job sources");
+		this.name = "PluginJobSourceDisposeError";
+		this.cause = errors[0];
+		this.errors = Object.freeze([...errors]);
+	}
+};
+function duplicatePluginJobId(jobId) {
+	return /* @__PURE__ */ new Error(`Duplicate plugin job id across combined sources: ${jobId}`);
+}
+function responseJobs(response) {
+	return "jobs" in response ? response.jobs : response;
+}
+function isSnapshotPayload(data) {
+	return "jobs" in data && Array.isArray(data.jobs);
+}
 function errorMessage(error, fallback) {
 	return error instanceof Error ? error.message : fallback;
 }
@@ -564,38 +617,94 @@ function errorMessage(error, fallback) {
 * source. The controller never mirrors source jobs into another ref.
 */
 function usePluginJobCenter(options = {}) {
+	const legacyOverride = shallowRef(null);
 	const isOpen = ref(false);
 	const activeTab = ref("active");
 	const isLoading = ref(false);
 	const error = shallowRef(null);
 	const pendingJobIds = ref(/* @__PURE__ */ new Set());
+	const jobRevisions = /* @__PURE__ */ new Map();
+	let stateRevision = 0;
 	let requestGeneration = 0;
 	let active = true;
 	const source = computed(() => toValue(options.source));
-	const jobs = computed(() => source.value ? [...toValue(source.value.jobs)] : []);
+	const adapter = computed(() => toValue(options.adapter));
+	const jobs = computed(() => {
+		const currentSource = source.value;
+		if (currentSource) return [...toValue(currentSource.jobs)].map(normalizeJobState);
+		const input = toValue(options.jobs);
+		const override = legacyOverride.value;
+		if (override && override.input === input) return override.jobs;
+		return input ? [...input].map(normalizeJobState) : [];
+	});
 	const activeJobs = computed(() => jobs.value.filter((job) => isActiveJobStatus(job.status)));
 	const historyJobs = computed(() => jobs.value.filter((job) => !isActiveJobStatus(job.status)));
 	const deletableJobs = computed(() => historyJobs.value.filter((job) => job.can_delete));
 	const featuredJob = computed(() => activeJobs.value[0] ?? historyJobs.value[0] ?? null);
-	const canRefresh = computed(() => Boolean(source.value?.refreshJobs));
-	const canCancel = computed(() => Boolean(source.value?.cancelJob));
-	const canDelete = computed(() => Boolean(source.value?.deleteJob));
-	const canClearFinished = computed(() => Boolean(source.value?.clearFinishedJobs || source.value?.deleteJob));
+	const canRefresh = computed(() => Boolean(source.value?.refreshJobs || adapter.value?.listJobs));
+	const canCancel = computed(() => Boolean(source.value?.cancelJob || adapter.value?.cancelJob));
+	const canDelete = computed(() => Boolean(source.value?.deleteJob || adapter.value?.deleteJob));
+	const canClearFinished = computed(() => Boolean(source.value?.clearFinishedJobs || source.value?.deleteJob || adapter.value?.clearFinishedJobs || adapter.value?.deleteJob));
+	function bumpJobRevision(jobId) {
+		jobRevisions.set(jobId, (jobRevisions.get(jobId) ?? 0) + 1);
+	}
+	function replaceLegacyJobs(nextJobs) {
+		const normalized = nextJobs.map(normalizeJobState);
+		new Set([...jobs.value.map((job) => job.job_id), ...normalized.map((job) => job.job_id)]).forEach(bumpJobRevision);
+		legacyOverride.value = {
+			input: toValue(options.jobs),
+			jobs: normalized
+		};
+		stateRevision += 1;
+	}
+	function upsertLegacyJob(nextJob) {
+		const normalized = normalizeJobState(nextJob);
+		const existingIndex = jobs.value.findIndex((job) => job.job_id === normalized.job_id);
+		const nextJobs = [...jobs.value];
+		if (existingIndex === -1) nextJobs.unshift(normalized);
+		else nextJobs[existingIndex] = normalized;
+		legacyOverride.value = {
+			input: toValue(options.jobs),
+			jobs: nextJobs
+		};
+		bumpJobRevision(normalized.job_id);
+		stateRevision += 1;
+	}
+	function removeLegacyJobs(jobIds) {
+		legacyOverride.value = {
+			input: toValue(options.jobs),
+			jobs: jobs.value.filter((job) => !jobIds.has(job.job_id))
+		};
+		jobIds.forEach(bumpJobRevision);
+		stateRevision += 1;
+	}
 	function setPending(jobId, pending) {
 		const next = new Set(pendingJobIds.value);
 		if (pending) next.add(jobId);
 		else next.delete(jobId);
 		pendingJobIds.value = next;
 	}
+	function applyStreamMessage(message) {
+		if (!active || source.value) return;
+		if (message.event === "snapshot" && isSnapshotPayload(message.data)) {
+			replaceLegacyJobs(message.data.jobs);
+			return;
+		}
+		if ((message.event === "job" || message.event === "terminal") && !isSnapshotPayload(message.data)) upsertLegacyJob(message.data);
+	}
 	async function refresh() {
-		const refreshJobs = source.value?.refreshJobs;
-		if (!refreshJobs) return false;
+		const currentSource = source.value;
+		const listJobs = currentSource?.refreshJobs ?? adapter.value?.listJobs;
+		if (!listJobs) return false;
 		const generation = ++requestGeneration;
+		const revision = stateRevision;
 		isLoading.value = true;
 		error.value = null;
 		try {
-			await refreshJobs();
-			return active && generation === requestGeneration;
+			const response = await listJobs();
+			if (!active || generation !== requestGeneration || revision !== stateRevision) return false;
+			if (!currentSource && response) replaceLegacyJobs(responseJobs(response));
+			return true;
 		} catch (cause) {
 			if (active && generation === requestGeneration) error.value = errorMessage(cause, "Failed to load jobs");
 			return false;
@@ -605,12 +714,17 @@ function usePluginJobCenter(options = {}) {
 	}
 	async function cancelJob(job) {
 		const sourceCancel = source.value?.cancelJob;
-		if (!job.can_cancel || !sourceCancel || pendingJobIds.value.has(job.job_id)) return false;
+		const adapterCancel = adapter.value?.cancelJob;
+		if (!job.can_cancel || !sourceCancel && !adapterCancel || pendingJobIds.value.has(job.job_id)) return false;
+		const revision = jobRevisions.get(job.job_id) ?? 0;
 		setPending(job.job_id, true);
 		error.value = null;
 		try {
-			await sourceCancel(job.job_id);
-			return active;
+			const updated = sourceCancel ? await sourceCancel(job.job_id) : await adapterCancel(job);
+			if (!active) return false;
+			if (!sourceCancel && revision === (jobRevisions.get(job.job_id) ?? 0)) if (updated) upsertLegacyJob(updated);
+			else await refresh();
+			return true;
 		} catch (cause) {
 			if (active) error.value = errorMessage(cause, "Failed to cancel job");
 			return false;
@@ -620,12 +734,16 @@ function usePluginJobCenter(options = {}) {
 	}
 	async function deleteJob(job) {
 		const sourceDelete = source.value?.deleteJob;
-		if (!job.can_delete || !sourceDelete || pendingJobIds.value.has(job.job_id)) return false;
+		const adapterDelete = adapter.value?.deleteJob;
+		if (!job.can_delete || !sourceDelete && !adapterDelete || pendingJobIds.value.has(job.job_id)) return false;
 		setPending(job.job_id, true);
 		error.value = null;
 		try {
-			const deleted = await sourceDelete(job.job_id);
-			return active && deleted !== false;
+			const deleted = sourceDelete ? await sourceDelete(job.job_id) : await adapterDelete(job);
+			if (!active) return false;
+			if (!sourceDelete) if (deleted === false) await refresh();
+			else removeLegacyJobs(new Set([job.job_id]));
+			return deleted !== false;
 		} catch (cause) {
 			if (active) error.value = errorMessage(cause, "Failed to delete job");
 			return false;
@@ -645,12 +763,30 @@ function usePluginJobCenter(options = {}) {
 				return typeof deleted !== "number" || deleted === targets.length;
 			}
 			if (currentSource?.deleteJob) return (await Promise.all(targets.map((job) => deleteJob(job)))).every(Boolean);
-			return false;
+			const currentAdapter = adapter.value;
+			if (currentAdapter?.clearFinishedJobs) {
+				const deleted = await currentAdapter.clearFinishedJobs(targets);
+				if (!active) return false;
+				if (typeof deleted === "number" && deleted !== targets.length) {
+					await refresh();
+					return false;
+				}
+				removeLegacyJobs(new Set(targets.map((job) => job.job_id)));
+				return true;
+			}
+			if (!currentAdapter?.deleteJob) return false;
+			return (await Promise.all(targets.map((job) => deleteJob(job)))).every(Boolean);
 		} catch (cause) {
 			if (active) error.value = errorMessage(cause, "Failed to clear jobs");
 			return false;
 		}
 	}
+	if (options.eventStream !== void 0) watch(() => toValue(options.eventStream)?.lastMessage.value ?? null, (message) => {
+		if (message) applyStreamMessage(message);
+	}, { immediate: true });
+	onMounted(() => {
+		if (options.loadOnMount !== false) refresh();
+	});
 	onUnmounted(() => {
 		active = false;
 		requestGeneration += 1;
@@ -680,12 +816,17 @@ function usePluginJobCenter(options = {}) {
 			isOpen.value = !isOpen.value;
 		},
 		refresh,
+		applyStreamMessage,
 		cancelJob,
 		deleteJob,
 		clearFinished,
 		isPending: (job) => pendingJobIds.value.has(job.job_id)
 	};
 }
+/** @deprecated Use `usePluginJobCenter()` for the plugin job-center controller. */
+function useJobsStatusTray(options = {}) {
+	return usePluginJobCenter(options);
+}
 //#endregion
 //#region src/composables/useDoseCalculator.ts
 var VOLUME_UNITS = [
@@ -2285,6 +2426,14 @@ function parseCSV(text) {
 //#endregion
 //#region src/composables/useAutoGroup.ts
 var STRUCTURED_MISSING_GROUP = "Outlier";
+var deprecationWarned = false;
+var outlierDeprecationWarned = false;
+function warnDeprecated(api) {
+	if (deprecationWarned) return;
+	if (typeof process !== "undefined" && process.env.NODE_ENV === "production") return;
+	console.warn(`[useAutoGroup] ${api} is deprecated; use the new class-first API (setClassDisposition / toggleGroupBy / setValueOps).`);
+	deprecationWarned = true;
+}
 function useAutoGroup() {
 	const inputMode = ref("paste");
 	const rawText = ref("");
@@ -2617,6 +2766,54 @@ function useAutoGroup() {
 		document.body.removeChild(a);
 		URL.revokeObjectURL(url);
 	}
+	/** Test seam — exposes the template content/filename without triggering a browser download. */
+	function composeTemplateForTest(opts) {
+		return composeTemplate(samples.value, opts.mode === "prefilled" ? Object.values(schemas.value) : null, opts.mode === "prefilled" ? classes.value : null, {
+			...opts,
+			tokenizedSamples: tokenized.value
+		});
+	}
+	const outliers = ref([]);
+	const hasOutliers = computed(() => outliers.value.length > 0);
+	const conformingSamples = computed(() => samples.value);
+	const dominantFieldCount = computed(() => tokenized.value[0]?.length ?? 0);
+	const minFieldCount = computed(() => {
+		if (tokenized.value.length === 0) return 0;
+		return Math.min(...tokenized.value.map((t) => t.length));
+	});
+	const fields = computed(() => activeSchema.value?.columns ?? []);
+	const fieldNames = computed(() => {
+		const out = {};
+		for (const c of fields.value) out[c.index] = c.displayName ?? c.name;
+		return out;
+	});
+	const enabledFields = computed(() => activeSchema.value ? new Set(activeSchema.value.groupBy) : /* @__PURE__ */ new Set());
+	const effectiveColumns = fields;
+	const allSingletons = computed(() => groups.value.length > 1 && groups.value.every((g) => g.samples.length === 1));
+	function setOutlierAction(_, __) {
+		if (!outlierDeprecationWarned) {
+			if (typeof process === "undefined" || process.env.NODE_ENV !== "production") {
+				console.warn("[useAutoGroup] setOutlierAction is deprecated AND inactive in the class-first redesign. Use setClassDisposition('iqc' | 'eqc' | …, 'group' | 'overlay' | 'exclude') instead.");
+				outlierDeprecationWarned = true;
+			}
+		}
+	}
+	function setAllOutlierActions(__) {
+		if (!outlierDeprecationWarned) {
+			if (typeof process === "undefined" || process.env.NODE_ENV !== "production") {
+				console.warn("[useAutoGroup] setAllOutlierActions is deprecated AND inactive in the class-first redesign. Use setClassDisposition('iqc' | 'eqc' | …, 'group' | 'overlay' | 'exclude') instead.");
+				outlierDeprecationWarned = true;
+			}
+		}
+	}
+	function toggleField(index) {
+		warnDeprecated("toggleField");
+		if (activeClassKey.value) toggleGroupBy(activeClassKey.value, index);
+	}
+	function renameField(index, name) {
+		warnDeprecated("renameField");
+		if (activeClassKey.value) setColumnName(activeClassKey.value, index, name);
+	}
 	function loadExperimentData(rawData, options = {}) {
 		const parsed = extractSamplesFromDesignData(rawData, options);
 		if (!parsed) return false;
@@ -2633,6 +2830,7 @@ function useAutoGroup() {
 		schemas.value = {};
 		activeClassKey.value = "";
 		tokenized.value = [];
+		outliers.value = [];
 		sampleTypeHints.value = [];
 	}
 	return {
@@ -2644,6 +2842,8 @@ function useAutoGroup() {
 		schemas,
 		activeClassKey,
 		delimiter,
+		dominantFieldCount,
+		minFieldCount,
 		samples,
 		tokenized,
 		activeSchema,
@@ -2654,6 +2854,14 @@ function useAutoGroup() {
 		excludedSamples,
 		result,
 		fingerprint,
+		fields,
+		fieldNames,
+		enabledFields,
+		effectiveColumns,
+		hasOutliers,
+		outliers,
+		conformingSamples,
+		allSingletons,
 		canDownloadTemplate,
 		setClassDisposition,
 		setClassDispositions,
@@ -2669,8 +2877,13 @@ function useAutoGroup() {
 		loadFingerprint,
 		parseInput,
 		downloadTemplate,
+		composeTemplateForTest,
 		loadExperimentData,
-		reset
+		reset,
+		setOutlierAction,
+		setAllOutlierActions,
+		toggleField,
+		renameField
 	};
 }
 function extractSamplesFromDesignData(rawData, options = {}) {
@@ -4147,6 +4360,328 @@ function mergeInitialValues(controlOptions, initialValues) {
 	};
 }
 //#endregion
+//#region src/composables/useRackEditor.ts
+var SLOT_CYCLE = [
+	"R",
+	"G",
+	"B",
+	"Y"
+];
+var PLATE_CONFIGS = {
+	6: {
+		rows: 2,
+		cols: 3
+	},
+	12: {
+		rows: 3,
+		cols: 4
+	},
+	24: {
+		rows: 4,
+		cols: 6
+	},
+	48: {
+		rows: 6,
+		cols: 8
+	},
+	54: {
+		rows: 6,
+		cols: 9
+	},
+	96: {
+		rows: 8,
+		cols: 12
+	},
+	384: {
+		rows: 16,
+		cols: 24
+	}
+};
+var globalIdCounter = 0;
+function generateId() {
+	globalIdCounter++;
+	return `rack-${Date.now()}-${globalIdCounter}`;
+}
+/** Manages a set of sample racks with well-level assignment, series fill, and multi-rack reordering. */
+function useRackEditor(initialRacks, options) {
+	const defaultFormat = options?.defaultFormat ?? 54;
+	const defaultInjVol = options?.defaultInjectionVolume ?? 5;
+	const maxRacks = options?.maxRacks ?? 10;
+	const minRacks = options?.minRacks ?? 1;
+	function createDefaultRack(name, slotIndex) {
+		const slot = SLOT_CYCLE[(slotIndex ?? 0) % SLOT_CYCLE.length];
+		return {
+			id: generateId(),
+			name: name ?? `Rack ${racks.value.length + 1}`,
+			format: defaultFormat,
+			slot,
+			injectionVolume: defaultInjVol,
+			wells: {}
+		};
+	}
+	const racks = ref(initialRacks && initialRacks.length > 0 ? initialRacks.map((r) => ({ ...r })) : [createDefaultRack("Rack 1", 0)]);
+	const activeRackId = ref(racks.value[0]?.id ?? "");
+	const activeRack = computed(() => racks.value.find((r) => r.id === activeRackId.value) ?? racks.value[0]);
+	function addRack(name) {
+		if (racks.value.length >= maxRacks) return racks.value[racks.value.length - 1];
+		const rack = createDefaultRack(name, racks.value.length);
+		racks.value.push(rack);
+		activeRackId.value = rack.id;
+		return rack;
+	}
+	function removeRack(rackId) {
+		if (racks.value.length <= minRacks) return;
+		const index = racks.value.findIndex((r) => r.id === rackId);
+		if (index === -1) return;
+		racks.value.splice(index, 1);
+		if (activeRackId.value === rackId && racks.value[0]) activeRackId.value = racks.value[0].id;
+	}
+	function reorderRacks(fromIndex, toIndex) {
+		if (fromIndex < 0 || fromIndex >= racks.value.length) return;
+		if (toIndex < 0 || toIndex >= racks.value.length) return;
+		if (fromIndex === toIndex) return;
+		const [moved] = racks.value.splice(fromIndex, 1);
+		if (moved) racks.value.splice(toIndex, 0, moved);
+	}
+	function updateRack(rackId, data) {
+		const rack = racks.value.find((r) => r.id === rackId);
+		if (!rack) return;
+		if (data.name !== void 0) rack.name = data.name;
+		if (data.format !== void 0) rack.format = data.format;
+		if (data.slot !== void 0) rack.slot = data.slot;
+		if (data.injectionVolume !== void 0) rack.injectionVolume = data.injectionVolume;
+		if (data.wells !== void 0) rack.wells = data.wells;
+	}
+	function setActiveRack(rackId) {
+		if (racks.value.some((r) => r.id === rackId)) activeRackId.value = rackId;
+	}
+	function setWellData(rackId, wellId, data) {
+		const rack = racks.value.find((r) => r.id === rackId);
+		if (!rack) return;
+		rack.wells[wellId] = {
+			...rack.wells[wellId],
+			...data
+		};
+	}
+	function clearWell(rackId, wellId) {
+		const rack = racks.value.find((r) => r.id === rackId);
+		if (!rack) return;
+		delete rack.wells[wellId];
+	}
+	function clearAllWells(rackId) {
+		const rack = racks.value.find((r) => r.id === rackId);
+		if (!rack) return;
+		rack.wells = {};
+	}
+	function fillSeries(rackId, prefix = "S") {
+		const rack = racks.value.find((r) => r.id === rackId);
+		if (!rack) return;
+		const config = PLATE_CONFIGS[rack.format];
+		if (!config) return;
+		let counter = 1;
+		for (let row = 0; row < config.rows; row++) for (let col = 0; col < config.cols; col++) {
+			const wellId = `${String.fromCharCode(65 + row)}${col + 1}`;
+			if (!rack.wells[wellId]?.sampleType) {
+				const paddedNum = String(counter).padStart(3, "0");
+				rack.wells[wellId] = {
+					id: wellId,
+					row,
+					col,
+					state: "filled",
+					sampleType: "sample",
+					metadata: {
+						label: `${prefix}${paddedNum}`,
+						injectionVolume: rack.injectionVolume,
+						injectionCount: 1
+					}
+				};
+			}
+			counter++;
+		}
+	}
+	function getAllWells() {
+		const result = [];
+		for (const rack of racks.value) for (const [wellId, well] of Object.entries(rack.wells)) result.push({
+			rackId: rack.id,
+			wellId,
+			well
+		});
+		return result;
+	}
+	const totalSampleCount = computed(() => {
+		let count = 0;
+		for (const rack of racks.value) count += Object.keys(rack.wells).length;
+		return count;
+	});
+	function reset() {
+		const rack = createDefaultRack("Rack 1", 0);
+		racks.value = [rack];
+		activeRackId.value = rack.id;
+	}
+	return {
+		racks,
+		activeRack,
+		activeRackId,
+		addRack,
+		removeRack,
+		reorderRacks,
+		updateRack,
+		setActiveRack,
+		setWellData,
+		clearWell,
+		clearAllWells,
+		fillSeries,
+		getAllWells,
+		totalSampleCount,
+		reset
+	};
+}
+//#endregion
+//#region src/composables/useGroupAssignment.ts
+/** Shared two-zone group assignment model for control/treatment style workflows. */
+function useGroupAssignment(options) {
+	const groups = computed(() => [...toValue(options.groups)]);
+	const group1 = computed(() => [...toValue(options.group1)]);
+	const group2 = computed(() => [...toValue(options.group2)]);
+	const label1 = computed(() => toValue(options.label1) || "Control");
+	const label2 = computed(() => toValue(options.label2) || "Treatment");
+	const minPerGroup = computed(() => normalizeMinimum(toValue(options.minPerGroup)));
+	const group1Set = computed(() => new Set(group1.value));
+	const group2Set = computed(() => new Set(group2.value));
+	const unassignedGroups = computed(() => groups.value.filter((group) => !group1Set.value.has(group.name) && !group2Set.value.has(group.name)));
+	const zone1Groups = computed(() => groups.value.filter((group) => group1Set.value.has(group.name)));
+	const zone2Groups = computed(() => groups.value.filter((group) => group2Set.value.has(group.name)));
+	const zone1Count = computed(() => zone1Groups.value.reduce((sum, group) => sum + group.count, 0));
+	const zone2Count = computed(() => zone2Groups.value.reduce((sum, group) => sum + group.count, 0));
+	const isValid = computed(() => group1.value.length >= minPerGroup.value && group2.value.length >= minPerGroup.value);
+	const validationMessage = computed(() => {
+		if (isValid.value) return null;
+		const missing1 = Math.max(0, minPerGroup.value - group1.value.length);
+		const missing2 = Math.max(0, minPerGroup.value - group2.value.length);
+		const parts = [];
+		if (missing1 > 0) parts.push(`${missing1} more to ${label1.value}`);
+		if (missing2 > 0) parts.push(`${missing2} more to ${label2.value}`);
+		return `Add ${parts.join(" and ")}`;
+	});
+	function getZoneForGroup(groupName) {
+		if (group1Set.value.has(groupName)) return "zone1";
+		if (group2Set.value.has(groupName)) return "zone2";
+		return null;
+	}
+	function assignToZone(groupName, zone) {
+		const next = removeFromBoth(groupName);
+		if (zone === "zone1") return {
+			group1: [...next.group1, groupName],
+			group2: next.group2
+		};
+		return {
+			group1: next.group1,
+			group2: [...next.group2, groupName]
+		};
+	}
+	function removeFromZone(groupName, zone) {
+		if (zone === "zone1") return {
+			group1: group1.value.filter((name) => name !== groupName),
+			group2: group2.value
+		};
+		return {
+			group1: group1.value,
+			group2: group2.value.filter((name) => name !== groupName)
+		};
+	}
+	function clearAll() {
+		return {
+			group1: [],
+			group2: []
+		};
+	}
+	function removeFromBoth(groupName) {
+		return {
+			group1: group1.value.filter((name) => name !== groupName),
+			group2: group2.value.filter((name) => name !== groupName)
+		};
+	}
+	return {
+		unassignedGroups,
+		zone1Groups,
+		zone2Groups,
+		zone1Count,
+		zone2Count,
+		isValid,
+		validationMessage,
+		getZoneForGroup,
+		assignToZone,
+		removeFromZone,
+		clearAll
+	};
+}
+function normalizeMinimum(value) {
+	if (value === null || value === void 0 || !Number.isFinite(value)) return 1;
+	return Math.max(0, Math.floor(value));
+}
+//#endregion
+//#region src/composables/useReagentSeries.ts
+var DEFAULT_PRESETS = [
+	{
+		label: "2x",
+		factor: 2
+	},
+	{
+		label: "3x",
+		factor: 3
+	},
+	{
+		label: "½ log",
+		factor: "half-log"
+	},
+	{
+		label: "10x",
+		factor: 10
+	}
+];
+var DEFAULT_UNITS = [
+	"µM",
+	"nM",
+	"mM",
+	"pM"
+];
+function resolveFactor(factor) {
+	return factor === "half-log" ? Math.sqrt(10) : factor;
+}
+function roundToSignificant(value, digits = 4) {
+	if (value === 0) return 0;
+	const magnitude = Math.floor(Math.log10(Math.abs(value))) + 1;
+	const factor = Math.pow(10, digits - magnitude);
+	return Math.round(value * factor) / factor;
+}
+function generateDilutionSeries(startConcentration, count, factor, defaultReplicates = 1) {
+	if (count < 1 || startConcentration <= 0) return [];
+	const divisor = resolveFactor(factor);
+	const levels = [];
+	for (let i = 0; i < count; i++) levels.push({
+		value: roundToSignificant(startConcentration / Math.pow(divisor, i)),
+		replicates: defaultReplicates
+	});
+	return levels;
+}
+/** Generates and sorts geometric dilution series (2x, 3x, ½ log, 10x) for plate-based experiments. */
+function useReagentSeries() {
+	function generateSeries(start, count, factor, defaultReplicates = 1) {
+		return generateDilutionSeries(start, count, factor, defaultReplicates);
+	}
+	function sortLevels(levels, order = "desc") {
+		return [...levels].sort((a, b) => order === "desc" ? b.value - a.value : a.value - b.value);
+	}
+	function totalPositions(levels) {
+		return levels.reduce((sum, l) => sum + l.replicates, 0);
+	}
+	return {
+		generateSeries,
+		sortLevels,
+		totalPositions
+	};
+}
+//#endregion
 //#region src/composables/protocolTemplateCatalog.ts
 var BUILT_IN_PROTOCOL_TEMPLATES = [
 	{
@@ -4609,4 +5144,6 @@ function useProtocolTemplates() {
 	};
 }
 //#endregion
-export { useSortedItems as $, extractSampleOptionsFromDesignData as A, useMobileSupportGate as B, readFileAsText as C, useAutoGroup as D, extractSamplesFromDesignData as E, usePluginJobCenter as F, getPresenceClientId as G, useAppExperiment as H, isActiveJobStatus as I, useToast as J, usePresenceHeartbeat as K, jobStatusLabel as L, DEFAULT_COLORS as M, useWellPlateEditor as N, parseCSV as O, useDoseCalculator as P, compareSortValues as Q, normalizeJobPercent as R, parseDelimitedText as S, validateImportFile as T, getInjectedFrontendRevision as U, APP_EXPERIMENT_KEY as V, useRuntimeAlignment as W, normalizeSearchQuery as X, candidateMatchesSearch as Y, useTextSearch as Z, getSampleGroupParentPath as _, getBioTemplateComponentProps as a, hslToHex as b, useBioTemplateControls as c, useScheduleDrag as d, useExperimentSamples as f, getSampleGroupMajorPrefix as g, useSampleGroups as h, useBioTemplateWorkspace as i, unwrapExperimentDesignData as j, extractSampleNamesFromDesignData as k, useTemplateCollection as l, useExpansionSet as m, useBioTemplatePresetWorkspace as n, toBioTemplateComponentPropsByComponent as o, useExperimentData as p, useTheme as q, useBioTemplatePackWorkspace as r, useBioTemplateComponents as s, useProtocolTemplates as t, useExperimentSave as u, deriveShade as v, useFileImport as w, detectDelimiter as x, hexToHsl as y, DEFAULT_MOBILE_VIEWPORT_QUERY as z };
+export { useToast as $, useFileImport as A, useDoseCalculator as B, getSampleGroupParentPath as C, detectDelimiter as D, hslToHex as E, extractSampleNamesFromDesignData as F, useMobileSupportGate as G, useJobsStatusTray as H, extractSampleOptionsFromDesignData as I, getInjectedFrontendRevision as J, APP_EXPERIMENT_KEY as K, unwrapExperimentDesignData as L, extractSamplesFromDesignData as M, useAutoGroup as N, parseDelimitedText as O, parseCSV as P, useTheme as Q, DEFAULT_COLORS as R, getSampleGroupMajorPrefix as S, hexToHsl as T, usePluginJobCenter as U, combinePluginJobSources as V, DEFAULT_MOBILE_VIEWPORT_QUERY as W, getPresenceClientId as X, useRuntimeAlignment as Y, usePresenceHeartbeat as Z, useScheduleDrag as _, useReagentSeries as a, useExpansionSet as b, useBioTemplatePresetWorkspace as c, getBioTemplateComponentProps as d, candidateMatchesSearch as et, toBioTemplateComponentPropsByComponent as f, useExperimentSave as g, useTemplateCollection as h, generateDilutionSeries as i, useSortedItems as it, validateImportFile as j, readFileAsText as k, useBioTemplatePackWorkspace as l, useBioTemplateControls as m, DEFAULT_PRESETS as n, useTextSearch as nt, useGroupAssignment as o, useBioTemplateComponents as p, useAppExperiment as q, DEFAULT_UNITS as r, compareSortValues as rt, useRackEditor as s, useProtocolTemplates as t, normalizeSearchQuery as tt, useBioTemplateWorkspace as u, useExperimentSamples as v, deriveShade as w, useSampleGroups as x, useExperimentData as y, useWellPlateEditor as z };
+
+//# sourceMappingURL=useProtocolTemplates-BWhQIWV5.js.map