From b2b9c56317f52a96b0d874f2fbc1800240bcb224 Mon Sep 17 00:00:00 2001
From: kbirk <birk.kevin@gmail.com>
Date: Thu, 17 Oct 2024 10:55:49 -0400
Subject: [PATCH 1/2] First pass

---
 .../stratify-mira/tera-stratify-drilldown.vue | 30 ++++----
 .../client/hmi-client/src/services/model.ts   |  9 +++
 .../dataservice/ModelController.java          | 70 ++++++++++++++++++-
 .../models/dataservice/model/Model.java       | 51 ++++++++++++++
 .../dataservice/modelparts/ModelMetadata.java | 46 +++++++++++-
 .../terarium/hmiserver/utils/JsonUtil.java    | 11 +++
 6 files changed, 200 insertions(+), 17 deletions(-)

diff --git a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-drilldown.vue b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-drilldown.vue
index 264e26f23f..4e9d00ae67 100644
--- a/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-drilldown.vue
+++ b/packages/client/hmi-client/src/components/workflow/ops/stratify-mira/tera-stratify-drilldown.vue
@@ -94,29 +94,29 @@
 </template>
 
 <script setup lang="ts">
-import { onMounted, onUnmounted, ref, watch } from 'vue';
-import { cloneDeep, debounce, isEqual, last } from 'lodash';
+import '@/ace-config';
 import TeraDrilldownPreview from '@/components/drilldown/tera-drilldown-preview.vue';
 import TeraDrilldownSection from '@/components/drilldown/tera-drilldown-section.vue';
 import TeraDrilldown from '@/components/drilldown/tera-drilldown.vue';
+import TeraNotebookError from '@/components/drilldown/tera-notebook-error.vue';
+import TeraNotebookJupyterInput from '@/components/llm/tera-notebook-jupyter-input.vue';
+import TeraModel from '@/components/model/tera-model.vue';
 import TeraOperatorPlaceholder from '@/components/operator/tera-operator-placeholder.vue';
+import TeraProgressSpinner from '@/components/widgets/tera-progress-spinner.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';
+import { KernelSessionManager } from '@/services/jupyter';
+import { createModelFromOld, getModel } from '@/services/model';
+import { getModelIdFromModelConfigurationId } from '@/services/model-configurations';
+import type { Model } from '@/types/Types';
+import { AMRSchemaNames } from '@/types/common';
+import { OperatorStatus, WorkflowNode } from '@/types/workflow';
 import { logger } from '@/utils/logger';
+import { cloneDeep, debounce, isEqual, last } from 'lodash';
 import Button from 'primevue/button';
 import { v4 as uuidv4 } from 'uuid';
+import { onMounted, onUnmounted, ref, watch } from 'vue';
 import { VAceEditor } from 'vue3-ace-editor';
 import { VAceEditorInstance } from 'vue3-ace-editor/types';
-import '@/ace-config';
-import TeraNotebookError from '@/components/drilldown/tera-notebook-error.vue';
-import type { Model } from '@/types/Types';
-import { AMRSchemaNames } from '@/types/common';
-import { getModelIdFromModelConfigurationId } from '@/services/model-configurations';
-import TeraProgressSpinner from '@/components/widgets/tera-progress-spinner.vue';
-import { KernelSessionManager } from '@/services/jupyter';
-import TeraModel from '@/components/model/tera-model.vue';
 import { blankStratifyGroup, StratifyGroup, StratifyOperationStateMira } from './stratify-mira-operation';
 
 const props = defineProps<{
@@ -234,6 +234,8 @@ const stratifyModel = () => {
 };
 
 const handleModelPreview = async (data: any) => {
+	if (!amr.value) return;
+
 	const amrResponse = data.content['application/json'] as Model;
 	isStratifyInProgress.value = false;
 	if (!amrResponse) {
@@ -250,7 +252,7 @@ const handleModelPreview = async (data: any) => {
 	amrResponse.header.name = newName;
 
 	// Create output
-	const modelData = await createModel(amrResponse);
+	const modelData = await createModelFromOld(amr.value, amrResponse);
 	if (!modelData) return;
 	outputAmr.value = modelData;
 
diff --git a/packages/client/hmi-client/src/services/model.ts b/packages/client/hmi-client/src/services/model.ts
index 6a94a38cba..6216a2a38a 100644
--- a/packages/client/hmi-client/src/services/model.ts
+++ b/packages/client/hmi-client/src/services/model.ts
@@ -15,6 +15,15 @@ export async function createModel(model: Model): Promise<Model | null> {
 	return response?.data ?? null;
 }
 
+export async function createModelFromOld(oldModel: Model, newModel: Model): Promise<Model | null> {
+	delete newModel.id;
+	const response = await API.post(`/models/new-from-old`, {
+		newModel,
+		oldModel
+	});
+	return response?.data ?? null;
+}
+
 export async function createModelAndModelConfig(file: File, progress?: Ref<number>): Promise<Model | null> {
 	const formData = new FormData();
 	formData.append('file', file);
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
index 3b783a8ed9..5a2287cec5 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
@@ -190,7 +190,8 @@ ResponseEntity<Model> getModel(
 								new TypeReference<>() {}
 							);
 
-							// Append the Document extractions to the Model extractions, just for the front-end.
+							// Append the Document extractions to the Model extractions, just for the
+							// front-end.
 							// Those are NOT to be saved back to the data-service.
 							if (extractions != null) {
 								model.get().getMetadata().getAttributes().addAll(extractions);
@@ -473,6 +474,73 @@ ResponseEntity<Model> createModel(
 		}
 	}
 
+	public static class CreateModelFromOldRequest {
+
+		Model oldModel;
+		Model newModel;
+	}
+
+	@PostMapping("/new-from-old")
+	@Secured(Roles.USER)
+	@Operation(summary = "Create a new model from an old model")
+	@ApiResponses(
+		value = {
+			@ApiResponse(
+				responseCode = "201",
+				description = "Model created.",
+				content = @Content(
+					mediaType = "application/json",
+					schema = @io.swagger.v3.oas.annotations.media.Schema(implementation = Model.class)
+				)
+			),
+			@ApiResponse(responseCode = "500", description = "There was an issue creating the model", content = @Content)
+		}
+	)
+	ResponseEntity<Model> createModelFromOld(
+		@RequestBody final CreateModelFromOldRequest req,
+		@RequestParam(name = "project-id", required = false) final UUID projectId
+	) {
+		final Schema.Permission permission = projectService.checkPermissionCanWrite(
+			currentUserService.get().getId(),
+			projectId
+		);
+
+		try {
+			req.newModel.retainMetadataFields(req.oldModel);
+
+			// Set the model name from the AMR header name.
+			// TerariumAsset have a name field, but it's not used for the model name outside
+			// the front-end.
+			req.newModel.setName(req.newModel.getHeader().getName());
+			final Model created = modelService.createAsset(req.newModel, projectId, permission);
+
+			// create default configuration
+			final ModelConfiguration modelConfiguration = ModelConfigurationService.modelConfigurationFromAMR(
+				created,
+				null,
+				null
+			);
+			modelConfigurationService.createAsset(modelConfiguration, projectId, permission);
+
+			// add default model configuration to project
+			final Optional<Project> project = projectService.getProject(projectId);
+			if (project.isPresent()) {
+				projectAssetService.createProjectAsset(
+					project.get(),
+					AssetType.MODEL_CONFIGURATION,
+					modelConfiguration,
+					permission
+				);
+			}
+
+			return ResponseEntity.status(HttpStatus.CREATED).body(created);
+		} catch (final IOException e) {
+			final String error = "Unable to create model";
+			log.error(error, e);
+			throw new ResponseStatusException(org.springframework.http.HttpStatus.INTERNAL_SERVER_ERROR, error);
+		}
+	}
+
 	@GetMapping("/{id}/model-configurations")
 	@Secured(Roles.USER)
 	@Operation(summary = "Gets all model configurations for a model")
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
index 122c5b313c..ab6fcb3510 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import io.hypersistence.utils.hibernate.type.json.JsonType;
 import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
@@ -26,6 +27,7 @@
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.ModelSemantics;
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.semantics.Initial;
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.semantics.Observable;
+import software.uncharted.terarium.hmiserver.utils.JsonUtil;
 
 @EqualsAndHashCode(callSuper = true)
 @Data
@@ -64,6 +66,55 @@ public class Model extends TerariumAssetThatSupportsAdditionalProperties {
 	@Column(columnDefinition = "json")
 	private ModelMetadata metadata;
 
+	public void retainMetadataFields(final Model other) {
+		final Map<String, JsonNode> props = getAdditionalProperties();
+		final Map<String, JsonNode> otherProps = other.getAdditionalProperties();
+
+		if (metadata == null) {
+			metadata = other.getMetadata();
+		} else {
+			metadata.retainMetadataFields(other.getMetadata());
+		}
+
+		final List<String> propertiesToPreserve = List.of(
+			"states",
+			"metadata",
+			"units",
+			"vertices",
+			"edges",
+			"parameters",
+			"initials"
+		);
+
+		for (final String property : propertiesToPreserve) {
+			if (!otherProps.containsKey(property) || !otherProps.get(property).isArray()) {
+				continue;
+			}
+
+			if (!props.containsKey(property) || !props.get(property).isArray()) {
+				continue;
+			}
+
+			final ArrayNode otherProperty = (ArrayNode) otherProps.get(property);
+			final ArrayNode thisProperty = (ArrayNode) props.get(property);
+
+			for (final JsonNode element : otherProperty) {
+				final JsonNode matching = JsonUtil.getFirstByPredicate(thisProperty, (final JsonNode node) -> {
+					// Check if the 'state' object has a 'name' field
+					return node.has("id");
+				});
+
+				if (matching == null) {
+					// does not exist in current model, we can add the old one, otherwise keep the
+					// new one
+					thisProperty.add(element);
+				}
+			}
+
+			props.put(property, thisProperty);
+		}
+	}
+
 	public ModelMetadata getMetadata() {
 		if (metadata == null) {
 			return new ModelMetadata();
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
index 83228f37f7..198b894825 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
@@ -84,6 +84,48 @@ public class ModelMetadata extends SupportAdditionalProperties implements Serial
 	@JdbcTypeCode(Types.BINARY)
 	private byte[] description;
 
+	public void retainMetadataFields(final ModelMetadata other) {
+		if (gollmCard == null) {
+			gollmCard = other.gollmCard;
+		}
+		if (gollmExtractions == null) {
+			gollmExtractions = other.gollmExtractions;
+		}
+		if (provenance == null) {
+			provenance = other.provenance;
+		}
+		if (templateCard == null) {
+			templateCard = other.templateCard;
+		}
+		if (codeId == null) {
+			codeId = other.codeId;
+		}
+		if (source == null) {
+			source = other.source;
+		}
+		if (processedBy == null) {
+			processedBy = other.processedBy;
+		}
+		if (variableStatements == null) {
+			variableStatements = other.variableStatements;
+		}
+		if (annotations == null) {
+			annotations = other.annotations;
+		}
+		if (attributes == null) {
+			attributes = other.attributes;
+		}
+		if (initials == null) {
+			initials = other.initials;
+		}
+		if (parameters == null) {
+			parameters = other.parameters;
+		}
+		if (card == null) {
+			card = other.card;
+		}
+	}
+
 	@Override
 	public ModelMetadata clone() {
 		final ModelMetadata clone = (ModelMetadata) super.clone();
@@ -92,7 +134,7 @@ public ModelMetadata clone() {
 
 		if (this.variableStatements != null) {
 			clone.variableStatements = new ArrayList<>();
-			for (VariableStatement variableStatement : this.variableStatements) {
+			for (final VariableStatement variableStatement : this.variableStatements) {
 				clone.variableStatements.add(variableStatement.clone());
 			}
 		}
@@ -103,7 +145,7 @@ public ModelMetadata clone() {
 
 		if (this.attributes != null) {
 			clone.attributes = new ArrayList<>();
-			for (JsonNode attribute : this.attributes) {
+			for (final JsonNode attribute : this.attributes) {
 				clone.attributes.add(attribute.deepCopy());
 			}
 		}
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/utils/JsonUtil.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/utils/JsonUtil.java
index 712d01a74f..1cfcb7047f 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/utils/JsonUtil.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/utils/JsonUtil.java
@@ -1,9 +1,11 @@
 package software.uncharted.terarium.hmiserver.utils;
 
 import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import java.util.Iterator;
 import java.util.Map;
+import java.util.function.Predicate;
 
 public class JsonUtil {
 
@@ -17,6 +19,15 @@ public static void setAll(final ObjectNode dest, final JsonNode src) {
 			});
 	}
 
+	public static JsonNode getFirstByPredicate(final ArrayNode node, final Predicate<JsonNode> predicate) {
+		for (final JsonNode element : node) {
+			if (predicate.test(element)) {
+				return element;
+			}
+		}
+		return null; // Return null if no element matches the predicate
+	}
+
 	public static void recursiveSetAll(final ObjectNode dest, final JsonNode src) {
 		if (src.isObject()) {
 			final Iterator<Map.Entry<String, JsonNode>> fields = src.fields();

From de7bf6501044fe1fb454395cb23bdf42803eedbe Mon Sep 17 00:00:00 2001
From: kbirk <birk.kevin@gmail.com>
Date: Thu, 17 Oct 2024 11:10:27 -0400
Subject: [PATCH 2/2] Fix couple bugs

---
 .../hmiserver/controller/dataservice/ModelController.java     | 2 ++
 .../terarium/hmiserver/models/dataservice/model/Model.java    | 4 ++++
 .../models/dataservice/modelparts/ModelMetadata.java          | 3 +++
 3 files changed, 9 insertions(+)

diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
index 5a2287cec5..dceec93086 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/controller/dataservice/ModelController.java
@@ -15,6 +15,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.UUID;
+import lombok.Data;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.data.domain.PageRequest;
@@ -474,6 +475,7 @@ ResponseEntity<Model> createModel(
 		}
 	}
 
+	@Data
 	public static class CreateModelFromOldRequest {
 
 		Model oldModel;
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
index ab6fcb3510..3a635d6bf9 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/model/Model.java
@@ -76,6 +76,10 @@ public void retainMetadataFields(final Model other) {
 			metadata.retainMetadataFields(other.getMetadata());
 		}
 
+		if (getDescription() == null) {
+			setDescription(other.getDescription());
+		}
+
 		final List<String> propertiesToPreserve = List.of(
 			"states",
 			"metadata",
diff --git a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
index 198b894825..0bd131ef41 100644
--- a/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
+++ b/packages/server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/ModelMetadata.java
@@ -85,6 +85,9 @@ public class ModelMetadata extends SupportAdditionalProperties implements Serial
 	private byte[] description;
 
 	public void retainMetadataFields(final ModelMetadata other) {
+		if (description == null) {
+			description = other.description;
+		}
 		if (gollmCard == null) {
 			gollmCard = other.gollmCard;
 		}