From 7ced17c412ce149101ea6cdbbb577bb3396539d8 Mon Sep 17 00:00:00 2001
From: Daniel Chang <mwdchang@gmail.com>
Date: Tue, 7 May 2024 09:39:23 -0700
Subject: [PATCH 1/5] upgrade pyodide, fix mmt init problems (#3557)

---
 packages/client/hmi-client/package.json             |  2 +-
 .../workflow/ops/model-config/tera-model-config.vue |  4 ++--
 .../client/hmi-client/src/python/PyodideWorker.ts   |  2 +-
 yarn.lock                                           | 13 ++++++-------
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/packages/client/hmi-client/package.json b/packages/client/hmi-client/package.json
index 04554beabf..3620896a41 100644
--- a/packages/client/hmi-client/package.json
+++ b/packages/client/hmi-client/package.json
@@ -64,7 +64,7 @@
 		"primeflex": "3.3.1",
 		"primeicons": "6.0.1",
 		"primevue": "3.43.0",
-		"pyodide": "0.23.4",
+		"pyodide": "0.25.1",
 		"sass": "1.56.1",
 		"uuid": "9.0.1",
 		"vue": "3.3.13",
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
index 3c1d1223be..eb29814a6a 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
@@ -116,7 +116,7 @@
 								Initial variable values<span class="artifact-amount">({{ numInitials }})</span>
 							</template>
 							<tera-initial-table
-								v-if="!isEmpty(knobs.transientModelConfig)"
+								v-if="!isEmpty(knobs.transientModelConfig) && !isEmpty(mmt.initials)"
 								:model="knobs.transientModelConfig.configuration"
 								:mmt="mmt"
 								:mmt-params="mmtParams"
@@ -158,7 +158,7 @@
 							Parameters<span class="artifact-amount">({{ numParameters }})</span>
 						</template>
 						<tera-parameter-table
-							v-if="!isEmpty(knobs.transientModelConfig)"
+							v-if="!isEmpty(knobs.transientModelConfig) && !isEmpty(mmt.parameters)"
 							:model-configurations="suggestedConfigurationContext.tableData"
 							:model="knobs.transientModelConfig.configuration"
 							:mmt="mmt"
diff --git a/packages/client/hmi-client/src/python/PyodideWorker.ts b/packages/client/hmi-client/src/python/PyodideWorker.ts
index e839782939..fc14d4d2f5 100644
--- a/packages/client/hmi-client/src/python/PyodideWorker.ts
+++ b/packages/client/hmi-client/src/python/PyodideWorker.ts
@@ -11,7 +11,7 @@ const variableMap: Object = {
 };
 
 const pyodide = await loadPyodide({
-	indexURL: 'https://cdn.jsdelivr.net/pyodide/v0.23.4/full'
+	indexURL: 'https://cdn.jsdelivr.net/pyodide/v0.25.1/full'
 });
 await pyodide.loadPackage('sympy');
 pyodide.runPython('import sympy');
diff --git a/yarn.lock b/yarn.lock
index 493284e0df..7d8aa5fec7 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -8458,7 +8458,7 @@ __metadata:
     primeflex: "npm:3.3.1"
     primeicons: "npm:6.0.1"
     primevue: "npm:3.43.0"
-    pyodide: "npm:0.23.4"
+    pyodide: "npm:0.25.1"
     sass: "npm:1.56.1"
     typescript: "npm:5.3.3"
     uuid: "npm:9.0.1"
@@ -11033,7 +11033,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"node-fetch@npm:^2.6.0, node-fetch@npm:^2.6.1":
+"node-fetch@npm:^2.6.0":
   version: 2.7.0
   resolution: "node-fetch@npm:2.7.0"
   dependencies:
@@ -11955,14 +11955,13 @@ __metadata:
   languageName: node
   linkType: hard
 
-"pyodide@npm:0.23.4":
-  version: 0.23.4
-  resolution: "pyodide@npm:0.23.4"
+"pyodide@npm:0.25.1":
+  version: 0.25.1
+  resolution: "pyodide@npm:0.25.1"
   dependencies:
     base-64: "npm:^1.0.0"
-    node-fetch: "npm:^2.6.1"
     ws: "npm:^8.5.0"
-  checksum: 9f85790565fdd2ea9e39f7f18e81ff7dce2d8aeace2d5cb9c62e068258ceca511da501cabd67f68d16d011aaf854047bd8691fd9f402d4700b6e5aec9da6a44f
+  checksum: 6a2aa972ce15565089469524231da03706886d3f0c87fa411444c501300d7765f04576d889683a43fcd9fdb1a44c8bafd829bd223057a9dd2c5eec4399672eae
   languageName: node
   linkType: hard
 

From 967c0fa11085ade23644c3c11cc0a6289404bae7 Mon Sep 17 00:00:00 2001
From: Cole Blanchard <33158416+blanchco@users.noreply.github.com>
Date: Tue, 7 May 2024 15:39:23 -0400
Subject: [PATCH 2/5] Const distrib fix (#3560)

Co-authored-by: Cole Blanchard <cblanchard@Cole-Blanchards-MacBook-Pro.local>
---
 .../model/petrinet/tera-parameter-table.vue   | 190 ++----------------
 1 file changed, 21 insertions(+), 169 deletions(-)

diff --git a/packages/client/hmi-client/src/components/model/petrinet/tera-parameter-table.vue b/packages/client/hmi-client/src/components/model/petrinet/tera-parameter-table.vue
index 217db99a94..7c190e86d3 100644
--- a/packages/client/hmi-client/src/components/model/petrinet/tera-parameter-table.vue
+++ b/packages/client/hmi-client/src/components/model/petrinet/tera-parameter-table.vue
@@ -42,45 +42,6 @@
 			</template>
 		</Column>
 
-		<Column header="Concept" class="w-1">
-			<template #body="{ data }">
-				<template v-if="data.concept?.identifiers && !isEmpty(data.concept.identifiers)">
-					{{
-						getNameOfCurieCached(
-							nameOfCurieCache,
-							getCurieFromGroudingIdentifier(data.concept.identifiers)
-						)
-					}}
-
-					<a
-						target="_blank"
-						rel="noopener noreferrer"
-						:href="getCurieUrl(getCurieFromGroudingIdentifier(data.concept.identifiers))"
-						@click.stop
-						aria-label="Open Concept"
-					>
-						<i class="pi pi-external-link" />
-					</a>
-				</template>
-				<template v-else>--</template>
-			</template>
-			<template v-if="!configView && !readonly" #editor="{ data }">
-				<AutoComplete
-					v-model="conceptSearchTerm.name"
-					:suggestions="curies"
-					@complete="onSearch"
-					@item-select="
-						updateParamValue(data.value, 'grounding', {
-							identifiers: parseCurie($event.value.curie)
-						})
-					"
-					optionLabel="name"
-					:forceSelection="true"
-					:inputStyle="{ width: '100%' }"
-				/>
-			</template>
-		</Column>
-
 		<Column header="Unit" class="w-1">
 			<template #body="slotProps">
 				<InputText
@@ -99,8 +60,8 @@
 			</template>
 		</Column>
 
-		<!-- Value type: Matrix or a Dropdown with: Constant, Distribution (with icons) -->
-		<Column field="type" header="Value Type" class="w-2">
+		<!-- Value type: Matrix or a Contant -->
+		<Column field="type" header="Constant" class="pl-2 pr-6 w-2">
 			<template #body="slotProps">
 				<Button
 					text
@@ -110,38 +71,20 @@
 					@click="openMatrixModal(slotProps.data)"
 					class="p-0"
 				/>
-				<Dropdown
+				<tera-input-number
 					v-else
-					class="value-type-dropdown w-9"
-					:model-value="slotProps.data.type"
-					:options="typeOptions"
-					optionLabel="label"
-					optionValue="value"
-					placeholder="Select a parameter type"
+					class="constant-number"
+					v-model.lazy="slotProps.data.value.value"
+					:min-fraction-digits="1"
+					:max-fraction-digits="10"
 					:disabled="readonly"
-					@update:model-value="(val) => (slotProps.data.type = val)"
-				>
-					<template #value="slotProps">
-						<span class="flex align-items-center">
-							<span
-								class="p-dropdown-item-icon mr-2"
-								:class="typeOptions[slotProps.value].icon"
-							></span>
-							<span>{{ typeOptions[slotProps.value].label }}</span>
-						</span>
-					</template>
-					<template #option="slotProps">
-						<span class="flex align-items-center">
-							<span class="p-dropdown-item-icon mr-2" :class="slotProps.option.icon"></span>
-							<span>{{ slotProps.option.label }}</span>
-						</span>
-					</template>
-				</Dropdown>
+					@update:model-value="emit('update-value', [slotProps.data.value])"
+				/>
 			</template>
 		</Column>
 
 		<!-- Value: the thing we show depends on the type of number -->
-		<Column field="value" header="Value" class="w-2 pr-2">
+		<Column field="value" header="Distribution" class="w-4 pl-2 pr-2">
 			<template #body="slotProps">
 				<!-- Matrix -->
 				<span
@@ -151,10 +94,7 @@
 					>Open matrix</span
 				>
 				<!-- Distribution -->
-				<div
-					v-else-if="slotProps.data.type === ParamType.DISTRIBUTION"
-					class="distribution-container"
-				>
+				<div v-else class="distribution-container">
 					<label>Min</label>
 					<tera-input-number
 						class="distribution-item min-value"
@@ -174,57 +114,6 @@
 						@update:model-value="emit('update-value', [slotProps.data.value])"
 					/>
 				</div>
-
-				<!-- Constant: Includes the value, a button and input box to convert it into a distributions with a customizable range -->
-				<span
-					v-else-if="slotProps.data.type === ParamType.CONSTANT"
-					class="flex align-items-center"
-				>
-					<tera-input-number
-						class="constant-number"
-						v-model.lazy="slotProps.data.value.value"
-						:min-fraction-digits="1"
-						:max-fraction-digits="10"
-						:disabled="readonly"
-						@update:model-value="emit('update-value', [slotProps.data.value])"
-					/>
-					<!-- This is a button with an input field inside it, weird huh?, but it works -->
-					<!--
-					<Button
-						v-if="!readonly"
-						class="ml-2 pt-0 pb-0 w-5"
-						text
-						@click="changeType(slotProps.data.value, 1)"
-						v-tooltip="'Convert to distribution'"
-					>
-						<span class="white-space-nowrap text-sm">Add ±</span>
-						<InputNumber
-							v-model="addPlusMinus"
-
-							text
-							class="constant-number add-plus-minus w-full"
-							inputId="convert-to-distribution"
-							suffix="%"
-							:min="0"
-							:max="100"
-							:disabled="readonly"
-							@click.stop
-						/>
-					-->
-				</span>
-			</template>
-		</Column>
-
-		<!-- Source  -->
-		<Column field="source" header="Source" class="w-2">
-			<template #body="{ data }">
-				<InputText
-					v-if="data.type !== ParamType.MATRIX"
-					class="w-full"
-					v-model.lazy="data.source"
-					:disabled="readonly"
-					@update:model-value="(val) => updateMetadataFromInput(data.value.id, 'source', val)"
-				/>
 			</template>
 		</Column>
 
@@ -277,6 +166,7 @@
 		<tera-modal
 			v-if="suggestedValuesModalContext.isOpen"
 			@modal-mask-clicked="onCloseSuggestedValuesModal"
+			:width="1000"
 		>
 			<template #header
 				><h5>Suggested configurations for {{ suggestedValuesModalContext.id }}</h5></template
@@ -285,7 +175,7 @@
 				:value="suggestedValues"
 				dataKey="index"
 				v-model:selection="selectedValue"
-				tableStyle="min-width: 50rem"
+				tableStyle="min-width: 80rem"
 			>
 				<Column selectionMode="single" class="w-3rem"></Column>
 				<Column header="Symbol">
@@ -307,22 +197,16 @@
 						{{ data.configuration?.name }}
 					</template>
 				</Column>
-				<Column header="Value type">
+				<Column header="Constant">
 					<template #body="{ data }">
-						{{ typeOptions[getParamType(data.parameter)].label }}
+						{{ data.parameter.value }}
 					</template>
 				</Column>
-				<Column header="Value">
+				<Column header="Distribution">
 					<template #body="{ data }">
-						<span v-if="getParamType(data.parameter) === ParamType.CONSTANT">
-							{{ data.parameter.value }}
-						</span>
-						<div
-							class="distribution-container"
-							v-else-if="getParamType(data.parameter) === ParamType.DISTRIBUTION"
-						>
-							<span>Min: {{ data.parameter.distribution.parameters.minimum }}</span>
-							<span>Max: {{ data.parameter.distribution.parameters.maximum }}</span>
+						<div class="distribution-container">
+							<span>Min: {{ data.parameter.distribution?.parameters.minimum }}</span>
+							<span>Max: {{ data.parameter.distribution?.parameters.maximum }}</span>
 						</div>
 					</template>
 				</Column>
@@ -351,22 +235,13 @@
 import { computed, ref, watch } from 'vue';
 import { cloneDeep, isEmpty } from 'lodash';
 import Button from 'primevue/button';
-import type { DKG, Model, ModelConfiguration, ModelParameter } from '@/types/Types';
-import Dropdown from 'primevue/dropdown';
+import type { Model, ModelConfiguration, ModelParameter } from '@/types/Types';
 import InputText from 'primevue/inputtext';
 import Datatable from 'primevue/datatable';
 import Column from 'primevue/column';
 import { StratifiedMatrix } from '@/types/Model';
 import TeraStratifiedMatrixModal from '@/components/model/petrinet/model-configurations/tera-stratified-matrix-modal.vue';
 import { AMRSchemaNames, ModelConfigTableData, ParamType } from '@/types/common';
-import {
-	getCurieFromGroudingIdentifier,
-	getCurieUrl,
-	getNameOfCurieCached,
-	parseCurie,
-	searchCuriesEntities
-} from '@/services/concept';
-import AutoComplete, { AutoCompleteCompleteEvent } from 'primevue/autocomplete';
 
 import { getModelType } from '@/services/model';
 import { matrixEffect } from '@/utils/easter-eggs';
@@ -375,8 +250,7 @@ import { isStratifiedModel, collapseParameters } from '@/model-representation/mi
 import {
 	updateVariable,
 	getParameterMetadata,
-	getParameters,
-	updateParameterMetadata
+	getParameters
 } from '@/model-representation/service';
 import TeraModal from '@/components/widgets/tera-modal.vue';
 import TeraInputNumber from '@/components/widgets/tera-input-number.vue';
@@ -392,11 +266,6 @@ const props = defineProps<{
 	configView?: boolean; // if the table is in the model config view we have limited functionality
 }>();
 
-const typeOptions = [
-	{ label: 'Constant', value: ParamType.CONSTANT, icon: 'pi pi-hashtag' },
-	{ label: 'Distribution', value: ParamType.DISTRIBUTION, icon: 'custom-icon-distribution' }
-];
-
 const emit = defineEmits(['update-value', 'update-model']);
 
 const isStratified = computed(() => isStratifiedModel(props.mmt));
@@ -545,9 +414,6 @@ const conceptSearchTerm = ref({
 	curie: '',
 	name: ''
 });
-const nameOfCurieCache = ref(new Map<string, string>());
-
-const curies = ref<DKG[]>([]);
 
 const modelType = computed(() => getModelType(props.model));
 
@@ -581,20 +447,6 @@ const updateParamValue = (param: ModelParameter, key: string, value: any) => {
 	emit('update-value', [clonedParam]);
 };
 
-const updateMetadataFromInput = (id: string, key: string, value: any) => {
-	const clonedModel = cloneDeep(props.model);
-	updateParameterMetadata(clonedModel, id, key, value);
-	emit('update-model', clonedModel);
-};
-
-async function onSearch(event: AutoCompleteCompleteEvent) {
-	const query = event.query;
-	if (query.length > 2) {
-		const response = await searchCuriesEntities(query);
-		curies.value = response;
-	}
-}
-
 const openSuggestedValuesModal = (id: string) => {
 	suggestedValuesModalContext.value.isOpen = true;
 	suggestedValuesModalContext.value.id = id;

From 854d6e967b09a89240bd055c4c7598c0909f05ac Mon Sep 17 00:00:00 2001
From: Daniel Chang <mwdchang@gmail.com>
Date: Tue, 7 May 2024 13:06:39 -0700
Subject: [PATCH 3/5] Llm stratify (#3558)

---
 .../ops/stratify-mira/tera-stratify-mira.vue  | 26 +++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
index bc2ca325bd..0cfe92b89c 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
@@ -41,8 +41,14 @@
 			</tera-drilldown-section>
 		</div>
 		<div :tabName="StratifyTabs.Notebook">
-			<tera-drilldown-section>
-				<p class="mt-3 ml-4">Code Editor - Python</p>
+			<tera-drilldown-section class="notebook-section">
+				<tera-notebook-jupyter-input
+					:kernel-manager="kernelManager"
+					:default-options="[]"
+					:context-language="'python3'"
+					@llm-output="(data: any) => processLLMOutput(data)"
+				/>
+
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initialize"
@@ -123,6 +129,7 @@ import TeraOperatorPlaceholder from '@/components/operator/tera-operator-placeho
 import TeraModelSemanticTables from '@/components/model/tera-model-semantic-tables.vue';
 import TeraSaveModelModal from '@/page/project/components/tera-save-model-modal.vue';
 import TeraStratificationGroupForm from '@/components/workflow/ops/stratify-mira/tera-stratification-group-form.vue';
+import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
 
 import { createModel, getModel } from '@/services/model';
 import { WorkflowNode, OperatorStatus } from '@/types/workflow';
@@ -200,6 +207,11 @@ const stratifyModel = () => {
 	stratifyRequest();
 };
 
+const processLLMOutput = (data: any) => {
+	codeText.value = data.content.code;
+	saveCodeToState(data.content.code, false);
+};
+
 const resetModel = () => {
 	if (!amr.value) return;
 	kernelManager
@@ -483,6 +495,16 @@ onUnmounted(() => {
 </script>
 
 <style scoped>
+.notebook-section:deep(main .notebook-toolbar),
+.notebook-section:deep(main .ai-assistant) {
+	padding-left: var(--gap-medium);
+}
+
+.notebook-section:deep(main) {
+	gap: var(--gap-small);
+	position: relative;
+}
+
 .code-executed-warning {
 	background-color: #ffe6e6;
 	color: #cc0000;

From 121c6c83e7ad1ed8ae5ab6d12e8c19d86800d626 Mon Sep 17 00:00:00 2001
From: Tom Szendrey <T.Szendrey@hotmail.com>
Date: Wed, 8 May 2024 09:28:37 -0400
Subject: [PATCH 4/5] Ts/llm thought output for release (#3565)

---
 .../llm/tera-notebook-jupyter-input.vue       |  8 +++--
 .../tera-notebook-jupyter-thought-output.vue  | 31 +++++++++++++++++++
 .../decapodes/tera-decapodes-drilldown.vue    |  5 +++
 .../tera-model-comparison.vue                 | 22 +++++++++----
 .../ops/model-config/tera-model-config.vue    | 25 ++++++++++-----
 .../ops/model-edit/tera-model-edit.vue        | 26 ++++++++++------
 .../ops/stratify-mira/tera-stratify-mira.vue  | 22 +++++++------
 7 files changed, 104 insertions(+), 35 deletions(-)
 create mode 100644 packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue

diff --git a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
index 586b297fa7..61e977caef 100644
--- a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
+++ b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
@@ -58,12 +58,12 @@ const props = defineProps<{
 	contextLanguage: string;
 }>();
 
-const emit = defineEmits(['llm-output']);
+const emit = defineEmits(['llm-output', 'llm-thought-output']);
 
 const questionString = ref('');
 const kernelStatus = ref<string>('');
-
 const showAssistant = ref(true);
+const thoughts = ref();
 
 // FIXME: If the language is changed here it should mutate the beaker instance in the parent component
 
@@ -80,6 +80,10 @@ const submitQuestion = () => {
 	message.register('code_cell', (data) => {
 		emit('llm-output', data);
 	});
+	message.register('llm_thought', (data) => {
+		thoughts.value = data;
+		emit('llm-thought-output', data);
+	});
 };
 </script>
 
diff --git a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue
new file mode 100644
index 0000000000..a769fda59e
--- /dev/null
+++ b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue
@@ -0,0 +1,31 @@
+<template>
+	<p v-if="showThoughts" class="thought-bubble">
+		{{ thought }}
+	</p>
+	<Button
+		v-if="thought"
+		link
+		:label="`${showThoughts ? 'Hide' : 'Show'} thoughts`"
+		@click="() => (showThoughts = !showThoughts)"
+	/>
+</template>
+
+<script setup lang="ts">
+import { ref, computed } from 'vue';
+import Button from 'primevue/button';
+
+const props = defineProps<{
+	llmThought?: any;
+}>();
+const showThoughts = ref(false);
+const thought = computed(() => props?.llmThought?.content?.thought ?? '');
+</script>
+
+<style scoped>
+.thought-bubble {
+	border: 1px solid var(--surface-border-light);
+	border-radius: var(--border-radius);
+	padding: var(--gap-small);
+	margin-top: var(--gap-small);
+}
+</style>
diff --git a/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue b/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
index 6dbb615f4a..e7b30439a4 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
@@ -31,8 +31,10 @@
 						:defaultOptions="sampleAgentQuestions"
 						:context-language="contextLanguage"
 						@llm-output="(data: any) => appendCode(data, 'code')"
+						@llm-thought-output="(data: any) => (llmThought = data)"
 					/>
 				</Suspense>
+				<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initializeEditor"
@@ -65,6 +67,8 @@ import TeraDrilldown from '@/components/drilldown/tera-drilldown.vue';
 import TeraNotebookError from '@/components/drilldown/tera-notebook-error.vue';
 import TeraDrilldownSection from '@/components/drilldown/tera-drilldown-section.vue';
 import TeraDrilldownPreview from '@/components/drilldown/tera-drilldown-preview.vue';
+import teraNotebookJupyterThoughtOutput from '@/components/llm/tera-notebook-jupyter-thought-output.vue';
+
 import { KernelSessionManager } from '@/services/jupyter';
 import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
 import { VAceEditorInstance } from 'vue3-ace-editor/types';
@@ -114,6 +118,7 @@ const initializeEditor = (editorInstance: any) => {
 	editor = editorInstance;
 };
 const codeText = ref();
+const llmThought = ref();
 
 const buildJupyterContext = () => ({
 	context: 'decapodes',
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue b/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
index 25c56c4839..c48fd69831 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
@@ -81,12 +81,16 @@
 						@click="runCode"
 					/>
 				</div>
-				<tera-notebook-jupyter-input
-					:kernelManager="kernelManager"
-					:defaultOptions="sampleAgentQuestions"
-					@llm-output="appendCode"
-					:context-language="contextLanguage"
-				/>
+				<div class="toolbar">
+					<tera-notebook-jupyter-input
+						:kernelManager="kernelManager"
+						:defaultOptions="sampleAgentQuestions"
+						@llm-output="appendCode"
+						@llm-thought-output="(data: any) => (llmThought = data)"
+						:context-language="contextLanguage"
+					/>
+					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+				</div>
 				<v-ace-editor
 					v-model:value="code"
 					@init="initializeAceEditor"
@@ -158,6 +162,8 @@ import { VAceEditorInstance } from 'vue3-ace-editor/types';
 import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
 import Image from 'primevue/image';
 import TeraProgressSpinner from '@/components/widgets/tera-progress-spinner.vue';
+import teraNotebookJupyterThoughtOutput from '@/components/llm/tera-notebook-jupyter-thought-output.vue';
+
 import { saveCodeToState } from '@/services/notebook';
 import { getImages, addImage, deleteImages } from '@/services/image';
 import { ModelComparisonOperationState } from './model-comparison-operation';
@@ -185,6 +191,7 @@ const isLoadingStructuralComparisons = ref(false);
 const structuralComparisons = ref<string[]>([]);
 const llmAnswer = ref('');
 const code = ref(props.node.state.notebookHistory?.[0]?.code ?? '');
+const llmThought = ref();
 const isKernelReady = ref(false);
 const modelsToCompare = ref<Model[]>([]);
 const contextLanguage = ref<string>('python3');
@@ -403,6 +410,9 @@ ul {
 	gap: var(--gap-small);
 	position: relative;
 }
+.toolbar {
+	padding-left: var(--gap-medium);
+}
 
 .toolbar-right-side {
 	position: absolute;
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
index eb29814a6a..6c7df18536 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
@@ -233,14 +233,18 @@
 						@click="runFromCode"
 					/>
 				</div>
-				<Suspense>
-					<tera-notebook-jupyter-input
-						:kernel-manager="kernelManager"
-						:defaultOptions="sampleAgentQuestions"
-						:context-language="contextLanguage"
-						@llm-output="(data: any) => appendCode(data, 'code')"
-					/>
-				</Suspense>
+				<div class="toolbar">
+					<Suspense>
+						<tera-notebook-jupyter-input
+							:kernel-manager="kernelManager"
+							:defaultOptions="sampleAgentQuestions"
+							:context-language="contextLanguage"
+							@llm-output="(data: any) => appendCode(data, 'code')"
+							@llm-thought-output="(data: any) => (llmThought = data)"
+						/>
+					</Suspense>
+					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+				</div>
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initializeEditor"
@@ -345,6 +349,7 @@ import TeraModelDiagram from '@/components/model/petrinet/model-diagrams/tera-mo
 import TeraModelSemanticTables from '@/components/model/tera-model-semantic-tables.vue';
 import teraModelIntervention from '@/components/model/petrinet/tera-model-intervention.vue';
 import TeraModal from '@/components/widgets/tera-modal.vue';
+import teraNotebookJupyterThoughtOutput from '@/components/llm/tera-notebook-jupyter-thought-output.vue';
 
 import { FatalError } from '@/api/api';
 import TeraInitialTable from '@/components/model/petrinet/tera-initial-table.vue';
@@ -437,6 +442,7 @@ const buildJupyterContext = () => {
 const codeText = ref(
 	'# This environment contains the variable "model_config" to be read and updated'
 );
+const llmThought = ref();
 const notebookResponse = ref();
 const executeResponse = ref({
 	status: OperatorStatus.DEFAULT,
@@ -1042,6 +1048,9 @@ onUnmounted(() => {
 	display: flex;
 	align-items: center;
 }
+.toolbar {
+	padding-left: var(--gap-medium);
+}
 
 :deep(.p-datatable-loading-overlay.p-component-overlay) {
 	background-color: #fff;
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue b/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
index c983ab75e3..57a6adbc80 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
@@ -26,14 +26,18 @@
 						@click="runFromCodeWrapper"
 					/>
 				</div>
-				<Suspense>
-					<tera-notebook-jupyter-input
-						:kernel-manager="kernelManager"
-						:default-options="sampleAgentQuestions"
-						:context-language="contextLanguage"
-						@llm-output="(data: any) => appendCode(data, 'code')"
-					/>
-				</Suspense>
+				<div class="toolbar">
+					<Suspense>
+						<tera-notebook-jupyter-input
+							:kernel-manager="kernelManager"
+							:default-options="sampleAgentQuestions"
+							:context-language="contextLanguage"
+							@llm-output="(data: any) => appendCode(data, 'code')"
+							@llm-thought-output="(data: any) => (llmThought = data)"
+						/>
+					</Suspense>
+					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+				</div>
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initializeAceEditor"
@@ -110,6 +114,7 @@ import TeraDrilldownPreview from '@/components/drilldown/tera-drilldown-preview.
 import TeraDrilldownSection from '@/components/drilldown/tera-drilldown-section.vue';
 import TeraModelTemplateEditor from '@/components/model-template/tera-model-template-editor.vue';
 import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
+import teraNotebookJupyterThoughtOutput from '@/components/llm/tera-notebook-jupyter-thought-output.vue';
 
 import { KernelSessionManager } from '@/services/jupyter';
 import { getModelIdFromModelConfigurationId } from '@/services/model-configurations';
@@ -168,6 +173,8 @@ const contextLanguage = ref<string>('python3');
 const defaultCodeText =
 	'# This environment contains the variable "model" \n# which is displayed on the right';
 const codeText = ref(defaultCodeText);
+const llmThought = ref();
+
 const executeResponse = ref({
 	status: OperatorStatus.DEFAULT,
 	name: '',
@@ -401,8 +408,7 @@ onUnmounted(() => {
 	position: relative;
 }
 
-.notebook-section:deep(main .notebook-toolbar),
-.notebook-section:deep(main .ai-assistant) {
+.notebook-section:deep(main .toolbar) {
 	padding-left: var(--gap-medium);
 }
 .toolbar-right-side {
diff --git a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
index 0cfe92b89c..f7bb6104a4 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
@@ -42,13 +42,16 @@
 		</div>
 		<div :tabName="StratifyTabs.Notebook">
 			<tera-drilldown-section class="notebook-section">
-				<tera-notebook-jupyter-input
-					:kernel-manager="kernelManager"
-					:default-options="[]"
-					:context-language="'python3'"
-					@llm-output="(data: any) => processLLMOutput(data)"
-				/>
-
+				<div class="toolbar">
+					<tera-notebook-jupyter-input
+						:kernel-manager="kernelManager"
+						:default-options="[]"
+						:context-language="'python3'"
+						@llm-output="(data: any) => processLLMOutput(data)"
+						@llm-thought-output="(data: any) => (llmThought = data)"
+					/>
+					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+				</div>
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initialize"
@@ -130,6 +133,7 @@ import TeraModelSemanticTables from '@/components/model/tera-model-semantic-tabl
 import TeraSaveModelModal from '@/page/project/components/tera-save-model-modal.vue';
 import TeraStratificationGroupForm from '@/components/workflow/ops/stratify-mira/tera-stratification-group-form.vue';
 import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
+import teraNotebookJupyterThoughtOutput from '@/components/llm/tera-notebook-jupyter-thought-output.vue';
 
 import { createModel, getModel } from '@/services/model';
 import { WorkflowNode, OperatorStatus } from '@/types/workflow';
@@ -196,6 +200,7 @@ const kernelManager = new KernelSessionManager();
 
 let editor: VAceEditorInstance['_editor'] | null;
 const codeText = ref('');
+const llmThought = ref();
 
 const updateStratifyGroupForm = (config: StratifyGroup) => {
 	const state = _.cloneDeep(props.node.state);
@@ -495,8 +500,7 @@ onUnmounted(() => {
 </script>
 
 <style scoped>
-.notebook-section:deep(main .notebook-toolbar),
-.notebook-section:deep(main .ai-assistant) {
+.notebook-section:deep(main .toolbar) {
 	padding-left: var(--gap-medium);
 }
 

From 30088dc2416bfcbf9fe986ef01a9d23682a4f127 Mon Sep 17 00:00:00 2001
From: Tom Szendrey <T.Szendrey@hotmail.com>
Date: Thu, 9 May 2024 15:41:46 -0400
Subject: [PATCH 5/5] Ts/update stratify beaker context (#3584)

---
 .../llm/tera-notebook-jupyter-input.vue       |   7 +-
 .../tera-notebook-jupyter-thought-output.vue  |  12 ++-
 .../decapodes/tera-decapodes-drilldown.vue    |   7 +-
 .../tera-model-comparison.vue                 |   7 +-
 .../ops/model-config/tera-model-config.vue    |   7 +-
 .../ops/model-edit/tera-model-edit.vue        |  10 +-
 .../ops/stratify-mira/tera-stratify-mira.vue  |  32 +++---
 testing/Stratify-LLM-Tests.md                 | 101 ++++++++++++++++++
 8 files changed, 153 insertions(+), 30 deletions(-)
 create mode 100644 testing/Stratify-LLM-Tests.md

diff --git a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
index 61e977caef..480292eb44 100644
--- a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
+++ b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-input.vue
@@ -58,7 +58,7 @@ const props = defineProps<{
 	contextLanguage: string;
 }>();
 
-const emit = defineEmits(['llm-output', 'llm-thought-output']);
+const emit = defineEmits(['question-asked', 'llm-output', 'llm-thought-output']);
 
 const questionString = ref('');
 const kernelStatus = ref<string>('');
@@ -73,6 +73,7 @@ const submitQuestion = () => {
 	const message = props.kernelManager.sendMessage('llm_request', {
 		request: questionString.value
 	});
+	emit('question-asked');
 	// May prefer to use a manual status rather than following this. TBD. Both options work for now
 	message.register('status', (data) => {
 		kernelStatus.value = data.content.execution_state;
@@ -84,6 +85,10 @@ const submitQuestion = () => {
 		thoughts.value = data;
 		emit('llm-thought-output', data);
 	});
+	message.register('llm_response', (data) => {
+		thoughts.value = data;
+		emit('llm-thought-output', data);
+	});
 };
 </script>
 
diff --git a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue
index a769fda59e..a02d77c99f 100644
--- a/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue
+++ b/packages/client/hmi-client/src/components/llm/tera-notebook-jupyter-thought-output.vue
@@ -15,14 +15,22 @@ import { ref, computed } from 'vue';
 import Button from 'primevue/button';
 
 const props = defineProps<{
-	llmThought?: any;
+	llmThoughts: any[];
 }>();
 const showThoughts = ref(false);
-const thought = computed(() => props?.llmThought?.content?.thought ?? '');
+const thought = computed(() => {
+	let aString = '';
+	props.llmThoughts.forEach((ele) => {
+		const llmResponse = ele.content?.thought ?? ele.content?.text ?? '';
+		aString = aString.concat(llmResponse, '\n \n');
+	});
+	return aString;
+});
 </script>
 
 <style scoped>
 .thought-bubble {
+	white-space: pre-line;
 	border: 1px solid var(--surface-border-light);
 	border-radius: var(--border-radius);
 	padding: var(--gap-small);
diff --git a/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue b/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
index e7b30439a4..f1bb185b4a 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/decapodes/tera-decapodes-drilldown.vue
@@ -31,10 +31,11 @@
 						:defaultOptions="sampleAgentQuestions"
 						:context-language="contextLanguage"
 						@llm-output="(data: any) => appendCode(data, 'code')"
-						@llm-thought-output="(data: any) => (llmThought = data)"
+						@llm-thought-output="(data: any) => llmThoughts.push(data)"
+						@question-asked="llmThoughts = []"
 					/>
 				</Suspense>
-				<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+				<tera-notebook-jupyter-thought-output :llm-thoughts="llmThoughts" />
 				<v-ace-editor
 					v-model:value="codeText"
 					@init="initializeEditor"
@@ -118,7 +119,7 @@ const initializeEditor = (editorInstance: any) => {
 	editor = editorInstance;
 };
 const codeText = ref();
-const llmThought = ref();
+const llmThoughts = ref<any[]>([]);
 
 const buildJupyterContext = () => ({
 	context: 'decapodes',
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue b/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
index c48fd69831..dc48f20ded 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-comparison/tera-model-comparison.vue
@@ -86,10 +86,11 @@
 						:kernelManager="kernelManager"
 						:defaultOptions="sampleAgentQuestions"
 						@llm-output="appendCode"
-						@llm-thought-output="(data: any) => (llmThought = data)"
+						@llm-thought-output="(data: any) => llmThoughts.push(data)"
+						@question-asked="llmThoughts = []"
 						:context-language="contextLanguage"
 					/>
-					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+					<tera-notebook-jupyter-thought-output :llm-thoughts="llmThoughts" />
 				</div>
 				<v-ace-editor
 					v-model:value="code"
@@ -191,7 +192,7 @@ const isLoadingStructuralComparisons = ref(false);
 const structuralComparisons = ref<string[]>([]);
 const llmAnswer = ref('');
 const code = ref(props.node.state.notebookHistory?.[0]?.code ?? '');
-const llmThought = ref();
+const llmThoughts = ref<any[]>([]);
 const isKernelReady = ref(false);
 const modelsToCompare = ref<Model[]>([]);
 const contextLanguage = ref<string>('python3');
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
index 6c7df18536..5e6c512384 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-config/tera-model-config.vue
@@ -240,10 +240,11 @@
 							:defaultOptions="sampleAgentQuestions"
 							:context-language="contextLanguage"
 							@llm-output="(data: any) => appendCode(data, 'code')"
-							@llm-thought-output="(data: any) => (llmThought = data)"
+							@llm-thought-output="(data: any) => llmThoughts.push(data)"
+							@question-asked="llmThoughts = []"
 						/>
 					</Suspense>
-					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+					<tera-notebook-jupyter-thought-output :llm-thoughts="llmThoughts" />
 				</div>
 				<v-ace-editor
 					v-model:value="codeText"
@@ -442,7 +443,7 @@ const buildJupyterContext = () => {
 const codeText = ref(
 	'# This environment contains the variable "model_config" to be read and updated'
 );
-const llmThought = ref();
+const llmThoughts = ref<any[]>([]);
 const notebookResponse = ref();
 const executeResponse = ref({
 	status: OperatorStatus.DEFAULT,
diff --git a/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue b/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
index 57a6adbc80..7bb5b08851 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/model-edit/tera-model-edit.vue
@@ -33,10 +33,11 @@
 							:default-options="sampleAgentQuestions"
 							:context-language="contextLanguage"
 							@llm-output="(data: any) => appendCode(data, 'code')"
-							@llm-thought-output="(data: any) => (llmThought = data)"
+							@llm-thought-output="(data: any) => llmThoughts.push(data)"
+							@question-asked="llmThoughts = []"
 						/>
 					</Suspense>
-					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+					<tera-notebook-jupyter-thought-output :llm-thoughts="llmThoughts" />
 				</div>
 				<v-ace-editor
 					v-model:value="codeText"
@@ -165,7 +166,8 @@ const sampleAgentQuestions = [
 	'Add a new transition from S (to nowhere) with a rate constant of v with unit Days. The Rate depends on R',
 	'Add an observable titled sample with the expression A * B  * p.',
 	'Rename the state S to Susceptible in the infection transition.',
-	'Rename the transition infection to inf.'
+	'Rename the transition infection to inf.',
+	'Change rate law of inf to S * I * z.'
 ];
 
 const contextLanguage = ref<string>('python3');
@@ -173,7 +175,7 @@ const contextLanguage = ref<string>('python3');
 const defaultCodeText =
 	'# This environment contains the variable "model" \n# which is displayed on the right';
 const codeText = ref(defaultCodeText);
-const llmThought = ref();
+const llmThoughts = ref<any[]>([]);
 
 const executeResponse = ref({
 	status: OperatorStatus.DEFAULT,
diff --git a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
index f7bb6104a4..4252cac991 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-mira.vue
@@ -45,12 +45,13 @@
 				<div class="toolbar">
 					<tera-notebook-jupyter-input
 						:kernel-manager="kernelManager"
-						:default-options="[]"
+						:default-options="sampleAgentQuestions"
 						:context-language="'python3'"
 						@llm-output="(data: any) => processLLMOutput(data)"
-						@llm-thought-output="(data: any) => (llmThought = data)"
+						@llm-thought-output="(data: any) => llmThoughts.push(data)"
+						@question-asked="llmThoughts = []"
 					/>
-					<tera-notebook-jupyter-thought-output :llm-thought="llmThought" />
+					<tera-notebook-jupyter-thought-output :llm-thoughts="llmThoughts" />
 				</div>
 				<v-ace-editor
 					v-model:value="codeText"
@@ -200,7 +201,13 @@ const kernelManager = new KernelSessionManager();
 
 let editor: VAceEditorInstance['_editor'] | null;
 const codeText = ref('');
-const llmThought = ref();
+const llmThoughts = ref<any[]>([]);
+
+const sampleAgentQuestions = [
+	'Stratify my model by the ages young and old',
+	'Stratify my model by the locations Toronto and Montreal where Toronto and Montreal cannot interact',
+	'What is cartesian_control in stratify?'
+];
 
 const updateStratifyGroupForm = (config: StratifyGroup) => {
 	const state = _.cloneDeep(props.node.state);
@@ -253,16 +260,13 @@ const stratifyRequest = () => {
 	});
 
 	const messageContent = {
-		stratify_args: {
-			key: strataOption.name,
-			strata: strataOption.groupLabels.split(',').map((d) => d.trim()),
-			concepts_to_stratify: conceptsToStratify,
-			params_to_stratify: parametersToStratify,
-			cartesian_control: strataOption.cartesianProduct,
-			structure: strataOption.useStructure === true ? null : []
-		}
+		key: strataOption.name,
+		strata: strataOption.groupLabels.split(',').map((d) => d.trim()),
+		concepts_to_stratify: conceptsToStratify,
+		params_to_stratify: parametersToStratify,
+		cartesian_control: strataOption.cartesianProduct,
+		structure: strataOption.useStructure === true ? null : []
 	};
-
 	kernelManager.sendMessage('reset_request', {}).register('reset_response', () => {
 		kernelManager
 			.sendMessage('stratify_request', messageContent)
@@ -311,7 +315,7 @@ const buildJupyterContext = () => {
 	}
 
 	return {
-		context: 'mira_model',
+		context: 'mira_model_edit',
 		language: 'python3',
 		context_info: {
 			id: amr.value.id
diff --git a/testing/Stratify-LLM-Tests.md b/testing/Stratify-LLM-Tests.md
new file mode 100644
index 0000000000..58d6d13607
--- /dev/null
+++ b/testing/Stratify-LLM-Tests.md
@@ -0,0 +1,101 @@
+## [Name of the Test Scenario]
+Please go through __every__ step of the test scenario.\
+When blocked, an error, or a UI/UX anomaly occurs, please report which scenario and step to [\#askem-testing](https://unchartedsoftware.slack.com/archives/C06FGLXB2CE).
+
+### 1. Begin test
+1. Login to https://app.staging.terarium.ai using the test account
+    ```
+    email: qa@test.io
+    password: askem-quality-assurance
+    ```
+2. Create, or open, project named `Q&A [Your Name] [YYMMDD]`
+
+### 2. Test Stratify LLM Responses
+1. Make sure you have a model in your project.
+2. Create a workflow
+    Drop in your model in the workflow
+    Create a Stratify node
+    Connect the model to the stratify node
+3. Drill down into the Stratify node and go to the notebook section.
+
+Ask the follow questions one at a time, wait for the response, check the response matches
+reset the code block move on to the next.
+
+Q) "Stratify my model by the ages young and old",
+A) 
+model = stratify(
+    template_model=model,
+    key= "Age",
+    strata=['young', 'old'],
+    structure= [],
+    directed=False,
+    cartesian_control=False,
+    modify_names=True
+)
+
+Q) Stratify my model by the ages young and old where young can transition to old
+A) 
+model = stratify(
+    template_model=model,
+    key= "Age",
+    strata=['young', 'old'],
+    structure= [['young', 'old']],
+    directed=True,
+    cartesian_control=False,
+    modify_names=True
+)
+
+Q) Stratify my model by the ages young and old where young and old can become old, but old cannot become young
+A) 
+model = stratify(
+    template_model=model,
+    key= "Age",
+    strata=['young', 'old'],
+    structure= [['young', 'old']],
+    directed=False,
+    cartesian_control=False,
+    modify_names=True
+)
+
+Q) Stratify my model by the locations Toronto and Montreal where Toronto and Montreal cannot interact
+A) 
+model = stratify(
+    template_model=model,
+    key= "Location",
+    strata=['Toronto', 'Montreal'],
+    structure= [],
+    directed=False,
+    cartesian_control=False,
+    modify_names=True
+)
+
+Q) Stratify my model by the locations Toronto and Montreal where Toronto and Montreal can interact
+A) 
+model = stratify(
+    template_model=model,
+    key= "Location",
+    strata=['Toronto', 'Montreal'],
+    structure= [['Toronto', 'Montreal'], ['Montreal', 'Toronto']],
+    directed=False,
+    cartesian_control=True,
+    modify_names=True
+)
+
+OR
+model = stratify(
+    template_model=model,
+    key= "Location",
+    strata=['Toronto', 'Montreal'],
+    structure= [['Toronto', 'Montreal']],
+    directed=True,
+    cartesian_control=True,
+    modify_names=True
+)
+
+Q) What is cartesian_control in stratify?
+A)
+No code response, instead just a message in the thought section.
+
+
+### 4. End test
+1. logout of the application